Mercurial > repos > iuc > lineagespot
changeset 0:6ddf5a9ce4a5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NC_045512.2_annot.gff3 Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,28 @@ +##sequence-region NC_045512.2 1 29903 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049 +NC_045512.2 Giorgi CDS 266 805 . + . NSP1 Leader protein +NC_045512.2 Giorgi CDS 806 2719 . + . NSP2 Non-Structural protein 2 +NC_045512.2 Giorgi CDS 2720 8554 . + . NSP3 Predicted phosphoesterase, papain-like proteinase +NC_045512.2 Giorgi CDS 8555 10054 . + . NSP4 Transmembrane protein +NC_045512.2 Giorgi CDS 10055 10972 . + . NSP5 3C-like proteinase +NC_045512.2 Giorgi CDS 10973 11842 . + . NSP6 Transmembrane protein +NC_045512.2 Giorgi CDS 11843 12091 . + . NSP7 Non-Structural Protein 7 +NC_045512.2 Giorgi CDS 12092 12685 . + . NSP8 Non-Structural Protein 8 +NC_045512.2 Giorgi CDS 12686 13024 . + . NSP9 ssRNA-binding protein +NC_045512.2 Giorgi CDS 13025 13441 . + . NSP10 Growth-factor-like protein +NC_045512.2 Giorgi CDS 13442 13468 . + . NSP12a RNA-dependent RNA polymerase, pre-ribosomal frameshift +NC_045512.2 Giorgi CDS 13468 16236 . + . NSP12b RNA-dependent RNA polymerase, post-ribosomal frameshift +NC_045512.2 Giorgi CDS 16237 18039 . + . NSP13 Helicase +NC_045512.2 Giorgi CDS 18040 19620 . + . NSP14 3'-to-5' exonuclease +NC_045512.2 Giorgi CDS 19621 20658 . + . NSP15 endoRNAse +NC_045512.2 Giorgi CDS 20659 21552 . + . NSP16 2'-O-ribose methyltransferase +NC_045512.2 Giorgi CDS 21563 25384 . + . S Spike +NC_045512.2 Giorgi CDS 25393 26220 . + . ORF3a ORF3a protein +NC_045512.2 Giorgi CDS 26245 26472 . + . E Envelope +NC_045512.2 Giorgi CDS 26523 27191 . + . M Membrane +NC_045512.2 Giorgi CDS 27202 27387 . + . ORF6 ORF6 protein +NC_045512.2 Giorgi CDS 27394 27759 . + . ORF7a ORF7a protein +NC_045512.2 Giorgi CDS 27756 27887 . + . ORF7b ORF7b protein +NC_045512.2 Giorgi CDS 27894 28259 . + . ORF8 ORF8 protein +NC_045512.2 Giorgi CDS 28274 29533 . + . N Nucleocapsid protein +NC_045512.2 Giorgi CDS 29558 29674 . + . ORF10 ORF10 protein
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert_lineage_defs.py Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,173 @@ +# Try to convert constellations files into the format expected by lineagespot. +# Constellations files can define parent lineages, in which case the script +# parses parent mutations recursively and adds them to the signature of the +# child. + +# CURRENT AND GENERAL LIMITATIONS +# Important to understand, please read carefully +# 1. Constellations sometimes uses base instead of amino acid positions for +# defining mutations. These can take two forms like in these examples: +# "nuc:C8986T", i.e. a SNV given in base coordinates +# "del:22029:6", i.e. a deletion of 6 bases given in base coordinates +# The current version of the script makes no attempt to convert such lines to +# amino acid coordinates, but simply drops them. +# 2. In other cases, constellations lists deletions in amino acid poisitions like +# this: +# "s:HV69-" +# While this notation could be parsed such lines are currently *also* dropped +# because it's not entirely clear how lineagespot describes deletions. +# 3. In some cases, constellation also provides mutations in mature peptide +# coordinates, like "nsp15:K259R". Lines like this are currently dropped, too. +# 4. The constellations data provided by +# https://github.com/cov-lineages/constellations +# lists mostly lineage-defining mutations that can be used to *distinguish* +# between lineages, but makes no attempt to provide complete lists of mutations +# (even through parent lineage definitions) for any lineage. + +import argparse +import json +import os +import re +import sys + + +genes_names_translation = { + "orf1a": "ORF1a", + "orf1ab": "ORF1ab", + "1ab": "ORF1ab", + "orf1b": "ORF1b", + "s": "S", + "spike": "S", + "orf3a": "ORF3a", + "e": "E", + "m": "M", + "n": "N", + "orf6": "ORF6", + "orf7a": "ORF7a", + "orf7b": "ORF7b", + "orf8": "ORF8", + "8": "ORF8", + "n": "N", + # NOTE: in constellations, mutations are sometimes, but not always, given + # in nsp coordinates instead of ORF1a/b ones. Currently, we drop these, + # while we should convert instead!!! + "nsp2": "NSP2", + "nsp3": "NSP3", + "nsp4": "NSP4", + "nsp5": "NSP5", + "nsp6": "NSP6", + "nsp7": "NSP7", + "nsp8": "NSP8", + "nsp9": "NSP9", + "nsp10": "NSP10", + "nsp12": "NSP12", + "nsp13": "NSP13", + "nsp14": "NSP14", + "nsp15": "NSP15", + "nsp16": "NSP16", +} + + +lineagespot_template = dict.fromkeys(["ORF1a", "ORF1b", "S", "ORF3a", "M", "ORF6", "ORF7a", "ORF7b", "ORF8", "E", "N"]) +definitions = {} + +pat = re.compile(r'(?P<gene>.+):(?P<ref>[A-Z]+)(?P<pos>\d+)(?P<alt>[A-Z*]+)') + + +def read_lineage_variants(x, lineage_name): + data = json.load(x) + + sites = {} + for mut in data["sites"]: + match = pat.match(mut) + if match is None: + # Likely a del or nuc mutation given at the base level + continue + # try to get a canonical gene name + gene = genes_names_translation.get( + match.group('gene'), + match.group('gene') + ) + pos = int(match.group('pos')) + if gene == 'ORF1ab': + # constellations isn't very consistent in representing ORF1ab + # mutations. They may be provided in ORF1a or ORF1b coordinates, + # but could also just be given as ORF1ab. + if pos <= 4401: + gene = 'ORF1a' + else: + gene = 'ORF1b' + # 4715 == 314 in constellations + pos = pos - 4401 + if gene not in sites: + sites[gene] = {} + sites[gene][pos] = (match.group('ref'), match.group('alt')) + + # recursively parse parent lineages and + # add their mutations to the global definitions + if "parent_lineage" in data["variant"]: + x_parent = data["variant"]["parent_lineage"] + if x_parent not in definitions: + parent_filename = f"c{x_parent}.json" + lineage_def_dir = os.path.dirname(x.name) + parent_file = os.path.join(lineage_def_dir, parent_filename) + if not os.path.isfile(parent_file): + raise FileNotFoundError( + f"{x_parent} is defined as a parent of {lineage_name}, but " + f"definitions file {parent_filename} not found in " + f"{lineage_def_dir}." + ) + with open(parent_file) as parent_in: + read_lineage_variants(parent_in, x_parent) + + # update the sites dictionary to include also mutations defined for the parent + for gene, muts in definitions[x_parent].items(): + if gene in sites: + for pos, ref_alt in muts.items(): + if pos in sites[gene]: + # exotic case of a parent site being affected in the child + # lineage again. Kepp the child site unaltered. + continue + sites[gene][pos] = ref_alt + else: + # only the parent has mutations in this gene listed + sites[gene] = muts + # done with this lineage and all of its parents + definitions[lineage_name] = sites + + +parser = argparse.ArgumentParser() +parser.add_argument( + "-i", "--input", required=True, + help="Name of the input folder" +) +parser.add_argument( + "-o", "--output", required=True, + help="Name of the output folder" +) +if len(sys.argv) < 2: + sys.exit('Please run with -h / --help for help.') + +args = parser.parse_args() + +for definitions_file in os.listdir(args.input): + # In constellations, the only reliable way to get the lineage name is from + # the file name by stripping the .json suffix from it and dropping the + # leading 'c' (e.g. cBA.5.json holds the definition for lineage BA.5). + if definitions_file[0] != 'c' or definitions_file[-5:] != '.json': + continue + lineage_name_from_file = definitions_file[1:-5] + if lineage_name_from_file in definitions: + # seems we have parsed this lineage already as a parent of another lineage + continue + with open(os.path.join(args.input, definitions_file)) as data_in: + read_lineage_variants(data_in, lineage_name_from_file) + +for lineage, sites in definitions.items(): + # if path isn't there, create one could be added + with open(os.path.join(args.output, lineage) + '.txt', "w") as data_out: + data_out.write('gene\tamino acid\n') + for gene, muts in sites.items(): + if gene in lineagespot_template: + for pos, ref_alt in muts.items(): + data_out.write(f'{gene}\t{ref_alt[0]}{pos}{ref_alt[1]}\n')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lineagespot_verbose.R Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,64 @@ +## How to execute this tool + +# A command-line interface to lineagespot for use with Galaxy +# +# The following arguments are required: +# +# 'in_vcf' a character vector of paths to VCF files object from Galaxy lineagespot/test-data +# 'in_gff3' a character vector of path to GFF3 file containing SARS-CoV-2 gene coordinates object from Galaxy lineagespot/test-data +# 'in_ref' a character vector of path to a folder containing lineage reports object from Galaxy lineagespot/test-data +# 'in_voc' a character vector containing the names of the lineages of interest +# 'in_threshold' a parameter indicating the AF threshold for identifying variants per sample +# +# Rscript ${__tool_directory__}/lineagespot_verbose.R --in_vcf ${__tool_directory__}/test-data/extdata/vcf-files --in_gff3 ${__tool_directory__}/test-data/extdata/NC_045512.2_annot.gff3 --in_ref ${__tool_directory__}/test-data/extdata/ref --in_voc "B.1.617.2, B.1.1.7, B.1.351, P.1" --in_threshold 0.8 +# Set up R error handling to go to stderr +options(show.error.messages = FALSE, error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) +}) + +# Import required libraries + +library_path <- .libPaths() + +suppressPackageStartupMessages({ + library("getopt", lib.loc = library_path) + library("data.table", lib.loc = library_path) + library("lineagespot", lib.loc = library_path) +}) + + +options(stringAsfactors = FALSE, useFancyQuotes = FALSE) + +# Take in trailing command line arguments +args <- commandArgs(trailingOnly = TRUE) + +# Get options using the spec as defined by the enclosed list +# Read the options from the default: commandArgs(TRUE) +option_specification <- matrix(c( + "in_vcf", "vcf", 1, "character", + "in_gff3", "gff3", 1, "character", + "in_ref", "ref", 1, "character", + "in_voc", "voc", 2, "character", + "in_threshold", "thr", 2, "double" +), byrow = TRUE, ncol = 4) + +options <- getopt(option_specification) + +if (!is.null(options$in_voc) && is.character(options$in_voc)) { + options$in_voc <- unlist(strsplit(options$in_voc, split = ",")) +} + +result <- lineagespot(vcf_folder = options$in_vcf, + ref_folder = options$in_ref, + gff3_path = options$in_gff3, + voc = options$in_voc, + AF_threshold = options$in_threshold) + + +# Write output to new file which will be recognized by Galaxy +fwrite(result$variants.table, sep = "\t", file = "variants_table.txt", row.names = FALSE) +fwrite(result$lineage.hits, sep = "\t", file = "lineage_hits.txt", row.names = FALSE) +fwrite(result$lineage.report, sep = "\t", file = "lineage_report.txt", row.names = FALSE) + +cat("\n Process has been completed !\n")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lineagespot_wrapper.xml Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,221 @@ +<tool id="lineagespot" name="lineagespot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>identifies SARS-CoV-2 lineages contributing to metagenomic samples from per-sample variant files</description> + <macros> + <token name="@TOOL_VERSION@">1.4.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <xrefs> + <xref type="bio.tools">lineagespot</xref> + <xref type="bioconductor">lineagespot</xref> + </xrefs> + <requirements> + <requirement type="package" version="4.3.1">r-base</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-lineagespot</requirement> + <requirement type="package" version="3.11">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +## Prepare lineage definitions +mkdir refs && +#if str($voc_source.choice) == 'cached': + python '${__tool_directory__}/convert_lineage_defs.py' -i '${voc_source.constellations.fields.path}/definitions' -o refs && +#end if + +## Symlink the VCFs of all samples into a vcfs folder +## and all custom lineage definitions into refs/ +sh arrange_custom_inputs.sh && + +#if str($ann_data.choice) == 'custom': + ## lineagespot insists on a .gff3 suffix for the annotation file + ln -s '$ann_data.in_gff3' custom.gff3 && +#end if + +Rscript '${__tool_directory__}/lineagespot_verbose.R' + --in_vcf vcfs/ + --in_ref refs/ + #if str($ann_data.choice) == 'standard': + --in_gff3 '${__tool_directory__}/NC_045512.2_annot.gff3' + #else: + --in_gff3 custom.gff3 + #end if + --in_threshold $in_threshold + ]]></command> + <configfiles> + <configfile filename="arrange_custom_inputs.sh"><![CDATA[mkdir vcfs && +#for $vcf in $in_vcf: + #set $sample_name = $vcf.element_identifier.replace("'", '_').replace('/', '_') +ln -s '$vcf' 'vcfs/${sample_name}.vcf' && +#end for +#set $num_samples = len($in_vcf) +echo "Gathered $num_samples samples for lineagespot run." +#if str($voc_source.choice) == 'custom': + #for $lineage_def in $voc_source.collection: + #set $lineage_name = $lineage_def.element_identifier.replace("'", '_').replace('/', '_') +ln -s '$lineage_def' 'refs/${lineage_name}.txt' && +#set $num_lineages = len(list($voc_source.collection)) + #end for +echo "Gathered $num_lineages custom lineage definitions for the analysis." +#end if]]></configfile> + </configfiles> + <inputs> + <param type="data" name="in_vcf" format="vcf" multiple="true" label="Per-sample variant calling data" /> + <conditional name="voc_source"> + <param name="choice" type="select" + label="Source of lineage definitions" + help="Lineagespot detects lineage evidence based on lineage mutation patterns defined in tool-specific definition files. The Galaxy tool also has experimental support for reading lineage definitions from cached constellations data (see tool help below)."> + <option value="custom">Collection of lineagespot-specific definitions in history</option> + <option value="cached">Lineage definitions from cached constellations data</option> + </param> + <when value="custom"> + <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Collection of lineage definitions" /> + </when> + <when value="cached"> + <param name="constellations" label="Cached constellations release" type="select"> + <options from_data_table="pangolin_constellations"> + <column name="value" index="0" /> + <column name="description" index="1" /> + <column name="date" index="3" /> + <column name="path" index="4" /> + <filter type="sort_by" column="3" /> + <validator type="no_options" message="No cached constellations release available" /> + </options> + </param> + </when> + </conditional> + <conditional name="ann_data"> + <param name="choice" type="select" label="Source of genome feature annotations" help="Select built-in genome file to use built-in annotations for the SARS-CoV-2 reference sequence NC_045512.2."> + <option value="standard">Use built-in genome file</option> + <option value="custom">Provide custom genome file</option> + </param> + <when value="standard" /> + <when value="custom"> + <param name="in_gff3" type="data" format="gff3" label="Genes GFF" help="GFF3 input listing gene positions on the reference sequence" /> + </when> + </conditional> + <param type="float" name="in_threshold" value="0.8" label="AF threshold for identifying variants per sample" help="Variants in the input VCFs with an allele frequency less than the threshold will be ignored as noise in the lineage analysis."/> + </inputs> + <outputs> + <data name="lineage_hits" format="tabular" from_work_dir="lineage_hits.txt" label="${tool.name} on ${on_string}: Lineage Hits"/> + <data name="lineage_report" format="tabular" from_work_dir="lineage_report.txt" label="${tool.name} on ${on_string}: Lineage Report"/> + <data name="variants_table" format="tabular" from_work_dir="variants_table.txt" label="${tool.name} on ${on_string}: Variants Table"/> + </outputs> + <tests> + <!-- test with custom genome annotation and lineage definitions --> + <test expect_num_outputs="3"> + <param name="in_vcf" value="SampleA_freebayes_ann.vcf,SampleB_freebayes_ann.vcf,SampleC_freebayes_ann.vcf"/> + <conditional name="ann_data"> + <param name="choice" value="custom"/> + <param name="in_gff3" value="NC_045512.2_annot.gff3"/> + </conditional> + <conditional name="voc_source"> + <param name="choice" value="custom"/> + <param name="collection"> + <collection type="list"> + <element name="AY.1" ftype="tabular" value="AY.1.txt"/> + <element name="B.1.617.2" ftype="tabular" value="B.1.617.2.txt"/> + <element name="B.1.351" ftype="tabular" value="B.1.351.txt"/> + <element name="P.1" ftype="tabular" value="P.1.txt"/> + </collection> + </param> + </conditional> + <output name="lineage_hits"> + <assert_contents> + <has_n_lines n="208"/> + </assert_contents> + </output> + <output name="lineage_report"> + <assert_contents> + <has_n_lines n="13"/> + </assert_contents> + </output> + <output name="variants_table"> + <assert_contents> + <has_n_lines n="1829"/> + </assert_contents> + </output> + </test> + <!-- test with built-in genome annotation and cached constellations --> + <test expect_num_outputs="3"> + <param name="in_vcf" value="SampleA_freebayes_ann.vcf,SampleB_freebayes_ann.vcf,SampleC_freebayes_ann.vcf"/> + <conditional name="ann_data"> + <param name="choice" value="standard"/> + </conditional> + <conditional name="voc_source"> + <param name="choice" value="cached"/> + <param name="constellations" value="v0.1.12"/> + </conditional> + <output name="lineage_hits"> + <assert_contents> + <has_n_lines n="123"/> + </assert_contents> + </output> + <output name="lineage_report"> + <assert_contents> + <has_n_lines n="10"/> + </assert_contents> + </output> + <output name="variants_table"> + <assert_contents> + <has_n_lines n="1829"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**lineagespot** - Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing + +The Galaxy tool wraps the functionality of the `lineagespot Bioconductor package <https://doi.org/doi:10.18129/B9.bioc.lineagespot>`__. + +**Inputs** + +*VCF datasets with per-sample variant calls* + +The tool accepts any number of input datasets in VCF format, for which it will generate reports of SARS-CoV-2 lineage evidence. These datasets need to be annotated using the VCF annotation standard field 'ANN' as added, for example, by SnpEff. + +*Lineage definitions* + +The tool requires definitions of mutation profiles for lineages of interest (it cannot find evidence for lineages it does not know about). These can be provided as a collection of simple 2-columns tabular datasets, like this definition for lineage B.1.617.2:: + + gene amino acid + ORF1b P314L + ORF1b G662S + ORF1b P1000L + S T19R + S G142D + S E156G + S del157/158 + S L452R + S T478K + S D614G + S P681R + S D950N + ORF3a S26L + M I82T + ORF7a V82A + ORF7a T120I + ORF8 D119I + ORF8 del120/121 + N D63G + N R203M + N D377Y + +where the gene names should match those used by the upstream tool producing the VCF ANN field. + +Alternatively, lineage definitions can be extracted from `constellations <https://github.com/cov-lineages/constellations>`__ data cached on the Galaxy server. + +.. class:: Warning mark + + Please note that extraction of lineage definitions from constellations data is still **experimental**. + The conversion process may drop some lineage defining mutations and shouldn't be trusted blindly. + For full and up to date details see the `comments in the conversion script <https://github.com/search?q=repo%3Agalaxyproject%2Ftools-iuc+path%3A%2F%5Etools%5C%2Flineagespot%5C%2F%2F+convert_lineage_defs.py&type=code>`__. + +*Genome feature annotations* + +To learn about the position of the genes mentioned in VCF ANN fields and the lineage definitions on the genome, the tool requires an additional genome feature annotation input in gff3 format. +You should normally just use the offered built-in genome annotation file. +A custom annotation file would only be required if you've mapped your sequencing data to a different reference genome than NC_045512.2 that isn't positionally identical to it. + ]]></help> + <citations> + <citation type="doi">10.1038/s41598-022-06625-6</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AY.1.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,32 @@ +gene amino acid +ORF1a A1306S +ORF1a P2046L +ORF1a P2287S +ORF1a V2930L +ORF1a T3255I +ORF1a T3646A +ORF1b P314L +ORF1b G662S +ORF1b P1000L +ORF1b A1918V +S T19R +S E156G +S del157/158 +S W258L +S K417N +S L452R +S T478K +S D614G +S P681R +S D950N +ORF3a S26L +M I82T +ORF7a V82A +ORF7a T120I +ORF7b T40I +ORF8 D119I +ORF8 del120/121 +N D63G +N R203M +N G215C +N D377Y \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/B.1.351.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,19 @@ +gene amino acid +ORF1a T265I +ORF1a K1655N +ORF1a K3353R +ORF1a S3675K +ORF1a del3676/3678 +ORF1b P314L +S D80A +S D215G +S del241/243 +S K417N +S E484K +S N501Y +S D614G +S A701V +ORF3a Q57H +ORF3a S171L +E P71L +N T205I \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/B.1.617.2.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,22 @@ +gene amino acid +ORF1b P314L +ORF1b G662S +ORF1b P1000L +S T19R +S G142D +S E156G +S del157/158 +S L452R +S T478K +S D614G +S P681R +S D950N +ORF3a S26L +M I82T +ORF7a V82A +ORF7a T120I +ORF8 D119I +ORF8 del120/121 +N D63G +N R203M +N D377Y \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_045512.2_annot.gff3 Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,28 @@ +##sequence-region NC_045512.2 1 29903 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049 +NC_045512.2 Giorgi CDS 266 805 . + . NSP1 Leader protein +NC_045512.2 Giorgi CDS 806 2719 . + . NSP2 Non-Structural protein 2 +NC_045512.2 Giorgi CDS 2720 8554 . + . NSP3 Predicted phosphoesterase, papain-like proteinase +NC_045512.2 Giorgi CDS 8555 10054 . + . NSP4 Transmembrane protein +NC_045512.2 Giorgi CDS 10055 10972 . + . NSP5 3C-like proteinase +NC_045512.2 Giorgi CDS 10973 11842 . + . NSP6 Transmembrane protein +NC_045512.2 Giorgi CDS 11843 12091 . + . NSP7 Non-Structural Protein 7 +NC_045512.2 Giorgi CDS 12092 12685 . + . NSP8 Non-Structural Protein 8 +NC_045512.2 Giorgi CDS 12686 13024 . + . NSP9 ssRNA-binding protein +NC_045512.2 Giorgi CDS 13025 13441 . + . NSP10 Growth-factor-like protein +NC_045512.2 Giorgi CDS 13442 13468 . + . NSP12a RNA-dependent RNA polymerase, pre-ribosomal frameshift +NC_045512.2 Giorgi CDS 13468 16236 . + . NSP12b RNA-dependent RNA polymerase, post-ribosomal frameshift +NC_045512.2 Giorgi CDS 16237 18039 . + . NSP13 Helicase +NC_045512.2 Giorgi CDS 18040 19620 . + . NSP14 3'-to-5' exonuclease +NC_045512.2 Giorgi CDS 19621 20658 . + . NSP15 endoRNAse +NC_045512.2 Giorgi CDS 20659 21552 . + . NSP16 2'-O-ribose methyltransferase +NC_045512.2 Giorgi CDS 21563 25384 . + . S Spike +NC_045512.2 Giorgi CDS 25393 26220 . + . ORF3a ORF3a protein +NC_045512.2 Giorgi CDS 26245 26472 . + . E Envelope +NC_045512.2 Giorgi CDS 26523 27191 . + . M Membrane +NC_045512.2 Giorgi CDS 27202 27387 . + . ORF6 ORF6 protein +NC_045512.2 Giorgi CDS 27394 27759 . + . ORF7a ORF7a protein +NC_045512.2 Giorgi CDS 27756 27887 . + . ORF7b ORF7b protein +NC_045512.2 Giorgi CDS 27894 28259 . + . ORF8 ORF8 protein +NC_045512.2 Giorgi CDS 28274 29533 . + . N Nucleocapsid protein +NC_045512.2 Giorgi CDS 29558 29674 . + . ORF10 ORF10 protein
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/P.1.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,24 @@ +gene amino acid +ORF1a S1188L +ORF1a K1795Q +ORF1a S3675K +ORF1a del3676/3678 +ORF1b P314L +ORF1b E1264D +S L18F +S T20N +S P26S +S D138Y +S R190S +S K417T +S E484K +S N501Y +S D614G +S H655Y +S T1027I +S V1176F +ORF3a S253P +ORF8 E92K +N P80R +N R203K +N G204R \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SampleA_freebayes_ann.vcf Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,645 @@ +##fileformat=VCFv4.2 +##fileDate=20210401 +##source=freeBayes v1.3.2-dirty +##reference=NC_045512.fasta +##contig=<ID=NC_045512.2,length=29903> +##phasing=none +##commandline="freebayes -f NC_045512.fasta -F 0.01 -C 1 --pooled-continuous L4_S1_L001_sorted_uniq.bam" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##SnpEffVersion="5.0 (build 2020-08-09 21:23), by Pablo Cingolani" +##SnpEffCmd="SnpEff NC_045512.2 L4_S1_L001_freebayes.vcf " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +NC_045512.2 32 . C A 3.56727E-5 . AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7097;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=340;RO=10;RPL=0;RPP=5.18177;RPPR=24.725;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=24.725;SRR=0;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-234C>A|||||234| GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:10,1:10:340:1:34:-0.0875811,0,-27.6188 +NC_045512.2 117 . C A 2.06691E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.3774;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=707;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.44459;SRR=9;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-149C>A|||||149| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:707:1:19:0,-4.42166,-62.044 +NC_045512.2 123 . C A 1.76706E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.9102;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=705;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.44459;SRR=9;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-143C>A|||||143| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:705:1:8:0,-5.52163,-62.9622 +NC_045512.2 161 . A T 2.12537E-6 . AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=718;RO=19;RPL=0;RPP=7.35324;RPPR=44.2683;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-105A>T|||||105| GT:DP:AD:RO:QR:AO:QA:GL 0/1:21:19,2:19:718:2:76:-0.893181,0,-58.6313 +NC_045512.2 204 . G T 2.12537E-6 . AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=7.35324;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=695;RO=19;RPL=1;RPP=3.0103;RPPR=3.12459;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-62G>T|||||62| GT:DP:AD:RO:QR:AO:QA:GL 0/1:21:19,2:19:695:2:76:-0.893181,0,-56.5538 +NC_045512.2 241 . C T 616.567 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=21;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=48.6112;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=33.7174;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=769;QR=0;RO=0;RPL=11;RPP=3.1137;RPPR=0;RPR=10;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-25C>T|||||25| GT:DP:AD:RO:QR:AO:QA:GL 1/1:21:0,21:0:0:21:769:-69.5268,-6.32163,0 +NC_045512.2 328 . ACA ACCA 9.67365E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=36;DPB=36.3333;DPRA=0;EPP=5.18177;EPPR=68.4099;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=43.4814;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1233;RO=34;RPL=0;RPP=5.18177;RPPR=12.2071;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=15.5282;SRR=10;TYPE=ins;ANN=ACCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.64dupC|p.Gln22fs|65/21291|65/21291|22/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,1:34:1233:1:38:0,-6.98864,-107.578 +NC_045512.2 355 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7073;NS=1;NUMALT=1;ODDS=52.4278;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1555;RO=41;RPL=1;RPP=5.18177;RPPR=31.0276;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=31.0276;SRR=9;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.90C>T|p.Gly30Gly|90/21291|90/21291|30/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1555:1:38:0,-8.84599,-136.397 +NC_045512.2 366 . C T 186.222 . AB=0.333333;ABP=13.1438;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=33.4109;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=42.8793;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=528;QR=1064;RO=28;RPL=0;RPP=33.4109;RPPR=7.97367;RPR=14;RUN=1;SAF=14;SAP=33.4109;SAR=0;SRF=18;SRP=7.97367;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.101C>T|p.Ser34Phe|101/21291|101/21291|34/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:42:28,14:28:1064:14:528:-35.1856,0,-83.4276 +NC_045512.2 401 . CTTAA CTAA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D3M;DP=37;DPB=36.6;DPRA=0;EPP=7.35324;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=40.215;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=1319;RO=35;RPL=2;RPP=7.35324;RPPR=55.1877;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=32;SRP=55.1877;SRR=3;TYPE=del;ANN=CTAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.138delT|p.Asp48fs|138/21291|138/21291|46/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:35,2:35:1319:2:61:0,-5.34435,-113.176 +NC_045512.2 406 . AGA AA 1.27173E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=35;DPB=35.3333;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=44.6059;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=34;PRO=1;QA=34;QR=1277;RO=34;RPL=1;RPP=5.18177;RPPR=60.4905;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=60.4905;SRR=2;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.142delG|p.Asp48fs|142/21291|142/21291|48/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1277:1:34:0,-7.47703,-111.792 +NC_045512.2 421 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=53.0819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=42.906;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1265;RO=34;RPL=0;RPP=5.18177;RPPR=76.8404;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=53.0819;SRR=3;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.156C>A|p.Gly52Gly|156/21291|156/21291|52/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1265:1:38:0,-6.73878,-110.313 +NC_045512.2 442 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=89.6368;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2254;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.177C>G|p.Gly59Gly|177/21291|177/21291|59/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2254:1:7:0,-18.5659,-202.353 +NC_045512.2 445 . T C 647.516 . AB=0.484375;ABP=3.14602;AC=1;AF=0.5;AN=2;AO=31;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.08035;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=59.2258;MQMR=60;NS=1;NUMALT=1;ODDS=149.096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1087;QR=1196;RO=33;RPL=0;RPP=70.3259;RPPR=74.6689;RPR=31;RUN=1;SAF=16;SAP=3.08035;SAR=15;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.180T>C|p.Val60Val|180/21291|180/21291|60/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:64:33,31:33:1196:31:1087:-78.8078,0,-88.6688 +NC_045512.2 460 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=89.6368;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2266;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.195A>C|p.Glu65Asp|195/21291|195/21291|65/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2266:1:7:0,-18.5659,-203.41 +NC_045512.2 505 . T A 1.73301E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=139.813;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=59.8095;NS=1;NUMALT=1;ODDS=84.1303;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=2312;RO=63;RPL=1;RPP=5.18177;RPPR=3.04477;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.240T>A|p.Pro80Pro|240/21291|240/21291|80/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2312:1:31:0,-16.1745,-205.204 +NC_045512.2 541 . CGA CA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D1M;DP=64;DPB=63.3333;DPRA=0;EPP=7.35324;EPPR=137.642;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=71.879;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2328;RO=62;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=31;SRP=3.0103;SRR=31;TYPE=del;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.277delG|p.Glu93fs|277/21291|277/21291|93/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,2:62:2328:2:76:0,-12.0511,-202.468 +NC_045512.2 560 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=7.35324;EPPR=137.642;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=71.879;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2315;RO=62;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=31;SRP=3.0103;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.295C>T|p.Arg99Cys|295/21291|295/21291|99/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,2:62:2315:2:76:0,-12.0511,-201.298 +NC_045512.2 577 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=89.1762;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2353;RO=63;RPL=1;RPP=5.18177;RPPR=131.265;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.312T>G|p.Leu104Leu|312/21291|312/21291|104/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2353:1:9:0,-18.3659,-211.033 +NC_045512.2 578 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=84.3418;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=2356;RO=63;RPL=1;RPP=5.18177;RPPR=131.265;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.313G>A|p.Gly105Ser|313/21291|313/21291|105/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2356:1:30:0,-16.2664,-209.204 +NC_045512.2 583 . CC TT,TC 601.468 . AB=0.09375,0.4375;ABP=94.755,5.18177;AC=0,1;AF=0,0.5;AN=2;AO=6,28;CIGAR=2X,1X1M;DP=64;DPB=64;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.0103;GTI=0;LEN=2,1;MEANALT=2,2;MQM=60,59.1429;MQMR=60;NS=1;NUMALT=2;ODDS=138.493;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=218,1009;QR=1114;RO=30;RPL=6,28;RPP=16.0391,63.8115;RPPR=68.1545;RPR=0,0;RUN=1,1;SAF=3,14;SAP=3.0103,3.0103;SAR=3,14;SRF=15;SRP=3.0103;SRR=15;TYPE=complex,snp;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.318_319delCCinsTT|p.Leu107Phe|318/21291|318/21291|106/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:64:30,6,28:30:1114:6,28:218,1009:-73.2231,-64.4502,-153.815,0,-73.3701,-82.7431 +NC_045512.2 593 . C T 610.965 . AB=0.4375;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=28;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=140.68;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1038;QR=1263;RO=36;RPL=28;RPP=63.8115;RPPR=81.1833;RPR=0;RUN=1;SAF=14;SAP=3.0103;SAR=14;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.328C>T|p.His110Tyr|328/21291|328/21291|110/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:64:36,28:36:1263:28:1038:-74.3936,0,-94.685 +NC_045512.2 643 . C T 202.452 . AB=0.358974;ABP=9.74743;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=33.4109;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=46.6162;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=532;QR=920;RO=25;RPL=14;RPP=33.4109;RPPR=13.5202;RPR=0;RUN=1;SAF=0;SAP=33.4109;SAR=14;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.378C>T|p.Asn126Asn|378/21291|378/21291|126/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:39:25,14:25:920:14:532:-36.4501,0,-71.3774 +NC_045512.2 657 . C T 154.161 . AB=0.28;ABP=24.0302;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=33.4109;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=35.4969;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=532;QR=1361;RO=36;RPL=14;RPP=33.4109;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=33.4109;SAR=14;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.392C>T|p.Ala131Val|392/21291|392/21291|131/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:50:36,14:36:1361:14:532:-33.1387,0,-107.731 +NC_045512.2 663 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=105.24;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=66.0771;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1930;RO=51;RPL=1;RPP=5.18177;RPPR=8.16222;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=10.206;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.398G>C|p.Gly133Ala|398/21291|398/21291|133/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1930:1:38:0,-11.8563,-170.124 +NC_045512.2 666 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=105.24;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=66.0771;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1936;RO=51;RPL=0;RPP=5.18177;RPPR=10.206;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=12.5903;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.401A>T|p.His134Leu|401/21291|401/21291|134/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1936:1:38:0,-11.8563,-170.663 +NC_045512.2 682 . T C 342.715 . AB=0.346154;ABP=13.7006;AC=1;AF=0.5;AN=2;AO=18;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=33.8935;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=78.913;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=665;QR=1292;RO=34;RPL=6;RPP=7.35324;RPPR=23.7032;RPR=12;RUN=1;SAF=11;SAP=4.9405;SAR=7;SRF=8;SRP=23.7032;SRR=26;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.417T>C|p.Asp139Asp|417/21291|417/21291|139/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:52:34,18:34:1292:18:665:-44.5238,0,-100.888 +NC_045512.2 721 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=7.35324;EPPR=94.401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7391;NS=1;NUMALT=1;ODDS=59.7474;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1691;RO=46;RPL=2;RPP=7.35324;RPPR=4.70971;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=19;SRP=6.03148;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.456T>G|p.Asp152Glu|456/21291|456/21291|152/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:46,2:46:1691:2:39:0,-10.7447,-148.746 +NC_045512.2 724 . T G 3.40528E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=83.5666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7073;NS=1;NUMALT=1;ODDS=54.0345;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1474;RO=41;RPL=1;RPP=5.18177;RPPR=3.06326;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.48696;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.459T>G|p.Pro153Pro|459/21291|459/21291|153/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1474:1:31:0,-9.54381,-129.836 +NC_045512.2 725 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.3595;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1335;RO=37;RPL=1;RPP=5.18177;RPPR=3.5385;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.460T>G|p.Tyr154Asp|460/21291|460/21291|154/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1335:1:32:0,-8.23983,-117.246 +NC_045512.2 729 . A G 2.90829E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1342;RO=36;RPL=0;RPP=5.18177;RPPR=81.1833;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.464A>G|p.Glu155Gly|464/21291|464/21291|155/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1342:1:38:0,-7.34084,-117.278 +NC_045512.2 737 . C A 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.8841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1332;RO=37;RPL=0;RPP=5.18177;RPPR=83.3548;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.472C>A|p.Gln158Lys|472/21291|472/21291|158/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1332:1:8:0,-10.6391,-119.367 +NC_045512.2 913 . C T 595.642 . AB=0.684211;ABP=14.2105;AC=1;AF=0.5;AN=2;AO=26;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.1502;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=935;QR=445;RO=12;RPL=26;RPP=59.4686;RPPR=29.068;RPR=0;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.648C>T|p.Ser216Ser|648/21291|648/21291|216/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:38:12,26:12:445:26:935:-73.017,0,-28.9551 +NC_045512.2 924 . A T 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.8841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1322;RO=37;RPL=1;RPP=5.18177;RPPR=83.3548;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.659A>T|p.Asp220Val|659/21291|659/21291|220/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1322:1:8:0,-10.6391,-118.459 +NC_045512.2 929 . A T 6.26083E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.6539;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1298;RO=37;RPL=1;RPP=5.18177;RPPR=83.3548;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.664A>T|p.Ile222Phe|664/21291|664/21291|222/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1298:1:9:0,-10.5391,-116.202 +NC_045512.2 932 . G T 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.8841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1322;RO=37;RPL=1;RPP=5.18177;RPPR=83.3548;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.667G>T|p.Asp223Tyr|667/21291|667/21291|223/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1322:1:8:0,-10.6391,-118.464 +NC_045512.2 946 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=47.41;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.5293;PAIRED=1;PAIREDR=0.93617;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1674;RO=47;RPL=0;RPP=5.18177;RPPR=5.27418;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=6.75262;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.681T>G|p.Gly227Gly|681/21291|681/21291|227/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1674:1:34:0,-11.0505,-147.539 +NC_045512.2 949 . A G 1.43295E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=83.8559;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.3616;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1883;RO=52;RPL=0;RPP=5.18177;RPPR=4.51363;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=11.1951;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.684A>G|p.Val228Val|684/21291|684/21291|228/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1883:1:34:0,-12.5557,-166.334 +NC_045512.2 954 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=107.408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.4248;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1958;RO=52;RPL=0;RPP=5.18177;RPPR=9.02361;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=11.1951;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.689G>T|p.Cys230Phe|689/21291|689/21291|230/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1958:1:12:0,-14.7546,-175.276 +NC_045512.2 968 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1898;RO=50;RPL=1;RPP=5.18177;RPPR=14.1282;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=14.1282;SRR=17;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.703G>T|p.Glu235*|703/21291|703/21291|235/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1898:1:38:0,-11.5553,-167.28 +NC_045512.2 973 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1897;RO=50;RPL=0;RPP=5.18177;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.708T>A|p.His236Gln|708/21291|708/21291|236/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1897:1:38:0,-11.5553,-167.19 +NC_045512.2 998 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1892;RO=50;RPL=0;RPP=5.18177;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.733T>C|p.Ser245Pro|733/21291|733/21291|245/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1892:1:38:0,-11.5553,-166.741 +NC_045512.2 1019 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1892;RO=50;RPL=0;RPP=5.18177;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.754C>T|p.Gln252*|754/21291|754/21291|252/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1892:1:38:0,-11.5553,-166.741 +NC_045512.2 1026 . C T 6.48614E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.8949;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1730;RO=48;RPL=1;RPP=5.18177;RPPR=17.6677;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=17.6677;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.761C>T|p.Pro254Leu|761/21291|761/21291|254/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1730:1:34:0,-11.3516,-152.571 +NC_045512.2 1044 . C T 3.11712E-4 . AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.54195;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=334;QR=2013;RO=56;RPL=0;RPP=22.5536;RPPR=124.613;RPR=9;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.779C>T|p.Ala260Val|779/21291|779/21291|260/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:65:56,9:56:2013:9:334:-10.8453,0,-161.85 +NC_045512.2 1069 . G A 8.67461E-8 . AB=0.123077;ABP=83.2212;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.0103;EPPR=3.0484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.7288;PAIRED=1;PAIREDR=0.877193;PAO=0;PQA=0;PQR=0;PRO=0;QA=299;QR=2032;RO=57;RPL=0;RPP=20.3821;RPPR=126.784;RPR=8;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=29;SRP=3.0484;SRR=28;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.804G>A|p.Gly268Gly|804/21291|804/21291|268/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:65:57,8:57:2032:8:299:-7.69887,0,-163.558 +NC_045512.2 1076 . C T 8.85674E-4 . AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.49761;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=339;QR=2022;RO=56;RPL=0;RPP=22.5536;RPPR=124.613;RPR=9;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.811C>T|p.Pro271Ser|811/21291|811/21291|271/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:65:56,9:56:2022:9:339:-11.2989,0,-162.66 +NC_045512.2 1126 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=141.985;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0865;PAIRED=1;PAIREDR=0.890625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2381;RO=64;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.861G>T|p.Arg287Ser|861/21291|861/21291|287/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2381:1:11:0,-18.467,-213.416 +NC_045512.2 1142 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=141.985;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0865;PAIRED=0;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2404;RO=64;RPL=0;RPP=5.18177;RPPR=3.14602;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.14602;SRR=31;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.877C>G|p.Leu293Val|877/21291|877/21291|293/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2404:1:11:0,-18.467,-215.488 +NC_045512.2 1153 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=7.35324;EPPR=139.813;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.2341;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2338;RO=63;RPL=1;RPP=3.0103;RPPR=3.04477;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.888T>C|p.Phe296Phe|888/21291|888/21291|296/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:63,2:63:2338:2:76:0,-12.3521,-203.432 +NC_045512.2 1193 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.14602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0865;PAIRED=0;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2417;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.14602;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.928A>T|p.Asn310Tyr|928/21291|928/21291|310/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2417:1:11:0,-18.467,-216.656 +NC_045512.2 1205 . C T 0.0010911 . AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.289;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=340;QR=2079;RO=56;RPL=9;RPP=22.5536;RPPR=124.613;RPR=0;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.940C>T|p.Gln314*|940/21291|940/21291|314/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:65:56,9:56:2079:9:340:-11.3895,0,-167.79 +NC_045512.2 1213 . C T 3.11242E-4 . AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.54346;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=334;QR=2086;RO=56;RPL=9;RPP=22.5536;RPPR=124.613;RPR=0;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.948C>T|p.Cys316Cys|948/21291|948/21291|316/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:65:56,9:56:2086:9:334:-10.8446,0,-168.42 +NC_045512.2 1222 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.7773;PAIRED=0;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2374;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.957T>C|p.Thr319Thr|957/21291|957/21291|319/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2374:1:8:0,-18.767,-213.093 +NC_045512.2 1224 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.7773;PAIRED=1;PAIREDR=0.890625;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2363;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.959T>C|p.Leu320Pro|959/21291|959/21291|320/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2363:1:8:0,-18.767,-212.104 +NC_045512.2 1254 . C T 4.88136E-8 . AB=0.121951;ABP=53.9075;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=13.8677;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.3038;PAIRED=0.8;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=189;QR=1353;RO=36;RPL=5;RPP=13.8677;RPPR=22.5536;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=22.5536;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.989C>T|p.Ser330Leu|989/21291|989/21291|330/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:36,5:36:1353:5:189:-5.03372,0,-109.719 +NC_045512.2 1288 . C T 4.88136E-8 . AB=0.121951;ABP=53.9075;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=13.8677;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.3038;PAIRED=0.8;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=189;QR=1362;RO=36;RPL=5;RPP=13.8677;RPPR=22.5536;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=22.5536;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1023C>T|p.Cys341Cys|1023/21291|1023/21291|341/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:36,5:36:1362:5:189:-5.03372,0,-110.53 +NC_045512.2 1292 . T C 0.189044 . AB=0.170732;ABP=41.6201;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=18.2106;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.11248;PAIRED=1;PAIREDR=0.882353;PAO=0;PQA=0;PQR=0;PRO=0;QA=266;QR=1290;RO=34;RPL=0;RPP=18.2106;RPPR=60.4905;RPR=7;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=2;SRP=60.4905;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1027T>C|p.Phe343Leu|1027/21291|1027/21291|343/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:34,7:34:1290:7:266:-11.9603,0,-104.054 +NC_045512.2 1314 . C T 1.71007E-8 . AB=0.119048;ABP=55.9529;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=13.8677;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.0541;NS=1;NUMALT=1;ODDS=19.3527;PAIRED=0.8;PAIREDR=0.891892;PAO=0;PQA=0;PQR=0;PRO=0;QA=190;QR=1385;RO=37;RPL=5;RPP=13.8677;RPPR=19.9713;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=24.1968;SRR=28;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1049C>T|p.Thr350Ile|1049/21291|1049/21291|350/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:42:37,5:37:1385:5:190:-4.82418,0,-111.803 +NC_045512.2 1336 . T G 3.36083E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.6538;NS=1;NUMALT=1;ODDS=32.9924;PAIRED=1;PAIREDR=0.807692;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=908;RO=26;RPL=1;RPP=5.18177;RPPR=8.35546;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=8.35546;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1071T>G|p.Cys357Trp|1071/21291|1071/21291|357/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:908:1:34:0,-4.7289,-77.5254 +NC_045512.2 1406 . G T 7.97288E-5 . AB=0.111111;ABP=26.6552;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=7.35324;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.9054;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=581;RO=16;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=3.0103;SRR=8;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1141G>T|p.Glu381*|1141/21291|1141/21291|381/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:16,2:16:581:2:75:-1.7018,0,-47.2006 +NC_045512.2 1441 . C T 366.029 . AB=0.833333;ABP=20.3821;AC=1;AF=0.5;AN=2;AO=15;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=35.5824;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.41326;PAIRED=1;PAIREDR=0.666667;PAO=0;PQA=0;PQR=0;PRO=0;QA=567;QR=114;RO=3;RPL=7;RPP=3.15506;RPPR=3.73412;RPR=8;RUN=1;SAF=7;SAP=3.15506;SAR=8;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1176C>T|p.Gly392Gly|1176/21291|1176/21291|392/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:3,15:3:114:15:567:-45.9537,0,-5.21381 +NC_045512.2 1456 . T C 8.91572E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=645;RO=17;RPL=1;RPP=5.18177;RPPR=3.13803;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=3.13803;SRR=9;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1191T>C|p.Leu397Leu|1191/21291|1191/21291|397/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:645:1:38:0,-1.62127,-54.5906 +NC_045512.2 1534 . G T 3.33317E-5 . AB=0.111111;ABP=26.6552;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7775;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=556;RO=16;RPL=2;RPP=7.35324;RPPR=37.7539;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=3.0103;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1269G>T|p.Trp423Cys|1269/21291|1269/21291|423/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:16,2:16:556:2:71:-1.32304,0,-44.9385 +NC_045512.2 1580 . GTTGG GTTTGG 1.41193E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=14;DPB=14.2;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.9391;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=488;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=7.18621;SRR=9;TYPE=ins;ANN=GTTTGG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1317dupT|p.Gly440fs|1318/21291|1318/21291|440/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:488:1:37:0,-0.516591,-40.5677 +NC_045512.2 1601 . C T 1.77522E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=494;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=7.18621;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1336C>T|p.Leu446Phe|1336/21291|1336/21291|446/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:494:1:38:0,-0.417151,-41.0105 +NC_045512.2 1609 . C T 1.77522E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=494;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=7.18621;SRR=9;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1344C>T|p.Asp448Asp|1344/21291|1344/21291|448/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:494:1:38:0,-0.417151,-41.0105 +NC_045512.2 1684 . C T 0.895072 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.47459;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=269;RO=8;RPL=0;RPP=7.35324;RPPR=20.3821;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1419C>T|p.Ile473Ile|1419/21291|1419/21291|473/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:269:2:73:-3.9208,0,-21.5227 +NC_045512.2 1759 . A T 1.58317 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.821324;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=304;RO=8;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1494A>T|p.Ala498Ala|1494/21291|1494/21291|498/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:304:2:76:-4.20451,0,-24.7098 +NC_045512.2 1841 . C T 1.58317 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.821324;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=301;RO=8;RPL=2;RPP=7.35324;RPPR=20.3821;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1576C>T|p.Gln526*|1576/21291|1576/21291|526/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:301:2:76:-4.20451,0,-24.4375 +NC_045512.2 1883 . G A 1.32389E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.6087;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=444;RO=12;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.73412;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1618G>A|p.Ala540Thr|1618/21291|1618/21291|540/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:444:1:11:0,-2.81339,-39.2047 +NC_045512.2 1902 . C T 6.59366E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.398;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=456;RO=12;RPL=1;RPP=5.18177;RPPR=5.9056;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=5.9056;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1637C>T|p.Ser546Leu|1637/21291|1637/21291|546/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:456:1:38:0,-0.116121,-37.593 +NC_045512.2 1943 . C T 6.59366E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.398;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=456;RO=12;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.73412;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1678C>T|p.Arg560Cys|1678/21291|1678/21291|560/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:456:1:38:0,-0.116121,-37.593 +NC_045512.2 2134 . A C 3.80095E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.1592;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=509;RO=14;RPL=1;RPP=5.18177;RPPR=33.4109;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1869A>C|p.Lys623Asn|1869/21291|1869/21291|623/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:509:1:7:0,-3.81545,-45.4449 +NC_045512.2 2166 . A C 3.80095E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.1592;PAIRED=1;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=482;RO=14;RPL=1;RPP=5.18177;RPPR=33.4109;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1901A>C|p.Lys634Thr|1901/21291|1901/21291|634/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:482:1:7:0,-3.81545,-42.9993 +NC_045512.2 2659 . G T 103.718 . AB=0.4;ABP=4.31318;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=16.0391;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.882;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=224;QR=342;RO=9;RPL=3;RPP=3.0103;RPPR=3.25157;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2394G>T|p.Lys798Asn|2394/21291|2394/21291|798/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:15:9,6:9:342:6:224:-16.0044,0,-26.6222 +NC_045512.2 2714 . G C 0.00435058 . AB=0.133333;ABP=20.5268;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=7.35324;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.9055;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=494;RO=13;RPL=1;RPP=3.0103;RPPR=3.17734;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2449G>C|p.Gly817Arg|2449/21291|2449/21291|817/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:15:13,2:13:494:2:76:-2.69936,0,-40.2923 +NC_045512.2 2719 . TGC TC 198.79 . AB=0.6;ABP=4.31318;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1M1D1M;DP=15;DPB=12;DPRA=0;EPP=22.5536;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.3031;PAIRED=0.888889;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=226;RO=6;RPL=5;RPP=3.25157;RPPR=3.0103;RPR=4;RUN=1;SAF=5;SAP=3.25157;SAR=4;SRF=3;SRP=3.0103;SRR=3;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2455delG|p.Ala819fs|2455/21291|2455/21291|819/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:15:6,9:6:226:9:342:-26.6222,0,-16.1872 +NC_045512.2 2811 . T C 5.82418E-4 . AB=0.142857;ABP=10.7656;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.91681;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=228;RO=6;RPL=1;RPP=5.18177;RPPR=16.0391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=16.0391;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2546T>C|p.Ile849Thr|2546/21291|2546/21291|849/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:6,1:6:228:1:24:-0.292681,0,-18.7778 +NC_045512.2 2828 . G T 1.90019E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.9447;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=504;RO=14;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2563G>T|p.Glu855*|2563/21291|2563/21291|855/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:504:1:34:0,-1.11654,-42.2968 +NC_045512.2 2873 . G T 2.35276E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3362;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=682;RO=18;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=4.9405;SRR=7;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2608G>T|p.Glu870*|2608/21291|2608/21291|870/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:19:18,1:18:682:1:38:0,-1.9223,-57.9181 +NC_045512.2 2891 . GCA GCCA 2.35276E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=19;DPB=19.3333;DPRA=0;EPP=5.18177;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3362;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=677;RO=18;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=4.9405;SRR=7;TYPE=ins;ANN=GCCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2627dupC|p.Asp877fs|2628/21291|2628/21291|876/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:19:18,1:18:677:1:38:0,-1.9223,-57.4672 +NC_045512.2 2942 . C T 8.20418E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.7846;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=735;RO=20;RPL=0;RPP=7.35324;RPPR=46.4397;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2677C>T|p.Leu893Leu|2677/21291|2677/21291|893/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:20,2:20:735:2:67:0,-0.260581,-60.1116 +NC_045512.2 3037 . C T 682.489 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=42.4916;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=35.1036;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=831;QR=0;RO=0;RPL=12;RPP=3.40511;RPPR=0;RPR=10;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:22:0,22:0:0:22:831:-75.1154,-6.62266,0 +NC_045512.2 3061 . A G 1.70196E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2658;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=760;RO=21;RPL=1;RPP=5.18177;RPPR=32.8939;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.1137;SRR=10;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2796A>G|p.Glu932Glu|2796/21291|2796/21291|932/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:760:1:34:0,-3.22375,-65.3167 +NC_045512.2 3073 . TGAAGAAGAAGAGT TGAAGAAGAGT 5.84477E-7 . AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M3D10M;DP=22;DPB=21.5714;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.8211;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=725;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=del;ANN=TGAAGAAGAGT|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2817_2819delAGA|p.Glu940del|2817/21291|2817/21291|939/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:22:20,2:20:725:2:76:-0.592151,0,-58.9509 +NC_045512.2 3105 . A G 4.70219E-7 . AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.0386;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=700;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2840A>G|p.Tyr947Cys|2840/21291|2840/21291|947/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:22:20,2:20:700:2:75:-0.497684,0,-56.6876 +NC_045512.2 3110 . T C 5.9668E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.0197;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=788;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2845T>C|p.Tyr949His|2845/21291|2845/21291|949/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:788:1:9:0,-5.72266,-70.3482 +NC_045512.2 3113 . G T 5.84477E-7 . AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.8211;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=713;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2848G>T|p.Gly950Cys|2848/21291|2848/21291|950/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:22:20,2:20:713:2:76:-0.592151,0,-57.8648 +NC_045512.2 3118 . T A 2.44527E-7 . AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.6925;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=668;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2853T>A|p.Thr951Thr|2853/21291|2853/21291|951/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:22:20,2:20:668:2:72:-0.213711,0,-53.7961 +NC_045512.2 3244 . C A 4.31238E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1143;PAIRED=1;PAIREDR=0.969697;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1214;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2979C>A|p.Gly993Gly|2979/21291|2979/21291|993/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1214:2:75:0,-3.41571,-102.438 +NC_045512.2 3267 . C T 1053.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=35;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.07234;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=53.1255;PAIRED=0.971429;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1304;QR=0;RO=0;RPL=0;RPP=79.0118;RPPR=0;RPR=35;RUN=1;SAF=17;SAP=3.07234;SAR=18;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3002C>T|p.Thr1001Ile|3002/21291|3002/21291|1001/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:35:0,35:0:0:35:1304:-117.653,-10.5361,0 +NC_045512.2 3462 . A C 1.99799E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=48.9587;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.1744;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=925;RO=25;RPL=0;RPP=5.18177;RPPR=17.6895;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3197A>C|p.Lys1066Thr|3197/21291|3197/21291|1066/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:925:1:23:0,-5.52687,-81.2678 +NC_045512.2 3464 . C A 2.15924E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=53.2759;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=982;RO=27;RPL=0;RPP=5.18177;RPPR=12.7417;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=9.52472;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3199C>A|p.His1067Asn|3199/21291|3199/21291|1067/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:982:1:34:0,-5.02993,-85.2914 +NC_045512.2 3465 . A C 8.04008E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=7.35324;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5855;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=954;RO=26;RPL=0;RPP=7.35324;RPPR=11.3621;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=11.3621;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3200A>C|p.His1067Pro|3200/21291|3200/21291|1067/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:26,2:26:954:2:46:0,-4.05988,-81.806 +NC_045512.2 3528 . A T 3.52281E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.754;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1113;RO=31;RPL=1;RPP=5.18177;RPPR=3.08035;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3263A>T|p.Asp1088Val|3263/21291|3263/21291|1088/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1113:1:34:0,-6.23405,-97.0776 +NC_045512.2 3529 . T G 2.61878E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=7.35324;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.0666;PAIRED=0.5;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1050;RO=29;RPL=2;RPP=7.35324;RPPR=3.68421;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=16;SRP=3.68421;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3264T>G|p.Asp1088Glu|3264/21291|3264/21291|1088/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:29,2:29:1050:2:39:0,-5.62714,-91.105 +NC_045512.2 3562 . G T 9.89491E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.1374;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1042;RO=30;RPL=0;RPP=7.35324;RPPR=68.1545;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3297G>T|p.Val1099Val|3297/21291|3297/21291|1099/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1042:2:75:0,-2.51262,-86.9511 +NC_045512.2 3647 . ATTCA ATCA 1.19167E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D3M;DP=32;DPB=31.6;DPRA=0;EPP=7.35324;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.9199;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1121;RO=30;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=del;ANN=ATCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3384delT|p.Gln1129fs|3384/21291|3384/21291|1128/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1121:2:76:0,-2.41815,-93.9829 +NC_045512.2 3728 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.7382;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1142;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3463G>T|p.Gly1155Cys|3463/21291|3463/21291|1155/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1142:1:8:0,-8.83296,-102.283 +NC_045512.2 4060 . A C 2.8418E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=42.621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.046;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1077;RO=29;RPL=0;RPP=5.18177;RPPR=24.6501;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=42.621;SRR=3;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3795A>C|p.Pro1265Pro|3795/21291|3795/21291|1265/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1077:1:34:0,-5.63199,-93.8409 +NC_045512.2 4126 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=3.0103;EPPR=4.03458;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.9256;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1938;RO=53;RPL=0;RPP=7.35324;RPPR=93.5156;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3861G>T|p.Val1287Val|3861/21291|3861/21291|1287/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:53,2:53:1938:2:75:0,-9.43631,-167.557 +NC_045512.2 4142 . G A 6.61515E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=3.16006;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.7866;PAIRED=0;PAIREDR=0.982759;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2071;RO=58;RPL=0;RPP=5.18177;RPPR=104.246;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.60933;SRR=31;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3877G>A|p.Glu1293Lys|3877/21291|3877/21291|1293/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2071:1:7:0,-17.0608,-185.929 +NC_045512.2 4163 . G T 5.12534E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.0484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.203;PAIRED=1;PAIREDR=0.964912;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2120;RO=57;RPL=1;RPP=5.18177;RPPR=118.251;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.35316;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3898G>T|p.Val1300Phe|3898/21291|3898/21291|1300/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2120:1:34:0,-14.0608,-187.646 +NC_045512.2 4304 . A T 7.3231E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=3.93042;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.9416;PAIRED=1;PAIREDR=0.966102;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2177;RO=59;RPL=0;RPP=5.18177;RPPR=106.394;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=30;SRP=3.0471;SRR=29;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4039A>T|p.Lys1347*|4039/21291|4039/21291|1347/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2177:1:34:0,-14.6629,-192.771 +NC_045512.2 4391 . C T 2.89298E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=50.3001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1356;RO=36;RPL=1;RPP=5.18177;RPPR=27.1378;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=50.3001;SRR=32;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4126C>T|p.Arg1376*|4126/21291|4126/21291|1376/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1356:1:38:0,-7.34084,-118.536 +NC_045512.2 4397 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=50.3001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.5403;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1364;RO=36;RPL=1;RPP=5.18177;RPPR=27.1378;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=50.3001;SRR=32;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4132A>G|p.Met1378Val|4132/21291|4132/21291|1378/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1364:1:34:0,-7.7392,-119.653 +NC_045512.2 4404 . C A 2.89298E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=50.3001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1342;RO=36;RPL=1;RPP=5.18177;RPPR=27.1378;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=50.3001;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4139C>A|p.Ala1380Glu|4139/21291|4139/21291|1380/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1342:1:38:0,-7.34084,-117.273 +NC_045512.2 4751 . A C 1.35112E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.496;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1051;RO=28;RPL=0;RPP=7.35324;RPPR=63.8115;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4486A>C|p.Thr1496Pro|4486/21291|4486/21291|1496/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:28,2:28:1051:2:75:0,-1.91056,-87.7804 +NC_045512.2 4850 . A C 1.68301E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=7.35324;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2785;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1064;RO=28;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4585A>C|p.Lys1529Gln|4585/21291|4585/21291|1529/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:28,2:28:1064:2:76:0,-1.81609,-88.8561 +NC_045512.2 4890 . C A 1.35112E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.496;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1050;RO=28;RPL=2;RPP=7.35324;RPPR=63.8115;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4625C>A|p.Thr1542Asn|4625/21291|4625/21291|1542/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:28,2:28:1050:2:75:0,-1.91056,-87.6907 +NC_045512.2 5014 . T G 9.40218E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.2535;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=640;RO=18;RPL=1;RPP=5.18177;RPPR=4.9405;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=4.9405;SRR=11;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4749T>G|p.Val1583Val|4749/21291|4749/21291|1583/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:19:18,1:18:640:1:34:0,-2.32066,-54.5285 +NC_045512.2 5016 . T G 1.34597E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=29.6108;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5921;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=575;RO=16;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.55317;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4751T>G|p.Val1584Gly|4751/21291|4751/21291|1584/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:575:1:34:0,-1.7186,-48.6833 +NC_045512.2 5037 . G A 40.1272 . AB=0.285714;ABP=8.59409;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.23953;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=146;QR=353;RO=10;RPL=0;RPP=11.6962;RPPR=24.725;RPR=4;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4772G>A|p.Gly1591Glu|4772/21291|4772/21291|1591/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:14:10,4:10:353:4:146:-9.28272,0,-27.8893 +NC_045512.2 5172 . A G 3.56433E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9208;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=494;RO=13;RPL=1;RPP=5.18177;RPPR=31.2394;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4907A>G|p.His1636Arg|4907/21291|4907/21291|1636/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:494:1:11:0,-3.11442,-43.7078 +NC_045512.2 5267 . A T 3.19931E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2968;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=892;RO=24;RPL=0;RPP=5.18177;RPPR=12.0581;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=12.0581;SRR=7;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5002A>T|p.Lys1668*|5002/21291|5002/21291|1668/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:24,1:24:892:1:34:0,-4.12684,-77.2009 +NC_045512.2 5289 . A T 3.73074E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.7763;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1057;RO=28;RPL=0;RPP=5.18177;RPPR=18.2106;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=18.2106;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5024A>T|p.Tyr1675Phe|5024/21291|5024/21291|1675/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:28,1:28:1057:1:38:0,-4.9326,-91.6435 +NC_045512.2 5360 . T C 1.21146E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1273;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1551;RO=42;RPL=0;RPP=7.35324;RPPR=94.2121;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5095T>C|p.Tyr1699His|5095/21291|5095/21291|1699/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:42,2:42:1551:2:75:0,-6.12498,-132.75 +NC_045512.2 5367 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.9098;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1513;RO=42;RPL=0;RPP=7.35324;RPPR=94.2121;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5102G>T|p.Arg1701Ile|5102/21291|5102/21291|1701/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:42,2:42:1513:2:76:0,-6.03051,-129.224 +NC_045512.2 5368 . A G 1.12861E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1573;RO=43;RPL=0;RPP=5.18177;RPPR=96.3836;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0608;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5103A>G|p.Arg1701Arg|5103/21291|5103/21291|1701/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1573:1:9:0,-12.3453,-140.947 +NC_045512.2 5376 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.9098;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1536;RO=42;RPL=0;RPP=7.35324;RPPR=94.2121;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5111C>A|p.Ala1704Asp|5111/21291|5111/21291|1704/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:42,2:42:1536:2:76:0,-6.03051,-131.304 +NC_045512.2 5388 . C A 798.742 . AB=0.727273;ABP=22.751;AC=1;AF=0.5;AN=2;AO=32;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.6329;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1212;QR=439;RO=12;RPL=0;RPP=72.4974;RPPR=29.068;RPR=32;RUN=1;SAF=16;SAP=3.0103;SAR=16;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5123C>A|p.Ala1708Asp|5123/21291|5123/21291|1708/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:44:12,32:12:439:32:1212:-96.1364,0,-26.605 +NC_045512.2 5489 . G T 1.21146E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=85.7331;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1273;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1573;RO=42;RPL=2;RPP=7.35324;RPPR=3.21711;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5224G>T|p.Asp1742Tyr|5224/21291|5224/21291|1742/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:42,2:42:1573:2:75:0,-6.12498,-134.726 +NC_045512.2 5523 . A C 8.61891E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.5948;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1575;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5258A>C|p.Lys1753Thr|5258/21291|5258/21291|1753/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1575:1:10:0,-12.2453,-141.027 +NC_045512.2 5544 . C A 1.12861E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1552;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5279C>A|p.Thr1760Lys|5279/21291|5279/21291|1760/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1552:1:9:0,-12.3453,-139.057 +NC_045512.2 5546 . A C 1.12861E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1541;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5281A>C|p.Thr1761Pro|5281/21291|5281/21291|1761/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1541:1:9:0,-12.3453,-138.068 +NC_045512.2 5553 . A C 8.30273E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.0553;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1557;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5288A>C|p.Lys1763Thr|5288/21291|5288/21291|1763/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1557:1:8:0,-12.4453,-139.607 +NC_045512.2 5641 . A G 3.1823E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1067;RO=30;RPL=1;RPP=5.18177;RPPR=5.61607;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5376A>G|p.Gln1792Gln|5376/21291|5376/21291|1792/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1067:1:34:0,-5.93302,-92.9399 +NC_045512.2 5824 . T G 2.95401E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1313;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=828;RO=22;RPL=1;RPP=5.18177;RPPR=50.7827;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5559T>G|p.Leu1853Leu|5559/21291|5559/21291|1853/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:23:22,1:22:828:1:10:0,-5.92369,-73.8461 +NC_045512.2 5852 . ATTAC ATAC,ACTAC 3.07172E-7 . AB=0.0869565,0.0434783;ABP=37.093,44.6459;AC=1,0;AF=0.5,0;AN=2;AO=2,1;CIGAR=1M1D3M,1M1X3M;DP=23;DPB=22.6;DPRA=0,0;EPP=3.0103,5.18177;EPPR=3.0103;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=16.4644;PAIRED=1,0;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=75,9;QR=726;RO=20;RPL=2,1;RPP=7.35324,5.18177;RPPR=46.4397;RPR=0,0;RUN=1,1;SAF=1,1;SAP=3.0103,5.18177;SAR=1,0;SRF=10;SRP=3.0103;SRR=10;TYPE=del,snp;ANN=ATAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5589delT|p.Thr1864fs|5589/21291|5589/21291|1863/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:23:20,2,1:20:726:2,1:75,9:-0.312765,0,-58.9375,-5.91932,-59.0435,-64.8871 +NC_045512.2 5869 . C A 8.91572E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=24.5973;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=613;RO=17;RPL=1;RPP=5.18177;RPPR=9.26925;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=4.1599;SRR=10;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5604C>A|p.Tyr1868*|5604/21291|5604/21291|1868/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:613:1:38:0,-1.62127,-51.7006 +NC_045512.2 5952 . T G 4.17411E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.9892;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=746;RO=20;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5687T>G|p.Leu1896Trp|5687/21291|5687/21291|1896/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:746:1:12:0,-5.12164,-66.269 +NC_045512.2 5986 . C T 571.853 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=19;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=3.12459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=30.9448;PAIRED=0.947368;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=712;QR=0;RO=0;RPL=0;RPP=44.2683;RPPR=0;RPR=19;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721C>T|p.Phe1907Phe|5721/21291|5721/21291|1907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:19:0,19:0:0:19:712:-64.4128,-5.71957,0 +NC_045512.2 6193 . A G 4.07431E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1100;RO=29;RPL=1;RPP=5.18177;RPPR=15.6647;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=15.6647;SRR=8;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5928A>G|p.Thr1976Thr|5928/21291|5928/21291|1976/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1100:1:38:0,-5.23363,-95.5115 +NC_045512.2 6241 . G T 4.07431E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1085;RO=29;RPL=1;RPP=5.18177;RPPR=15.6647;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=15.6647;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5976G>T|p.Trp1992Cys|5976/21291|5976/21291|1992/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1085:1:38:0,-5.23363,-94.1611 +NC_045512.2 6250 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=10.8184;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.5202;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1680;RO=47;RPL=0;RPP=5.18177;RPPR=41.8658;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=4.16534;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5985C>A|p.Asn1995Lys|5985/21291|5985/21291|1995/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1680:1:21:0,-12.3495,-149.361 +NC_045512.2 6279 . C T 5.28897E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.4488;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1441;RO=40;RPL=0;RPP=7.35324;RPPR=89.8692;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6014C>T|p.Pro2005Leu|6014/21291|6014/21291|2005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,2:40:1441:2:75:0,-5.52292,-122.849 +NC_045512.2 6280 . A G 5.28897E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.4488;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1425;RO=40;RPL=0;RPP=7.35324;RPPR=89.8692;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6015A>G|p.Pro2005Pro|6015/21291|6015/21291|2005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,2:40:1425:2:75:0,-5.52292,-121.408 +NC_045512.2 6359 . G T 2.78774E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9548;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1540;RO=41;RPL=1;RPP=5.18177;RPPR=3.06326;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6094G>T|p.Asp2032Tyr|6094/21291|6094/21291|2032/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1540:1:27:0,-9.94348,-136.18 +NC_045512.2 6433 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.2313;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1451;RO=40;RPL=2;RPP=7.35324;RPPR=89.8692;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6168C>T|p.Thr2056Thr|6168/21291|6168/21291|2056/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,2:40:1451:2:76:0,-5.42845,-123.655 +NC_045512.2 6439 . G T 6.90097E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1502;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6174G>T|p.Gln2058His|6174/21291|6174/21291|2058/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1502:1:11:0,-11.5433,-134.358 +NC_045512.2 6447 . T G 1.49216E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.3292;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1457;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6182T>G|p.Val2061Gly|6182/21291|6182/21291|2061/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1457:1:8:0,-11.8433,-130.607 +NC_045512.2 6455 . T G 1.03067E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.5595;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1524;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6190T>G|p.Cys2064Gly|6190/21291|6190/21291|2064/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1524:1:7:0,-11.9433,-136.744 +NC_045512.2 6593 . C A 1.37118E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.2645;PAIRED=0;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1475;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6328C>A|p.Pro2110Thr|6328/21291|6328/21291|2110/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1475:1:30:0,-9.64369,-130.032 +NC_045512.2 6643 . T C 6.90097E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1540;RO=41;RPL=1;RPP=5.18177;RPPR=3.48696;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.48696;SRR=22;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6378T>C|p.Gly2126Gly|6378/21291|6378/21291|2126/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1540:1:11:0,-11.5433,-137.782 +NC_045512.2 6722 . A C,T 1.28098E-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=42;DPB=42;DPRA=0,0;EPP=5.18177,5.18177;EPPR=29.2851;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=57.518;PAIRED=0,1;PAIREDR=0.975;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,10;QR=1508;RO=40;RPL=0,1;RPP=5.18177,5.18177;RPPR=16.9077;RPR=1,0;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=19;SRP=3.22745;SRR=21;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6457A>C|p.Thr2153Pro|6457/21291|6457/21291|2153/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,1,1:40:1508:1,1:11,10:0,-11.3472,-134.903,-11.4472,-134.611,-134.993 +NC_045512.2 6742 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4278;PAIRED=0;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1504;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6477G>A|p.Arg2159Arg|6477/21291|6477/21291|2159/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1504:1:38:0,-8.84599,-131.839 +NC_045512.2 6744 . GTTTA ATTTT 2.78774E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9548;PAIRED=0;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1521;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=complex;ANN=ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6479_6483delGTTTAinsATTTT|p.CysLeu2160TyrPhe|6479/21291|6479/21291|2160/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1521:1:27:0,-9.94348,-134.474 +NC_045512.2 6762 . C A 6.90097E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1505;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6497C>A|p.Thr2166Asn|6497/21291|6497/21291|2166/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1505:1:11:0,-11.5433,-134.631 +NC_045512.2 6828 . C T 1.7035E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2658;PAIRED=1;PAIREDR=0.904762;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=797;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=48.6112;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6563C>T|p.Ser2188Phe|6563/21291|6563/21291|2188/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:797:1:34:0,-3.22375,-68.6592 +NC_045512.2 6839 . G T 9.29677E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5592;PAIRED=0;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=783;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=48.6112;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6574G>T|p.Ala2192Ser|6574/21291|6574/21291|2192/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:783:1:11:0,-5.52266,-69.6938 +NC_045512.2 7975 . G A 1.77522E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=493;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=31.2394;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7710G>A|p.Leu2570Leu|7710/21291|7710/21291|2570/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:493:1:38:0,-0.417151,-40.9202 +NC_045512.2 8252 . A C 5.07863E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.5668;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=562;RO=15;RPL=0;RPP=5.18177;RPPR=20.5268;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7987A>C|p.Ile2663Leu|7987/21291|7987/21291|2663/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:562:1:24:0,-2.41659,-48.5206 +NC_045512.2 8254 . AGA AA 5.06717E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=16;DPB=15.6667;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.2665;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=564;RO=15;RPL=0;RPP=5.18177;RPPR=20.5268;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=20.5268;SRR=13;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7990delG|p.Glu2664fs|7990/21291|7990/21291|2664/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:564:1:34:0,-1.41757,-47.7023 +NC_045512.2 8335 . T G 1.26801E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.3492;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=550;RO=15;RPL=0;RPP=5.18177;RPPR=10.1038;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=10.1038;SRR=11;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8070T>G|p.Ala2690Ala|8070/21291|8070/21291|2690/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:550:1:38:0,-1.01921,-46.0397 +NC_045512.2 8339 . A T 1.66407E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7748;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=426;RO=12;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.73412;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8074A>T|p.Ile2692Phe|8074/21291|8074/21291|2692/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:426:1:32:0,-0.714077,-35.4767 +NC_045512.2 8340 . T G 6.15389E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.0721;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=392;RO=11;RPL=1;RPP=5.18177;RPPR=3.20771;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.20771;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8075T>G|p.Ile2692Ser|8075/21291|8075/21291|2692/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:392:1:12:0,-2.41237,-34.4184 +NC_045512.2 8375 . G T 0.293568 . AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.66021;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=302;RO=9;RPL=0;RPP=7.35324;RPPR=22.5536;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8110G>T|p.Ala2704Ser|8110/21291|8110/21291|2704/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:302:2:73:-3.61977,0,-24.1879 +NC_045512.2 8480 . C T 0.547656 . AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.00695;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=337;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8215C>T|p.Pro2739Ser|8215/21291|8215/21291|2739/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:337:2:76:-3.90348,0,-27.3727 +NC_045512.2 8656 . T C 1.2603E-4 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.4475;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=190;RO=5;RPL=1;RPP=5.18177;RPPR=13.8677;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=13.8677;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8391T>C|p.Ser2797Ser|8391/21291|8391/21291|2797/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:6:5,1:5:190:1:12:0,-0.606186,-16.2674 +NC_045512.2 8891 . A C 9.75095E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.3093;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=352;RO=11;RPL=0;RPP=5.18177;RPPR=26.8965;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=26.8965;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8626A>C|p.Thr2876Pro|8626/21291|8626/21291|2876/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:352:1:24:0,-1.21247,-29.5902 +NC_045512.2 8897 . A T 3.56285E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9213;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=633;RO=17;RPL=0;RPP=5.18177;RPPR=39.9253;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=39.9253;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8632A>T|p.Asn2878Tyr|8632/21291|8632/21291|2878/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:633:1:34:0,-2.01963,-53.9064 +NC_045512.2 8966 . A G 9.29677E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=20.4855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5592;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=789;RO=21;RPL=0;RPP=5.18177;RPPR=48.6112;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=20.4855;SRR=4;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8701A>G|p.Lys2901Glu|8701/21291|8701/21291|2901/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:789:1:11:0,-5.52266,-70.2371 +NC_045512.2 8975 . G T 2.27069E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1894;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=1245;RO=34;RPL=0;RPP=7.35324;RPPR=76.8404;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8710G>T|p.Glu2904*|8710/21291|8710/21291|2904/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1245:2:67:0,-4.475,-105.982 +NC_045512.2 8991 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.9354;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1296;RO=35;RPL=0;RPP=5.18177;RPPR=79.0118;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8726C>A|p.Ala2909Glu|8726/21291|8726/21291|2909/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1296:1:9:0,-9.93708,-116.035 +NC_045512.2 9041 . T C 2.59963E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=48.239;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1814;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1308;RO=35;RPL=0;RPP=5.18177;RPPR=8.03571;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8776T>C|p.Ser2926Pro|8776/21291|8776/21291|2926/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1308:1:34:0,-7.43817,-114.613 +NC_045512.2 9049 . G T 1.87615E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.4749;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1309;RO=35;RPL=0;RPP=5.18177;RPPR=3.07234;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8784G>T|p.Lys2928Asn|8784/21291|8784/21291|2928/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1309:1:11:0,-9.73708,-117.004 +NC_045512.2 9123 . G C 3.26967E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2259;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1286;RO=34;RPL=2;RPP=7.35324;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8858G>C|p.Arg2953Pro|8858/21291|8858/21291|2953/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1286:2:76:0,-3.62227,-108.822 +NC_045512.2 9269 . G T 9.72896E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.009;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=382;RO=11;RPL=1;RPP=5.18177;RPPR=12.6832;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=12.6832;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9004G>T|p.Gly3002Cys|9004/21291|9004/21291|3002/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:382:1:34:0,-0.213449,-31.3145 +NC_045512.2 10040 . T C 4.11236E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.1727;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=297;RO=9;RPL=1;RPP=5.18177;RPPR=22.5536;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9775T>C|p.Ser3259Pro|9775/21291|9775/21291|3259/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:10:9,1:9:297:1:9:0,-2.1103,-26.1442 +NC_045512.2 10168 . T G 1.04727E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=5.99147;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.0048;PAIRED=1;PAIREDR=0.779661;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=2057;RO=59;RPL=1;RPP=5.18177;RPPR=98.7391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.0471;SRR=29;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9903T>G|p.Cys3301Trp|9903/21291|9903/21291|3301/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2057:1:12:0,-16.8618,-184.171 +NC_045512.2 10169 . CCAAG CG,CTAAG,CCGAG 1.54596E-14 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=2,1,2;CIGAR=1M3D1M,1M1X3M,2M1X2M;DP=55;DPB=56;DPRA=0,0,0;EPP=3.0103,5.18177,3.0103;EPPR=3.70517;GTI=0;LEN=3,1,1;MEANALT=3,3,3;MQM=60,60,60;MQMR=60;NS=1;NUMALT=3;ODDS=56.5225;PAIRED=1,0,1;PAIREDR=0.76;PAO=0.25,0.25,1.25;PQA=8.5,8.5,42.5;PQR=110.5;PRO=3.25;QA=67,27,76;QR=1794;RO=50;RPL=0,0,0;RPP=7.35324,5.18177,7.35324;RPPR=111.584;RPR=2,1,2;RUN=1,1,1;SAF=1,1,1;SAP=3.0103,5.18177,3.0103;SAR=1,0,1;SRF=27;SRP=3.70517;SRR=23;TYPE=del,snp,snp;ANN=CTAAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9905C>T|p.Pro3302Leu|9905/21291|9905/21291|3302/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:50,2,1,2:50:1794:2,1,2:67,27,76:0,-9.63806,-155.337,-12.9384,-153.812,-158.935,-8.81225,-149.705,-153.002,-154.527 +NC_045512.2 10282 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=111.745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.7867;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1943;RO=54;RPL=1;RPP=5.18177;RPPR=3.17115;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10017G>T|p.Arg3339Ser|10017/21291|10017/21291|3339/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1943:1:31:0,-13.4572,-172.017 +NC_045512.2 10300 . GCAA TCAC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=111.745;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.3184;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=2010;RO=54;RPL=1;RPP=5.18177;RPPR=3.17115;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=complex;ANN=TCAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10035_10038delGCAAinsTCAC|p.MetGln3345IleHis|10035/21291|10035/21291|3345/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:2010:1:20:0,-14.5567,-179.154 +NC_045512.2 10314 . T A 4.92735E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=3.0103;EPPR=4.03458;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.7081;PAIRED=1;PAIREDR=0.754717;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1976;RO=53;RPL=2;RPP=7.35324;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=4.03458;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10049T>A|p.Leu3350His|10049/21291|10049/21291|3350/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:53,2:53:1976:2:76:0,-9.34184,-170.875 +NC_045512.2 10323 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2005;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10058A>C|p.Lys3353Thr|10058/21291|10058/21291|3353/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:2005:1:9:0,-15.6567,-179.804 +NC_045512.2 10335 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6277;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=1968;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10070C>A|p.Ala3357Asp|10070/21291|10070/21291|3357/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1968:1:23:0,-14.2567,-175.07 +NC_045512.2 10344 . A C 1.28079E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.4696;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1964;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10079A>C|p.Lys3360Thr|10079/21291|10079/21291|3360/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1964:1:15:0,-15.0567,-175.516 +NC_045512.2 10352 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1966;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10087A>C|p.Lys3363Gln|10087/21291|10087/21291|3363/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1966:1:9:0,-15.6567,-176.293 +NC_045512.2 10355 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=1;PAIREDR=0.759259;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1971;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10090T>C|p.Tyr3364His|10090/21291|10090/21291|3364/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1971:1:9:0,-15.6567,-176.746 +NC_045512.2 10358 . AA TC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1937;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=complex;ANN=TC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10093_10094delAAinsTC|p.Lys3365Ser|10093/21291|10093/21291|3365/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1937:1:9:0,-15.6567,-173.683 +NC_045512.2 10364 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=84.7931;PAIRED=1;PAIREDR=0.796875;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2326;RO=64;RPL=0;RPP=5.18177;RPPR=74.8046;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=9.66043;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10099G>T|p.Val3367Phe|10099/21291|10099/21291|3367/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2326:1:34:0,-16.168,-206.182 +NC_045512.2 10377 . C A 7.68684E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=15.1406;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.3261;PAIRED=1;PAIREDR=0.87931;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2116;RO=58;RPL=1;RPP=5.18177;RPPR=41.348;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=5.40641;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10112C>A|p.Pro3371Gln|10112/21291|10112/21291|3371/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2116:1:9:0,-16.8608,-189.785 +NC_045512.2 10454 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.5895;PAIRED=1;PAIREDR=0.891892;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1359;RO=37;RPL=1;RPP=5.18177;RPPR=10.1116;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=7.76406;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10189T>G|p.Phe3397Val|10189/21291|10189/21291|3397/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1359:1:31:0,-8.33969,-119.502 +NC_045512.2 10548 . T G 2.08611E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6358;PAIRED=0;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1025;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10283T>G|p.Met3428Arg|10283/21291|10283/21291|3428/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1025:1:11:0,-7.32884,-91.4635 +NC_045512.2 10602 . G T 2.08611E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6358;PAIRED=0;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=989;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10337G>T|p.Gly3446Val|10337/21291|10337/21291|3446/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:989:1:11:0,-7.32884,-88.2152 +NC_045512.2 10649 . A C 2.08611E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=4.34659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.2069;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=967;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=4.34659;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10384A>C|p.Thr3462Pro|10384/21291|10384/21291|3462/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:967:1:7:0,-7.42781,-86.6456 +NC_045512.2 10672 . T G 1.34597E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5921;PAIRED=1;PAIREDR=0.875;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=606;RO=16;RPL=0;RPP=5.18177;RPPR=29.6108;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=29.6108;SRR=15;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10407T>G|p.Ala3469Ala|10407/21291|10407/21291|3469/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:606:1:34:0,-1.7186,-51.4813 +NC_045512.2 10725 . C A 3.92939E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.4284;PAIRED=0;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=722;RO=19;RPL=1;RPP=5.18177;RPPR=12.2676;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=12.2676;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10460C>A|p.Thr3487Asn|10460/21291|10460/21291|3487/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:722:1:26:0,-3.42077,-62.7132 +NC_045512.2 10735 . T C 6.19167E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.6712;PAIRED=1;PAIREDR=0.894737;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=712;RO=19;RPL=1;RPP=5.18177;RPPR=12.2676;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=12.2676;SRR=14;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10470T>C|p.Leu3490Leu|10470/21291|10470/21291|3490/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:712:1:38:0,-2.22333,-60.6137 +NC_045512.2 11001 . C A 4.479E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.6076;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=768;RO=22;RPL=0;RPP=5.18177;RPPR=17.2236;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=17.2236;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10736C>A|p.Thr3579Lys|10736/21291|10736/21291|3579/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:23:22,1:22:768:1:34:0,-3.52478,-66.0411 +NC_045512.2 11002 . A C 5.28118E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=7.35324;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.437;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=791;RO=23;RPL=0;RPP=7.35324;RPPR=18.9659;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=18;SRP=18.9659;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10737A>C|p.Thr3579Thr|10737/21291|10737/21291|3579/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:23,2:23:791:2:47:0,-3.06093,-67.0399 +NC_045512.2 11030 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3837;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1136;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10765A>T|p.Thr3589Ser|10765/21291|10765/21291|3589/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1136:1:8:0,-8.53193,-101.747 +NC_045512.2 11035 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3837;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1137;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10770A>T|p.Ser3590Ser|10770/21291|10770/21291|3590/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1137:1:8:0,-8.53193,-101.836 +NC_045512.2 11038 . T A 2.14262E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=59.7581;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.9404;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1136;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=26.4622;SRR=6;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10773T>A|p.Leu3591Leu|10773/21291|10773/21291|3591/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1136:1:36:0,-5.73365,-98.9484 +NC_045512.2 11047 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3837;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1132;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10782A>C|p.Leu3594Phe|10782/21291|10782/21291|3594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1132:1:8:0,-8.53193,-101.387 +NC_045512.2 11074 . CTTTTTTTTGTATGA CTTTTTTTGTATGA,CTTTTTTTTTTATGA 32.7069 . AB=0.0344828,0.206897;ABP=57.5966,24.6501;AC=0,1;AF=0,0.5;AN=2;AO=1,6;CIGAR=1M1D13M,9M1X5M;DP=29;DPB=28.9333;DPRA=0,0;EPP=5.18177,8.80089;EPPR=34.9902;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=7.53051;PAIRED=1,1;PAIREDR=0.954545;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,227;QR=823;RO=22;RPL=0,0;RPP=5.18177,16.0391;RPPR=50.7827;RPR=1,6;RUN=1,1;SAF=1,5;SAP=5.18177,8.80089;SAR=0,1;SRF=20;SRP=34.9902;SRR=2;TYPE=del,snp;ANN=CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817delT|p.Leu3606fs|10817/21291|10817/21291|3606/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:29:22,1,6:22:823:1,6:38,227:-11.9855,-15.4914,-82.5863,0,-64.2769,-65.5874 +NC_045512.2 11094 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=3.40914;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.2452;PAIRED=0;PAIREDR=0.959184;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1679;RO=49;RPL=0;RPP=5.18177;RPPR=109.412;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.40914;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10829C>G|p.Ala3610Gly|10829/21291|10829/21291|3610/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1679:1:8:0,-14.2515,-150.57 +NC_045512.2 11127 . T G 1.11656E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.1156;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1951;RO=52;RPL=0;RPP=5.18177;RPPR=115.927;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10862T>G|p.Met3621Arg|10862/21291|10862/21291|3621/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1951:1:9:0,-15.0546,-174.948 +NC_045512.2 11148 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=7.18621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.132;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=1961;RO=52;RPL=0;RPP=5.18177;RPPR=83.8559;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10883T>C|p.Phe3628Ser|10883/21291|10883/21291|3628/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1961:1:35:0,-12.456,-173.247 +NC_045512.2 11152 . CAAACAT CAACAT 3.57126E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D5M;DP=53;DPB=52.7143;DPRA=0;EPP=7.35324;EPPR=55.1682;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.8816;PAIRED=1;PAIREDR=0.921569;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1886;RO=51;RPL=1;RPP=3.0103;RPPR=15.3153;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.05288;SRR=26;TYPE=del;ANN=CAACAT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10890delA|p.Lys3630fs|10890/21291|10890/21291|3630/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:51,2:51:1886:2:72:0,-9.11822,-163.168 +NC_045512.2 11208 . C A 1.36065E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=99.2232;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1950;RO=52;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10943C>A|p.Ala3648Asp|10943/21291|10943/21291|3648/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1950:1:11:0,-14.8546,-174.655 +NC_045512.2 11234 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=63.3104;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.3616;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1919;RO=52;RPL=0;RPP=5.18177;RPPR=11.1951;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10969G>A|p.Ala3657Thr|10969/21291|10969/21291|3657/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1919:1:34:0,-12.5557,-169.565 +NC_045512.2 11242 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=5.68288;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1915;RO=52;RPL=1;RPP=5.18177;RPPR=83.8559;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10977G>T|p.Trp3659Cys|10977/21291|10977/21291|3659/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1915:1:11:0,-14.8546,-171.508 +NC_045512.2 11261 . T G 1.36065E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1870;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10996T>G|p.Trp3666Gly|10996/21291|10996/21291|3666/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1870:1:11:0,-14.8546,-167.457 +NC_045512.2 11262 . G A 5.89167E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.7413;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=1853;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10997G>A|p.Trp3666*|10997/21291|10997/21291|3666/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1853:1:28:0,-13.1549,-164.222 +NC_045512.2 11269 . TA GT 1.36065E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1870;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11004_11005delTAinsGT|p.AspMet3668GluLeu|11004/21291|11004/21291|3668/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1870:1:11:0,-14.8546,-167.46 +NC_045512.2 11271 . TGGT CGGG 1.39076E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.1946;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1883;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=complex;ANN=CGGG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11006_11009delTGGTinsCGGG|p.MetVal3669ThrGly|11006/21291|11006/21291|3669/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1883:1:13:0,-14.6546,-168.432 +NC_045512.2 11276 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.5761;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1851;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11011G>T|p.Asp3671Tyr|11011/21291|11011/21291|3671/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1851:1:7:0,-15.2546,-166.142 +NC_045512.2 11277 . ATAC TTCT 1.11656E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M2X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.1156;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1816;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=complex;ANN=TTCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11012_11015delATACinsTTCT|p.AspThr3671ValLeu|11012/21291|11012/21291|3671/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1816:1:9:0,-15.0546,-162.795 +NC_045512.2 11287 . GTCTGGTTTTAAG GAAG,GTCTGGTTTTTAAG 655.65 . AB=0.681818,0.181818;ABP=15.6443,41.702;AC=1,1;AF=0.5,0.5;AN=2;AO=30,8;CIGAR=1M9D3M,6M1I7M;DP=44;DPB=23.8462;DPRA=0,0;EPP=4.16842,7.35324;EPPR=4.45795;GTI=0;LEN=9,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=12.3816;PAIRED=0.933333,0.875;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=977,299;QR=220;RO=6;RPL=30,8;RPP=68.1545,20.3821;RPPR=16.0391;RPR=0,0;RUN=1,1;SAF=13,2;SAP=4.16842,7.35324;SAR=17,6;SRF=2;SRP=4.45795;SRR=4;TYPE=del,ins;ANN=GTCTGGTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11031dupT|p.Lys3678fs|11032/21291|11032/21291|3678/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/2:44:6,30,8:6:220:30,8:977,299:-83.515,-6.50958,-15.4575,-60.8267,0,-76.4071 +NC_045512.2 11308 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=29.2231;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.8341;PAIRED=1;PAIREDR=0.946429;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1967;RO=56;RPL=0;RPP=5.18177;RPPR=33.4109;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11043C>A|p.Asp3681Glu|11043/21291|11043/21291|3681/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:1967:1:34:0,-13.7598,-173.887 +NC_045512.2 11324 . T C 9.58348E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=88.4369;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.612;PAIRED=1;PAIREDR=0.93617;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1724;RO=47;RPL=0;RPP=5.18177;RPPR=8.60069;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=5.27418;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11059T>C|p.Ser3687Pro|11059/21291|11059/21291|3687/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1724:1:38:0,-10.6522,-151.622 +NC_045512.2 11369 . G T 6.14782E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2468;PAIRED=1;PAIREDR=0.934783;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1747;RO=46;RPL=1;RPP=5.18177;RPPR=3.76559;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.76559;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11104G>T|p.Asp3702Tyr|11104/21291|11104/21291|3702/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:47:46,1:46:1747:1:38:0,-10.3511,-153.7 +NC_045512.2 11377 . T G 1.36214E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.1244;PAIRED=1;PAIREDR=0.931818;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1650;RO=44;RPL=1;RPP=5.18177;RPPR=3.20771;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.20771;SRR=23;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11112T>G|p.Gly3704Gly|11112/21291|11112/21291|3704/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1650:1:31:0,-10.4469,-145.676 +NC_045512.2 11437 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.5065;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1504;RO=40;RPL=0;RPP=5.18177;RPPR=89.8692;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11172T>G|p.Gly3724Gly|11172/21291|11172/21291|3724/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1504:1:10:0,-11.3422,-134.644 +NC_045512.2 11515 . T G 3.51075E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.2763;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1511;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11250T>G|p.Thr3750Thr|11250/21291|11250/21291|3750/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1511:1:11:0,-11.2422,-135.173 +NC_045512.2 11516 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=7.35324;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.8938;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1423;RO=39;RPL=1;RPP=3.0103;RPPR=3.06598;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11251G>A|p.Val3751Ile|11251/21291|11251/21291|3751/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:39,2:39:1423:2:76:0,-5.12742,-121.131 +NC_045512.2 11586 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=18.709;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.2051;PAIRED=1;PAIREDR=0.934426;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2258;RO=61;RPL=1;RPP=5.18177;RPPR=15.8611;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=18.709;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11321A>T|p.Asn3774Ile|11321/21291|11321/21291|3774/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2258:1:10:0,-17.6639,-202.456 +NC_045512.2 11589 . C T 3.76714E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=15.8611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.2224;PAIRED=0;PAIREDR=0.95082;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=2222;RO=61;RPL=0;RPP=5.18177;RPPR=18.709;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=18.709;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11324C>T|p.Thr3775Ile|11324/21291|11324/21291|3775/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2222:1:36:0,-15.0656,-196.615 +NC_045512.2 11803 . T C 9.08766E-17 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.538;PAIRED=1;PAIREDR=0.925;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=1458;RO=40;RPL=2;RPP=7.35324;RPPR=89.8692;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11538T>C|p.Gly3846Gly|11538/21291|11538/21291|3846/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,2:40:1458:2:70:0,-5.99593,-124.851 +NC_045512.2 11808 . GTGGC TTGGT 9.40266E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.4872;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1496;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=complex;ANN=TTGGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11543_11547delGTGGCinsTTGGT|p.Gly3848Val|11543/21291|11543/21291|3848/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1496:1:16:0,-11.0433,-133.323 +NC_045512.2 11824 . C A 1.79352E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.8687;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1525;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11559C>A|p.Ile3853Ile|11559/21291|11559/21291|3853/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1525:1:10:0,-11.6433,-136.532 +NC_045512.2 11828 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.257;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1546;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11563G>T|p.Val3855Leu|11563/21291|11563/21291|3855/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1546:1:17:0,-10.9433,-137.722 +NC_045512.2 11833 . C T 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1449;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11568C>T|p.Ala3856Ala|11568/21291|11568/21291|3856/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1449:1:9:0,-11.7433,-129.785 +NC_045512.2 11840 . C T 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1510;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11575C>T|p.Gln3859*|11575/21291|11575/21291|3859/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1510:1:9:0,-11.7433,-135.281 +NC_045512.2 11854 . A G 1.67144E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=3.0103;EPPR=26.1727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.6781;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=908;RO=24;RPL=2;RPP=7.35324;RPPR=55.1256;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=26.1727;SRR=20;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11589A>G|p.Ser3863Ser|11589/21291|11589/21291|3863/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:24,2:24:908:2:73:0,-0.895676,-75.11 +NC_045512.2 11880 . TAC TC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=41;DPB=40.6667;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.0656;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1520;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.22745;SRR=21;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11616delA|p.Leu3872fs|11616/21291|11616/21291|3872/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1520:1:38:0,-8.54496,-133.284 +NC_045512.2 11886 . C T 48.6984 . AB=0.219512;ABP=31.0276;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=22.5536;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.2132;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=1216;RO=32;RPL=9;RPP=22.5536;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=20;SRP=7.35324;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11621C>T|p.Ser3874Leu|11621/21291|11621/21291|3874/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:32,9:32:1216:9:342:-18.7954,0,-97.3988 +NC_045512.2 11896 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.0656;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1520;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.22745;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11631A>G|p.Gln3877Gln|11631/21291|11631/21291|3877/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1520:1:38:0,-8.54496,-133.284 +NC_045512.2 11919 . C T 48.6984 . AB=0.219512;ABP=31.0276;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=22.5536;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.2132;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=1214;RO=32;RPL=9;RPP=22.5536;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=20;SRP=7.35324;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11654C>T|p.Ser3885Phe|11654/21291|11654/21291|3885/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:32,9:32:1214:9:342:-18.7954,0,-97.2191 +NC_045512.2 11928 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.0656;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1499;RO=40;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11663G>A|p.Trp3888*|11663/21291|11663/21291|3888/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1499:1:38:0,-8.54496,-131.397 +NC_045512.2 11948 . C A 3.52281E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=61.9202;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.754;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1140;RO=31;RPL=1;RPP=5.18177;RPPR=14.8483;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=11.486;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11683C>A|p.His3895Asn|11683/21291|11683/21291|3895/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1140:1:34:0,-6.23405,-99.5067 +NC_045512.2 11984 . G T 3.95377E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=3.0103;EPPR=3.9754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8889;PAIRED=1;PAIREDR=0.972222;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1299;RO=36;RPL=0;RPP=7.35324;RPPR=81.1833;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11719G>T|p.Ala3907Ser|11719/21291|11719/21291|3907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:36,2:36:1299:2:76:0,-4.22433,-109.984 +NC_045512.2 12244 . TGA TA 1.54744E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D1M;DP=40;DPB=39.3333;DPRA=0;EPP=7.35324;EPPR=8.7247;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.9438;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1417;RO=38;RPL=2;RPP=7.35324;RPPR=8.7247;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=21.525;SRR=28;TYPE=del;ANN=TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11980delG|p.Asp3994fs|11980/21291|11980/21291|3994/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:38,2:38:1417:2:76:0,-4.82639,-120.603 +NC_045512.2 12259 . A T 2.26316E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=5.3706;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2448;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=874;RO=23;RPL=0;RPP=5.18177;RPPR=52.9542;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=5.3706;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11994A>T|p.Gln3998His|11994/21291|11994/21291|3998/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:874:1:11:0,-6.12472,-77.8832 +NC_045512.2 12410 . A T 1.70989E-6 . AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=8.61041;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7476;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=701;RO=19;RPL=2;RPP=7.35324;RPPR=44.2683;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=8.61041;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12145A>T|p.Ile4049Phe|12145/21291|12145/21291|4049/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:21:19,2:19:701:2:75:-0.798713,0,-57.0966 +NC_045512.2 12419 . G T 2.15846E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=968;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12154G>T|p.Ala4052Ser|12154/21291|12154/21291|4052/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:968:1:34:0,-5.02993,-84.0341 +NC_045512.2 12491 . G T 1.62542E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.0087;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=760;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=46.4397;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12226G>T|p.Asp4076Tyr|12226/21291|12226/21291|4076/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:760:1:38:0,-2.52436,-64.9333 +NC_045512.2 12674 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.0103;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.8938;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1444;RO=39;RPL=2;RPP=7.35324;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12409G>C|p.Val4137Leu|12409/21291|12409/21291|4137/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:39,2:39:1444:2:76:0,-5.12742,-123.031 +NC_045512.2 12748 . T C 4.07431E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1090;RO=29;RPL=0;RPP=5.18177;RPPR=12.0706;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=12.0706;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12483T>C|p.Thr4161Thr|12483/21291|12483/21291|4161/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1090:1:38:0,-5.23363,-94.6098 +NC_045512.2 12795 . G T 1.63938E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=51.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1092;RO=30;RPL=1;RPP=5.18177;RPPR=5.61607;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=10.2485;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12530G>T|p.Gly4177Val|12530/21291|12530/21291|4177/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1092:1:34:0,-5.93302,-95.187 +NC_045512.2 12862 . T C 5.18713E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=18.6449;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.4565;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=751;RO=20;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12597T>C|p.Ser4199Ser|12597/21291|12597/21291|4199/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:751:1:23:0,-4.02172,-65.6201 +NC_045512.2 12864 . A T 2.12537E-6 . AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=22.325;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=717;RO=19;RPL=0;RPP=7.35324;RPPR=8.61041;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=9;SRP=3.12459;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12599A>T|p.Asp4200Val|12599/21291|12599/21291|4200/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:21:19,2:19:717:2:76:-0.893181,0,-58.5411 +NC_045512.2 13010 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=34.5724;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.0711;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1481;RO=43;RPL=0;RPP=5.18177;RPPR=3.46479;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=25.2805;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12745A>C|p.Thr4249Pro|12745/21291|12745/21291|4249/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1481:1:34:0,-9.84641,-130.176 +NC_045512.2 13012 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=66.97;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.4981;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1565;RO=44;RPL=0;RPP=5.18177;RPPR=12.6832;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=26.8965;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12747A>C|p.Thr4249Thr|12747/21291|12747/21291|4249/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1565:1:12:0,-12.3464,-139.935 +NC_045512.2 13015 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=88.4369;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.2188;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1739;RO=47;RPL=0;RPP=5.18177;RPPR=23.3852;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=31.8863;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12750A>C|p.Val4250Val|12750/21291|12750/21291|4250/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1739:1:31:0,-11.35,-153.682 +NC_045512.2 13022 . CAAGC CAAAGC 6.14782E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=47;DPB=47.2;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2468;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1746;RO=46;RPL=0;RPP=5.18177;RPPR=30.2009;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=30.2009;SRR=11;TYPE=ins;ANN=CAAAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12759dupA|p.Ala4254fs|12760/21291|12760/21291|4254/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:47:46,1:46:1746:1:38:0,-10.3511,-153.61 +NC_045512.2 13050 . C T 6.14782E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2468;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1721;RO=46;RPL=0;RPP=5.18177;RPPR=30.2009;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=30.2009;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12785C>T|p.Ala4262Val|12785/21291|12785/21291|4262/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:47:46,1:46:1721:1:38:0,-10.3511,-151.356 +NC_045512.2 13088 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=8.46682;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=103.089;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2892;RO=78;RPL=1;RPP=5.18177;RPPR=96.662;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=4.01252;SRR=42;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12823G>T|p.Asp4275Tyr|12823/21291|12823/21291|4275/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2892:1:38:0,-19.9841,-256.684 +NC_045512.2 13090 . T A 8.10661E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=3.0103;EPPR=9.35551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=92.4668;PAIRED=1;PAIREDR=0.961039;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=2841;RO=77;RPL=0;RPP=7.35324;RPPR=88.3181;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=35;SRP=4.39215;SRR=42;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12825T>A|p.Asp4275Glu|12825/21291|12825/21291|4275/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:77,2:77:2841:2:75:0,-16.661,-248.778 +NC_045512.2 13118 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=3.0103;EPPR=3.04177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=81.5914;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=2581;RO=69;RPL=0;RPP=7.35324;RPPR=152.842;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=35;SRP=3.04177;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12853G>T|p.Ala4285Ser|12853/21291|12853/21291|4285/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:69,2:69:2581:2:75:0,-14.2528,-225.389 +NC_045512.2 13168 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=157.185;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.3068;PAIRED=0;PAIREDR=0.957746;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=2691;RO=71;RPL=0;RPP=5.18177;RPPR=3.04088;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12903C>A|p.His4301Gln|12903/21291|12903/21291|4301/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2691:1:17:0,-19.9742,-240.697 +NC_045512.2 13174 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=157.185;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6883;PAIRED=0;PAIREDR=0.957746;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2694;RO=71;RPL=0;RPP=5.18177;RPPR=3.04088;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12909T>G|p.Gly4303Gly|12909/21291|12909/21291|4303/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2694:1:11:0,-20.5742,-241.567 +NC_045512.2 13190 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=157.185;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6883;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2678;RO=71;RPL=1;RPP=5.18177;RPPR=3.04088;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.04088;SRR=36;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12925A>T|p.Thr4309Ser|12925/21291|12925/21291|4309/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2678:1:11:0,-20.5742,-240.128 +NC_045512.2 13232 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=109.474;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=93.7066;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=2685;RO=71;RPL=1;RPP=5.18177;RPPR=8.17902;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12967G>A|p.Gly4323Ser|12967/21291|12967/21291|4323/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2685:1:37:0,-17.9763,-238.162 +NC_045512.2 13235 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=16.4979;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=95.3144;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=2650;RO=71;RPL=1;RPP=5.18177;RPPR=82.5596;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12970G>A|p.Ala4324Thr|12970/21291|12970/21291|4324/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2650:1:30:0,-18.6746,-235.707 +NC_045512.2 13238 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=4.50892;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6883;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2680;RO=71;RPL=1;RPP=5.18177;RPPR=124.399;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.04088;SRR=36;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12973T>A|p.Ser4325Thr|12973/21291|12973/21291|4325/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2680:1:11:0,-20.5742,-240.31 +NC_045512.2 13326 . CAACT CAAACT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=40;DPB=40.2;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.137;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1436;RO=38;RPL=0;RPP=5.18177;RPPR=69.0688;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=69.0688;SRR=36;TYPE=ins;ANN=CAAACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13063dupA|p.Thr4355fs|13064/21291|13064/21291|4355/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:38,1:38:1436:1:38:0,-8.28774,-125.764 +NC_045512.2 13384 . C G 3.19931E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2968;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=842;RO=24;RPL=1;RPP=5.18177;RPPR=26.1727;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=26.1727;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13119C>G|p.Cys4373Trp|13119/21291|13119/21291|4373/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:24,1:24:842:1:34:0,-4.12684,-72.6983 +NC_045512.2 13385 . G C 2.47418E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.5885;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=674;RO=19;RPL=1;RPP=5.18177;RPPR=16.8392;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=16.8392;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13120G>C|p.Gly4374Arg|13120/21291|13120/21291|4374/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:674:1:34:0,-2.62169,-57.5867 +NC_045512.2 13605 . C A 7.3683E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=58.6;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.046;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1403;RO=40;RPL=0;RPP=5.18177;RPPR=34.2795;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=58.6;SRR=4;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13341C>A|p.Arg4447Arg|13341/21291|13341/21291|4447/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1403:1:12:0,-11.1422,-125.355 +NC_045512.2 13690 . G T 1.34405E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9749;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2274;RO=61;RPL=0;RPP=5.18177;RPPR=135.47;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13426G>T|p.Glu4476*|13426/21291|13426/21291|4476/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2274:1:11:0,-17.5639,-203.8 +NC_045512.2 13724 . C T 1.34405E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9749;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2292;RO=61;RPL=0;RPP=5.18177;RPPR=135.47;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13460C>T|p.Ala4487Val|13460/21291|13460/21291|4487/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2292:1:11:0,-17.5639,-205.418 +NC_045512.2 13748 . A T 1.34405E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.0459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9749;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2297;RO=61;RPL=0;RPP=5.18177;RPPR=118.668;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13484A>T|p.Lys4495Met|13484/21291|13484/21291|4495/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2297:1:11:0,-17.5639,-205.865 +NC_045512.2 13796 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=126.927;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.7642;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2317;RO=61;RPL=1;RPP=5.18177;RPPR=3.90025;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13532T>C|p.Leu4511Pro|13532/21291|13532/21291|4511/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2317:1:38:0,-14.8666,-204.963 +NC_045512.2 13835 . G A 3.76714E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.90025;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.2224;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=2306;RO=61;RPL=1;RPP=5.18177;RPPR=135.47;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.90025;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13571G>A|p.Arg4524Lys|13571/21291|13571/21291|4524/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2306:1:36:0,-15.0656,-204.175 +NC_045512.2 13932 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.5097;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1404;RO=37;RPL=1;RPP=5.18177;RPPR=24.1968;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=24.1968;SRR=28;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13668T>G|p.Asp4556Glu|13668/21291|13668/21291|4556/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1404:1:27:0,-8.73936,-123.949 +NC_045512.2 13971 . CTTAG CTAG,CTTG 3.76391E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=2,1;CIGAR=1M1D3M,3M1D1M;DP=38;DPB=37.4;DPRA=0,0;EPP=7.35324,5.18177;EPPR=70.5741;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=37.8173;PAIRED=0.5,1;PAIREDR=0.971429;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,38;QR=1299;RO=35;RPL=2,1;RPP=7.35324,5.18177;RPPR=16.9698;RPR=0,0;RUN=1,1;SAF=0,0;SAP=7.35324,5.18177;SAR=2,1;SRF=9;SRP=20.9405;SRR=26;TYPE=del,del;ANN=CTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13709delT|p.Leu4570fs|13709/21291|13709/21291|4570/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:35,2,1:35:1299:2,1:76,38:0,-4.30303,-109.993,-7.41954,-107.478,-113.411 +NC_045512.2 13983 . T G 3.56286E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=31.7504;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9213;PAIRED=1;PAIREDR=0.882353;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=616;RO=17;RPL=1;RPP=5.18177;RPPR=4.1599;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.13803;SRR=8;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13719T>G|p.Arg4573Arg|13719/21291|13719/21291|4573/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:616:1:34:0,-2.01963,-52.3727 +NC_045512.2 14038 . G A 3.36415E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2194;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=732;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13774G>A|p.Gly4592Ser|13774/21291|13774/21291|4592/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:732:1:11:0,-5.22163,-65.104 +NC_045512.2 14176 . A G 2.12537E-6 . AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=710;RO=19;RPL=2;RPP=7.35324;RPPR=44.2683;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=4.03889;SRR=11;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13912A>G|p.Thr4638Ala|13912/21291|13912/21291|4638/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:21:19,2:19:710:2:76:-0.893181,0,-57.9105 +NC_045512.2 14269 . G A 2.90829E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1368;RO=36;RPL=1;RPP=5.18177;RPPR=18.4519;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=18.4519;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14005G>A|p.Glu4669Lys|14005/21291|14005/21291|4669/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1368:1:38:0,-7.34084,-119.614 +NC_045512.2 14290 . G T 6.2985E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.9827;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1383;RO=37;RPL=1;RPP=5.18177;RPPR=19.9713;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=16.2152;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14026G>T|p.Asp4676Tyr|14026/21291|14026/21291|4676/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1383:1:38:0,-7.64187,-120.964 +NC_045512.2 14327 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=3.0103;EPPR=3.19126;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1782;RO=48;RPL=0;RPP=7.35324;RPPR=107.241;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14063C>T|p.Pro4688Leu|14063/21291|14063/21291|4688/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,2:48:1782:2:76:0,-7.83669,-153.432 +NC_045512.2 14407 . CCTACAAGT CT,CTTACAAGT 1314.95 . AB=0.28,0.72;ABP=24.0302,24.0302;AC=1,1;AF=0.5,0.5;AN=2;AO=14,36;CIGAR=1M7D1M,1M1X7M;DP=50;DPB=39.1111;DPRA=0,0;EPP=33.4109,81.1833;EPPR=0;GTI=0;LEN=7,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=48.6802;PAIRED=0.928571,0.944444;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=518,1367;QR=0;RO=0;RPL=8,18;RPP=3.63072,3.0103;RPPR=0;RPR=6,18;RUN=1,1;SAF=8,18;SAP=3.63072,3.0103;SAR=6,18;SRF=0;SRP=0;SRR=0;TYPE=del,snp;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144_14150delCTACAAG|p.Pro4715fs|14144/21291|14144/21291|4715/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/2:50:0,14,36:0:0:14,36:518,1367:-154.858,-112.484,-108.27,-42.7461,0,-31.9091 +NC_045512.2 14435 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=7.35324;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1765;RO=48;RPL=1;RPP=3.0103;RPPR=3.19126;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14171A>T|p.Lys4724Ile|14171/21291|14171/21291|4724/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,2:48:1765:2:76:0,-7.83669,-151.894 +NC_045512.2 14442 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=7.35324;EPPR=90.593;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1805;RO=48;RPL=1;RPP=3.0103;RPPR=4.6389;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14178T>C|p.Phe4726Phe|14178/21291|14178/21291|4726/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,2:48:1805:2:76:0,-7.83669,-155.498 +NC_045512.2 14450 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=19.0083;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.7847;PAIRED=1;PAIREDR=0.938776;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1849;RO=49;RPL=1;RPP=5.18177;RPPR=45.5977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.05462;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14186G>T|p.Gly4729Val|14186/21291|14186/21291|4729/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1849:1:10:0,-14.0515,-165.672 +NC_045512.2 14531 . C A 3.80608E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2448;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=872;RO=23;RPL=1;RPP=5.18177;RPPR=52.9542;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=52.9542;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14267C>A|p.Ser4756Tyr|14267/21291|14267/21291|4756/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:872:1:11:0,-6.12472,-77.7033 +NC_045512.2 14549 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9631;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1354;RO=37;RPL=0;RPP=5.18177;RPPR=10.1116;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=10.1116;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14285A>C|p.Glu4762Ala|14285/21291|14285/21291|4762/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1354:1:12:0,-10.2391,-120.954 +NC_045512.2 14550 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.87;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1385;RO=38;RPL=0;RPP=5.18177;RPPR=8.7247;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=8.7247;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14286A>C|p.Glu4762Asp|14286/21291|14286/21291|4762/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1385:1:27:0,-9.04039,-122.243 +NC_045512.2 14553 . A C 1.30189E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.0447;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1634;RO=44;RPL=0;RPP=5.18177;RPPR=3.79993;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.79993;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14289A>C|p.Leu4763Phe|14289/21291|14289/21291|4763/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1634:1:27:0,-10.8466,-144.637 +NC_045512.2 14594 . GTA GA 8.14122E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=40;DPB=39.6667;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.6212;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1445;RO=39;RPL=1;RPP=5.18177;RPPR=4.40227;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=4.40227;SRR=17;TYPE=del;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14331delT|p.Asn4778fs|14331/21291|14331/21291|4777/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1445:1:34:0,-8.64229,-126.939 +NC_045512.2 14598 . T G 1.37871E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.8709;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1275;RO=35;RPL=1;RPP=5.18177;RPPR=8.03571;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=8.03571;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14334T>G|p.Asn4778Lys|14334/21291|14334/21291|4778/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1275:1:31:0,-7.73763,-111.948 +NC_045512.2 14667 . T G 1.65791E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=3.0103;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.2506;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1615;RO=43;RPL=0;RPP=7.35324;RPPR=96.3836;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14403T>G|p.Thr4801Thr|14403/21291|14403/21291|4801/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:43,2:43:1615:2:76:0,-6.33154,-138.413 +NC_045512.2 14672 . AACCC GACCT,AACCT 443.765 . AB=0.0444444,0.444444;ABP=84.1269,4.21667;AC=0,1;AF=0,0.5;AN=2;AO=2,20;CIGAR=1X3M1X,4M1X;DP=45;DPB=45;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.10471;GTI=0;LEN=5,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=102.181;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,754;QR=858;RO=23;RPL=0,0;RPP=7.35324,46.4397;RPPR=52.9542;RPR=2,20;RUN=1,1;SAF=1,10;SAP=3.0103,3.0103;SAR=1,10;SRF=11;SRP=3.10471;SRR=12;TYPE=complex,snp;ANN=GACCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14408_14412delAACCCinsGACCT|p.Lys4803Arg|14408/21291|14408/21291|4803/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:45:23,2,20:23:858:2,20:76,754:-54.8669,-55.5573,-125.2,0,-64.0069,-64.2199 +NC_045512.2 14694 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.3544;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1654;RO=44;RPL=0;RPP=5.18177;RPPR=98.5551;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.20771;SRR=23;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14430C>T|p.Asp4810Asp|14430/21291|14430/21291|4810/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1654:1:30:0,-10.5468,-146.133 +NC_045512.2 14708 . C A 1.65791E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=7.35324;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.2506;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1631;RO=43;RPL=1;RPP=3.0103;RPPR=3.0608;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14444C>A|p.Ala4815Asp|14444/21291|14444/21291|4815/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:43,2:43:1631:2:76:0,-6.33154,-139.85 +NC_045512.2 14794 . G A 1.65791E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=3.0103;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.2506;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1619;RO=43;RPL=2;RPP=7.35324;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14530G>A|p.Asp4844Asn|14530/21291|14530/21291|4844/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:43,2:43:1619:2:76:0,-6.33154,-138.77 +NC_045512.2 14902 . ATTAA ATAA 1.31392E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=40;DPB=39.8;DPRA=0;EPP=5.18177;EPPR=79.2345;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.704;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1474;RO=39;RPL=1;RPP=5.18177;RPPR=4.40227;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=5.73856;SRR=23;TYPE=del;ANN=ATAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14640delT|p.Asn4881fs|14640/21291|14640/21291|4880/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1474:1:38:0,-8.24393,-129.148 +NC_045512.2 14924 . T G 1.49624E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=61.9202;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.3638;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1110;RO=31;RPL=1;RPP=5.18177;RPPR=3.64073;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14660T>G|p.Val4887Gly|14660/21291|14660/21291|4887/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1110:1:27:0,-6.93318,-97.5053 +NC_045512.2 14978 . G T 3.63991E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=3.0103;EPPR=3.08518;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8156;PAIRED=1;PAIREDR=0.965517;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1087;RO=29;RPL=0;RPP=7.35324;RPPR=65.983;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14714G>T|p.Arg4905Ile|14714/21291|14714/21291|4905/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:29,2:29:1087:2:75:0,-2.21159,-91.0197 +NC_045512.2 14990 . A T 1.00355E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=3.0103;EPPR=3.08518;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6172;PAIRED=1;PAIREDR=0.965517;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1082;RO=29;RPL=0;RPP=7.35324;RPPR=65.983;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14726A>T|p.Asp4909Val|14726/21291|14726/21291|4909/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:29,2:29:1082:2:21:0,-7.33694,-95.6944 +NC_045512.2 15096 . T A 2.34019E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=26.4622;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6929;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1132;RO=30;RPL=1;RPP=5.18177;RPPR=17.1973;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.29983;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14832T>A|p.Asn4944Lys|14832/21291|14832/21291|4944/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1132:1:11:0,-8.23193,-101.087 +NC_045512.2 15173 . C T 7.79043E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=64.083;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.1095;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1139;RO=32;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.28173;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14909C>T|p.Ser4970Leu|14909/21291|14909/21291|4970/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1139:1:34:0,-6.53508,-99.4146 +NC_045512.2 15174 . A C 5.56019E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=7.35324;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.0378;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1124;RO=32;RPL=0;RPP=7.35324;RPPR=3.28173;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=3.28173;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14910A>C|p.Ser4970Ser|14910/21291|14910/21291|4970/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:32,2:32:1124:2:39:0,-6.53023,-97.7544 +NC_045512.2 15175 . A C 9.77912E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.4331;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1213;RO=34;RPL=0;RPP=5.18177;RPPR=4.03217;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=4.03217;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14911A>C|p.Ile4971Leu|14911/21291|14911/21291|4971/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1213:1:27:0,-7.83627,-106.772 +NC_045512.2 15245 . T G 1.11955E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=5.18177;EPPR=66.2462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.466;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1219;RO=33;RPL=1;RPP=5.18177;RPPR=22.0271;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=24;SRP=17.8158;SRR=9;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14981T>G|p.Leu4994*|14981/21291|14981/21291|4994/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:33,1:33:1219:1:34:0,-6.83611,-106.612 +NC_045512.2 15269 . A C 9.53827E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=3.79993;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8073;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1589;RO=44;RPL=0;RPP=5.18177;RPPR=98.5551;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=24;SRP=3.79993;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15005A>C|p.Glu5002Ala|15005/21291|15005/21291|5002/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1589:1:15:0,-12.0464,-141.784 +NC_045512.2 15279 . C T 422.797 . AB=0.434783;ABP=4.70971;AC=1;AF=0.5;AN=2;AO=20;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=3.44459;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=97.3526;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=739;QR=958;RO=26;RPL=0;RPP=46.4397;RPPR=59.4686;RPR=20;RUN=1;SAF=11;SAP=3.44459;SAR=9;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15015C>T|p.His5005His|15015/21291|15015/21291|5005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:46:26,20:26:958:20:739:-52.9896,0,-72.6862 +NC_045512.2 15334 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=7.35324;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.8099;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1626;RO=44;RPL=1;RPP=3.0103;RPPR=3.20771;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=23;SRP=3.20771;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15070A>G|p.Ile5024Val|15070/21291|15070/21291|5024/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:44,2:44:1626:2:75:0,-6.72704,-139.49 +NC_045512.2 15355 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=92.2337;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.0927;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1679;RO=45;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15091G>T|p.Ala5031Ser|15091/21291|15091/21291|5031/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1679:1:11:0,-12.7474,-150.281 +NC_045512.2 15374 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=92.2337;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.0927;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1657;RO=45;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15110G>T|p.Cys5037Phe|15110/21291|15110/21291|5037/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1657:1:11:0,-12.7474,-148.296 +NC_045512.2 15401 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=92.2337;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.3229;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1669;RO=45;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15137G>T|p.Arg5046Ile|15137/21291|15137/21291|5046/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1669:1:10:0,-12.8474,-149.48 +NC_045512.2 15406 . G T 1.41529E-12 . AB=0.0869565;ABP=71.1757;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=11.6962;EPPR=55.9529;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.7552;PAIRED=1;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=1534;RO=42;RPL=2;RPP=3.0103;RPPR=10.4553;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=22;SRP=3.21711;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15142G>T|p.Ala5048Ser|15142/21291|15142/21291|5048/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:46:42,4:42:1534:4:152:-0.202515,0,-124.49 +NC_045512.2 15412 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.7188;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1679;RO=45;RPL=1;RPP=5.18177;RPPR=100.727;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=24;SRP=3.44459;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15148G>A|p.Glu5050Lys|15148/21291|15148/21291|5050/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1679:1:30:0,-10.8478,-148.381 +NC_045512.2 15414 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=3.05855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.0927;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1674;RO=45;RPL=1;RPP=5.18177;RPPR=100.727;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15150G>T|p.Glu5050Asp|15150/21291|15150/21291|5050/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1674:1:11:0,-12.7474,-149.833 +NC_045512.2 15432 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=3.05855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.5532;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1663;RO=45;RPL=1;RPP=5.18177;RPPR=100.727;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15168T>G|p.Ser5056Arg|15168/21291|15168/21291|5056/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1663:1:9:0,-12.9474,-149.045 +NC_045512.2 15461 . A T 1.51432E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=3.05855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7834;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1605;RO=45;RPL=1;RPP=5.18177;RPPR=100.727;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15197A>T|p.Tyr5066Phe|15197/21291|15197/21291|5066/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1605:1:8:0,-13.0474,-143.921 +NC_045512.2 15463 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=3.05855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.3229;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1602;RO=45;RPL=1;RPP=5.18177;RPPR=100.727;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15199G>T|p.Val5067Phe|15199/21291|15199/21291|5067/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1602:1:10:0,-12.8474,-143.45 +NC_045512.2 15539 . TCAC TC,TCCC 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M2D1M,2M1X1M;DP=56;DPB=55.5;DPRA=0,0;EPP=5.18177,5.18177;EPPR=120.27;GTI=0;LEN=2,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=70.8934;PAIRED=1,1;PAIREDR=0.962963;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,24;QR=2029;RO=54;RPL=0,0;RPP=5.18177,5.18177;RPPR=8.80089;RPR=1,1;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=33;SRP=8.80089;SRR=21;TYPE=del,snp;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15277_15278delAC|p.Thr5093fs|15277/21291|15277/21291|5093/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:56:54,1,1:54:2029:1,1:38,24:0,-13.0692,-179.13,-14.4666,-177.574,-180.39 +NC_045512.2 15552 . TAATG TATG,TAATC 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D3M,4M1X;DP=53;DPB=52.8;DPRA=0,0;EPP=5.18177,5.18177;EPPR=113.755;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=66.9515;PAIRED=1,1;PAIREDR=0.960784;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,38;QR=1894;RO=51;RPL=1,0;RPP=5.18177,5.18177;RPPR=21.7871;RPR=0,1;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=36;SRP=21.7871;SRR=15;TYPE=del,snp;ANN=TATG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15290delA|p.Asn5097fs|15290/21291|15290/21291|5097/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:51,1,1:51:1894:1,1:38,38:0,-12.236,-166.927,-12.236,-164.111,-166.927 +NC_045512.2 15593 . A T 1.72677E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=75;DPB=75;DPRA=0;EPP=5.18177;EPPR=3.12768;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.0539;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=2752;RO=74;RPL=0;RPP=5.18177;RPPR=163.699;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=3.12768;SRR=38;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15329A>T|p.Lys5110Met|15329/21291|15329/21291|5110/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:75:74,1:74:2752:1:36:0,-18.979,-244.296 +NC_045512.2 15597 . T G 6.31357E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=107.474;PAIRED=0;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2761;RO=76;RPL=0;RPP=5.18177;RPPR=168.042;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=37;SRP=3.12459;SRR=39;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15333T>G|p.Tyr5111*|15333/21291|15333/21291|5111/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2761:1:7:0,-22.4793,-248.003 +NC_045512.2 15600 . C A 1.93471E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=3.73412;EPPR=3.12768;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=84.8607;PAIRED=1;PAIREDR=0.959459;PAO=0;PQA=0;PQR=0;PRO=0;QA=90;QR=2662;RO=74;RPL=0;RPP=9.52472;RPPR=163.699;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=36;SRP=3.12768;SRR=38;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15336C>A|p.Val5112Val|15336/21291|15336/21291|5112/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:74,3:74:2662:3:90:0,-14.7844,-231.406 +NC_045512.2 15645 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=122.159;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.944;PAIRED=0;PAIREDR=0.974026;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=2850;RO=77;RPL=1;RPP=5.18177;RPPR=11.1604;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=3.71532;SRR=41;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15381A>G|p.Arg5127Arg|15381/21291|15381/21291|5127/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2850:1:37:0,-19.7825,-252.999 +NC_045512.2 15736 . T G 6.31357E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=6.42261;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=107.926;PAIRED=1;PAIREDR=0.961039;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2875;RO=77;RPL=0;RPP=5.18177;RPPR=114.94;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=37;SRP=3.26411;SRR=40;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15472T>G|p.Phe5158Val|15472/21291|15472/21291|5158/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2875:1:11:0,-22.3803,-257.85 +NC_045512.2 15737 . T G 1.34102E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=3.0385;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=107.235;PAIRED=1;PAIREDR=0.961039;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2864;RO=77;RPL=1;RPP=5.18177;RPPR=145.171;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=3.71532;SRR=41;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15473T>G|p.Phe5158Cys|15473/21291|15473/21291|5158/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2864:1:14:0,-22.0803,-256.563 +NC_045512.2 15741 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=3.0103;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=95.0347;PAIRED=1;PAIREDR=0.960526;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=2837;RO=76;RPL=2;RPP=7.35324;RPPR=159.471;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=36;SRP=3.46745;SRR=40;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15477T>A|p.Asn5159Lys|15477/21291|15477/21291|5159/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:76,2:76:2837:2:57:0,-18.0661,-250.12 +NC_045512.2 15768 . G T 2.90829E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.46745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=106.553;PAIRED=1;PAIREDR=0.960526;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2773;RO=76;RPL=1;RPP=5.18177;RPPR=168.042;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.46745;SRR=40;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15504G>T|p.Val5168Val|15504/21291|15504/21291|5168/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2773:1:11:0,-22.0793,-248.675 +NC_045512.2 15770 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=106.783;PAIRED=0;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2765;RO=76;RPL=1;RPP=5.18177;RPPR=168.042;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=4.03889;SRR=41;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15506C>T|p.Ala5169Val|15506/21291|15506/21291|5169/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2765:1:10:0,-22.1793,-248.061 +NC_045512.2 15873 . ATTTTGC ATTTGC 9.4175E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D5M;DP=57;DPB=56.8571;DPRA=0;EPP=5.18177;EPPR=124.613;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.9168;PAIRED=1;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2088;RO=56;RPL=1;RPP=5.18177;RPPR=25.3454;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=25.3454;SRR=40;TYPE=del;ANN=ATTTGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15613delT|p.Cys5205fs|15613/21291|15613/21291|5205/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2088:1:38:0,-13.3614,-184.374 +NC_045512.2 15885 . A C 4.21917E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.9828;PAIRED=1;PAIREDR=0.85;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1424;RO=40;RPL=1;RPP=5.18177;RPPR=6.48466;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=6.48466;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15621A>C|p.Gln5207His|15621/21291|15621/21291|5207/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1424:1:34:0,-8.94332,-125.054 +NC_045512.2 15976 . G T 2.08611E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6358;PAIRED=0;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1026;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.73412;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15712G>T|p.Asp5238Tyr|15712/21291|15712/21291|5238/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1026:1:11:0,-7.32884,-91.5534 +NC_045512.2 15995 . G T 2.08611E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6358;PAIRED=0;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1024;RO=27;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.73412;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15731G>T|p.Gly5244Val|15731/21291|15731/21291|5244/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1024:1:11:0,-7.32884,-91.3736 +NC_045512.2 16061 . A G 2.15846E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=5.02092;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=0.851852;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1013;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=5.02092;SRR=11;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15797A>G|p.Asn5266Ser|15797/21291|15797/21291|5266/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1013:1:34:0,-5.02993,-88.0831 +NC_045512.2 16078 . GTCTTTCA TTTTTTAC 9.28165E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X3M2X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=8;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.4056;PAIRED=0;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1005;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.73412;SRR=12;TYPE=complex;ANN=TTTTTTAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15814_15821delGTCTTTCAinsTTTTTTAC|p.ValPheHis5272PhePheThr|15814/21291|15814/21291|5272/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1005:1:12:0,-7.22885,-89.5643 +NC_045512.2 16158 . G T 7.48846E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.3796;PAIRED=1;PAIREDR=0.958333;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=909;RO=24;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.0103;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15894G>T|p.Met5298Ile|15894/21291|15894/21291|5298/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:24,1:24:909:1:38:0,-3.72848,-78.3336 +NC_045512.2 16176 . T C 259.683 . AB=0.48;ABP=3.09716;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=29.068;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.7942;PAIRED=0.916667;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=454;QR=494;RO=13;RPL=6;RPP=3.0103;RPPR=3.17734;RPR=6;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15912T>C|p.Thr5304Thr|15912/21291|15912/21291|5304/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:25:13,12:13:494:12:454:-33.6837,0,-37.282 +NC_045512.2 16217 . C A 1.06229E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=3.86001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.1658;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=811;RO=23;RPL=0;RPP=5.18177;RPPR=52.9542;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.86001;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15953C>A|p.Thr5318Lys|15953/21291|15953/21291|5318/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:811:1:7:0,-6.52472,-72.5979 +NC_045512.2 16421 . A C 2.49957E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=44.6459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.5611;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=814;RO=23;RPL=0;RPP=5.18177;RPPR=3.10471;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.10471;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16157A>C|p.Gln5386Pro|16157/21291|16157/21291|5386/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:814:1:27:0,-4.52494,-70.8769 +NC_045512.2 16479 . T C 1.32901E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=51.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.4822;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1110;RO=30;RPL=0;RPP=5.18177;RPPR=7.64277;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=4.16842;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16215T>C|p.Phe5405Phe|16215/21291|16215/21291|5405/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1110:1:38:0,-5.53466,-96.4027 +NC_045512.2 16493 . A T 2.41553E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=51.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6929;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1137;RO=30;RPL=0;RPP=5.18177;RPPR=7.64277;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=4.16842;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16229A>T|p.Asn5410Ile|16229/21291|16229/21291|5410/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1137:1:11:0,-8.23193,-101.536 +NC_045512.2 16508 . G T 3.36083E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=43.4331;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.9924;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=965;RO=26;RPL=1;RPP=5.18177;RPPR=24.391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=15.0369;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16244G>T|p.Gly5415Val|16244/21291|16244/21291|5415/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:965:1:34:0,-4.7289,-83.7669 +NC_045512.2 16536 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.0421;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1355;RO=37;RPL=0;RPP=5.18177;RPPR=83.3548;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16272C>A|p.Ser5424Arg|16272/21291|16272/21291|5424/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1355:1:16:0,-9.83916,-120.64 +NC_045512.2 16596 . C A 6.99161E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=77.0689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.784;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1440;RO=38;RPL=0;RPP=5.18177;RPPR=3.23888;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.0103;SRR=19;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16332C>A|p.Tyr5444*|16332/21291|16332/21291|5444/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1440:1:10:0,-10.7402,-128.887 +NC_045512.2 16603 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=69.0688;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5537;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1412;RO=38;RPL=1;RPP=5.18177;RPPR=3.23888;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16339G>T|p.Ala5447Ser|16339/21291|16339/21291|5447/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1412:1:11:0,-10.6402,-126.264 +NC_045512.2 16630 . C A 4.29279E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=7.35324;EPPR=59.4099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.2225;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1367;RO=37;RPL=1;RPP=3.0103;RPPR=3.06899;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16366C>A|p.Leu5456Ile|16366/21291|16366/21291|5456/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:37,2:37:1367:2:76:0,-4.52536,-116.103 +NC_045512.2 16663 . G T 4.29279E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=7.35324;EPPR=59.4099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.2225;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1327;RO=37;RPL=1;RPP=3.0103;RPPR=4.47751;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16399G>T|p.Glu5467*|16399/21291|16399/21291|5467/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:37,2:37:1327:2:76:0,-4.52536,-112.495 +NC_045512.2 16700 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.784;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1396;RO=38;RPL=1;RPP=5.18177;RPPR=85.5263;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16436G>T|p.Arg5479Leu|16436/21291|16436/21291|5479/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1396:1:10:0,-10.7402,-124.93 +NC_045512.2 16710 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.0142;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1369;RO=38;RPL=1;RPP=5.18177;RPPR=85.5263;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16446G>T|p.Leu5482Leu|16446/21291|16446/21291|5482/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1369:1:9:0,-10.8402,-122.596 +NC_045512.2 16718 . G T 1.50154E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=19.3799;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.7464;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=970;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=19.3799;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16454G>T|p.Arg5485Ile|16454/21291|16454/21291|5485/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:970:1:9:0,-7.22781,-86.7148 +NC_045512.2 16751 . C A 3.1823E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=59.7581;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1095;RO=30;RPL=0;RPP=5.18177;RPPR=13.4334;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=10.2485;SRR=20;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16487C>A|p.Pro5496His|16487/21291|16487/21291|5496/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1095:1:34:0,-5.93302,-95.4585 +NC_045512.2 16985 . C A 1.35112E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=7.35324;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.496;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1060;RO=28;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16721C>A|p.Thr5574Asn|16721/21291|16721/21291|5574/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:28,2:28:1060:2:75:0,-1.91056,-88.5912 +NC_045512.2 17078 . AGGGAC AGGGGAC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I5M;DP=42;DPB=42.1667;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4278;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1552;RO=41;RPL=0;RPP=5.18177;RPPR=9.41879;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=9.41879;SRR=15;TYPE=ins;ANN=AGGGGAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16817dupG|p.Pro5607fs|16818/21291|16818/21291|5606/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1552:1:38:0,-8.84599,-136.163 +NC_045512.2 17103 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4278;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1556;RO=41;RPL=1;RPP=5.18177;RPPR=11.961;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=11.961;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16839T>A|p.Ser5613Arg|16839/21291|16839/21291|5613/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1556:1:38:0,-8.84599,-136.522 +NC_045512.2 17146 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=53.3238;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.5293;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1730;RO=47;RPL=1;RPP=5.18177;RPPR=23.3852;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=5.27418;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16882A>T|p.Ile5628Leu|16882/21291|16882/21291|5628/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1730:1:34:0,-11.0505,-152.569 +NC_045512.2 17150 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=25.858;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.164;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1696;RO=46;RPL=1;RPP=5.18177;RPPR=51.3492;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=6.03148;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16886T>G|p.Val5629Gly|16886/21291|16886/21291|5629/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:47:46,1:46:1696:1:34:0,-10.7495,-149.516 +NC_045512.2 17183 . C A 1.52941E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.6209;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2030;RO=54;RPL=0;RPP=5.18177;RPPR=120.27;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.0103;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16919C>A|p.Ala5640Glu|16919/21291|16919/21291|5640/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:2030:1:10:0,-15.5567,-181.953 +NC_045512.2 17298 . G A 4.95725E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=7.35324;EPPR=42.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.7081;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1984;RO=53;RPL=1;RPP=3.0103;RPPR=21.0786;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17034G>A|p.Gln5678Gln|17034/21291|17034/21291|5678/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:53,2:53:1984:2:76:0,-9.34184,-171.595 +NC_045512.2 17437 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.3438;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1832;RO=49;RPL=0;RPP=5.18177;RPPR=4.11819;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=4.11819;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17173G>T|p.Asp5725Tyr|17173/21291|17173/21291|5725/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1832:1:38:0,-11.2542,-161.339 +NC_045512.2 17442 . T G 7.21786E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.3242;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1838;RO=49;RPL=1;RPP=5.18177;RPPR=3.40914;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=3.40914;SRR=26;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17178T>G|p.Pro5726Pro|17178/21291|17178/21291|5726/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1838:1:12:0,-13.8515,-164.484 +NC_045512.2 17445 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.1884;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1771;RO=48;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=3.73412;SRR=26;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17181T>C|p.Ala5727Ala|17181/21291|17181/21291|5727/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1771:1:11:0,-13.6505,-158.56 +NC_045512.2 17463 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=3.05855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.0204;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1582;RO=45;RPL=0;RPP=5.18177;RPPR=100.727;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=3.05855;SRR=22;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17199C>A|p.Arg5733Arg|17199/21291|17199/21291|5733/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1582:1:20:0,-11.8474,-140.648 +NC_045512.2 17504 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=3.42611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.8227;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1752;RO=47;RPL=0;RPP=5.18177;RPPR=105.07;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=3.42611;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17240A>T|p.Asn5747Ile|17240/21291|17240/21291|5747/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1752:1:11:0,-13.3494,-156.848 +NC_045512.2 17506 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=3.0565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.9888;PAIRED=0;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1712;RO=47;RPL=0;RPP=5.18177;RPPR=105.07;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=3.0565;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17242T>C|p.Ser5748Pro|17242/21291|17242/21291|5748/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1712:1:32:0,-11.2501,-151.145 +NC_045512.2 17531 . T G 3.33041E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=8.60069;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.4488;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1766;RO=47;RPL=0;RPP=5.18177;RPPR=73.2828;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=3.42611;SRR=25;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17267T>G|p.Ile5756Arg|17267/21291|17267/21291|5756/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1766:1:30:0,-11.4499,-156.207 +NC_045512.2 17659 . T A 9.86952E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=3.0103;EPPR=3.19912;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.8036;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=1718;RO=46;RPL=2;RPP=7.35324;RPPR=102.898;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=22;SRP=3.19912;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17395T>A|p.Phe5799Ile|17395/21291|17395/21291|5799/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:46,2:46:1718:2:69:0,-7.89678,-148.339 +NC_045512.2 17669 . G T 5.86201E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=3.42611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.4412;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1715;RO=47;RPL=1;RPP=5.18177;RPPR=105.07;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=3.42611;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17405G>T|p.Gly5802Val|17405/21291|17405/21291|5802/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1715:1:17:0,-12.7495,-152.92 +NC_045512.2 17676 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=5.5839;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.0972;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1982;RO=54;RPL=0;RPP=5.18177;RPPR=73.9451;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17412C>T|p.Ile5804Ile|17412/21291|17412/21291|5804/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1982:1:34:0,-13.1577,-175.24 +NC_045512.2 17696 . C T 1.16929E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.4817;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=1323;RO=35;RPL=1;RPP=5.18177;RPPR=13.4954;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=13.4954;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17432C>T|p.Ala5811Val|17432/21291|17432/21291|5811/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1323:1:24:0,-8.43719,-116.965 +NC_045512.2 17697 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.2642;PAIRED=0;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1303;RO=35;RPL=1;RPP=5.18177;RPPR=13.4954;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=13.4954;SRR=24;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17433A>G|p.Ala5811Ala|17433/21291|17433/21291|5811/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1303:1:38:0,-7.03981,-113.762 +NC_045512.2 17707 . CCAC CC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M2D1M;DP=36;DPB=35.5;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.2642;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1325;RO=35;RPL=0;RPP=5.18177;RPPR=16.9698;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=16.9698;SRR=25;TYPE=del;ANN=CC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17446_17447delCA|p.Gln5816fs|17446/21291|17446/21291|5816/7096||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1325:1:38:0,-7.03981,-115.747 +NC_045512.2 17723 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.2642;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1326;RO=35;RPL=0;RPP=5.18177;RPPR=16.9698;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=16.9698;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17459T>C|p.Val5820Ala|17459/21291|17459/21291|5820/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1326:1:38:0,-7.03981,-115.837 +NC_045512.2 17727 . A C 3.26967E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.6122;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1290;RO=34;RPL=2;RPP=7.35324;RPPR=12.2071;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=12.2071;SRR=23;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17463A>C|p.Arg5821Ser|17463/21291|17463/21291|5821/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1290:2:76:0,-3.62227,-109.182 +NC_045512.2 17760 . A G 1.63863E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=44.7026;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1038;RO=30;RPL=1;RPP=5.18177;RPPR=3.29983;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=7.64277;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17496A>G|p.Lys5832Lys|17496/21291|17496/21291|5832/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1038:1:34:0,-5.93302,-90.3224 +NC_045512.2 17815 . G T 1.60035E-7 . AB=0.0869565;ABP=37.093;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=3.0103;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1164;PAIRED=1;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=776;RO=21;RPL=0;RPP=7.35324;RPPR=48.6112;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17551G>T|p.Gly5851*|17551/21291|17551/21291|5851/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:23:21,2:21:776:2:76:-0.291121,0,-63.2405 +NC_045512.2 17859 . T C 1.60035E-7 . AB=0.0869565;ABP=37.093;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=7.35324;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1164;PAIRED=1;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=792;RO=21;RPL=1;RPP=3.0103;RPPR=3.1137;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17595T>C|p.Tyr5865Tyr|17595/21291|17595/21291|5865/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:23:21,2:21:792:2:76:-0.291121,0,-64.684 +NC_045512.2 17931 . T A 3.46558E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=3.40511;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.9011;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=829;RO=22;RPL=1;RPP=5.18177;RPPR=50.7827;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.40511;SRR=12;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17667T>A|p.Ile5889Ile|17667/21291|17667/21291|5889/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:23:22,1:22:829:1:11:0,-5.82369,-73.8357 +NC_045512.2 17985 . C T 1.32901E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=59.7581;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.4822;PAIRED=1;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1139;RO=30;RPL=0;RPP=5.18177;RPPR=4.16842;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=5.61607;SRR=12;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17721C>T|p.Asp5907Asp|17721/21291|17721/21291|5907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1139:1:38:0,-5.53466,-99.0189 +NC_045512.2 18061 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=7.10075;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.6809;PAIRED=1;PAIREDR=0.906977;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1543;RO=43;RPL=1;RPP=5.18177;RPPR=39.8243;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=5.48477;SRR=25;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17797T>G|p.Phe5933Val|17797/21291|17797/21291|5933/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1543:1:27:0,-10.5455,-136.449 +NC_045512.2 18086 . C A 2.92764E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8968;PAIRED=1;PAIREDR=0.909091;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1222;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0761;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17822C>A|p.Thr5941Asn|17822/21291|17822/21291|5941/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1222:2:76:0,-3.32124,-103.063 +NC_045512.2 18088 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.5772;PAIRED=1;PAIREDR=0.911765;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1256;RO=34;RPL=0;RPP=5.18177;RPPR=76.8404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17824G>A|p.Gly5942Arg|17824/21291|17824/21291|5942/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1256:1:9:0,-9.63605,-112.434 +NC_045512.2 18092 . T C 2.92764E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8968;PAIRED=1;PAIREDR=0.909091;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1244;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0761;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17828T>C|p.Leu5943Ser|17828/21291|17828/21291|5943/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1244:2:76:0,-3.32124,-105.045 +NC_045512.2 18105 . G T 2.92764E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8968;PAIRED=1;PAIREDR=0.909091;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1252;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0761;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17841G>T|p.Gln5947His|17841/21291|17841/21291|5947/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1252:2:76:0,-3.32124,-105.764 +NC_045512.2 18221 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.1167;PAIRED=0;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1283;RO=34;RPL=1;RPP=5.18177;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17957A>C|p.Lys5986Thr|17957/21291|17957/21291|5986/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1283:1:11:0,-9.43605,-114.668 +NC_045512.2 18342 . T G 3.39045E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.0345;PAIRED=1;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1531;RO=41;RPL=1;RPP=5.18177;RPPR=7.30028;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=7.30028;SRR=16;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18078T>G|p.Val6026Val|18078/21291|18078/21291|6026/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1531:1:31:0,-9.54381,-134.971 +NC_045512.2 18346 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.8999;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1350;RO=37;RPL=1;RPP=5.18177;RPPR=12.9286;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=12.9286;SRR=12;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18082A>C|p.Thr6028Pro|18082/21291|18082/21291|6028/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1350:1:34:0,-8.04023,-118.396 +NC_045512.2 18395 . CTGT CT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M2D1M;DP=50;DPB=49;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.4044;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=1788;RO=48;RPL=0;RPP=7.35324;RPPR=107.241;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=24;SRP=3.0103;SRR=24;TYPE=del;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18133_18134delGT|p.Val6045fs|18133/21291|18133/21291|6045/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,2:48:1788:2:74:0,-8.02573,-154.164 +NC_045512.2 18411 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=7.35324;EPPR=98.736;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1786;RO=48;RPL=1;RPP=3.0103;RPPR=3.19126;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=24;SRP=3.0103;SRR=24;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18147T>A|p.Tyr6049*|18147/21291|18147/21291|6049/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,2:48:1786:2:76:0,-7.83669,-153.791 +NC_045512.2 18468 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=7.35324;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.3154;PAIRED=1;PAIREDR=0.959184;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1807;RO=49;RPL=1;RPP=3.0103;RPPR=3.05462;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=24;SRP=3.05462;SRR=25;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18204A>G|p.Gly6068Gly|18204/21291|18204/21291|6068/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:49,2:49:1807:2:76:0,-8.13772,-155.675 +NC_045512.2 18483 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=7.35324;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.3154;PAIRED=1;PAIREDR=0.959184;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1849;RO=49;RPL=1;RPP=3.0103;RPPR=3.05462;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=24;SRP=3.05462;SRR=25;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18219C>T|p.His6073His|18219/21291|18219/21291|6073/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:49,2:49:1849:2:76:0,-8.13772,-159.457 +NC_045512.2 18506 . G T 4.32464E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.3815;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1885;RO=50;RPL=1;RPP=5.18177;RPPR=3.18402;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=3.18402;SRR=26;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18242G>T|p.Gly6081Val|18242/21291|18242/21291|6081/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1885:1:9:0,-14.4525,-169.01 +NC_045512.2 18556 . A C 7.05188E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=24.9965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.403;PAIRED=0;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1205;RO=32;RPL=1;RPP=5.18177;RPPR=72.4974;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=24.9965;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18292A>C|p.Thr6098Pro|18292/21291|18292/21291|6098/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1205:1:11:0,-8.83399,-107.653 +NC_045512.2 18619 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=124.613;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.1275;PAIRED=0;PAIREDR=0.875;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2110;RO=56;RPL=1;RPP=5.18177;RPPR=4.40625;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=31;SRP=4.40625;SRR=25;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18355T>G|p.Ser6119Ala|18355/21291|18355/21291|6119/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2110:1:11:0,-16.0587,-189.045 +NC_045512.2 18659 . GTTGTC GTGTC 9.4328E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D4M;DP=57;DPB=56.8333;DPRA=0;EPP=5.18177;EPPR=116.082;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.9168;PAIRED=1;PAIREDR=0.857143;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2092;RO=56;RPL=1;RPP=5.18177;RPPR=8.59409;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=6.88793;SRR=23;TYPE=del;ANN=GTGTC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18397delT|p.Cys6133fs|18397/21291|18397/21291|6133/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2092:1:38:0,-13.3614,-184.732 +NC_045512.2 18668 . G A 9.44787E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=71.4117;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.9168;PAIRED=1;PAIREDR=0.857143;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2008;RO=56;RPL=0;RPP=5.18177;RPPR=21.778;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=5.49198;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18404G>A|p.Cys6135Tyr|18404/21291|18404/21291|6135/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2008:1:38:0,-13.3614,-177.179 +NC_045512.2 18714 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=5.18177;EPPR=3.1419;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=91.217;PAIRED=0;PAIREDR=0.848485;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=2412;RO=66;RPL=0;RPP=5.18177;RPPR=146.327;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.1419;SRR=32;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18450C>A|p.Ala6150Ala|18450/21291|18450/21291|6150/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:66,1:66:2412:1:18:0,-18.369,-215.506 +NC_045512.2 18754 . C T 1.26872E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=5.18177;EPPR=98.9499;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.6181;PAIRED=0;PAIREDR=0.848485;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2467;RO=66;RPL=1;RPP=5.18177;RPPR=7.74806;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=3.0103;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18490C>T|p.Pro6164Ser|18490/21291|18490/21291|6164/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:66,1:66:2467:1:38:0,-16.3717,-218.458 +NC_045512.2 18758 . TTAT TT 1.50375E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M2D1M;DP=67;DPB=66;DPRA=0;EPP=7.35324;EPPR=104.067;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.9456;PAIRED=1;PAIREDR=0.830769;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2453;RO=65;RPL=1;RPP=3.0103;RPPR=5.71629;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=33;SRP=3.04371;SRR=32;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18496_18497delAT|p.Met6166fs|18496/21291|18496/21291|6166/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:65,2:65:2453:2:76:0,-12.9542,-213.781 +NC_045512.2 18786 . TAC TC 1.50375E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D1M;DP=67;DPB=66.3333;DPRA=0;EPP=3.0103;EPPR=127.319;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.9456;PAIRED=1;PAIREDR=0.830769;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2445;RO=65;RPL=0;RPP=7.35324;RPPR=3.31097;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=33;SRP=3.04371;SRR=32;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18523delA|p.Thr6175fs|18523/21291|18523/21291|6175/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:65,2:65:2445:2:76:0,-12.9542,-213.061 +NC_045512.2 18795 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=5.18177;EPPR=121.454;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=92.8288;PAIRED=0;PAIREDR=0.848485;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2474;RO=66;RPL=0;RPP=5.18177;RPPR=3.53672;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.1419;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18531C>A|p.Asn6177Lys|18531/21291|18531/21291|6177/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:66,1:66:2474:1:11:0,-19.069,-221.783 +NC_045512.2 18807 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=5.18177;EPPR=137.773;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.9868;PAIRED=0;PAIREDR=0.848485;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=2477;RO=66;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.1419;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18543C>A|p.Asn6181Lys|18543/21291|18543/21291|6181/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:66,1:66:2477:1:19:0,-18.269,-221.252 +NC_045512.2 18936 . T C 4.28528E-14 . AB=0.0909091;ABP=82.96;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=13.8677;EPPR=79.6198;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.9661;PAIRED=1;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=190;QR=1865;RO=50;RPL=0;RPP=13.8677;RPPR=24.0302;RPR=5;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=16;SRP=17.0814;SRR=34;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18672T>C|p.Ile6224Ile|18672/21291|18672/21291|6224/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:55:50,5:50:1865:5:190:-0.910787,0,-151.552 +NC_045512.2 18964 . T G 6.63211E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=90.593;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.8949;PAIRED=1;PAIREDR=0.895833;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1801;RO=48;RPL=1;RPP=5.18177;RPPR=7.5342;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=7.5342;SRR=29;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18700T>G|p.Cys6234Gly|18700/21291|18700/21291|6234/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1801:1:34:0,-11.3516,-158.954 +NC_045512.2 18978 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=77.0689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.2602;PAIRED=1;PAIREDR=0.868421;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1362;RO=38;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18714A>C|p.Gln6238His|18714/21291|18714/21291|6238/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1362:1:34:0,-8.34126,-119.475 +NC_045512.2 19036 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4815;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1418;RO=38;RPL=0;RPP=5.18177;RPPR=85.5263;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18772G>T|p.Gly6258Cys|18772/21291|18772/21291|6258/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1418:1:20:0,-9.74021,-125.908 +NC_045512.2 19103 . C T 4.29279E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=7.35324;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.2225;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1401;RO=37;RPL=1;RPP=3.0103;RPPR=3.06899;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.5385;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18839C>T|p.Pro6280Leu|18839/21291|18839/21291|6280/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:37,2:37:1401:2:76:0,-4.52536,-119.165 +NC_045512.2 19208 . A C 1.67554E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=53.2759;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.9522;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1005;RO=27;RPL=0;RPP=5.18177;RPPR=26.2531;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=21.1059;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18944A>C|p.Asp6315Ala|18944/21291|18944/21291|6315/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1005:1:27:0,-5.72906,-88.0637 +NC_045512.2 19220 . C G 3.73074E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.7763;PAIRED=1;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1056;RO=28;RPL=1;RPP=5.18177;RPPR=14.1779;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=14.1779;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18956C>G|p.Ala6319Gly|18956/21291|18956/21291|6319/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:28,1:28:1056:1:38:0,-4.9326,-91.5533 +NC_045512.2 19227 . C T 3.39026E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.4251;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1012;RO=27;RPL=1;RPP=5.18177;RPPR=12.7417;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=12.7417;SRR=19;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18963C>T|p.Ser6321Ser|18963/21291|18963/21291|6321/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1012:1:38:0,-4.63157,-87.5933 +NC_045512.2 19284 . TGGTGGC TGTGGC 3.39026E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D5M;DP=28;DPB=27.8571;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.4251;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1005;RO=27;RPL=1;RPP=5.18177;RPPR=12.7417;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=12.7417;SRR=19;TYPE=del;ANN=TGTGGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19022delG|p.Gly6341fs|19022/21291|19022/21291|6341/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1005:1:38:0,-4.63157,-86.9677 +NC_045512.2 19295 . T G 1.12247E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.329;PAIRED=0;PAIREDR=0.904762;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=732;RO=21;RPL=1;RPP=5.18177;RPPR=5.59539;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=5.59539;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19031T>G|p.Leu6344Trp|19031/21291|19031/21291|6344/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:732:1:12:0,-5.42267,-64.9974 +NC_045512.2 19437 . A T 0.00124347 . AB=0.125;ABP=22.5536;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=7.35324;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.15826;PAIRED=1;PAIREDR=0.857143;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=532;RO=14;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19173A>T|p.Val6391Val|19173/21291|19173/21291|6391/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:16:14,2:14:532:2:76:-2.39833,0,-43.4088 +NC_045512.2 19478 . G T 36.2105 . AB=0.25;ABP=11.6962;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.33754;PAIRED=1;PAIREDR=0.833333;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=449;RO=12;RPL=4;RPP=11.6962;RPPR=29.068;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19214G>T|p.Gly6405Val|19214/21291|19214/21291|6405/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:16:12,4:12:449:4:152:-9.23341,0,-35.9409 +NC_045512.2 19550 . C G 3.56727E-5 . AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7097;PAIRED=1;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=372;RO=10;RPL=0;RPP=5.18177;RPPR=10.8276;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=10.8276;SRR=8;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19286C>G|p.Ala6429Gly|19286/21291|19286/21291|6429/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:10,1:10:372:1:34:-0.0875811,0,-30.5188 +NC_045512.2 19621 . A T 0.0495762 . AB=0.166667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.46708;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=187;RO=5;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19357A>T|p.Ser6453Cys|19357/21291|19357/21291|6453/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:5,1:5:187:1:38:-1.99109,0,-15.3865 +NC_045512.2 19630 . A G 0.0495762 . AB=0.166667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.46708;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=190;RO=5;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19366A>G|p.Asn6456Asp|19366/21291|19366/21291|6456/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:5,1:5:190:1:38:-1.99109,0,-15.6613 +NC_045512.2 20219 . T A 1.77522E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=494;RO=13;RPL=1;RPP=5.18177;RPPR=3.17734;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19955T>A|p.Leu6652*|19955/21291|19955/21291|6652/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:494:1:38:0,-0.417151,-41.0105 +NC_045512.2 20498 . C G 1.07327E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.52;NS=1;NUMALT=1;ODDS=31.6439;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=946;RO=25;RPL=0;RPP=5.18177;RPPR=17.6895;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=17.6895;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20234C>G|p.Ser6745Cys|20234/21291|20234/21291|6745/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:946:1:34:0,-4.42787,-82.0243 +NC_045512.2 20593 . A T 2.09141E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6842;NS=1;NUMALT=1;ODDS=40.4289;PAIRED=1;PAIREDR=0.921053;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1379;RO=38;RPL=0;RPP=7.35324;RPPR=85.5263;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=19;SRP=3.0103;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20329A>T|p.Thr6777Ser|20329/21291|20329/21291|6777/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:38,2:38:1379:2:72:0,-5.20483,-117.526 +NC_045512.2 20621 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=60;NS=1;NUMALT=1;ODDS=55.9148;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1469;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20357A>T|p.Lys6786Ile|20357/21291|20357/21291|6786/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1469:1:11:0,-10.9413,-131.397 +NC_045512.2 20696 . A C 9.08766E-17 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=79.2345;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6923;NS=1;NUMALT=1;ODDS=55.9147;PAIRED=0;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1454;RO=39;RPL=1;RPP=5.18177;RPPR=3.06598;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20432A>C|p.Asn6811Thr|20432/21291|20432/21291|6811/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1454:1:11:0,-10.9412,-130.009 +NC_045512.2 20726 . A G 1.54744E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=7.35324;EPPR=77.0689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6842;NS=1;NUMALT=1;ODDS=39.5575;PAIRED=1;PAIREDR=0.921053;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1401;RO=38;RPL=1;RPP=3.0103;RPPR=3.23888;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=19;SRP=3.0103;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20462A>G|p.Glu6821Gly|20462/21291|20462/21291|6821/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:38,2:38:1401:2:76:0,-4.82639,-119.131 +NC_045512.2 20732 . G T 2.26485E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=56.5176;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6923;NS=1;NUMALT=1;ODDS=53.8424;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1424;RO=39;RPL=1;RPP=5.18177;RPPR=5.73856;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20468G>T|p.Cys6823Phe|20468/21291|20468/21291|6823/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1424:1:20:0,-10.0412,-126.428 +NC_045512.2 20745 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6923;NS=1;NUMALT=1;ODDS=56.3752;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1454;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20481T>G|p.Asn6827Lys|20481/21291|20481/21291|6827/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1454:1:9:0,-11.1412,-130.218 +NC_045512.2 20766 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6923;NS=1;NUMALT=1;ODDS=56.1449;PAIRED=0;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1442;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20502A>C|p.Leu6834Phe|20502/21291|20502/21291|6834/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1442:1:10:0,-11.0412,-129.04 +NC_045512.2 20772 . A G 2.58426E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=3.0103;EPPR=20.744;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.2424;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=907;RO=24;RPL=2;RPP=7.35324;RPPR=55.1256;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=5;SRP=20.744;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20508A>G|p.Lys6836Lys|20508/21291|20508/21291|6836/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:24,2:24:907:2:75:0,-0.706436,-74.8308 +NC_045512.2 20789 . T G 5.7184E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=62.6327;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.2446;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1268;RO=35;RPL=0;RPP=5.18177;RPPR=6.05036;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=6.05036;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20525T>G|p.Val6842Gly|20525/21291|20525/21291|6842/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1268:1:12:0,-9.63709,-113.219 +NC_045512.2 20988 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=68.4099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.347;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1271;RO=34;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.26577;SRR=18;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20724T>G|p.Thr6908Thr|20724/21291|20724/21291|6908/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1271:1:10:0,-9.53605,-113.685 +NC_045512.2 21005 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=68.4099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.1167;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1289;RO=34;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.26577;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20741C>T|p.Ala6914Val|20741/21291|20741/21291|6914/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1289:1:11:0,-9.43605,-115.207 +NC_045512.2 21056 . A T 3.31339E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.0778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=1194;RO=33;RPL=2;RPP=7.35324;RPPR=74.6689;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20792A>T|p.Asp6931Val|20792/21291|20792/21291|6931/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1194:2:66:0,-4.26844,-101.489 +NC_045512.2 21065 . CTAAAAATG CGAAAATG,CTAAAATG 429.131 . AB=0.0285714,0.571429;ABP=70.5741,4.56135;AC=0,1;AF=0,0.5;AN=2;AO=1,20;CIGAR=1M1D1X6M,2M1D6M;DP=35;DPB=32.6667;DPRA=0,0;EPP=5.18177,3.44459;EPPR=3.0103;GTI=0;LEN=8,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=63.1396;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=8,707;QR=512;RO=14;RPL=1,20;RPP=5.18177,46.4397;RPPR=33.4109;RPR=0,0;RUN=1,1;SAF=1,9;SAP=5.18177,3.44459;SAR=0,11;SRF=7;SRP=3.0103;SRR=7;TYPE=complex,del;ANN=GAAAATG|frameshift_variant&synonymous_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20802_20803delTAinsG|p.Lys6935fs|20802/21291|20802/21291|6934/7096||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/2:35:14,1,20:14:512:1,20:8,707:-53.6158,-57.4243,-98.9672,0,-41.7054,-36.0848 +NC_045512.2 21132 . A G 2.92095E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.0341;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=873;RO=23;RPL=1;RPP=5.18177;RPPR=10.6577;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=10.6577;SRR=16;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20868A>G|p.Gln6956Gln|20868/21291|20868/21291|6956/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:873:1:38:0,-3.42745,-75.096 +NC_045512.2 21168 . G A 1.70196E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=8.07707;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2658;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=762;RO=21;RPL=1;RPP=5.18177;RPPR=8.07707;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=8.07707;SRR=14;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20904G>A|p.Lys6968Lys|20904/21291|20904/21291|6968/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:762:1:34:0,-3.22375,-65.5064 +NC_045512.2 21304 . C T 0.00630843 . AB=0.142857;ABP=18.5208;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=3.0103;EPPR=14.5915;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.53369;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=453;RO=12;RPL=2;RPP=7.35324;RPPR=5.9056;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21040C>T|p.Arg7014Cys|21040/21291|21040/21291|7014/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:14:12,2:12:453:2:72:-2.62195,0,-36.9048 +NC_045512.2 21395 . A G 4.75505E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.0274;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=532;RO=14;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21131A>G|p.Asp7044Gly|21131/21291|21131/21291|7044/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:532:1:38:0,-0.718181,-44.428 +NC_045512.2 21661 . A C 1.2418E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.278;PAIRED=1;PAIREDR=0.894737;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=652;RO=19;RPL=0;RPP=5.18177;RPPR=4.03889;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=4.03889;SRR=8;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.99A>C|p.Thr33Thr|99/3822|99/3822|33/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:652:1:31:0,-2.92115,-55.8954 +NC_045512.2 21735 . T G 5.71063E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=10.5174;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.2446;PAIRED=1;PAIREDR=0.885714;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1235;RO=35;RPL=1;RPP=5.18177;RPPR=30.3709;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.56868;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.173T>G|p.Phe58Cys|173/3822|173/3822|58/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1235:1:12:0,-9.63709,-110.233 +NC_045512.2 21764 . ATACATGTCTC AGCTC,ATCTA,ATCTC 389.593 . AB=0.0322581,0.0322581,0.580645;ABP=61.9202,61.9202,4.76149;AC=0,0,1;AF=0,0,0.5;AN=2;AO=1,1,18;CIGAR=1M6D1X3M,1M6D3M1X,1M6D4M;DP=31;DPB=20.0909;DPRA=0,0,0;EPP=5.18177,5.18177,3.0103;EPPR=4.78696;GTI=0;LEN=5,5,6;MEANALT=3,3,3;MQM=60,60,60;MQMR=60;NS=1;NUMALT=3;ODDS=46.8485;PAIRED=0,0,1;PAIREDR=0.818182;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=10,18,640;QR=411;RO=11;RPL=0,0,0;RPP=5.18177,5.18177,42.0968;RPPR=26.8965;RPR=1,1,18;RUN=1,1,1;SAF=0,0,9;SAP=5.18177,5.18177,3.0103;SAR=1,1,9;SRF=7;SRP=4.78696;SRR=4;TYPE=complex,complex,del;ANN=GCTC|missense_variant&disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.203_209delTACATGTinsG|p.Ile68_Val70delinsSer|203/3822|203/3822|68/1273||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/3:31:11,1,1,18:11:411:1,1,18:10,18,640:-49.0321,-51.7568,-85.1206,-51.0326,-84.1088,-84.398,0,-33.2732,-32.5465,-28.4338 +NC_045512.2 21776 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=3.29983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.9232;PAIRED=0;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1111;RO=30;RPL=0;RPP=5.18177;RPPR=68.1545;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.29983;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.214G>A|p.Gly72Arg|214/3822|214/3822|72/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1111:1:10:0,-8.33193,-99.2969 +NC_045512.2 21801 . A C 202.492 . AB=0.354839;ABP=8.68415;AC=1;AF=0.5;AN=2;AO=11;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=4.78696;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.6255;PAIRED=0.818182;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=417;QR=736;RO=20;RPL=0;RPP=26.8965;RPPR=46.4397;RPR=11;RUN=1;SAF=7;SAP=4.78696;SAR=4;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.239A>C|p.Asp80Ala|239/3822|239/3822|80/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:31:20,11:20:736:11:417:-28.5504,0,-57.2326 +NC_045512.2 21904 . C A 2.34019E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6929;PAIRED=0;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1129;RO=30;RPL=1;RPP=5.18177;RPPR=68.1545;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.342C>A|p.Thr114Thr|342/3822|342/3822|114/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1129:1:11:0,-8.23193,-100.817 +NC_045512.2 21910 . C A 2.34019E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6929;PAIRED=0;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1121;RO=30;RPL=1;RPP=5.18177;RPPR=68.1545;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.348C>A|p.Ser116Ser|348/3822|348/3822|116/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1121:1:11:0,-8.23193,-100.093 +NC_045512.2 21990 . TTTATTAC TTTAC 759.795 . AB=0.875;ABP=42.0968;AC=1;AF=0.5;AN=2;AO=28;CIGAR=1M3D4M;DP=32;DPB=21.5;DPRA=0;EPP=55.4358;EPPR=11.6962;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.4431;PAIRED=0.928571;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1057;QR=152;RO=4;RPL=11;RPP=5.80219;RPPR=11.6962;RPR=17;RUN=1;SAF=16;SAP=4.25114;SAR=12;SRF=0;SRP=11.6962;SRR=4;TYPE=del;ANN=TTTAC|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.432_434delTTA|p.Tyr145del|432/3822|432/3822|144/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:32:4,28:4:152:28:1057:-85.8083,0,-4.41693 +NC_045512.2 22084 . T C 4.31238E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.60252;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1143;PAIRED=1;PAIREDR=0.939394;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1227;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.60252;SRR=18;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.522T>C|p.Pro174Pro|522/3822|522/3822|174/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1227:2:75:0,-3.41571,-103.609 +NC_045512.2 22088 . C A 2.92764E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.60252;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8968;PAIRED=1;PAIREDR=0.939394;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1214;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.60252;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.526C>A|p.Leu176Ile|526/3822|526/3822|176/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1214:2:76:0,-3.32124,-102.343 +NC_045512.2 22096 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.347;PAIRED=0;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1263;RO=34;RPL=0;RPP=5.18177;RPPR=76.8404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.26577;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.534C>A|p.Asp178Glu|534/3822|534/3822|178/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1263:1:10:0,-9.53605,-112.968 +NC_045512.2 22133 . G A 2.72423E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=7.35324;EPPR=66.2462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.4214;PAIRED=1;PAIREDR=0.939394;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=1233;RO=33;RPL=1;RPP=3.0103;RPPR=3.0761;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.60252;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.571G>A|p.Glu191Lys|571/3822|571/3822|191/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1233:2:69:0,-3.98339,-104.715 +NC_045512.2 22194 . A G 2.92919E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=7.35324;EPPR=58.3499;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8968;PAIRED=1;PAIREDR=0.939394;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1247;RO=33;RPL=1;RPP=3.0103;RPPR=3.0761;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.60252;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.632A>G|p.Asn211Ser|632/3822|632/3822|211/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1247:2:76:0,-3.32124,-105.315 +NC_045512.2 22248 . TG GT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=4.03217;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.1167;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1270;RO=34;RPL=1;RPP=5.18177;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=4.03217;SRR=19;TYPE=complex;ANN=GT|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.686_687delTGinsGT|p.Leu229Cys|686/3822|686/3822|229/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1270:1:11:0,-9.43605,-113.5 +NC_045512.2 22267 . C A 1.32901E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=13.4334;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.4822;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1108;RO=30;RPL=1;RPP=5.18177;RPPR=44.7026;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.705C>A|p.Ile235Ile|705/3822|705/3822|235/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1108:1:38:0,-5.53466,-96.2304 +NC_045512.2 22304 . T C 1.62542E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.0087;PAIRED=1;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=758;RO=20;RPL=1;RPP=5.18177;RPPR=24.2907;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=24.2907;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.742T>C|p.Tyr248His|742/3822|742/3822|248/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:758:1:38:0,-2.52436,-64.7532 +NC_045512.2 22535 . T A 8.91572E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=18.4661;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=642;RO=17;RPL=0;RPP=5.18177;RPPR=6.20364;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=18.4661;SRR=3;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.973T>A|p.Ser325Thr|973/3822|973/3822|325/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:642:1:38:0,-1.62127,-54.3198 +NC_045512.2 22801 . G T 2.20891E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=4.88226;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5862;NS=1;NUMALT=1;ODDS=39.3463;PAIRED=1;PAIREDR=0.965517;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=1064;RO=29;RPL=1;RPP=5.18177;RPPR=42.621;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1239G>T|p.Gly413Gly|1239/3822|1239/3822|413/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1064:1:24:0,-6.63101,-93.6329 +NC_045512.2 22893 . A G 3.36816E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=29.6108;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.25;NS=1;NUMALT=1;ODDS=18.6749;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=607;RO=16;RPL=1;RPP=5.18177;RPPR=16.582;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=11.6962;SRR=12;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1331A>G|p.Lys444Arg|1331/3822|1331/3822|444/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:607:1:38:0,-1.32024,-51.138 +NC_045512.2 23063 . A T 179.773 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=12.9229;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=227;QR=0;RO=0;RPL=6;RPP=16.0391;RPPR=0;RPR=0;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:6:0,6:0:0:6:227:-20.7938,-1.80618,0 +NC_045512.2 23125 . A C 1.72869E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=7.35324;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.5702;PAIRED=1;PAIREDR=0.85;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=692;RO=20;RPL=0;RPP=7.35324;RPPR=24.2907;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=24.2907;SRR=3;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1563A>C|p.Pro521Pro|1563/3822|1563/3822|521/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:20,2:20:692:2:24:0,-4.34267,-60.3218 +NC_045512.2 23137 . T C 2.92095E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.0341;PAIRED=1;PAIREDR=0.869565;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=873;RO=23;RPL=1;RPP=5.18177;RPPR=37.093;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=37.093;SRR=2;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1575T>C|p.Cys525Cys|1575/3822|1575/3822|525/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:873:1:38:0,-3.42745,-75.096 +NC_045512.2 23205 . G C 6.06637E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=46.8017;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.6085;PAIRED=0;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=910;RO=24;RPL=0;RPP=5.18177;RPPR=32.3252;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=26.1727;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1643G>C|p.Gly548Ala|1643/3822|1643/3822|548/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:24,1:24:910:1:37:0,-3.82792,-78.5231 +NC_045512.2 23212 . T C 9.54179E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=3.0103;EPPR=44.6459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.9361;PAIRED=1;PAIREDR=0.869565;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=859;RO=23;RPL=0;RPP=7.35324;RPPR=37.093;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=30.2953;SRR=3;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1650T>C|p.Gly550Gly|1650/3822|1650/3822|550/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:23,2:23:859:2:75:0,-0.405406,-70.5117 +NC_045512.2 23233 . A C 1.79352E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.8687;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1476;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1671A>C|p.Lys557Asn|1671/3822|1671/3822|557/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1476:1:10:0,-11.6433,-132.116 +NC_045512.2 23236 . GT CG 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1498;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=complex;ANN=CG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1674_1675delGTinsCG|p.LysPhe558AsnVal|1674/3822|1674/3822|558/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1498:1:9:0,-11.7433,-134.201 +NC_045512.2 23249 . CA AC 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1508;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=complex;ANN=AC|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1687_1688delCAinsAC|p.Gln563Thr|1687/3822|1687/3822|563/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1508:1:9:0,-11.7433,-135.101 +NC_045512.2 23252 . C A 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1501;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1690C>A|p.Gln564Lys|1690/3822|1690/3822|564/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1501:1:9:0,-11.7433,-134.468 +NC_045512.2 23257 . T G 1.03067E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.5595;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1523;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1695T>G|p.Phe565Leu|1695/3822|1695/3822|565/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1523:1:7:0,-11.9433,-136.652 +NC_045512.2 23258 . G T 6.90097E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1498;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1696G>T|p.Gly566Cys|1696/3822|1696/3822|566/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1498:1:11:0,-11.5433,-133.998 +NC_045512.2 23264 . G T 5.78596E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.1058;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1526;RO=41;RPL=0;RPP=5.18177;RPPR=83.5666;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1702G>T|p.Asp568Tyr|1702/3822|1702/3822|568/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1526:1:22:0,-10.4433,-135.42 +NC_045512.2 23270 . GC TA,GA 1246.7 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=1,41;CIGAR=2X,1M1X;DP=42;DPB=42;DPRA=0,0;EPP=5.18177,3.06326;EPPR=0;GTI=0;LEN=2,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=54.2645;PAIRED=0,0.829268;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=30,1525;QR=0;RO=0;RPL=0,1;RPP=5.18177,83.5666;RPPR=0;RPR=1,40;RUN=1,1;SAF=0,21;SAP=5.18177,3.06326;SAR=1,20;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=GA|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273|| GT:DP:AD:RO:QR:AO:QA:GL 2/2:42:0,1,41:0:0:1,41:30,1525:-137.224,-134.827,-134.526,-12.3422,-9.64369,0 +NC_045512.2 23295 . A C 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1545;RO=41;RPL=0;RPP=5.18177;RPPR=3.06326;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1733A>C|p.Asp578Ala|1733/3822|1733/3822|578/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1545:1:9:0,-11.7433,-138.431 +NC_045512.2 23310 . A G 6.9085E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=83.5666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=0.804878;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1528;RO=41;RPL=0;RPP=5.18177;RPPR=3.48696;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1748A>G|p.Glu583Gly|1748/3822|1748/3822|583/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1528:1:11:0,-11.5433,-136.7 +NC_045512.2 23329 . A C 6.9085E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=83.5666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1519;RO=41;RPL=0;RPP=5.18177;RPPR=3.48696;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1767A>C|p.Pro589Pro|1767/3822|1767/3822|589/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1519:1:11:0,-11.5433,-135.886 +NC_045512.2 23356 . A C 1.79352E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=83.5666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.8687;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1550;RO=41;RPL=0;RPP=5.18177;RPPR=3.48696;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1794A>C|p.Ile598Ile|1794/3822|1794/3822|598/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1550:1:10:0,-11.6433,-138.781 +NC_045512.2 23374 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.2313;PAIRED=1;PAIREDR=0.8;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1499;RO=40;RPL=2;RPP=7.35324;RPPR=81.4005;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1812T>C|p.Thr604Thr|1812/3822|1812/3822|604/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,2:40:1499:2:76:0,-5.42845,-127.981 +NC_045512.2 23386 . T G 6.90097E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=0;PAIREDR=0.829268;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1524;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1824T>G|p.Val608Val|1824/3822|1824/3822|608/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1524:1:11:0,-11.5433,-136.342 +NC_045512.2 23403 . A G,T 1091.29 . AB=0,0;ABP=0,0;AC=2,0;AF=1,0;AN=2;AO=40,1;CIGAR=1X,1X;DP=41;DPB=41;DPRA=0,0;EPP=3.22745,5.18177;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=57.5065;PAIRED=0.85,0;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=1365,10;QR=0;RO=0;RPL=40,1;RPP=89.8692,5.18177;RPPR=0;RPR=0,0;RUN=1,1;SAF=19,1;SAP=3.22745,5.18177;SAR=21,0;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:41:0,40,1:0:0:40,1:1365,10:-123.016,-12.0412,0,-122.423,-11.3422,-122.122 +NC_045512.2 23431 . T A 1.62542E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.0087;PAIRED=1;PAIREDR=0.75;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=758;RO=20;RPL=1;RPP=5.18177;RPPR=46.4397;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=46.4397;SRR=20;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1869T>A|p.Ala623Ala|1869/3822|1869/3822|623/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:758:1:38:0,-2.52436,-64.7533 +NC_045512.2 23445 . A C 7.32844E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=7.35324;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.4076;PAIRED=1;PAIREDR=0.785714;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=1030;RO=28;RPL=0;RPP=7.35324;RPPR=18.2106;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=7;SRP=18.2106;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1883A>C|p.Gln628Pro|1883/3822|1883/3822|628/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:28,2:28:1030:2:68:0,-2.57297,-86.5537 +NC_045512.2 23446 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.3638;PAIRED=1;PAIREDR=0.806452;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1125;RO=31;RPL=0;RPP=5.18177;RPPR=11.486;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=11.486;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1884A>C|p.Gln628His|1884/3822|1884/3822|628/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1125:1:27:0,-6.93318,-98.8556 +NC_045512.2 23450 . A C 1.37871E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.8709;PAIRED=1;PAIREDR=0.828571;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1287;RO=35;RPL=0;RPP=5.18177;RPPR=4.56135;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=4.56135;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1888A>C|p.Thr630Pro|1888/3822|1888/3822|630/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1287:1:31:0,-7.73763,-113.025 +NC_045512.2 23469 . A C 5.28897E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.8338;PAIRED=0;PAIREDR=0.861111;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1358;RO=36;RPL=1;RPP=5.18177;RPPR=3.25157;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.25157;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1907A>C|p.Tyr636Ser|1907/3822|1907/3822|636/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1358:1:11:0,-10.0381,-121.412 +NC_045512.2 23521 . T G 3.36083E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.9924;PAIRED=0;PAIREDR=0.807692;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=950;RO=26;RPL=1;RPP=5.18177;RPPR=8.35546;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=8.35546;SRR=9;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1959T>G|p.Ala653Ala|1959/3822|1959/3822|653/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:950:1:34:0,-4.7289,-82.4166 +NC_045512.2 23571 . T C 5.28144E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=51.3959;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1273;RO=35;RPL=0;RPP=5.18177;RPPR=79.0118;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2009T>C|p.Ile670Thr|2009/3822|2009/3822|670/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1273:1:7:0,-10.1371,-114.156 +NC_045512.2 23604 . C A 239.33 . AB=0.361111;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=31.2394;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=59.0769;MQMR=60;NS=1;NUMALT=1;ODDS=55.1078;PAIRED=1;PAIREDR=0.913043;PAO=0;PQA=0;PQR=0;PRO=0;QA=480;QR=868;RO=23;RPL=6;RPP=3.17734;RPPR=3.10471;RPR=7;RUN=1;SAF=6;SAP=3.17734;SAR=7;SRF=11;SRP=3.10471;SRR=12;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2042C>A|p.Pro681His|2042/3822|2042/3822|681/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:36:23,13:23:868:13:480:-32.6775,0,-67.6063 +NC_045512.2 23606 . C A 1.56708E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=34.4434;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1258;RO=34;RPL=1;RPP=3.0103;RPPR=3.26577;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=3.26577;SRR=18;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2044C>A|p.Arg682Arg|2044/3822|2044/3822|682/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1258:2:75:0,-3.71674,-106.363 +NC_045512.2 23656 . A C 1.86862E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=50.4749;PAIRED=0;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1321;RO=35;RPL=1;RPP=5.18177;RPPR=3.56868;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.56868;SRR=19;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2094A>C|p.Ser698Ser|2094/3822|2094/3822|698/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1321:1:11:0,-9.73708,-118.05 +NC_045512.2 23664 . C T 538.189 . AB=0.638889;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=23;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=52.9542;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.0769;NS=1;NUMALT=1;ODDS=57.7969;PAIRED=0.913043;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=848;QR=493;RO=13;RPL=11;RPP=3.10471;RPPR=3.17734;RPR=12;RUN=1;SAF=11;SAP=3.10471;SAR=12;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2102C>T|p.Ala701Val|2102/3822|2102/3822|701/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:36:13,23:13:493:23:848:-65.8013,0,-33.8453 +NC_045512.2 23709 . C T 249.204 . AB=0.361111;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.17734;EPPR=3.10471;GTI=0;LEN=1;MEANALT=1;MQM=59.0769;MQMR=60;NS=1;NUMALT=1;ODDS=57.3813;PAIRED=1;PAIREDR=0.913043;PAO=0;PQA=0;PQR=0;PRO=0;QA=491;QR=838;RO=23;RPL=13;RPP=31.2394;RPPR=52.9542;RPR=0;RUN=1;SAF=6;SAP=3.17734;SAR=7;SRF=11;SRP=3.10471;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2147C>T|p.Thr716Ile|2147/3822|2147/3822|716/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:36:23,13:23:838:13:491:-33.6648,0,-64.8978 +NC_045512.2 23766 . C T 218.163 . AB=0.631579;ABP=5.8675;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=29.068;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.2857;NS=1;NUMALT=1;ODDS=21.2039;PAIRED=0.916667;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=456;QR=266;RO=7;RPL=12;RPP=29.068;RPPR=18.2106;RPR=0;RUN=1;SAF=0;SAP=29.068;SAR=12;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2204C>T|p.Ser735Leu|2204/3822|2204/3822|735/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:19:7,12:7:266:12:456:-35.6707,0,-18.5476 +NC_045512.2 23820 . T C 2.92096E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4783;NS=1;NUMALT=1;ODDS=28.0341;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=874;RO=23;RPL=1;RPP=5.18177;RPPR=18.9659;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=18.9659;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2258T>C|p.Leu753Ser|2258/3822|2258/3822|753/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:874:1:38:0,-3.42745,-75.151 +NC_045512.2 24394 . A C 8.51412E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.6553;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=578;RO=16;RPL=0;RPP=5.18177;RPPR=3.55317;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.55317;SRR=9;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2832A>C|p.Ala944Ala|2832/3822|2832/3822|944/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:578:1:12:0,-3.91752,-51.153 +NC_045512.2 24506 . T G 741.097 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=26;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=40.6488;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=925;QR=0;RO=0;RPL=0;RPP=59.4686;RPPR=0;RPR=26;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:26:0,26:0:0:26:925:-83.5559,-7.82678,0 +NC_045512.2 24511 . T A 3.21218E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.0249;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=853;RO=24;RPL=0;RPP=7.35324;RPPR=55.1256;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=12;SRP=3.0103;SRR=12;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2949T>A|p.Arg983Arg|2949/3822|2949/3822|983/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:24,2:24:853:2:76:0,-0.611969,-69.861 +NC_045512.2 24536 . CAAAT AAAAG 1.64468E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=3.09716;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.0953;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=939;RO=25;RPL=0;RPP=5.18177;RPPR=57.2971;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.09716;SRR=12;TYPE=complex;ANN=AAAAG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2974_2978delCAAATinsAAAAG|p.GlnIle992LysSer|2974/3822|2974/3822|992/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:939:1:19:0,-5.92681,-82.9292 +NC_045512.2 24620 . G T 1.4036E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.9373;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=948;RO=25;RPL=1;RPP=5.18177;RPPR=3.09716;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.09716;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3058G>T|p.Ala1020Ser|3058/3822|3058/3822|1020/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:948:1:11:0,-6.72678,-84.5385 +NC_045512.2 24672 . C T 1.15872E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=3.09716;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.3978;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=936;RO=25;RPL=1;RPP=5.18177;RPPR=57.2971;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.09716;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3110C>T|p.Ser1037Leu|3110/3822|3110/3822|1037/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:936:1:9:0,-6.92678,-83.6596 +NC_045512.2 24700 . C G 1.29812E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=49.8093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.046;PAIRED=1;PAIREDR=0.896552;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1029;RO=29;RPL=0;RPP=5.18177;RPPR=3.08518;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.68421;SRR=13;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3138C>G|p.Gly1046Gly|3138/3822|3138/3822|1046/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1029:1:34:0,-5.63199,-89.5189 +NC_045512.2 24776 . G A 1.08534E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=31.4368;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.4259;PAIRED=1;PAIREDR=0.931818;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1621;RO=44;RPL=0;RPP=5.18177;RPPR=19.0002;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.20771;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3214G>A|p.Glu1072Lys|3214/3822|3214/3822|1072/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1621:1:21:0,-11.4464,-144.064 +NC_045512.2 24788 . A C 6.55441E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=8.60069;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.5135;PAIRED=0;PAIREDR=0.93617;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1692;RO=47;RPL=0;RPP=5.18177;RPPR=47.41;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=4.16534;SRR=26;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3226A>C|p.Thr1076Pro|3226/3822|3226/3822|1076/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1692:1:8:0,-13.6494,-151.753 +NC_045512.2 24795 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.51141;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.6054;PAIRED=0;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1431;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.51141;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3233C>A|p.Ala1078Asp|3233/3822|3233/3822|1078/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1431:1:8:0,-11.2412,-128.275 +NC_045512.2 24849 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=43.6001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.231;PAIRED=1;PAIREDR=0.897436;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1453;RO=39;RPL=0;RPP=5.18177;RPPR=9.74743;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3287T>C|p.Val1096Ala|3287/3822|3287/3822|1096/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1453:1:27:0,-9.34142,-128.353 +NC_045512.2 24870 . T G 9.08766E-17 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.9147;PAIRED=0;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1482;RO=39;RPL=1;RPP=5.18177;RPPR=3.06598;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3308T>G|p.Phe1103Cys|3308/3822|3308/3822|1103/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1482:1:11:0,-10.9412,-132.564 +NC_045512.2 24902 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.1449;PAIRED=0;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1478;RO=39;RPL=1;RPP=5.18177;RPPR=3.06598;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3340A>C|p.Ile1114Leu|3340/3822|3340/3822|1114/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1478:1:10:0,-11.0412,-132.305 +NC_045512.2 24914 . G C 1227.52 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=81.4005;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=60.0569;PAIRED=0.9;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1498;QR=0;RO=0;RPL=22;RPP=3.87889;RPPR=0;RPR=18;RUN=1;SAF=21;SAP=3.22745;SAR=19;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:40:0,40:0:0:40:1498:-135.101,-12.0412,0 +NC_045512.2 24949 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.0727;PAIRED=0;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1463;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3387A>C|p.Val1129Val|3387/3822|3387/3822|1129/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1463:1:19:0,-10.1412,-130.057 +NC_045512.2 25010 . G A 1.67105E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.8368;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1177;RO=31;RPL=1;RPP=5.18177;RPPR=4.76149;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=4.76149;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3448G>A|p.Glu1150Lys|3448/3822|3448/3822|1150/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1177:1:38:0,-5.83569,-102.436 +NC_045512.2 25231 . C A 5.04454E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=3.0103;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.1787;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=995;RO=27;RPL=2;RPP=7.35324;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3669C>A|p.Gly1223Gly|3669/3822|3669/3822|1223/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:27,2:27:995:2:75:0,-1.60953,-82.7372 +NC_045512.2 25238 . GCCAT GCAT 5.04454E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D3M;DP=29;DPB=28.6;DPRA=0;EPP=3.0103;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.1787;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1014;RO=27;RPL=2;RPP=7.35324;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.09072;SRR=14;TYPE=del;ANN=GCAT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3678delC|p.Ile1227fs|3678/3822|3678/3822|1226/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:27,2:27:1014:2:75:0,-1.60953,-84.4545 +NC_045512.2 25252 . G A 243.786 . AB=0.413793;ABP=4.88226;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=3.0103;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.1338;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=452;QR=634;RO=17;RPL=12;RPP=29.068;RPPR=39.9253;RPR=0;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=8;SRP=3.13803;SRR=9;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3690G>A|p.Val1230Val|3690/3822|3690/3822|1230/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:29:17,12:17:634:12:452:-32.2991,0,-48.6654 +NC_045512.2 25606 . GCAC GC 0.608654 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1M2D1M;DP=3;DPB=2.5;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.9186;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=71;RO=2;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=7.35324;SRR=0;TYPE=del;ANN=GC|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.216_217delAC|p.Ser74fs|216/828|216/828|72/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3:2,1:2:71:1:34:-2.49582,0,-5.83881 +NC_045512.2 25784 . G T 1.58317 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.821324;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=303;RO=8;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.392G>T|p.Trp131Leu|392/828|392/828|131/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:303:2:76:-4.20451,0,-24.619 +NC_045512.2 25805 . C A 1.58317 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.821324;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=304;RO=8;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.413C>A|p.Pro138Gln|413/828|413/828|138/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:304:2:76:-4.20451,0,-24.7098 +NC_045512.2 25904 . C T 3.56727E-5 . AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7097;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=353;RO=10;RPL=0;RPP=5.18177;RPPR=16.9077;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.512C>T|p.Ser171Leu|512/828|512/828|171/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:10,1:10:353:1:34:-0.0875811,0,-28.7936 +NC_045512.2 25905 . A C 4.66965E-4 . AB=0.111111;ABP=14.8328;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=12.7819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.13775;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=295;RO=8;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=4.09604;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.513A>C|p.Ser171Ser|513/828|513/828|171/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:8,1:8:295:1:34:-0.689641,0,-24.1931 +NC_045512.2 26010 . C T 50.7908 . AB=0.75;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=9.52472;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.09996;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=114;QR=38;RO=1;RPL=0;RPP=9.52472;RPPR=5.18177;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.618C>T|p.Tyr206Tyr|618/828|618/828|206/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:1,3:1:38:3:114:-9.42823,0,-2.59315 +NC_045512.2 26172 . G T 6.62674E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.3929;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=257;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.780G>T|p.Met260Ile|780/828|780/828|260/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:8:7,1:7:257:1:10:0,-1.40824,-22.4823 +NC_045512.2 26173 . G T 6.62674E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.3929;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=248;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=T|stop_gained|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.781G>T|p.Glu261*|781/828|781/828|261/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:8:7,1:7:248:1:10:0,-1.40824,-21.6609 +NC_045512.2 26203 . A C 2.41692E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=57.5966;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.7355;PAIRED=1;PAIREDR=0.965517;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1048;RO=29;RPL=0;RPP=5.18177;RPPR=30.0414;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=36.0317;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.811A>C|p.Thr271Pro|811/828|811/828|271/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1048:1:31:0,-5.93145,-91.5268 +NC_045512.2 26208 . C A 1.66952E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.8368;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1160;RO=31;RPL=0;RPP=5.18177;RPPR=40.0654;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=27;SRP=40.0654;SRR=4;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.816C>A|p.Ser272Arg|816/828|816/828|272/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1160:1:38:0,-5.83569,-100.907 +NC_045512.2 26305 . CTTGC CTGC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=60;DPB=59.8;DPRA=0;EPP=5.18177;EPPR=3.34154;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.0244;PAIRED=1;PAIREDR=0.966102;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2181;RO=59;RPL=1;RPP=5.18177;RPPR=106.394;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=28;SRP=3.34154;SRR=31;TYPE=del;ANN=CTGC|frameshift_variant|HIGH|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.63delT|p.Ala22fs|63/228|63/228|21/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2181:1:38:0,-14.2645,-192.739 +NC_045512.2 26346 . T C 5.12534E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.0484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.203;PAIRED=1;PAIREDR=0.964912;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2140;RO=57;RPL=0;RPP=5.18177;RPPR=126.784;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0484;SRR=29;TYPE=snp;ANN=C|synonymous_variant|LOW|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.102T>C|p.Leu34Leu|102/228|102/228|34/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2140:1:34:0,-14.0608,-189.445 +NC_045512.2 26349 . T C 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=60.9543;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.7335;PAIRED=1;PAIREDR=0.964912;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=2138;RO=57;RPL=0;RPP=5.18177;RPPR=16.763;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0484;SRR=29;TYPE=snp;ANN=C|synonymous_variant|LOW|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.105T>C|p.Thr35Thr|105/228|105/228|35/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2138:1:23:0,-15.1598,-190.365 +NC_045512.2 26416 . G T 475.296 . AB=0.37931;ABP=10.3484;AC=1;AF=0.5;AN=2;AO=22;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=42.4916;EPPR=72.7387;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.441;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=836;QR=1359;RO=36;RPL=10;RPP=3.40511;RPPR=3.25157;RPR=12;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.172G>T|p.Val58Phe|172/228|172/228|58/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:58:36,22:36:1359:22:836:-58.1059,0,-105.143 +NC_045512.2 26590 . T A 7.06671E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=64.083;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.403;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1157;RO=32;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=9.79615;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.68T>A|p.Val23Glu|68/669|68/669|23/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1157:1:11:0,-8.83399,-103.331 +NC_045512.2 26695 . G A 4.11803E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=7.35324;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.8506;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=1363;RO=36;RPL=1;RPP=3.0103;RPPR=3.9754;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;ANN=A|stop_gained|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.173G>A|p.Trp58*|173/669|173/669|58/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:36,2:36:1363:2:67:0,-5.0763,-116.599 +NC_045512.2 26736 . AGAA TGAC 1.44199E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.5816;PAIRED=0;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1397;RO=37;RPL=1;RPP=5.18177;RPPR=3.5385;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.5385;SRR=17;TYPE=complex;ANN=TGAC|stop_gained|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.214_217delAGAAinsTGAC|p.ArgIle72*|214/669|214/669|72/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1397:1:18:0,-9.63917,-124.221 +NC_045512.2 26758 . GAA TAC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=66.922;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.7329;PAIRED=0;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1394;RO=37;RPL=1;RPP=5.18177;RPPR=5.88603;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.5385;SRR=17;TYPE=complex;ANN=TAC|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.236_238delGAAinsTAC|p.GlyIle79ValLeu|236/669|236/669|79/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1394:1:13:0,-10.1391,-124.451 +NC_045512.2 26803 . G T 2.85555E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.2943;PAIRED=1;PAIREDR=0.972222;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1326;RO=36;RPL=1;RPP=5.18177;RPPR=81.1833;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.281G>T|p.Ser94Ile|281/669|281/669|94/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1326:1:9:0,-10.2381,-118.734 +NC_045512.2 26830 . T C 3.36816E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.6749;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=608;RO=16;RPL=1;RPP=5.18177;RPPR=37.7539;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=37.7539;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.308T>C|p.Phe103Ser|308/669|308/669|103/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:608:1:38:0,-1.32024,-51.2631 +NC_045512.2 26859 . A G 1.36409E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.7963;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=797;RO=21;RPL=1;RPP=5.18177;RPPR=15.5221;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=15.5221;SRR=16;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.337A>G|p.Asn113Asp|337/669|337/669|113/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:797:1:23:0,-4.32275,-69.7582 +NC_045512.2 26885 . C T 4.25981E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.3485;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=797;RO=21;RPL=1;RPP=5.18177;RPPR=15.5221;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=15.5221;SRR=16;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.363C>T|p.Asn121Asn|363/669|363/669|121/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:797:1:38:0,-2.82539,-68.2609 +NC_045512.2 27032 . T C 2.43458E-5 . AB=0.0833333;ABP=21.1059;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.0917;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=417;RO=11;RPL=0;RPP=5.18177;RPPR=3.20771;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.20771;SRR=6;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.510T>C|p.Val170Val|510/669|510/669|170/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:11,1:11:417:1:38:-0.184909,0,-34.2699 +NC_045512.2 27126 . G T 2.44993E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=4.78696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.9932;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=414;RO=11;RPL=1;RPP=5.18177;RPPR=26.8965;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=4.78696;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.604G>T|p.Gly202Cys|604/669|604/669|202/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:414:1:8:0,-2.81236,-36.8111 +NC_045512.2 27143 . C A 3.1823E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=59.7581;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=0.733333;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1036;RO=30;RPL=0;RPP=5.18177;RPPR=17.1973;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=21.5402;SRR=7;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.621C>A|p.Asn207Lys|621/669|621/669|207/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1036:1:34:0,-5.93302,-90.1485 +NC_045512.2 27144 . A C 2.53593E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=7.35324;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.514;PAIRED=1;PAIREDR=0.733333;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=1025;RO=30;RPL=0;RPP=7.35324;RPPR=21.5402;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=23;SRP=21.5402;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.622A>C|p.Thr208Pro|622/669|622/669|208/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1025:2:43:0,-5.54848,-88.4685 +NC_045512.2 27161 . C A 1.29584E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.9777;PAIRED=0;PAIREDR=0.854167;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1799;RO=48;RPL=0;RPP=5.18177;RPPR=55.3066;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=55.3066;SRR=7;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.639C>A|p.Ser213Arg|639/669|639/669|213/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1799:1:38:0,-10.9532,-158.376 +NC_045512.2 27171 . A G 1.29584E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.9777;PAIRED=1;PAIREDR=0.833333;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1811;RO=48;RPL=0;RPP=5.18177;RPPR=55.3066;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=55.3066;SRR=7;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.649A>G|p.Ile217Val|649/669|649/669|217/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1811:1:38:0,-10.9532,-159.455 +NC_045512.2 27191 . A T 3.07984E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.1884;PAIRED=0;PAIREDR=0.854167;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1821;RO=48;RPL=0;RPP=5.18177;RPPR=55.3066;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=55.3066;SRR=7;TYPE=snp;ANN=T|stop_lost&splice_region_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.669A>T|p.Ter223Tyrext*?|669/669|669/669|223/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1821:1:11:0,-13.6505,-163.053 +NC_045512.2 27196 . C G 1.64239E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.3438;PAIRED=1;PAIREDR=0.836735;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1846;RO=49;RPL=1;RPP=5.18177;RPPR=63.6786;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=63.6786;SRR=6;TYPE=snp;ANN=G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-6C>G|||||6| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1846:1:38:0,-11.2542,-162.603 +NC_045512.2 27201 . G T 1.64239E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.3438;PAIRED=1;PAIREDR=0.836735;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1858;RO=49;RPL=0;RPP=5.18177;RPPR=57.2971;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=57.2971;SRR=7;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1G>T|||||1| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1858:1:38:0,-11.2542,-163.683 +NC_045512.2 27206 . T C 1.97993E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.84;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1895;RO=50;RPL=0;RPP=5.18177;RPPR=59.2949;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=59.2949;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.5T>C|p.Phe2Ser|5/186|5/186|2/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1895:1:38:0,-11.5553,-167.011 +NC_045512.2 27212 . T A 1.64239E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.3438;PAIRED=1;PAIREDR=0.836735;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1826;RO=49;RPL=0;RPP=5.18177;RPPR=63.6786;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=63.6786;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.11T>A|p.Leu4His|11/186|11/186|4/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1826:1:38:0,-11.2542,-160.808 +NC_045512.2 27217 . G T 2.77291E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=84.1269;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.882;PAIRED=1;PAIREDR=0.822222;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1659;RO=45;RPL=0;RPP=5.18177;RPPR=100.727;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=84.1269;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.16G>T|p.Asp6Tyr|16/186|16/186|6/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1659:1:38:0,-10.0501,-145.779 +NC_045512.2 27337 . G T 2.85084E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=7.35324;EPPR=155.459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=93.6103;PAIRED=1;PAIREDR=0.897436;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2943;RO=78;RPL=1;RPP=3.0103;RPPR=3.45573;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=43;SRP=4.79202;SRR=35;TYPE=snp;ANN=T|stop_gained|HIGH|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.136G>T|p.Glu46*|136/186|136/186|46/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:80:78,2:78:2943:2:76:0,-16.8676,-257.847 +NC_045512.2 27361 . G T 8.03175E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=5.18177;EPPR=174.557;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=110.904;PAIRED=1;PAIREDR=0.898734;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2968;RO=79;RPL=1;RPP=5.18177;RPPR=4.35716;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=4.35716;SRR=36;TYPE=snp;ANN=T|stop_gained|HIGH|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.160G>T|p.Glu54*|160/186|160/186|54/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:80:79,1:79:2968:1:10:0,-23.0824,-266.31 +NC_045512.2 27423 . A T 1.06982E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=5.18177;EPPR=4.35716;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=111.134;PAIRED=0;PAIREDR=0.911392;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2940;RO=79;RPL=1;RPP=5.18177;RPPR=174.557;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=4.35716;SRR=36;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.30A>T|p.Ile10Ile|30/366|30/366|10/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:80:79,1:79:2940:1:9:0,-23.1824,-263.898 +NC_045512.2 27476 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=69.0688;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5537;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1443;RO=38;RPL=1;RPP=5.18177;RPPR=77.0689;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=61.5258;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.83C>A|p.Thr28Lys|83/366|83/366|28/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1443:1:11:0,-10.6402,-129.057 +NC_045512.2 27530 . T G 2.17147E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=9.52472;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.7194;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=89;QR=884;RO=26;RPL=3;RPP=9.52472;RPPR=51.1168;RPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=1;SRP=51.1168;SRR=25;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.137T>G|p.Phe46Cys|137/366|137/366|46/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:26,3:26:884:3:89:0,-0.42483,-71.5687 +NC_045512.2 27531 . T G 1.27668E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.329;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=696;RO=21;RPL=1;RPP=5.18177;RPPR=40.3389;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=40.3389;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.138T>G|p.Phe46Leu|138/366|138/366|46/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:696:1:12:0,-5.42267,-61.7502 +NC_045512.2 27758 . G T 28.9582 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1;CIGAR=1X;DP=1;DPB=1;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=5.99146;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=0;RO=0;RPL=1;RPP=5.18177;RPPR=0;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|stop_lost&splice_region_variant|HIGH|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.365G>T|p.Ter122Leuext*?|365/366|365/366|122/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:1:0,1:0:0:1:38:-3.79727,-0.30103,0 +NC_045512.2 27841 . G T 2.35057E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=5.18177;EPPR=66.2462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.5487;PAIRED=1;PAIREDR=0.878788;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1235;RO=33;RPL=1;RPP=5.18177;RPPR=74.6689;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=66.2462;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.86G>T|p.Trp29Leu|86/132|86/132|29/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:33,1:33:1235:1:38:0,-6.43775,-107.65 +NC_045512.2 27880 . ACG AG 106.243 . AB=0.2;ABP=53.8228;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1M1D1M;DP=65;DPB=60.6667;DPRA=0;EPP=3.17734;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.4634;PAIRED=0.923077;PAIREDR=0.865385;PAO=0;PQA=0;PQR=0;PRO=0;QA=483;QR=1851;RO=52;RPL=0;RPP=31.2394;RPPR=115.927;RPR=13;RUN=1;SAF=7;SAP=3.17734;SAR=6;SRF=26;SRP=3.0103;SRR=26;TYPE=del;ANN=AG|frameshift_variant|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.126delC|p.His42fs|126/132|126/132|42/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:65:52,13:52:1851:13:483:-24.247,0,-147.281 +NC_045512.2 27890 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=5.18177;EPPR=3.04371;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.9249;PAIRED=0;PAIREDR=0.876923;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=2360;RO=65;RPL=0;RPP=5.18177;RPPR=144.156;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.04371;SRR=32;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4G>T|||||4| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:65,1:65:2360:1:22:0,-17.668,-210.425 +NC_045512.2 27920 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.5896;PAIRED=1;PAIREDR=0.859375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2388;RO=64;RPL=0;RPP=7.35324;RPPR=141.985;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.27C>A|p.Ile9Ile|27/366|27/366|9/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:64,2:64:2388:2:76:0,-12.6532,-207.93 +NC_045512.2 27944 . C T 111.113 . AB=0.19697;ABP=55.6521;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=31.2394;EPPR=93.5156;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.5848;PAIRED=0.923077;PAIREDR=0.849057;PAO=0;PQA=0;PQR=0;PRO=0;QA=494;QR=1957;RO=53;RPL=7;RPP=3.17734;RPPR=5.01789;RPR=6;RUN=1;SAF=7;SAP=3.17734;SAR=6;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.51C>T|p.His17His|51/366|51/366|17/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:66:53,13:53:1957:13:494:-24.9398,0,-156.512 +NC_045512.2 27972 . C T 2074.42 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=66;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=121.454;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=96.1006;PAIRED=0.863636;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2494;QR=0;RO=0;RPL=32;RPP=3.1419;RPPR=0;RPR=34;RUN=1;SAF=33;SAP=3.0103;SAR=33;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:66:0,66:0:0:66:2494:-224.681,-19.868,0 +NC_045512.2 27998 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=7.35324;EPPR=109.412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.3403;PAIRED=0;PAIREDR=0.890625;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=2396;RO=64;RPL=0;RPP=7.35324;RPPR=4.23175;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=33;SRP=3.14602;SRR=31;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.105C>A|p.Asp35Glu|105/366|105/366|35/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:64,2:64:2396:2:56:0,-14.5486,-210.548 +NC_045512.2 28014 . T A 1.16329E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=3.0103;EPPR=52.0041;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.5896;PAIRED=1;PAIREDR=0.859375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2391;RO=64;RPL=2;RPP=7.35324;RPPR=25.9465;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.121T>A|p.Phe41Ile|121/366|121/366|41/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:64,2:64:2391:2:76:0,-12.6532,-208.2 +NC_045512.2 28016 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=5.18177;EPPR=43.9342;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=91.4576;PAIRED=0;PAIREDR=0.876923;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2432;RO=65;RPL=0;RPP=5.18177;RPPR=35.1147;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.04371;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.123C>A|p.Phe41Leu|123/366|123/366|41/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:65,1:65:2432:1:11:0,-18.768,-218.004 +NC_045512.2 28043 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.5896;PAIRED=1;PAIREDR=0.859375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2358;RO=64;RPL=2;RPP=7.35324;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.150A>T|p.Gly50Gly|150/366|150/366|50/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:64,2:64:2358:2:76:0,-12.6532,-205.239 +NC_045512.2 28048 . G T 2005.51 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=66;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=96.1006;PAIRED=0.863636;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2469;QR=0;RO=0;RPL=66;RPP=146.327;RPPR=0;RPR=0;RUN=1;SAF=33;SAP=3.0103;SAR=33;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:66:0,66:0:0:66:2469:-222.438,-19.868,0 +NC_045512.2 28077 . GTGG TTGA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=66;DPB=66;DPRA=0;EPP=5.18177;EPPR=3.04371;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.997;PAIRED=1;PAIREDR=0.861538;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=2271;RO=65;RPL=1;RPP=5.18177;RPPR=144.156;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.04371;SRR=33;TYPE=complex;ANN=TTGA|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.184_187delGTGGinsTTGA|p.ValAsp62LeuAsn|184/366|184/366|62/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:65,1:65:2271:1:13:0,-18.568,-203.328 +NC_045512.2 28087 . C A 1.28381E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=73.4498;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.2857;PAIRED=1;PAIREDR=0.877193;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2115;RO=57;RPL=1;RPP=5.18177;RPPR=19.8106;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=4.877;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.194C>A|p.Ala65Asp|194/366|194/366|65/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2115:1:38:0,-13.6625,-186.803 +NC_045512.2 28111 . A G 1843.24 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=59;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=114.344;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=86.3965;PAIRED=0.881356;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2233;QR=0;RO=0;RPL=34;RPP=5.99147;RPPR=0;RPR=25;RUN=1;SAF=27;SAP=3.93042;SAR=32;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:59:0,59:0:0:59:2233:-201.207,-17.7608,0 +NC_045512.2 28121 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=112.183;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.6549;PAIRED=0;PAIREDR=0.896552;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2196;RO=58;RPL=1;RPP=5.18177;RPPR=5.40641;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.60933;SRR=31;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.228C>A|p.Ile76Ile|228/366|228/366|76/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2196:1:38:0,-13.9635,-194.082 +NC_045512.2 28160 . T G 4.77691E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=97.0649;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.9786;PAIRED=1;PAIREDR=0.862745;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1869;RO=51;RPL=0;RPP=5.18177;RPPR=5.09662;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.3935;SRR=24;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.267T>G|p.Asn89Lys|267/366|267/366|89/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1869:1:8:0,-14.8536,-167.662 +NC_045512.2 28166 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=14.0512;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.149;PAIRED=1;PAIREDR=0.887324;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2570;RO=71;RPL=0;RPP=5.18177;RPPR=40.4758;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=11.8491;SRR=44;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.273G>A|p.Gln91Gln|273/366|273/366|91/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2570:1:9:0,-20.7742,-230.62 +NC_045512.2 28230 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.6488;PAIRED=0;PAIREDR=0.962264;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1989;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.337G>T|p.Asp113Tyr|337/366|337/366|113/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1989:1:30:0,-13.2561,-176.261 +NC_045512.2 28237 . G C 1.5522E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=7.35324;EPPR=51.2838;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.3588;PAIRED=1;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1895;RO=52;RPL=1;RPP=3.0103;RPPR=16.5402;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.344G>C|p.Arg115Pro|344/366|344/366|115/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:52,2:52:1895:2:76:0,-9.04081,-163.585 +NC_045512.2 28262 . G T 1.5369E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=7.35324;EPPR=99.2232;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.3588;PAIRED=1;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1937;RO=52;RPL=1;RPP=3.0103;RPPR=3.67845;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-12G>T|||||12| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:52,2:52:1937:2:76:0,-9.04081,-167.369 +NC_045512.2 28270 . TAAAATG TAAATG 1662.37 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=54;CIGAR=1M1D5M;DP=54;DPB=46.2857;DPRA=0;EPP=103.541;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=79.4651;PAIRED=0.944444;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2012;QR=0;RO=0;RPL=25;RPP=3.6537;RPPR=0;RPR=29;RUN=1;SAF=27;SAP=3.0103;SAR=27;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=TAAATG|frameshift_variant&start_lost|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1delA|p.Met1fs|1/1260|1/1260|1/419||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 1/1:54:0,54:0:0:54:2012:-181.332,-16.2556,0 +NC_045512.2 28280 . GAT CTA 1683.06 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=54;CIGAR=3X;DP=54;DPB=54;DPRA=0;EPP=103.541;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=79.4651;PAIRED=0.944444;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2035;QR=0;RO=0;RPL=25;RPP=3.6537;RPPR=0;RPR=29;RUN=1;SAF=27;SAP=3.0103;SAR=27;SRF=0;SRP=0;SRR=0;TYPE=complex;ANN=CTA|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.7_9delGATinsCTA|p.Asp3Leu|7/1260|7/1260|3/419|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:54:0,54:0:0:54:2035:-183.402,-16.2556,0 +NC_045512.2 28349 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.9437;PAIRED=0;PAIREDR=0.962264;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1959;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.76A>C|p.Ser26Arg|76/1260|76/1260|26/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1959:1:7:0,-15.5556,-175.864 +NC_045512.2 28372 . TGGGGCGCGA TGGGCGCGA,TGGGTCGCGA,TGGGGCGCTA 8.14122E-16 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=1,2,1;CIGAR=1M1D8M,4M1X5M,8M1X1M;DP=51;DPB=50.9;DPRA=0,0,0;EPP=5.18177,3.0103,5.18177;EPPR=3.42611;GTI=0;LEN=1,1,1;MEANALT=3,3,3;MQM=60,60,60;MQMR=60;NS=1;NUMALT=3;ODDS=52.5891;PAIRED=0,1,0;PAIREDR=1;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=35,75,20;QR=1688;RO=47;RPL=1,2,1;RPP=5.18177,7.35324,5.18177;RPPR=105.07;RPR=0,0,0;RUN=1,1,1;SAF=0,1,1;SAP=5.18177,3.0103,5.18177;SAR=1,1,0;SRF=22;SRP=3.42611;SRR=25;TYPE=del,snp,snp;ANN=TGGGCGCGA|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.103delG|p.Ala35fs|103/1260|103/1260|35/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:47,1,2,1:47:1688:1,2,1:35,75,20:0,-11.2923,-148.717,-7.95497,-142.874,-145.119,-12.6911,-147.522,-144.226,-150.069 +NC_045512.2 28435 . C A 9.58348E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=88.4369;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.612;PAIRED=0;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1781;RO=47;RPL=0;RPP=5.18177;RPPR=8.60069;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=5.27418;SRR=27;TYPE=snp;ANN=A|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.162C>A|p.Thr54Thr|162/1260|162/1260|54/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1781:1:38:0,-10.6522,-156.758 +NC_045512.2 28461 . A C 1.10297E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=43;DPB=43;DPRA=0;EPP=5.18177;EPPR=94.2121;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.7078;PAIRED=1;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1493;RO=42;RPL=1;RPP=5.18177;RPPR=3.83753;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.83753;SRR=23;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.188A>C|p.Asp63Ala|188/1260|188/1260|63/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:43:42,1:42:1493:1:34:0,-9.54538,-131.258 +NC_045512.2 28494 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.5245;PAIRED=0;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1268;RO=36;RPL=0;RPP=5.18177;RPPR=81.1833;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.221T>G|p.Ile74Ser|221/1260|221/1260|74/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1268:1:8:0,-10.3381,-113.603 +NC_045512.2 28501 . C A 1.81047E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.064;PAIRED=0;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1335;RO=36;RPL=0;RPP=5.18177;RPPR=81.1833;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=A|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.228C>A|p.Thr76Thr|228/1260|228/1260|76/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1335:1:10:0,-10.1381,-119.443 +NC_045512.2 28627 . A G 4.1589E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=32.2045;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.3011;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1363;RO=36;RPL=1;RPP=5.18177;RPPR=18.4519;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.354A>G|p.Glu118Glu|354/1260|354/1260|118/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1363:1:22:0,-8.93818,-120.762 +NC_045512.2 28648 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.5245;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1362;RO=36;RPL=1;RPP=5.18177;RPPR=81.1833;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.375T>G|p.Ala125Ala|375/1260|375/1260|125/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1362:1:8:0,-10.3381,-122.073 +NC_045512.2 28719 . G A 7.6429E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.3796;PAIRED=1;PAIREDR=0.958333;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=908;RO=24;RPL=0;RPP=5.18177;RPPR=16.0391;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=16.0391;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.446G>A|p.Arg149His|446/1260|446/1260|149/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:24,1:24:908:1:38:0,-3.72848,-78.2437 +NC_045512.2 28739 . G T 36.6325 . AB=0.24;ABP=17.6895;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=16.0391;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.43473;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=228;QR=721;RO=19;RPL=6;RPP=16.0391;RPPR=5.8675;RPR=0;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=7;SRP=5.8675;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.466G>T|p.Ala156Ser|466/1260|466/1260|156/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:25:19,6:19:721:6:228:-13.3592,0,-57.6973 +NC_045512.2 28767 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=26.4622;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.1534;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1120;RO=30;RPL=0;RPP=5.18177;RPPR=4.16842;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=21.5402;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.494C>A|p.Thr165Lys|494/1260|494/1260|165/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1120:1:9:0,-8.43193,-100.207 +NC_045512.2 28771 . ATTGC ATTTGC 1.96799E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=26;DPB=26.2;DPRA=0;EPP=5.18177;EPPR=13.5202;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.7266;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=889;RO=25;RPL=1;RPP=5.18177;RPPR=3.79203;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=13.5202;SRR=18;TYPE=ins;ANN=ATTTGC|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.500dupT|p.Leu167fs|501/1260|501/1260|167/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:889:1:38:0,-4.02951,-76.5246 +NC_045512.2 28881 . GGG AAC 423.825 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=3X;DP=14;DPB=14;DPRA=0;EPP=33.4109;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.0133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=529;QR=0;RO=0;RPL=7;RPP=3.0103;RPPR=0;RPR=7;RUN=1;SAF=7;SAP=3.0103;SAR=7;SRF=0;SRP=0;SRR=0;TYPE=complex;ANN=AAC|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608_610delGGGinsAAC|p.ArgGly203LysArg|608/1260|608/1260|203/419|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:14:0,14:0:0:14:529:-47.9547,-4.21442,0 +NC_045512.2 28923 . C A 0.0150634 . AB=0.142857;ABP=18.5208;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.6623;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=448;RO=12;RPL=2;RPP=7.35324;RPPR=29.068;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.650C>A|p.Ala217Asp|650/1260|650/1260|217/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:14:12,2:12:448:2:76:-3.00039,0,-36.4527 +NC_045512.2 28942 . G T 7.11169E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.2301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=476;RO=13;RPL=1;RPP=5.18177;RPPR=31.2394;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.669G>T|p.Leu223Leu|669/1260|669/1260|223/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:476:1:14:0,-2.81443,-41.7784 +NC_045512.2 28977 . C T 400.315 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.0133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=503;QR=0;RO=0;RPL=14;RPP=33.4109;RPPR=0;RPR=0;RUN=1;SAF=7;SAP=3.0103;SAR=7;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:14:0,14:0:0:14:503:-45.6037,-4.21442,0 +NC_045512.2 29438 . C T 5.172E-5 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.3382;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=336;RO=9;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=T|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1165C>T|p.Gln389*|1165/1260|1165/1260|389/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:10:9,1:9:336:1:30:0,-0.0107335,-27.5939 +NC_045512.2 29682 . TAATC TATC 0.1631 . AB=0.2;ABP=6.91895;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1M1D3M;DP=5;DPB=4.8;DPRA=0;EPP=5.18177;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.26311;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=151;RO=4;RPL=1;RPP=5.18177;RPPR=11.6962;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=11.6962;SRR=4;TYPE=del;ANN=TATC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4300delA|||||4300| GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:4,1:4:151:1:38:-2.29212,0,-12.4528
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SampleB_freebayes_ann.vcf Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,983 @@ +##fileformat=VCFv4.2 +##fileDate=20210521 +##source=freeBayes v1.3.2-dirty +##reference=NC_045512.fasta +##contig=<ID=NC_045512.2,length=29903> +##phasing=none +##commandline="freebayes -f NC_045512.fasta -F 0.01 -C 1 --pooled-continuous L14_S3_L001_sorted_uniq.bam" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##SnpEffVersion="5.0 (build 2020-08-09 21:23), by Pablo Cingolani" +##SnpEffCmd="SnpEff NC_045512.2 L14_S3_L001_freebayes.vcf " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +NC_045512.2 65 . TCTA CCTC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=43;DPB=43;DPRA=0;EPP=5.18177;EPPR=55.9529;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.3125;PAIRED=0;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1568;RO=42;RPL=0;RPP=5.18177;RPPR=94.2121;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=55.9529;SRR=5;TYPE=complex;ANN=CCTC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-201_-198delTCTAinsCCTC|||||201| GT:DP:AD:RO:QR:AO:QA:GL 0/0:43:42,1:42:1568:1:21:0,-10.8443,-139.299 +NC_045512.2 82 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=43;DPB=43;DPRA=0;EPP=5.18177;EPPR=55.9529;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4042;PAIRED=1;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1550;RO=42;RPL=0;RPP=5.18177;RPPR=94.2121;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=55.9529;SRR=5;TYPE=snp;ANN=G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-184A>G|||||184| GT:DP:AD:RO:QR:AO:QA:GL 0/0:43:42,1:42:1550:1:38:0,-9.14702,-135.981 +NC_045512.2 107 . A C 1.22653E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=11.2913;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=81.8488;PAIRED=1;PAIREDR=0.966102;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2154;RO=59;RPL=0;RPP=5.18177;RPPR=131.127;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=11.2913;SRR=22;TYPE=snp;ANN=C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-159A>C|||||159| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2154:1:11:0,-16.9618,-193.004 +NC_045512.2 119 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=7.35324;EPPR=3.12768;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.844;PAIRED=0.5;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=2684;RO=74;RPL=0;RPP=7.35324;RPPR=163.699;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=38;SRP=3.12768;SRR=36;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-147C>A|||||147| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:74,2:74:2684:2:18:0,-21.1683,-240.066 +NC_045512.2 125 . C A 6.08732E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.627;PAIRED=1;PAIREDR=0.934211;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2595;RO=76;RPL=0;RPP=5.18177;RPPR=168.042;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-141C>A|||||141| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2595:1:9:0,-22.2793,-232.855 +NC_045512.2 141 . T G 6.08732E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.627;PAIRED=1;PAIREDR=0.934211;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2769;RO=76;RPL=0;RPP=5.18177;RPPR=168.042;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-125T>G|||||125| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2769:1:9:0,-22.2793,-248.516 +NC_045512.2 148 . T G 3.1496E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.857;PAIRED=1;PAIREDR=0.934211;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2685;RO=76;RPL=0;RPP=5.18177;RPPR=159.471;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-118T>G|||||118| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2685:1:8:0,-22.3793,-241.055 +NC_045512.2 154 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.9556;PAIRED=1;PAIREDR=0.934211;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2753;RO=76;RPL=0;RPP=5.18177;RPPR=159.471;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-112T>G|||||112| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2753:1:38:0,-19.382,-244.175 +NC_045512.2 167 . G T 6.11769E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.627;PAIRED=1;PAIREDR=0.934211;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2801;RO=76;RPL=0;RPP=5.18177;RPPR=159.471;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-99G>T|||||99| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2801:1:9:0,-22.2793,-251.391 +NC_045512.2 176 . C T 3.42082E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=10.3247;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.397;PAIRED=0;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2827;RO=76;RPL=0;RPP=5.18177;RPPR=105.87;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-90C>T|||||90| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2827:1:10:0,-22.1793,-253.634 +NC_045512.2 195 . T C 8.14122E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=120.041;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.943;PAIRED=0;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=2845;RO=76;RPL=1;RPP=5.18177;RPPR=4.03889;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=3.12459;SRR=39;TYPE=snp;ANN=C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-71T>C|||||71| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2845:1:25:0,-20.6794,-253.751 +NC_045512.2 216 . G C 8.55864E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=127.47;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.166;PAIRED=0;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2776;RO=76;RPL=1;RPP=5.18177;RPPR=4.83891;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=3.12459;SRR=39;TYPE=snp;ANN=C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-50G>C|||||50| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2776:1:11:0,-22.0793,-248.946 +NC_045512.2 221 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=3.0103;EPPR=132.98;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.142;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2749;RO=75;RPL=2;RPP=7.35324;RPPR=4.429;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=37;SRP=3.03925;SRR=38;TYPE=snp;ANN=C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-45T>C|||||45| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:75,2:75:2749:2:76:0,-15.9645,-240.396 +NC_045512.2 234 . T G 3.43565E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=127.47;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.397;PAIRED=0;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2761;RO=76;RPL=1;RPP=5.18177;RPPR=4.83891;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=3.12459;SRR=39;TYPE=snp;ANN=G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-32T>G|||||32| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2761:1:10:0,-22.1793,-247.692 +NC_045512.2 238 . TTTC ATTT,TTTT 2349.85 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=1,76;CIGAR=1X2M1X,3M1X;DP=77;DPB=77;DPRA=0,0;EPP=5.18177,99.1265;EPPR=0;GTI=0;LEN=4,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=102.173;PAIRED=1,0.934211;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=24,2773;QR=0;RO=0;RPL=1,46;RPP=5.18177,10.3247;RPPR=0;RPR=0,30;RUN=1,1;SAF=1,37;SAP=5.18177,3.12459;SAR=0,39;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=ATTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-28_-25delTTTCinsATTT|||||28| GT:DP:AD:RO:QR:AO:QA:GL 2/2:77:0,1,76:0:0:1,76:24,2773:-249.528,-247.671,-247.37,-22.8783,-20.7794,0 +NC_045512.2 246 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=7.35324;EPPR=66.9674;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.142;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2743;RO=75;RPL=1;RPP=3.0103;RPPR=24.117;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=37;SRP=3.03925;SRR=38;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-20G>A|||||20| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:75,2:75:2743:2:76:0,-15.9645,-239.861 +NC_045512.2 269 . G C 4.54383E-17 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=5.18177;EPPR=3.27088;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=104.023;PAIRED=1;PAIREDR=0.946667;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2743;RO=75;RPL=1;RPP=5.18177;RPPR=165.871;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=3.27088;SRR=39;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4G>C|p.Glu2Gln|4/21291|4/21291|2/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:75,1:75:2743:1:10:0,-21.8783,-246.071 +NC_045512.2 276 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=75;DPB=75;DPRA=0;EPP=5.18177;EPPR=3.47981;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=103.111;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2642;RO=74;RPL=1;RPP=5.18177;RPPR=163.699;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.47981;SRR=39;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11T>G|p.Leu4Arg|11/21291|11/21291|4/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:75:74,1:74:2642:1:8:0,-21.7773,-237.181 +NC_045512.2 283 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=5.18177;EPPR=3.27088;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=104.484;PAIRED=1;PAIREDR=0.946667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2700;RO=75;RPL=1;RPP=5.18177;RPPR=165.871;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=3.27088;SRR=39;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.18T>G|p.Pro6Pro|18/21291|18/21291|6/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:75,1:75:2700:1:8:0,-22.0783,-242.401 +NC_045512.2 286 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=73;DPB=73;DPRA=0;EPP=5.18177;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.135;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2485;RO=72;RPL=1;RPP=5.18177;RPPR=159.356;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=4.09604;SRR=39;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.21T>G|p.Gly7Gly|21/21291|21/21291|7/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:73:72,1:72:2485:1:9:0,-21.0752,-222.952 +NC_045512.2 306 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.9997;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2554;RO=72;RPL=2;RPP=7.35324;RPPR=159.356;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=33;SRP=4.09604;SRR=39;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.41T>G|p.Val14Gly|41/21291|41/21291|14/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:74:72,2:72:2554:2:14:0,-20.9462,-228.74 +NC_045512.2 307 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=5.18177;EPPR=3.75395;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.738;PAIRED=1;PAIREDR=0.945205;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2498;RO=73;RPL=1;RPP=5.18177;RPPR=161.528;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=34;SRP=3.75395;SRR=39;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.42C>A|p.Val14Val|42/21291|42/21291|14/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:74:73,1:73:2498:1:8:0,-21.4762,-224.227 +NC_045512.2 320 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=4.55236;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=95.5576;PAIRED=1;PAIREDR=0.942029;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2450;RO=69;RPL=1;RPP=5.18177;RPPR=152.842;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=31;SRP=4.55236;SRR=38;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.55C>T|p.Pro19Ser|55/21291|55/21291|19/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2450:1:11:0,-19.9721,-219.621 +NC_045512.2 327 . T G 3.1795E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=112;DPB=112;DPRA=0;EPP=7.35324;EPPR=69.4179;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=140.786;PAIRED=0.5;PAIREDR=0.936364;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=4003;RO=110;RPL=2;RPP=7.35324;RPPR=10.9066;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=71;SRP=23.2247;SRR=39;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.62T>G|p.Leu21*|62/21291|62/21291|21/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:112:110,2:110:4003:2:60:0,-28.0166,-354.71 +NC_045512.2 332 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=160.476;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.055;PAIRED=1;PAIREDR=0.926316;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=3545;RO=95;RPL=0;RPP=5.18177;RPPR=3.58174;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=9.61615;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.67G>T|p.Val23Phe|67/21291|67/21291|23/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3545:1:12:0,-27.6989,-318.012 +NC_045512.2 338 . G T 3.70687E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=103;DPB=103;DPRA=0;EPP=7.35324;EPPR=211.559;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=125.397;PAIRED=1;PAIREDR=0.93;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=3699;RO=100;RPL=0;RPP=7.35324;RPPR=15.518;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=63;SRP=17.6895;SRR=37;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.73G>T|p.Asp25Tyr|73/21291|73/21291|25/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:103:100,2:100:3699:2:71:0,-24.2617,-326.351 +NC_045512.2 343 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=7.35324;EPPR=228.924;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=138.854;PAIRED=1;PAIREDR=0.935185;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=3976;RO=108;RPL=1;RPP=3.0103;RPPR=35.1803;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=75;SRP=38.4777;SRR=33;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.78G>A|p.Val26Val|78/21291|78/21291|26/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:110:108,2:108:3976:2:50:0,-28.3659,-353.228 +NC_045512.2 346 . C T 255.826 . AB=0.245455;ABP=64.917;AC=1;AF=0.5;AN=2;AO=27;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=61.6401;EPPR=174.661;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.9061;PAIRED=0.925926;PAIREDR=0.939759;PAO=0;PQA=0;PQR=0;PRO=0;QA=1019;QR=3127;RO=83;RPL=0;RPP=61.6401;RPPR=7.43173;RPR=27;RUN=1;SAF=27;SAP=61.6401;SAR=0;SRF=49;SRP=8.89682;SRR=34;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.81C>T|p.Leu27Leu|81/21291|81/21291|27/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:110:83,27:83:3127:27:1019:-58.9094,0,-248.5 +NC_045512.2 408 . A T 9.64351E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=186.228;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=133.352;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=3549;RO=96;RPL=0;RPP=5.18177;RPPR=120.27;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=81;SRP=101.541;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.143A>T|p.Asp48Val|143/21291|143/21291|48/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3549:1:8:0,-28.3999,-318.776 +NC_045512.2 416 . T G 5.09285E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=5.18177;EPPR=128.087;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=125.098;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=3368;RO=90;RPL=0;RPP=5.18177;RPPR=198.443;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=81;SRP=128.087;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.151T>G|p.Cys51Gly|151/21291|151/21291|51/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:90,1:90:3368:1:8:0,-26.5937,-302.488 +NC_045512.2 419 . G A 1.39225E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=101.541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.129;PAIRED=1;PAIREDR=0.947917;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=3565;RO=96;RPL=0;RPP=5.18177;RPPR=211.472;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=81;SRP=101.541;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.154G>A|p.Gly52Ser|154/21291|154/21291|52/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3565:1:22:0,-27,-318.807 +NC_045512.2 421 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=97.5925;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=134.958;PAIRED=1;PAIREDR=0.948454;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3543;RO=97;RPL=0;RPP=5.18177;RPPR=213.643;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=81;SRP=97.5925;SRR=16;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.156C>G|p.Gly52Gly|156/21291|156/21291|52/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3543:1:7:0,-28.8009,-318.321 +NC_045512.2 422 . T G 1.33202E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=91.8616;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=134.268;PAIRED=1;PAIREDR=0.948454;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3500;RO=97;RPL=0;RPP=5.18177;RPPR=213.643;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=80;SRP=91.8616;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.157T>G|p.Leu53Val|157/21291|157/21291|53/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3500:1:10:0,-28.5009,-314.159 +NC_045512.2 450 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=161;DPB=161;DPRA=0;EPP=3.0103;EPPR=3.06527;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=206.332;PAIRED=1;PAIREDR=0.924051;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=5583;RO=158;RPL=0;RPP=7.35324;RPPR=328.951;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=80;SRP=3.06527;SRR=78;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.185C>T|p.Pro62Leu|185/21291|185/21291|62/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:161:158,2:158:5583:2:57:0,-42.9465,-497.142 +NC_045512.2 452 . C A 7.53852E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=162;DPB=162;DPRA=0;EPP=7.35324;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=218.982;PAIRED=0.5;PAIREDR=0.925;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=5607;RO=160;RPL=0;RPP=7.35324;RPPR=324.877;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=81;SRP=3.06459;SRR=79;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.187C>A|p.Gln63Lys|187/21291|187/21291|63/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:162:160,2:160:5607:2:16:0,-47.2469,-503.155 +NC_045512.2 472 . G T 4.26437E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=158;DPB=158;DPRA=0;EPP=9.52472;EPPR=81.8137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=209.312;PAIRED=1;PAIREDR=0.941935;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=5614;RO=155;RPL=0;RPP=9.52472;RPPR=77.6669;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=81;SRP=3.69677;SRR=74;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.207G>T|p.Val69Val|207/21291|207/21291|69/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:158:155,3:155:5614:3:27:0,-45.0427,-502.776 +NC_045512.2 474 . T A 1.22354E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=164;DPB=164;DPRA=0;EPP=3.0103;EPPR=116.463;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=207.231;PAIRED=1;PAIREDR=0.91358;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5837;RO=162;RPL=0;RPP=7.35324;RPPR=72.4974;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=80;SRP=3.06392;SRR=82;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.209T>A|p.Phe70Tyr|209/21291|209/21291|70/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:164:162,2:162:5837:2:76:0,-42.1541,-518.145 +NC_045512.2 478 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=166;DPB=166;DPRA=0;EPP=7.35324;EPPR=140.766;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=224.259;PAIRED=0.5;PAIREDR=0.920732;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=5869;RO=164;RPL=0;RPP=7.35324;RPPR=57.2441;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=81;SRP=3.06326;SRR=83;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.213C>A|p.Ile71Ile|213/21291|213/21291|71/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:166:164,2:164:5869:2:17:0,-48.356,-526.612 +NC_045512.2 501 . C A 1.75688E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=166;DPB=166;DPRA=0;EPP=7.35324;EPPR=308.923;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=223.603;PAIRED=0.5;PAIREDR=0.920732;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=5870;RO=164;RPL=0;RPP=7.35324;RPPR=5.60547;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=81;SRP=3.06326;SRR=83;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.236C>A|p.Ala79Glu|236/21291|236/21291|79/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:166:164,2:164:5870:2:20:0,-48.071,-526.419 +NC_045512.2 556 . C T 1.56101E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=165;DPB=165;DPRA=0;EPP=7.35324;EPPR=331.382;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=208.605;PAIRED=1;PAIREDR=0.91411;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6065;RO=163;RPL=1;RPP=3.0103;RPPR=3.02362;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=79;SRP=3.34335;SRR=84;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.291C>T|p.Tyr97Tyr|291/21291|291/21291|97/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:165:163,2:163:6065:2:76:0,-42.4551,-538.641 +NC_045512.2 570 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=164;DPB=164;DPRA=0;EPP=3.73412;EPPR=220.549;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=202.409;PAIRED=0.666667;PAIREDR=0.925466;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=5743;RO=161;RPL=2;RPP=3.73412;RPPR=14.3532;RPR=1;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=78;SRP=3.34749;SRR=83;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.305A>G|p.Glu102Gly|305/21291|305/21291|102/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:164:161,3:161:5743:3:82:0,-41.7189,-509.257 +NC_045512.2 572 . A T 6.33311E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=164;DPB=164;DPRA=0;EPP=7.35324;EPPR=196.03;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=208.319;PAIRED=1;PAIREDR=0.919753;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=5890;RO=162;RPL=1;RPP=3.0103;RPPR=20.3821;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=78;SRP=3.49285;SRR=84;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.307A>T|p.Thr103Ser|307/21291|307/21291|103/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:164:162,2:162:5890:2:71:0,-42.627,-523.383 +NC_045512.2 576 . T G 1.33049E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=162;DPB=162;DPRA=0;EPP=7.35324;EPPR=73.366;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=217.158;PAIRED=1;PAIREDR=0.91875;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=5671;RO=160;RPL=1;RPP=3.0103;RPPR=89.8692;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=76;SRP=3.87889;SRR=84;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.311T>G|p.Leu104Arg|311/21291|311/21291|104/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:162:160,2:160:5671:2:18:0,-47.0569,-508.709 +NC_045512.2 581 . G T 3.91758E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=162;DPB=162;DPRA=0;EPP=7.35324;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=216.72;PAIRED=1;PAIREDR=0.91875;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=5851;RO=160;RPL=1;RPP=3.0103;RPPR=300.285;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=76;SRP=3.87889;SRR=84;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.316G>T|p.Val106Phe|316/21291|316/21291|106/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:162:160,2:160:5851:2:20:0,-46.8669,-524.718 +NC_045512.2 585 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=162;DPB=162;DPRA=0;EPP=7.35324;EPPR=3.06459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=208.413;PAIRED=1;PAIREDR=0.925;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=5884;RO=160;RPL=1;RPP=3.0103;RPPR=324.877;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=76;SRP=3.87889;SRR=84;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.320T>C|p.Leu107Pro|320/21291|320/21291|107/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:162:160,2:160:5884:2:58:0,-43.259,-524.081 +NC_045512.2 601 . C T 5.27969E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=160;DPB=160;DPRA=0;EPP=3.0103;EPPR=4.38465;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=202.388;PAIRED=1;PAIREDR=0.924051;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=5653;RO=158;RPL=2;RPP=7.35324;RPPR=346.103;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=74;SRP=4.38465;SRR=84;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.336C>T|p.Gly112Gly|336/21291|336/21291|112/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:160:158,2:158:5653:2:73:0,-41.2337,-501.892 +NC_045512.2 604 . A G 6.02707E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=160;DPB=160;DPRA=0;EPP=3.0103;EPPR=4.38465;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=201.735;PAIRED=1;PAIREDR=0.924051;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5603;RO=158;RPL=2;RPP=7.35324;RPPR=346.103;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=74;SRP=4.38465;SRR=84;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.339A>G|p.Glu113Glu|339/21291|339/21291|113/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:160:158,2:158:5603:2:76:0,-40.95,-497.101 +NC_045512.2 627 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=118;DPB=118;DPRA=0;EPP=7.35324;EPPR=57.5966;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=158.621;PAIRED=1;PAIREDR=0.913793;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=4111;RO=116;RPL=2;RPP=7.35324;RPPR=254.901;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=31;SRP=57.5966;SRR=85;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.362T>G|p.Val121Gly|362/21291|362/21291|121/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:118:116,2:116:4111:2:16:0,-34.0015,-368.598 +NC_045512.2 639 . A C 5.64739E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=5.18177;EPPR=157.426;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=122.335;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=3355;RO=90;RPL=1;RPP=5.18177;RPPR=198.443;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=157.426;SRR=85;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.374A>C|p.Lys125Thr|374/21291|374/21291|125/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:90,1:90:3355:1:20:0,-25.3938,-300.118 +NC_045512.2 682 . T C 1443.71 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=59;CIGAR=1X;DP=118;DPB=118;DPRA=0;EPP=114.344;EPPR=98.7391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=269.301;PAIRED=0.932203;PAIREDR=0.898305;PAO=0;PQA=0;PQR=0;PRO=0;QA=2208;QR=2186;RO=59;RPL=30;RPP=3.0471;RPPR=131.127;RPR=29;RUN=1;SAF=31;SAP=3.34154;SAR=28;SRF=4;SRP=98.7391;SRR=55;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.417T>C|p.Asp139Asp|417/21291|417/21291|139/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:118:59,59:59:2186:59:2208:-163.439,0,-161.455 +NC_045512.2 723 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=176.02;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=132.206;PAIRED=1;PAIREDR=0.905263;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3326;RO=95;RPL=0;RPP=5.18177;RPPR=19.6735;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=31.0109;SRR=65;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.458C>G|p.Pro153Arg|458/21291|458/21291|153/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3326:1:7:0,-28.1989,-298.854 +NC_045512.2 732 . A C 5.42434E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.35316;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.1101;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2091;RO=57;RPL=0;RPP=5.18177;RPPR=126.784;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.35316;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.467A>C|p.Asp156Ala|467/21291|467/21291|156/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2091:1:11:0,-16.3597,-187.34 +NC_045512.2 733 . T G 8.82986E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.35316;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.0311;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2060;RO=57;RPL=0;RPP=5.18177;RPPR=126.784;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.35316;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.468T>G|p.Asp156Glu|468/21291|468/21291|156/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2060:1:7:0,-16.7597,-184.946 +NC_045512.2 743 . A C 1.96114E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.0645;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=2181;RO=60;RPL=0;RPP=7.35324;RPPR=133.299;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=30;SRP=3.0103;SRR=30;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.478A>C|p.Asn160His|478/21291|478/21291|160/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:60,2:60:2181:2:17:0,-17.0489,-194.921 +NC_045512.2 754 . T A 2.07933E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=3.0103;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.3106;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=2108;RO=60;RPL=0;RPP=7.35324;RPPR=133.299;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=3.15506;SRR=31;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.489T>A|p.Thr163Thr|489/21291|489/21291|163/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:60,2:60:2108:2:69:0,-12.112,-183.402 +NC_045512.2 757 . A C 1.36666E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.0459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.2794;PAIRED=1;PAIREDR=0.95082;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2130;RO=61;RPL=0;RPP=5.18177;RPPR=135.47;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.0459;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.492A>C|p.Lys164Asn|492/21291|492/21291|164/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2130:1:8:0,-17.8639,-191.135 +NC_045512.2 775 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=3.0471;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=81.158;PAIRED=0;PAIREDR=0.983051;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2162;RO=59;RPL=0;RPP=5.18177;RPPR=131.127;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.0471;SRR=29;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.510C>T|p.Thr170Thr|510/21291|510/21291|170/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2162:1:14:0,-16.6618,-193.423 +NC_045512.2 783 . TC GT 1.05476E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=61;DPB=61;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.4488;PAIRED=0;PAIREDR=0.983333;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2240;RO=60;RPL=0;RPP=5.18177;RPPR=133.299;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.0103;SRR=30;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.518_519delTCinsGT|p.Leu173Arg|518/21291|518/21291|173/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:61:60,1:60:2240:1:10:0,-17.3628,-200.843 +NC_045512.2 820 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=131.265;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.5597;PAIRED=0;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2340;RO=63;RPL=0;RPP=5.18177;RPPR=3.872;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.32051;SRR=33;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.555T>G|p.Tyr185*|555/21291|555/21291|185/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2340:1:10:0,-18.2659,-209.83 +NC_045512.2 846 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=131.265;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.3294;PAIRED=0;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2372;RO=63;RPL=0;RPP=5.18177;RPPR=3.872;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.32051;SRR=33;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.581A>C|p.Asp194Ala|581/21291|581/21291|194/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2372:1:11:0,-18.1659,-212.611 +NC_045512.2 875 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=99.8304;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.3294;PAIRED=0;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2337;RO=63;RPL=0;RPP=5.18177;RPPR=4.69922;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.32051;SRR=33;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.610C>A|p.Leu204Ile|610/21291|610/21291|204/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2337:1:11:0,-18.1659,-209.457 +NC_045512.2 905 . AC CA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.0202;PAIRED=1;PAIREDR=0.936508;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2300;RO=63;RPL=1;RPP=5.18177;RPPR=131.265;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.872;SRR=34;TYPE=complex;ANN=CA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.640_641delACinsCA|p.Thr214His|640/21291|640/21291|214/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2300:1:8:0,-18.4659,-206.434 +NC_045512.2 909 . TGTCCGAA CGTCTGAA,TGTCTGAA 1799.65 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=1,61;CIGAR=1X3M1X3M,4M1X3M;DP=63;DPB=63;DPRA=0,0;EPP=5.18177,3.90025;EPPR=0;GTI=0;LEN=8,1;MEANALT=3,3;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=82.1941;PAIRED=1,0.95082;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=24,2228;QR=0;RO=0;RPL=1,61;RPP=5.18177,135.47;RPPR=0;RPR=0,0;RUN=1,1;SAF=1,28;SAP=5.18177,3.90025;SAR=0,33;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=CGTCTGAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.644_648delTGTCCinsCGTCT|p.Leu215Ser|644/21291|644/21291|215/7096|| GT:DP:AD:RO:QR:AO:QA:GL 2/2:63:0,1,61:0:0:1,61:24,2228:-200.488,-198.631,-198.33,-18.3628,-16.5239,0 +NC_045512.2 920 . C A,G 1.15272E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=64;DPB=64;DPRA=0,0;EPP=5.18177,5.18177;EPPR=4.27115;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=86.1661;PAIRED=1,1;PAIREDR=0.935484;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,7;QR=2300;RO=62;RPL=1,1;RPP=5.18177,5.18177;RPPR=137.642;RPR=0,0;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=28;SRP=4.27115;SRR=34;TYPE=snp,snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.655C>A|p.Leu219Met|655/21291|655/21291|219/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,1,1:62:2300:1,1:11,7:0,-17.9549,-206.146,-18.3549,-206.123,-206.507 +NC_045512.2 924 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.0103;EPPR=3.57068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.5179;PAIRED=1;PAIREDR=0.935484;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=2275;RO=62;RPL=2;RPP=7.35324;RPPR=137.642;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=3.57068;SRR=33;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.659A>G|p.Asp220Gly|659/21291|659/21291|220/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,2:62:2275:2:53:0,-14.2335,-199.954 +NC_045512.2 936 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.872;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.3294;PAIRED=1;PAIREDR=0.936508;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2268;RO=63;RPL=1;RPP=5.18177;RPPR=139.813;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.872;SRR=34;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.671C>A|p.Thr224Asn|671/21291|671/21291|224/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2268:1:11:0,-18.1659,-203.252 +NC_045512.2 937 . TAAG AAAA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=63;DPB=63.5;DPRA=0;EPP=5.18177;EPPR=4.27115;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.1661;PAIRED=1;PAIREDR=0.935484;PAO=0;PQA=0;PQR=26;PRO=1;QA=12;QR=2219;RO=62;RPL=1;RPP=5.18177;RPPR=137.642;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=4.27115;SRR=34;TYPE=complex;ANN=AAAA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.672_675delTAAGinsAAAA|p.226|672/21291|672/21291|224/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2219:1:12:0,-17.9549,-198.678 +NC_045512.2 943 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=3.57068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.1891;PAIRED=0;PAIREDR=0.951613;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2251;RO=62;RPL=1;RPP=5.18177;RPPR=137.642;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=29;SRP=3.57068;SRR=33;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.678G>C|p.Arg226Ser|678/21291|678/21291|226/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2251:1:10:0,-17.9649,-201.824 +NC_045512.2 946 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=56;DPB=56;DPRA=0;EPP=5.18177;EPPR=27.6861;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.8399;PAIRED=1;PAIREDR=0.927273;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=2029;RO=55;RPL=1;RPP=5.18177;RPPR=76.0113;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=9.68264;SRR=34;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.681T>G|p.Gly227Gly|681/21291|681/21291|227/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:56:55,1:55:2029:1:22:0,-14.6577,-180.664 +NC_045512.2 999 . C T 4.77347E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=11.6962;EPPR=92.2337;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.3365;PAIRED=1;PAIREDR=0.911111;PAO=0;PQA=0;PQR=0;PRO=0;QA=145;QR=1687;RO=45;RPL=0;RPP=11.6962;RPPR=33.1696;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=11;SRP=28.5372;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.734C>T|p.Ser245Phe|734/21291|734/21291|245/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:45,4:45:1687:4:145:0,-1.34605,-138.695 +NC_045512.2 1010 . T C 1.07135E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=7.35324;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.5924;PAIRED=1;PAIREDR=0.909091;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1649;RO=44;RPL=0;RPP=7.35324;RPPR=22.751;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=22.751;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.745T>C|p.Tyr249His|745/21291|745/21291|249/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:44,2:44:1649:2:76:0,-6.63257,-141.471 +NC_045512.2 1019 . C A 6.56972E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4183;PAIRED=1;PAIREDR=0.902439;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1557;RO=41;RPL=1;RPP=5.18177;RPPR=11.961;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=11.961;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.754C>A|p.Gln252Lys|754/21291|754/21291|252/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1557:1:32:0,-9.44395,-137.21 +NC_045512.2 1040 . T G 2.8252E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=5.3706;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8585;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=817;RO=23;RPL=0;RPP=5.18177;RPPR=52.9542;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=5.3706;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.775T>G|p.Leu259Val|775/21291|775/21291|259/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:817:1:11:0,-6.12472,-72.7395 +NC_045512.2 1060 . C T 2.79099E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=3.0103;EPPR=3.09716;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.1654;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=897;RO=25;RPL=0;RPP=7.35324;RPPR=57.2971;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.09716;SRR=12;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.795C>T|p.Thr265Thr|795/21291|795/21291|265/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:25,2:25:897:2:75:0,-1.00747,-73.9185 +NC_045512.2 1069 . G C 3.90747E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.1315;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=859;RO=26;RPL=0;RPP=7.35324;RPPR=59.4686;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.804G>C|p.Gly268Gly|804/21291|804/21291|268/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:26,2:26:859:2:72:0,-1.59247,-70.7604 +NC_045512.2 1083 . T G 4.62576E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=6.56362;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.903;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=802;RO=22;RPL=0;RPP=5.18177;RPPR=50.7827;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=6.56362;SRR=8;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.818T>G|p.Phe273Cys|818/21291|818/21291|273/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:23:22,1:22:802:1:18:0,-5.12372,-70.6952 +NC_045512.2 1085 . G T 2.13659E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.4798;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=940;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.820G>T|p.Val274Leu|820/21291|820/21291|274/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:940:1:10:0,-7.42884,-83.8972 +NC_045512.2 1092 . C A 2.05075E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.4157;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=891;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.827C>A|p.Pro276His|827/21291|827/21291|276/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:891:1:32:0,-5.22953,-77.2742 +NC_045512.2 1116 . T G 1.10528E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.2495;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=986;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.851T>G|p.Ile284Ser|851/21291|851/21291|284/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:986:1:11:0,-7.32884,-87.951 +NC_045512.2 1209 . T A 8.61161E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.71;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1018;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.944T>A|p.Met315Lys|944/21291|944/21291|315/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1018:1:9:0,-7.52884,-91.0342 +NC_045512.2 1218 . C A 8.61161E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.71;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=977;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.953C>A|p.Ser318*|953/21291|953/21291|318/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:977:1:9:0,-7.52884,-87.3331 +NC_045512.2 1232 . T G 1.10528E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.2495;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=969;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.967T>G|p.Cys323Gly|967/21291|967/21291|323/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:969:1:11:0,-7.32884,-86.4169 +NC_045512.2 1310 . T G 1.01839E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1736;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=542;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1045T>G|p.Leu349Val|1045/21291|1045/21291|349/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:542:1:11:0,-3.71648,-48.0072 +NC_045512.2 1441 . C T 119.939 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=8.76405;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=0;RO=0;RPL=2;RPP=3.0103;RPPR=0;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1176C>T|p.Gly392Gly|1176/21291|1176/21291|392/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:4:0,4:0:0:4:152:-14.0499,-1.20412,0 +NC_045512.2 1952 . C T 3.56629E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.2941;NS=1;NUMALT=1;ODDS=18.6177;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=645;RO=17;RPL=0;RPP=5.18177;RPPR=13.3567;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=13.3567;SRR=4;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1687C>T|p.Gln563*|1687/21291|1687/21291|563/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:645:1:38:0,-1.62127,-54.5556 +NC_045512.2 1970 . A T 1.76597E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5385;NS=1;NUMALT=1;ODDS=37.5904;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=955;RO=26;RPL=0;RPP=5.18177;RPPR=59.4686;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.34437;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1705A>T|p.Ile569Leu|1705/21291|1705/21291|569/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:955:1:8:0,-7.32781,-85.4272 +NC_045512.2 2011 . T G 9.74145E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5385;NS=1;NUMALT=1;ODDS=33.4461;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=982;RO=26;RPL=0;RPP=5.18177;RPPR=59.4686;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.34437;SRR=12;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1746T>G|p.Asp582Glu|1746/21291|1746/21291|582/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:982:1:26:0,-5.52798,-86.0617 +NC_045512.2 2023 . C A 2.13659E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=5.02092;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=38.4798;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=997;RO=27;RPL=0;RPP=5.18177;RPPR=38.4777;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1758C>A|p.Phe586Leu|1758/21291|1758/21291|586/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:997:1:10:0,-7.42884,-89.0116 +NC_045512.2 2024 . A G 6.04378E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=3.0103;EPPR=6.01695;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5385;NS=1;NUMALT=1;ODDS=22.6954;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=955;RO=26;RPL=0;RPP=7.35324;RPPR=36.4176;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1759A>G|p.Thr587Ala|1759/21291|1759/21291|587/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:26,2:26:955:2:74:0,-1.40307,-79.218 +NC_045512.2 2047 . T C 2.27971E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=60;NS=1;NUMALT=1;ODDS=38.2497;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=973;RO=27;RPL=1;RPP=5.18177;RPPR=3.09072;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1782T>C|p.Asn594Asn|1782/21291|1782/21291|594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:973:1:11:0,-7.32892,-86.7751 +NC_045512.2 2089 . G T 1.10528E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=38.2495;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1015;RO=27;RPL=1;RPP=5.18177;RPPR=3.09072;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1824G>T|p.Leu608Phe|1824/21291|1824/21291|608/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1015:1:11:0,-7.32884,-90.5359 +NC_045512.2 2124 . T A 1.10528E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=38.2495;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=990;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1859T>A|p.Val620Asp|1859/21291|1859/21291|620/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:990:1:11:0,-7.32884,-88.2918 +NC_045512.2 2130 . A C 2.06276E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5385;NS=1;NUMALT=1;ODDS=37.3601;PAIRED=0;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=948;RO=26;RPL=1;RPP=5.18177;RPPR=51.1168;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1865A>C|p.Glu622Ala|1865/21291|1865/21291|622/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:948:1:9:0,-7.22781,-84.6969 +NC_045512.2 2133 . A C 1.10528E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=38.2495;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=979;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1868A>C|p.Lys623Thr|1868/21291|1868/21291|623/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:979:1:11:0,-7.32884,-87.318 +NC_045512.2 2134 . A T 2.13659E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=38.4798;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=979;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1869A>T|p.Lys623Asn|1869/21291|1869/21291|623/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:979:1:10:0,-7.42884,-87.4031 +NC_045512.2 2136 . T C 6.04408E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5385;NS=1;NUMALT=1;ODDS=22.6954;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=951;RO=26;RPL=2;RPP=7.35324;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1871T>C|p.Leu624Pro|1871/21291|1871/21291|624/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:26,2:26:951:2:74:0,-1.40307,-78.8622 +NC_045512.2 2149 . T G 2.72046E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=32.9561;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=993;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1884T>G|p.Leu628Leu|1884/21291|1884/21291|628/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:993:1:34:0,-5.02993,-86.2692 +NC_045512.2 2161 . A C 2.10643E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5556;NS=1;NUMALT=1;ODDS=38.9403;PAIRED=1;PAIREDR=0.925926;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=935;RO=27;RPL=1;RPP=5.18177;RPPR=61.6401;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1896A>C|p.Glu632Asp|1896/21291|1896/21291|632/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:935:1:8:0,-7.62884,-83.6427 +NC_045512.2 2176 . A T 2.4933E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=12.2676;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.3684;NS=1;NUMALT=1;ODDS=28.1864;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=713;RO=19;RPL=1;RPP=5.18177;RPPR=44.2683;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=12.2676;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1911A>T|p.Glu637Asp|1911/21291|1911/21291|637/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:713:1:8:0,-5.2206,-63.6673 +NC_045512.2 2189 . C T 1.01839E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=20.5268;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.2;NS=1;NUMALT=1;ODDS=22.1736;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=564;RO=15;RPL=1;RPP=5.18177;RPPR=35.5824;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1924C>T|p.Leu642Phe|1924/21291|1924/21291|642/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:564:1:11:0,-3.71648,-49.9732 +NC_045512.2 2800 . T G 0.776404 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.63092;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=113;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2535T>G|p.Leu845Leu|2535/21291|2535/21291|845/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:3,1:3:113:1:34:-2.19479,0,-9.33542 +NC_045512.2 2895 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=23.7032;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1977;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1265;RO=34;RPL=0;RPP=5.18177;RPPR=60.4905;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=15.5282;SRR=10;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2630A>C|p.Asp877Ala|2630/21291|2630/21291|877/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1265:1:22:0,-8.33612,-111.946 +NC_045512.2 2941 . A C 9.9451E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.9952;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1822;RO=50;RPL=0;RPP=5.18177;RPPR=111.584;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2676A>C|p.Pro892Pro|2676/21291|2676/21291|892/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1822:1:9:0,-14.4525,-163.34 +NC_045512.2 2955 . T G 4.65589E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.3114;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=1836;RO=50;RPL=0;RPP=5.18177;RPPR=111.584;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2690T>G|p.Leu897*|2690/21291|2690/21291|897/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1836:1:25:0,-12.8527,-162.998 +NC_045512.2 2965 . G T 1.23858E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.5347;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1847;RO=50;RPL=0;RPP=5.18177;RPPR=111.584;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2700G>T|p.Trp900Cys|2700/21291|2700/21291|900/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1847:1:11:0,-14.2525,-165.388 +NC_045512.2 3037 . C T 1602.62 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=52;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=91.3725;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=75.3062;PAIRED=0.961538;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1925;QR=0;RO=0;RPL=27;RPP=3.17734;RPPR=0;RPR=25;RUN=1;SAF=26;SAP=3.0103;SAR=26;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:52:0,52:0:0:52:1925:-173.504,-15.6536,0 +NC_045512.2 3067 . T A 1.33652E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=3.05288;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.3621;PAIRED=1;PAIREDR=0.960784;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1859;RO=51;RPL=1;RPP=5.18177;RPPR=113.755;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.05288;SRR=26;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2802T>A|p.Gly934Gly|2802/21291|2802/21291|934/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1859:1:9:0,-14.7536,-166.672 +NC_045512.2 3076 . A C 1.67251E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=3.05288;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.7577;PAIRED=1;PAIREDR=0.960784;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1885;RO=51;RPL=1;RPP=5.18177;RPPR=113.755;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.05288;SRR=26;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2811A>C|p.Glu937Asp|2811/21291|2811/21291|937/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1885:1:29:0,-12.7539,-167.006 +NC_045512.2 3094 . A T 1.23858E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.5347;PAIRED=0;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1773;RO=50;RPL=1;RPP=5.18177;RPPR=111.584;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=3.0103;SRR=25;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2829A>T|p.Pro943Pro|2829/21291|2829/21291|943/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1773:1:11:0,-14.2525,-158.73 +NC_045512.2 3114 . G T 1.31091E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.2412;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1836;RO=50;RPL=1;RPP=5.18177;RPPR=111.584;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=3.18402;SRR=26;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2849G>T|p.Gly950Val|2849/21291|2849/21291|950/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1836:1:34:0,-11.9536,-162.104 +NC_045512.2 3216 . G T 37.7717 . AB=0.230769;ABP=19.3799;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=16.0391;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.6971;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=228;QR=749;RO=20;RPL=0;RPP=16.0391;RPPR=46.4397;RPR=6;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=20;SRP=46.4397;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2951G>T|p.Ser984Ile|2951/21291|2951/21291|984/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:26:20,6:20:749:6:228:-13.0582,0,-59.9124 +NC_045512.2 3222 . A C 1.96635E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.551;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=948;RO=25;RPL=0;RPP=5.18177;RPPR=57.2971;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=57.2971;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2957A>C|p.Gln986Pro|2957/21291|2957/21291|986/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:948:1:11:0,-6.72678,-84.5385 +NC_045512.2 3236 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=4.16534;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.6667;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1696;RO=47;RPL=0;RPP=5.18177;RPPR=105.07;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=4.16534;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2971C>A|p.Gln991Lys|2971/21291|2971/21291|991/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1696:1:10:0,-13.4494,-151.906 +NC_045512.2 3240 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=3.0103;EPPR=3.42611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.0124;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1682;RO=47;RPL=0;RPP=7.35324;RPPR=105.07;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.42611;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2975A>G|p.Asp992Gly|2975/21291|2975/21291|992/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:47,2:47:1682:2:45:0,-10.4781,-147.376 +NC_045512.2 3243 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=3.19126;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.5914;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1718;RO=48;RPL=0;RPP=5.18177;RPPR=107.241;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2978G>A|p.Gly993Asp|2978/21291|2978/21291|993/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1718:1:38:0,-10.9532,-151.09 +NC_045512.2 3252 . A G 1.07886E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=3.0103;EPPR=3.05462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.1466;PAIRED=1;PAIREDR=0.979592;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1804;RO=49;RPL=0;RPP=7.35324;RPPR=109.412;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.05462;SRR=24;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2987A>G|p.Asp996Gly|2987/21291|2987/21291|996/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:49,2:49:1804:2:75:0,-8.23219,-155.503 +NC_045512.2 3258 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=3.40914;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.5564;PAIRED=1;PAIREDR=0.979592;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1810;RO=49;RPL=0;RPP=5.18177;RPPR=109.412;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.40914;SRR=23;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2993A>C|p.Gln998Pro|2993/21291|2993/21291|998/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1810:1:18:0,-13.2515,-161.364 +NC_045512.2 3267 . C T 1535.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=51;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=3.05288;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=73.9199;PAIRED=0.980392;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1895;QR=0;RO=0;RPL=0;RPP=113.755;RPPR=0;RPR=51;RUN=1;SAF=26;SAP=3.05288;SAR=25;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3002C>T|p.Thr1001Ile|3002/21291|3002/21291|1001/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:51:0,51:0:0:51:1895:-170.809,-15.3525,0 +NC_045512.2 3285 . A G 9.9451E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.9952;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1817;RO=50;RPL=0;RPP=5.18177;RPPR=111.584;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3020A>G|p.Glu1007Gly|3020/21291|3020/21291|1007/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1817:1:9:0,-14.4525,-162.889 +NC_045512.2 3291 . A C 7.26259E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.7649;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1860;RO=50;RPL=0;RPP=5.18177;RPPR=111.584;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3026A>C|p.Gln1009Pro|3026/21291|3026/21291|1009/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1860:1:10:0,-14.3525,-166.662 +NC_045512.2 3343 . T C 1.24009E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.5347;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1884;RO=50;RPL=0;RPP=5.18177;RPPR=3.18402;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3078T>C|p.Asn1026Asn|3078/21291|3078/21291|1026/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1884:1:11:0,-14.2525,-168.72 +NC_045512.2 3416 . A C 3.02883E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=3.05462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.3343;PAIRED=1;PAIREDR=0.979592;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1794;RO=49;RPL=1;RPP=5.18177;RPPR=109.412;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=3.05462;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3151A>C|p.Lys1051Gln|3151/21291|3151/21291|1051/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1794:1:32:0,-11.8522,-158.52 +NC_045512.2 3425 . C A 6.96124E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.2254;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1866;RO=50;RPL=1;RPP=5.18177;RPPR=111.584;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.0103;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3160C>A|p.Pro1054Thr|3160/21291|3160/21291|1054/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1866:1:8:0,-14.5525,-167.402 +NC_045512.2 3426 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.4557;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1808;RO=50;RPL=1;RPP=5.18177;RPPR=111.584;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.0103;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3161C>A|p.Pro1054Gln|3161/21291|3161/21291|1054/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1808:1:7:0,-14.6525,-162.28 +NC_045512.2 3435 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.4557;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1783;RO=50;RPL=1;RPP=5.18177;RPPR=111.584;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.0103;SRR=25;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3170T>G|p.Val1057Gly|3170/21291|3170/21291|1057/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1783:1:7:0,-14.6525,-160.031 +NC_045512.2 3442 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.4557;PAIRED=1;PAIREDR=0.98;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1802;RO=50;RPL=1;RPP=5.18177;RPPR=111.584;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.0103;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3177T>A|p.Asn1059Lys|3177/21291|3177/21291|1059/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1802:1:7:0,-14.6525,-161.743 +NC_045512.2 3449 . A C 9.13121E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=6.48466;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.89;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1449;RO=40;RPL=1;RPP=5.18177;RPPR=89.8692;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=6.48466;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3184A>C|p.Asn1062His|3184/21291|3184/21291|1062/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1449:1:11:0,-11.2422,-129.591 +NC_045512.2 3454 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=7.35324;EPPR=16.9698;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.5757;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1292;RO=35;RPL=2;RPP=7.35324;RPPR=79.0118;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=16.9698;SRR=25;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3189T>G|p.Val1063Val|3189/21291|3189/21291|1063/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:35,2:35:1292:2:21:0,-9.14312,-114.577 +NC_045512.2 3459 . T G 3.43565E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=31.9633;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.7671;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1079;RO=30;RPL=1;RPP=5.18177;RPPR=68.1545;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=31.9633;SRR=25;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3194T>G|p.Leu1065Arg|3194/21291|3194/21291|1065/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1079:1:9:0,-8.43193,-96.5036 +NC_045512.2 3886 . TAAAGAGGAAGT TAAGAGGAAGT 129.731 . AB=0.75;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1M1D10M;DP=8;DPB=7.5;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.42806;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=224;QR=74;RO=2;RPL=0;RPP=16.0391;RPPR=7.35324;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=1;SRP=3.0103;SRR=1;TYPE=del;ANN=TAAGAGGAAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3624delA|p.Glu1209fs|3624/21291|3624/21291|1208/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:2,6:2:74:6:224:-18.1119,0,-4.61764 +NC_045512.2 4064 . T C 2.47659E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=16.8392;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.2849;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=718;RO=19;RPL=0;RPP=5.18177;RPPR=4.03889;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=16.8392;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3799T>C|p.Ser1267Pro|3799/21291|3799/21291|1267/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:718:1:38:0,-2.22333,-61.1557 +NC_045512.2 4095 . CTTTC TTTTT 21.84 . AB=0.235294;ABP=13.3567;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X3M1X;DP=17;DPB=17;DPRA=0;EPP=11.6962;EPPR=31.2394;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.02229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=492;RO=13;RPL=0;RPP=11.6962;RPPR=7.18621;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=9;SRP=7.18621;SRR=4;TYPE=complex;ANN=TTTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3830_3834delCTTTCinsTTTTT|p.Thr1277Ile|3830/21291|3830/21291|1277/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:17:13,4:13:492:4:152:-8.93238,0,-39.5096 +NC_045512.2 4107 . A C 5.68903E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.0587;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=645;RO=17;RPL=0;RPP=5.18177;RPPR=13.3567;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=13.3567;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3842A>C|p.Lys1281Thr|3842/21291|3842/21291|1281/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:645:1:10:0,-4.41854,-57.3879 +NC_045512.2 4124 . G T 1.16132E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=10.6577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.6478;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=831;RO=23;RPL=0;RPP=5.18177;RPPR=24.253;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.10471;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3859G>T|p.Val1287Leu|3859/21291|3859/21291|1287/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:831:1:38:0,-3.42745,-71.3089 +NC_045512.2 4128 . G A 9.3577E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.831;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1029;RO=28;RPL=0;RPP=5.18177;RPPR=34.0313;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.32051;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3863G>A|p.Gly1288Asp|3863/21291|3863/21291|1288/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:28,1:28:1029:1:10:0,-7.72987,-91.9201 +NC_045512.2 4132 . T G 1.01633E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.5218;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1006;RO=28;RPL=0;RPP=5.18177;RPPR=34.0313;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.32051;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3867T>G|p.Asp1289Glu|3867/21291|3867/21291|1289/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:28,1:28:1006:1:7:0,-8.02987,-90.1432 +NC_045512.2 4143 . A G 3.85731E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=4.76149;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3519;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1098;RO=31;RPL=0;RPP=5.18177;RPPR=40.0654;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.64073;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3878A>G|p.Glu1293Gly|3878/21291|3878/21291|1293/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1098:1:8:0,-8.83296,-98.3172 +NC_045512.2 4171 . T G 2.0394E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.868;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1001;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3906T>G|p.Pro1302Pro|3906/21291|3906/21291|1302/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1001:1:17:0,-6.72886,-88.7033 +NC_045512.2 4180 . G T 1.69817E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.4866;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=1000;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3915G>T|p.Lys1305Asn|3915/21291|3915/21291|1305/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:1000:1:23:0,-6.12893,-88.0107 +NC_045512.2 4206 . C T 201.582 . AB=0.357143;ABP=7.97367;AC=1;AF=0.5;AN=2;AO=10;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=10.8276;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.416;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=376;QR=681;RO=18;RPL=3;RPP=6.48466;RPPR=3.49285;RPR=7;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=9;SRP=3.0103;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3941C>T|p.Ala1314Val|3941/21291|3941/21291|1314/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:28:18,10:18:681:10:376:-25.7641,0,-53.1962 +NC_045512.2 4226 . C T 9.34035E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=7.35324;EPPR=51.1168;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.2601;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=936;RO=26;RPL=1;RPP=3.0103;RPPR=3.34437;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3961C>T|p.Pro1321Ser|3961/21291|3961/21291|1321/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:26,2:26:936:2:76:0,-1.21403,-77.3309 +NC_045512.2 4341 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=29.6215;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.1318;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1921;RO=51;RPL=1;RPP=5.18177;RPPR=3.3935;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=25.534;SRR=14;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4076T>G|p.Ile1359Ser|4076/21291|4076/21291|1359/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1921:1:10:0,-14.6536,-172.148 +NC_045512.2 4393 . A C 6.38137E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=15.1406;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.9398;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2171;RO=58;RPL=0;RPP=5.18177;RPPR=32.3626;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=5.40641;SRR=33;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4128A>C|p.Arg1376Arg|4128/21291|4128/21291|1376/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2171:1:9:0,-16.8608,-194.736 +NC_045512.2 4395 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=61;DPB=61;DPRA=0;EPP=5.18177;EPPR=10.1038;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.4488;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2246;RO=60;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=8.22183;SRR=36;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4130A>C|p.Glu1377Ala|4130/21291|4130/21291|1377/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:61:60,1:60:2246:1:10:0,-17.3628,-201.382 +NC_045512.2 4403 . G C 7.48861E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=9.02635;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=84.3583;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=2236;RO=61;RPL=1;RPP=5.18177;RPPR=41.7764;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=7.31765;SRR=36;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4138G>C|p.Ala1380Pro|4138/21291|4138/21291|1380/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2236:1:12:0,-17.4639,-200.281 +NC_045512.2 4404 . C A 1.94372E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=9.87495;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.1891;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2219;RO=62;RPL=0;RPP=5.18177;RPPR=43.4978;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=6.51267;SRR=36;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4139C>A|p.Ala1380Glu|4139/21291|4139/21291|1380/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2219:1:10:0,-17.9649,-198.942 +NC_045512.2 4420 . A G 1.04268E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.0103;EPPR=6.51267;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.4927;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2235;RO=62;RPL=0;RPP=7.35324;RPPR=53.5846;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=6.51267;SRR=36;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4155A>G|p.Thr1385Thr|4155/21291|4155/21291|1385/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,2:62:2235:2:76:0,-12.0511,-194.183 +NC_045512.2 4435 . T G 2.86308E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=7.35324;EPPR=4.6389;GTI=0;LEN=1;MEANALT=1;MQM=56;MQMR=60;NS=1;NUMALT=1;ODDS=61.7074;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1802;RO=48;RPL=0;RPP=7.35324;RPPR=107.241;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=27;SRP=4.6389;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4170T>G|p.Pro1390Pro|4170/21291|4170/21291|1390/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,2:48:1802:2:36:0,-11.6317,-159.027 +NC_045512.2 4442 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=3.0103;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8462;NS=1;NUMALT=1;ODDS=57.19;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1913;RO=52;RPL=0;RPP=7.35324;RPPR=107.408;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4177G>A|p.Val1393Met|4177/21291|4177/21291|1393/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:52,2:52:1913:2:75:0,-9.13528,-165.302 +NC_045512.2 4585 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8491;NS=1;NUMALT=1;ODDS=74.3272;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1898;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4320T>C|p.Asp1440Asp|4320/21291|4320/21291|1440/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1898:1:8:0,-15.4556,-170.271 +NC_045512.2 4586 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8491;NS=1;NUMALT=1;ODDS=74.0969;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1896;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4321C>T|p.Leu1441Leu|4321/21291|4321/21291|1441/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1896:1:9:0,-15.3556,-169.978 +NC_045512.2 4592 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8462;NS=1;NUMALT=1;ODDS=71.8083;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1843;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4327G>A|p.Glu1443Lys|4327/21291|4327/21291|1443/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1843:1:13:0,-14.6546,-164.814 +NC_045512.2 4593 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8462;NS=1;NUMALT=1;ODDS=70.8873;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1857;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4328A>T|p.Glu1443Val|4328/21291|4328/21291|1443/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1857:1:17:0,-14.2546,-165.675 +NC_045512.2 4605 . C T 2.91408E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=5.18177;EPPR=26.7649;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7576;NS=1;NUMALT=1;ODDS=40.1624;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1235;RO=33;RPL=1;RPP=5.18177;RPPR=74.6689;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=26.7649;SRR=26;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4340C>T|p.Thr1447Ile|4340/21291|4340/21291|1447/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:33,1:33:1235:1:38:0,-6.43775,-107.639 +NC_045512.2 4619 . T C 3.11299E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=38.0434;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7333;NS=1;NUMALT=1;ODDS=39.3135;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=1138;RO=30;RPL=1;RPP=5.18177;RPPR=68.1545;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=38.0434;SRR=26;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4354T>C|p.Tyr1452His|4354/21291|4354/21291|1452/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:31:30,1:30:1138:1:24:0,-6.93204,-100.314 +NC_045512.2 4639 . T A 4.42691E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=48.8827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.75;NS=1;NUMALT=1;ODDS=39.7232;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1183;RO=32;RPL=0;RPP=5.18177;RPPR=56.2114;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=35.8538;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4374T>A|p.Asn1458Lys|4374/21291|4374/21291|1458/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1183:1:34:0,-6.53508,-103.358 +NC_045512.2 4646 . G A 2.5736E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=48.8827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.75;NS=1;NUMALT=1;ODDS=38.806;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1209;RO=32;RPL=1;RPP=5.18177;RPPR=48.8827;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=30.1537;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4381G>A|p.Glu1461Lys|4381/21291|4381/21291|1461/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1209:1:38:0,-6.13672,-105.302 +NC_045512.2 4668 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=62.6327;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7714;NS=1;NUMALT=1;ODDS=49.5491;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1318;RO=35;RPL=1;RPP=5.18177;RPPR=35.8306;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=25.4075;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4403C>A|p.Ser1468Tyr|4403/21291|4403/21291|1468/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1318:1:9:0,-9.93708,-118.002 +NC_045512.2 4688 . G T 4.64233E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=30.2953;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6522;NS=1;NUMALT=1;ODDS=27.565;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=805;RO=23;RPL=1;RPP=5.18177;RPPR=14.4341;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=5.3706;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4423G>T|p.Val1475Phe|4423/21291|4423/21291|1475/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:805:1:34:0,-3.82581,-69.3627 +NC_045512.2 4693 . T A 0.194997 . AB=0.166667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.08079;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=189;RO=5;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4428T>A|p.Ser1476Ser|4428/21291|4428/21291|1476/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:5,1:5:189:1:38:-1.99109,0,-15.5698 +NC_045512.2 4724 . A C 1.95529E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.9161;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=399;RO=11;RPL=0;RPP=5.18177;RPPR=26.8965;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=3.20771;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4459A>C|p.Asn1487His|4459/21291|4459/21291|1487/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:399:1:11:0,-2.51236,-35.1508 +NC_045512.2 4995 . T G 1.42573E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5345;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=491;RO=13;RPL=0;RPP=5.18177;RPPR=3.17734;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4730T>G|p.Ile1577Ser|4730/21291|4730/21291|1577/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:491:1:11:0,-3.11442,-43.4369 +NC_045512.2 5046 . T G 1.01839E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1736;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=551;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4781T>G|p.Phe1594Cys|4781/21291|4781/21291|1594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:551:1:11:0,-3.71648,-48.8255 +NC_045512.2 5047 . T G 6.42557E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.6341;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=549;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=3.15506;SRR=7;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4782T>G|p.Phe1594Leu|4782/21291|4782/21291|1594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:549:1:9:0,-3.91648,-48.8442 +NC_045512.2 5060 . TT GG 4.05226E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.49;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=564;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=3.15506;SRR=7;TYPE=complex;ANN=GG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4795_4796delTTinsGG|p.Leu1599Gly|4795/21291|4795/21291|1599/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:564:1:27:0,-2.1167,-48.402 +NC_045512.2 5070 . C T 1.01838E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1736;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=564;RO=15;RPL=0;RPP=5.18177;RPPR=27.4756;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=3.15506;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4805C>T|p.Ala1602Val|4805/21291|4805/21291|1602/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:564:1:11:0,-3.71648,-50.0016 +NC_045512.2 5184 . C A 5.6477E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.5528;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=491;RO=13;RPL=1;RPP=5.18177;RPPR=31.2394;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=4.51363;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4919C>A|p.Pro1640His|4919/21291|4919/21291|1640/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:491:1:37:0,-0.516591,-40.8392 +NC_045512.2 5192 . C T 1.36128E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=7.35324;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5808;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=489;RO=13;RPL=2;RPP=7.35324;RPPR=31.2394;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.51363;SRR=8;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4927C>T|p.Leu1643Leu|4927/21291|4927/21291|1643/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:13,2:13:489:2:18:0,-2.80546,-42.6462 +NC_045512.2 5237 . T A 5.29557E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.2224;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=449;RO=12;RPL=1;RPP=5.18177;RPPR=29.068;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=5.9056;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4972T>A|p.Tyr1658Asn|4972/21291|4972/21291|1658/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:449:1:11:0,-2.81339,-39.6577 +NC_045512.2 5260 . T C 4.64232E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.565;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=808;RO=23;RPL=0;RPP=5.18177;RPPR=7.63648;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=7.63648;SRR=8;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4995T>C|p.Thr1665Thr|4995/21291|4995/21291|1665/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:808:1:34:0,-3.82581,-69.6398 +NC_045512.2 5330 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=51.8684;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.6793;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1487;RO=40;RPL=0;RPP=5.18177;RPPR=89.8692;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=51.8684;SRR=5;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5065A>G|p.Lys1689Glu|5065/21291|5065/21291|1689/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1487:1:38:0,-8.54496,-130.315 +NC_045512.2 5340 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=45.4803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.4388;PAIRED=1;PAIREDR=0.976744;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1574;RO=43;RPL=0;RPP=5.18177;RPPR=96.3836;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=45.4803;SRR=7;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5075C>A|p.Pro1692Gln|5075/21291|5075/21291|1692/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1574:1:9:0,-12.3453,-141.035 +NC_045512.2 5341 . A T 1.5522E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=39.8243;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.7675;PAIRED=1;PAIREDR=0.976744;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1587;RO=43;RPL=0;RPP=5.18177;RPPR=96.3836;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=39.8243;SRR=8;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5076A>T|p.Pro1692Pro|5076/21291|5076/21291|1692/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1587:1:38:0,-9.44805,-139.307 +NC_045512.2 5354 . G A 1.20998E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8235;NS=1;NUMALT=1;ODDS=94.1857;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2502;RO=68;RPL=0;RPP=5.18177;RPPR=150.67;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.13803;SRR=33;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5089G>A|p.Asp1697Asn|5089/21291|5089/21291|1697/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2502:1:11:0,-19.6711,-224.268 +NC_045512.2 5368 . A G 9.67365E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=3.52123;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8235;NS=1;NUMALT=1;ODDS=94.6462;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2447;RO=68;RPL=0;RPP=5.18177;RPPR=150.67;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.52123;SRR=32;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5103A>G|p.Arg1701Arg|5103/21291|5103/21291|1701/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2447:1:9:0,-19.8711,-219.518 +NC_045512.2 5388 . CT AG,AT 1964.73 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=1,68;CIGAR=2X,1X1M;DP=69;DPB=69;DPRA=0,0;EPP=5.18177,3.13803;EPPR=0;GTI=0;LEN=2,1;MEANALT=2,2;MQM=60,59.8235;MQMR=0;NS=1;NUMALT=2;ODDS=91.1926;PAIRED=1,0.985294;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=24,2434;QR=0;RO=0;RPL=0,0;RPP=5.18177,150.67;RPPR=0;RPR=1,68;RUN=1,1;SAF=1,35;SAP=5.18177,3.13803;SAR=0,33;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=AT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5123C>A|p.Ala1708Asp|5123/21291|5123/21291|1708/7096|| GT:DP:AD:RO:QR:AO:QA:GL 2/2:69:0,1,68:0:0:1,68:24,2434:-219,-217.142,-216.841,-20.47,-18.3712,0 +NC_045512.2 5395 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=96.9297;PAIRED=1;PAIREDR=0.985714;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2583;RO=70;RPL=0;RPP=5.18177;RPPR=146.452;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.13438;SRR=34;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5130T>G|p.Phe1710Leu|5130/21291|5130/21291|1710/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2583:1:11:0,-20.2731,-231.549 +NC_045512.2 5398 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=97.3902;PAIRED=1;PAIREDR=0.985714;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2536;RO=70;RPL=0;RPP=5.18177;RPPR=146.452;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.13438;SRR=34;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5133T>G|p.Cys1711Trp|5133/21291|5133/21291|1711/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2536:1:9:0,-20.4731,-227.519 +NC_045512.2 5434 . T A,C 2.66744E-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=71;DPB=71;DPRA=0,0;EPP=5.18177,5.18177;EPPR=135.974;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=59.6522;NS=1;NUMALT=2;ODDS=95.8109;PAIRED=1,1;PAIREDR=0.985507;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,11;QR=2567;RO=69;RPL=1,1;RPP=5.18177,5.18177;RPPR=3.04177;RPR=0,0;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=34;SRP=3.04177;SRR=35;TYPE=snp,snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5169T>A|p.Gly1723Gly|5169/21291|5169/21291|1723/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:69,1,1:69:2567:1,1:11,11:0,-20.0821,-230.078,-20.0821,-229.694,-230.078 +NC_045512.2 5482 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=93.4676;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=96.9297;PAIRED=1;PAIREDR=0.985714;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2604;RO=70;RPL=1;RPP=5.18177;RPPR=10.9517;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.0103;SRR=35;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5217C>A|p.Ala1739Ala|5217/21291|5217/21291|1739/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2604:1:11:0,-20.2731,-233.411 +NC_045512.2 5512 . C T 3.57126E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=68;DPB=68;DPRA=0;EPP=5.18177;EPPR=3.30199;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6418;NS=1;NUMALT=1;ODDS=93.0442;PAIRED=1;PAIREDR=0.985075;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2437;RO=67;RPL=1;RPP=5.18177;RPPR=148.499;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.30199;SRR=35;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5247C>T|p.Asn1749Asn|5247/21291|5247/21291|1749/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:68:67,1:67:2437:1:10:0,-19.47,-218.501 +NC_045512.2 5526 . C T 1.03969E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=3.04177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6522;NS=1;NUMALT=1;ODDS=95.7878;PAIRED=1;PAIREDR=0.985507;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2526;RO=69;RPL=1;RPP=5.18177;RPPR=152.842;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=34;SRP=3.04177;SRR=35;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5261C>T|p.Thr1754Ile|5261/21291|5261/21291|1754/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2526:1:10:0,-20.0721,-226.507 +NC_045512.2 5527 . T A 1.30789E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=3.04177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6522;NS=1;NUMALT=1;ODDS=96.0181;PAIRED=1;PAIREDR=0.985507;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2486;RO=69;RPL=1;RPP=5.18177;RPPR=152.842;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=34;SRP=3.04177;SRR=35;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5262T>A|p.Thr1754Thr|5262/21291|5262/21291|1754/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2486:1:9:0,-20.1721,-222.994 +NC_045512.2 5531 . G C 1.30789E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=3.04177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6522;NS=1;NUMALT=1;ODDS=96.0181;PAIRED=1;PAIREDR=0.985507;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2544;RO=69;RPL=1;RPP=5.18177;RPPR=152.842;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=34;SRP=3.04177;SRR=35;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5266G>C|p.Gly1756Arg|5266/21291|5266/21291|1756/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2544:1:9:0,-20.1721,-228.211 +NC_045512.2 5557 . T G 3.33041E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=7.35324;EPPR=4.23175;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.625;NS=1;NUMALT=1;ODDS=86.6087;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=2297;RO=64;RPL=2;RPP=7.35324;RPPR=141.985;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=29;SRP=4.23175;SRR=35;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5292T>G|p.Gly1764Gly|5292/21291|5292/21291|1764/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:64,2:64:2297:2:21:0,-17.873,-204.905 +NC_045512.2 5577 . T A 5.59032E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=66.2602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4894;NS=1;NUMALT=1;ODDS=66.3574;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1756;RO=47;RPL=1;RPP=5.18177;RPPR=47.41;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=23.3852;SRR=34;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5312T>A|p.Met1771Lys|5312/21291|5312/21291|1771/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1756:1:7:0,-13.7494,-157.536 +NC_045512.2 5683 . G A 2.30761E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8996;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=973;RO=26;RPL=0;RPP=5.18177;RPPR=59.4686;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5418G>A|p.Met1806Ile|5418/21291|5418/21291|1806/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:973:1:11:0,-7.02781,-86.7863 +NC_045512.2 5696 . C A 2.06351E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.3601;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=954;RO=26;RPL=0;RPP=5.18177;RPPR=59.4686;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5431C>A|p.Pro1811Thr|5431/21291|5431/21291|1811/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:954:1:9:0,-7.22781,-85.2705 +NC_045512.2 5727 . T G 2.30685E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=24.391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8996;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=963;RO=26;RPL=1;RPP=5.18177;RPPR=15.0369;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5462T>G|p.Phe1821Cys|5462/21291|5462/21291|1821/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:963:1:11:0,-7.02781,-85.8835 +NC_045512.2 5776 . A T 2.30761E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8996;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=974;RO=26;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5511A>T|p.Lys1837Asn|5511/21291|5511/21291|1837/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:974:1:11:0,-7.02781,-86.8767 +NC_045512.2 5789 . A C 2.30761E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8996;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=987;RO=26;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5524A>C|p.Lys1842Gln|5524/21291|5524/21291|1842/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:987:1:11:0,-7.02781,-88.0459 +NC_045512.2 5830 . G A 2.06351E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.3601;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=935;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5565G>A|p.Lys1855Lys|5565/21291|5565/21291|1855/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:935:1:9:0,-7.22781,-83.5593 +NC_045512.2 5835 . C A 1.79606E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.1299;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=963;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5570C>A|p.Ser1857*|5570/21291|5570/21291|1857/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:963:1:10:0,-7.12781,-85.9857 +NC_045512.2 5848 . T G 2.06351E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.3601;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=894;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5583T>G|p.Gly1861Gly|5583/21291|5583/21291|1861/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:894:1:9:0,-7.22781,-79.8563 +NC_045512.2 5850 . C A 2.30761E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8996;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=911;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5585C>A|p.Pro1862His|5585/21291|5585/21291|1862/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:27:26,1:26:911:1:11:0,-7.02781,-81.1948 +NC_045512.2 5876 . AAC CAG 3.77119E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=15.074;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.4699;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=669;RO=18;RPL=1;RPP=5.18177;RPPR=33.8935;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=10.7311;SRR=13;TYPE=complex;ANN=CAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5611_5613delAACinsCAG|p.Asn1871Gln|5611/21291|5611/21291|1871/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:19:18,1:18:669:1:14:0,-4.31958,-59.1436 +NC_045512.2 5881 . T C 7.15995E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=18.4661;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.8284;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=610;RO=17;RPL=1;RPP=5.18177;RPPR=31.7504;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=13.3567;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5616T>C|p.Ser1872Ser|5616/21291|5616/21291|1872/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:610:1:11:0,-4.31854,-54.1262 +NC_045512.2 5882 . T G 2.70525E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.4993;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=562;RO=16;RPL=1;RPP=5.18177;RPPR=29.6108;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=16.582;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5617T>G|p.Tyr1873Asp|5617/21291|5617/21291|1873/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:562:1:11:0,-4.01751,-49.7996 +NC_045512.2 5918 . G C 3.81893E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.8519;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=532;RO=14;RPL=1;RPP=5.18177;RPPR=25.3454;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=25.3454;SRR=13;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5653G>C|p.Asp1885His|5653/21291|5653/21291|1885/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:532:1:11:0,-3.41545,-47.1253 +NC_045512.2 5920 . T C 1.90202E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.6411;PAIRED=1;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=521;RO=14;RPL=1;RPP=5.18177;RPPR=25.3454;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=25.3454;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5655T>C|p.Asp1885Asp|5655/21291|5655/21291|1885/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:521:1:38:0,-0.718181,-43.4337 +NC_045512.2 5929 . T C 3.81893E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.8519;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=531;RO=14;RPL=1;RPP=5.18177;RPPR=25.3454;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=25.3454;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5664T>C|p.Val1888Val|5664/21291|5664/21291|1888/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:531:1:11:0,-3.41545,-47.0351 +NC_045512.2 5986 . CACA TACC,TACA 26.6711 . AB=0.5,0.5;ABP=3.0103,3.0103;AC=1,1;AF=0.5,0.5;AN=2;AO=1,1;CIGAR=1X2M1X,1X3M;DP=2;DPB=2;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;GTI=0;LEN=4,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=1.8518;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=24,38;QR=0;RO=0;RPL=0,0;RPP=5.18177,5.18177;RPPR=0;RPR=1,1;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=TACA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721C>T|p.Phe1907Phe|5721/21291|5721/21291|1907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/2:2:0,1,1:0:0:1,1:24,38:-5.28524,-3.49624,-3.19521,-2.09886,0,-1.79783 +NC_045512.2 6250 . C A 5.42761E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=3.94093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.41;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=739;RO=21;RPL=0;RPP=5.18177;RPPR=40.3389;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.1137;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5985C>A|p.Asn1995Lys|5985/21291|5985/21291|1995/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:739:1:23:0,-4.32275,-64.521 +NC_045512.2 6273 . ATAAA CTAAC 4.12779E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.3797;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=738;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.0103;SRR=10;TYPE=complex;ANN=CTAAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6008_6012delATAAAinsCTAAC|p.TyrLys2003SerAsn|6008/21291|6008/21291|2003/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:738:1:26:0,-3.7218,-64.1477 +NC_045512.2 6423 . A C 6.60632E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.5239;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=735;RO=20;RPL=1;RPP=5.18177;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6158A>C|p.Glu2053Ala|6158/21291|6158/21291|2053/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:735:1:8:0,-5.52163,-65.673 +NC_045512.2 6443 . G A 1.85746E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.8637;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=757;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6178G>A|p.Asp2060Asn|6178/21291|6178/21291|2060/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:757:1:8:0,-5.82266,-67.6481 +NC_045512.2 6505 . A G 1.90202E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.6411;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=531;RO=14;RPL=1;RPP=5.18177;RPPR=8.59409;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=8.59409;SRR=10;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6240A>G|p.Ala2080Ala|6240/21291|6240/21291|2080/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:531:1:38:0,-0.718181,-44.3378 +NC_045512.2 6721 . A C 4.70357E-5 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=12.7819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.4332;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=288;RO=8;RPL=1;RPP=5.18177;RPPR=4.09604;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6456A>C|p.Thr2152Thr|6456/21291|6456/21291|2152/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:9:8,1:8:288:1:18:0,-0.909297,-24.4659 +NC_045512.2 7281 . A T 2.10552E-5 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.2369;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=235;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7016A>T|p.Tyr2339Phe|7016/21291|7016/21291|2339/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:8:7,1:7:235:1:9:0,-1.50824,-20.5718 +NC_045512.2 7313 . T C 2.50102E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=22.325;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.1864;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=706;RO=19;RPL=1;RPP=5.18177;RPPR=5.8675;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=16.8392;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7048T>C|p.Phe2350Leu|7048/21291|7048/21291|2350/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:706:1:8:0,-5.2206,-63.0692 +NC_045512.2 7381 . A C 9.42858E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=12.8806;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5148;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=807;RO=22;RPL=0;RPP=5.18177;RPPR=22.3561;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=3.40511;SRR=10;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7116A>C|p.Val2372Val|7116/21291|7116/21291|2372/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:23:22,1:22:807:1:11:0,-5.82369,-71.8475 +NC_045512.2 7665 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.7142;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1180;RO=32;RPL=0;RPP=5.18177;RPPR=5.45321;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=5.45321;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7400A>T|p.Asp2467Val|7400/21291|7400/21291|2467/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1180:1:21:0,-7.83404,-104.396 +NC_045512.2 7670 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1200;RO=32;RPL=0;RPP=5.18177;RPPR=5.45321;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=5.45321;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7405G>T|p.Val2469Phe|7405/21291|7405/21291|2469/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1200:1:11:0,-8.83399,-107.202 +NC_045512.2 7675 . GAGAG TAGAT,GAGTG,GAGAT 2.38725 . AB=0.0344828,0.0344828,0.172414;ABP=57.5966,57.5966,30.0414;AC=0,0,1;AF=0,0,0.5;AN=2;AO=1,1,5;CIGAR=1X3M1X,3M1X1M,4M1X;DP=29;DPB=29;DPRA=0,0,0;EPP=5.18177,5.18177,13.8677;EPPR=50.7827;GTI=0;LEN=5,1,1;MEANALT=3,3,3;MQM=60,60,60;MQMR=60;NS=1;NUMALT=3;ODDS=0.311008;PAIRED=1,1,1;PAIREDR=1;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=27,38,190;QR=794;RO=22;RPL=0,0,0;RPP=5.18177,5.18177,13.8677;RPPR=4.58955;RPR=1,1,5;RUN=1,1,1;SAF=1,1,5;SAP=5.18177,5.18177,13.8677;SAR=0,0,0;SRF=13;SRP=4.58955;SRR=9;TYPE=complex,snp,snp;ANN=GAGTG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7413A>T|p.Arg2471Ser|7413/21291|7413/21291|2471/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/3:29:22,1,1,5:22:794:1,1,5:27,38,190:-8.9991,-13.5087,-77.9875,-12.5026,-75.1715,-76.9959,0,-62.7028,-61.7102,-63.3226 +NC_045512.2 7695 . T C 4.99826E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.4956;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=689;RO=19;RPL=0;RPP=5.18177;RPPR=44.2683;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=44.2683;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7430T>C|p.Phe2477Ser|7430/21291|7430/21291|2477/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:20:19,1:19:689:1:11:0,-4.9206,-61.2338 +NC_045512.2 7702 . A C 3.76329E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=32.8939;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.1729;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=772;RO=21;RPL=0;RPP=5.18177;RPPR=48.6112;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=32.8939;SRR=2;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7437A>C|p.Arg2479Ser|7437/21291|7437/21291|2479/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:772:1:11:0,-5.52266,-68.7019 +NC_045512.2 7705 . AAT GAG 5.91419E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=24.253;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.6352;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=832;RO=23;RPL=0;RPP=5.18177;RPPR=52.9542;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=24.253;SRR=4;TYPE=complex;ANN=GAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7440_7442delAATinsGAG|p.Ile2481Arg|7440/21291|7440/21291|2480/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:832:1:25:0,-4.72486,-72.6951 +NC_045512.2 7715 . A C 4.16923E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=26.1727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.8947;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=851;RO=24;RPL=0;RPP=5.18177;RPPR=55.1256;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=26.1727;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7450A>C|p.Thr2484Pro|7450/21291|7450/21291|2484/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:25:24,1:24:851:1:8:0,-6.72575,-76.0932 +NC_045512.2 7718 . G A 1.10528E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=12.7417;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.2495;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=952;RO=27;RPL=0;RPP=5.18177;RPPR=61.6401;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=12.7417;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7453G>A|p.Asp2485Asn|7453/21291|7453/21291|2485/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:27,1:27:952:1:11:0,-7.32884,-84.878 +NC_045512.2 7742 . A G 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1442;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7477A>G|p.Ser2493Gly|7477/21291|7477/21291|2493/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1442:1:11:0,-10.9412,-128.963 +NC_045512.2 7745 . G T 3.01588E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.2191;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1403;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7480G>T|p.Val2494Phe|7480/21291|7480/21291|2494/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1403:1:8:0,-11.2412,-125.751 +NC_045512.2 7747 . T G 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1407;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7482T>G|p.Val2494Val|7482/21291|7482/21291|2494/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1407:1:11:0,-10.9412,-125.81 +NC_045512.2 7761 . G T 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1403;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7496G>T|p.Gly2499Val|7496/21291|7496/21291|2499/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1403:1:11:0,-10.9412,-125.45 +NC_045512.2 7775 . T G 1.16021E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.9246;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.6347;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1385;RO=38;RPL=0;RPP=5.18177;RPPR=61.5258;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.23888;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7510T>G|p.Tyr2504Asp|7510/21291|7510/21291|2504/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1385:1:22:0,-9.54024,-122.735 +NC_045512.2 7788 . C T 5.84647E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=37.8095;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4561;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1404;RO=39;RPL=1;RPP=5.18177;RPPR=15.538;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7523C>T|p.Ala2508Val|7523/21291|7523/21291|2508/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1404:1:20:0,-10.0412,-124.641 +NC_045512.2 7807 . A T 5.71063E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1385;RO=39;RPL=1;RPP=5.18177;RPPR=3.06598;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7542A>T|p.Glu2514Asp|7542/21291|7542/21291|2514/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1385:1:11:0,-10.9412,-123.828 +NC_045512.2 7816 . T G 6.0294E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.7586;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1443;RO=39;RPL=0;RPP=5.18177;RPPR=3.06598;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7551T>G|p.Ser2517Ser|7551/21291|7551/21291|2517/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1443:1:10:0,-11.0412,-129.154 +NC_045512.2 7831 . T C 5.71063E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1436;RO=39;RPL=1;RPP=5.18177;RPPR=3.06598;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7566T>C|p.Val2522Val|7566/21291|7566/21291|2522/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1436:1:11:0,-10.9412,-128.421 +NC_045512.2 7846 . G A 5.71063E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1404;RO=39;RPL=1;RPP=5.18177;RPPR=3.06598;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7581G>A|p.Leu2527Leu|7581/21291|7581/21291|2527/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1404:1:11:0,-10.9412,-125.543 +NC_045512.2 7847 . A G 5.71063E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1371;RO=39;RPL=0;RPP=5.18177;RPPR=3.06598;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7582A>G|p.Arg2528Gly|7582/21291|7582/21291|2528/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1371:1:11:0,-10.9412,-122.567 +NC_045512.2 7871 . T A 2.31288E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.1674;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1398;RO=38;RPL=1;RPP=5.18177;RPPR=69.0688;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7606T>A|p.Leu2536Met|7606/21291|7606/21291|2536/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1398:1:11:0,-10.6402,-125.005 +NC_045512.2 7880 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.3977;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1327;RO=38;RPL=1;RPP=5.18177;RPPR=85.5263;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7615A>T|p.Asn2539Tyr|7615/21291|7615/21291|2539/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1327:1:10:0,-10.7402,-118.709 +NC_045512.2 7881 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.9754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.908;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1271;RO=36;RPL=1;RPP=5.18177;RPPR=81.1833;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.9754;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7616A>C|p.Asn2539Thr|7616/21291|7616/21291|2539/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1271:1:9:0,-10.2381,-113.775 +NC_045512.2 7924 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=4.56135;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.3978;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1196;RO=35;RPL=1;RPP=5.18177;RPPR=79.0118;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=4.56135;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7659T>C|p.Ser2553Ser|7659/21291|7659/21291|2553/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1196:1:14:0,-9.43709,-106.519 +NC_045512.2 7936 . G T 1.7207E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.0116;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=867;RO=25;RPL=1;RPP=5.18177;RPPR=57.2971;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=22.5536;SRR=20;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7671G>T|p.Ala2557Ala|7671/21291|7671/21291|2557/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:867:1:9:0,-6.92678,-77.4293 +NC_045512.2 8046 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.9754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.3752;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1322;RO=36;RPL=0;RPP=5.18177;RPPR=81.1833;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7781A>C|p.Tyr2594Ser|7781/21291|7781/21291|2594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1322:1:20:0,-9.13815,-117.273 +NC_045512.2 8087 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.9754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.908;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1335;RO=36;RPL=0;RPP=5.18177;RPPR=81.1833;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7822A>T|p.Lys2608*|7822/21291|7822/21291|2608/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1335:1:9:0,-10.2381,-119.544 +NC_045512.2 8089 . A C 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9889;PAIRED=1;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1430;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7824A>C|p.Lys2608Asn|7824/21291|7824/21291|2608/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1430:1:9:0,-11.1412,-128.088 +NC_045512.2 8164 . T C 2.10949E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=7.35324;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.1712;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1396;RO=38;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=19;SRP=3.0103;SRR=19;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7899T>C|p.Phe2633Phe|7899/21291|7899/21291|2633/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:38,2:38:1396:2:76:0,-4.82639,-118.712 +NC_045512.2 8196 . C T 6.0294E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.7586;PAIRED=1;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1422;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7931C>T|p.Ser2644Leu|7931/21291|7931/21291|2644/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1422:1:10:0,-11.0412,-127.262 +NC_045512.2 8201 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.6279;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1361;RO=38;RPL=1;RPP=5.18177;RPPR=85.5263;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.23888;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7936G>T|p.Val2646Leu|7936/21291|7936/21291|2646/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1361:1:9:0,-10.8402,-121.872 +NC_045512.2 8204 . G A 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9889;PAIRED=1;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1419;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06598;SRR=20;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7939G>A|p.Glu2647Lys|7939/21291|7939/21291|2647/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1419:1:9:0,-11.1412,-127.091 +NC_045512.2 8214 . A T 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1383;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7949A>T|p.Asp2650Val|7949/21291|7949/21291|2650/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1383:1:11:0,-10.9412,-123.649 +NC_045512.2 8242 . T C 2.12908E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=4.03217;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.0571;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1222;RO=34;RPL=2;RPP=7.35324;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=4.03217;SRR=19;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7977T>C|p.His2659His|7977/21291|7977/21291|2659/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1222:2:75:0,-3.71674,-103.151 +NC_045512.2 8253 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=23.254;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6612;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1119;RO=31;RPL=1;RPP=5.18177;RPPR=40.0654;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=8.68415;SRR=20;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7988T>A|p.Ile2663Lys|7988/21291|7988/21291|2663/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1119:1:11:0,-8.53296,-99.9092 +NC_045512.2 8255 . G C 1.86012E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=36.0317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.6597;PAIRED=1;PAIREDR=0.965517;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1051;RO=29;RPL=0;RPP=5.18177;RPPR=30.0414;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=12.0706;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7990G>C|p.Glu2664Gln|7990/21291|7990/21291|2664/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1051:1:34:0,-5.63199,-91.4917 +NC_045512.2 8304 . T C 8.04159E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.3403;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=937;RO=25;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=22.5536;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8039T>C|p.Val2680Ala|8039/21291|8039/21291|2680/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:937:1:38:0,-4.02951,-80.8508 +NC_045512.2 8325 . A G 4.5399E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.7813;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=942;RO=25;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=22.5536;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8060A>G|p.Asp2687Gly|8060/21291|8060/21291|2687/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:942:1:10:0,-6.82678,-84.0986 +NC_045512.2 8398 . G T 1.55314E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=4.78696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1464;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=408;RO=11;RPL=0;RPP=5.18177;RPPR=12.6832;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=3.20771;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8133G>T|p.Leu2711Phe|8133/21291|8133/21291|2711/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:408:1:10:0,-2.61236,-36.0676 +NC_045512.2 8535 . AGA TGT,TGA 1.91136E-4 . AB=0.0833333,0.0833333;ABP=21.1059,21.1059;AC=0,1;AF=0,0.5;AN=2;AO=1,1;CIGAR=1X1M1X,1X2M;DP=12;DPB=12;DPRA=0,0;EPP=5.18177,5.18177;EPPR=3.0103;GTI=0;LEN=3,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=10.039;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=17,38;QR=332;RO=10;RPL=1,1;RPP=5.18177,5.18177;RPPR=24.725;RPR=0,0;RUN=1,1;SAF=1,0;SAP=5.18177,5.18177;SAR=0,1;SRF=5;SRP=3.0103;SRR=5;TYPE=complex,snp;ANN=TGA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8270A>T|p.Lys2757Met|8270/21291|8270/21291|2757/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:12:10,1,1:10:332:1,1:17,38:-0.211077,-2.09729,-28.6059,0,-25.7861,-26.6993 +NC_045512.2 8538 . T C 1.95529E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.9161;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=371;RO=11;RPL=1;RPP=5.18177;RPPR=26.8965;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=3.20771;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8273T>C|p.Ile2758Thr|8273/21291|8273/21291|2758/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:371:1:11:0,-2.51236,-32.6082 +NC_045512.2 8543 . CT AC 1.55314E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=3.20771;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1464;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=389;RO=11;RPL=1;RPP=5.18177;RPPR=26.8965;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=3.20771;SRR=6;TYPE=complex;ANN=AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8278_8279delCTinsAC|p.Leu2760Thr|8278/21291|8278/21291|2760/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:12:11,1:11:389:1:10:0,-2.61236,-34.3442 +NC_045512.2 8551 . T G 7.36929E-5 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.9841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=226;RO=6;RPL=1;RPP=5.18177;RPPR=16.0391;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=0;SRP=16.0391;SRR=6;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8286T>G|p.Gly2762Gly|8286/21291|8286/21291|2762/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:7:6,1:6:226:1:9:0,-1.20721,-19.8027 +NC_045512.2 8920 . A G 9.41104E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.9499;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=675;RO=18;RPL=0;RPP=5.18177;RPPR=33.8935;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=33.8935;SRR=1;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8655A>G|p.Leu2885Leu|8655/21291|8655/21291|2885/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:19:18,1:18:675:1:38:0,-1.9223,-57.287 +NC_045512.2 8957 . A T 2.82955E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=3.0103;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.757;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=972;RO=27;RPL=0;RPP=7.35324;RPPR=53.2759;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=6.95112;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8692A>T|p.Thr2898Ser|8692/21291|8692/21291|2898/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:27,2:27:972:2:66:0,-2.46272,-81.5202 +NC_045512.2 9004 . TGTTT GGTTA,TTTTT,AGTTT 3.04519E-14 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=1,1,2;CIGAR=1X3M1X,1M1X3M,1X4M;DP=35;DPB=35;DPRA=0,0,0;EPP=5.18177,5.18177,3.0103;EPPR=3.08035;GTI=0;LEN=5,1,1;MEANALT=3,3,3;MQM=60,60,60;MQMR=60;NS=1;NUMALT=3;ODDS=36.0816;PAIRED=1,1,1;PAIREDR=0.967742;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=15,19,45;QR=1124;RO=31;RPL=0,0,0;RPP=5.18177,5.18177,7.35324;RPPR=70.3259;RPR=1,1,2;RUN=1,1,1;SAF=1,0,1;SAP=5.18177,5.18177,3.0103;SAR=0,1,1;SRF=16;SRP=3.08035;SRR=15;TYPE=complex,snp,snp;ANN=AGTTT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8739T>A|p.Cys2913*|8739/21291|8739/21291|2913/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:31,1,1,2:31:1124:1,1,2:15,19,45:0,-8.2988,-99.9026,-7.92549,-98.7995,-99.5414,-5.85663,-96.7636,-96.4023,-97.2042 +NC_045512.2 9014 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.6667;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1248;RO=34;RPL=0;RPP=5.18177;RPPR=76.8404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8749G>T|p.Ala2917Ser|8749/21291|8749/21291|2917/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1248:1:33:0,-7.23691,-109.316 +NC_045512.2 9023 . AC TA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.26577;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.9607;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1248;RO=34;RPL=0;RPP=5.18177;RPPR=76.8404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=complex;ANN=TA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8758_8759delACinsTA|p.Thr2920*|8758/21291|8758/21291|2920/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1248:1:10:0,-9.53605,-111.616 +NC_045512.2 9051 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.6582;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1227;RO=34;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8786C>A|p.Pro2929Gln|8786/21291|8786/21291|2929/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1227:1:20:0,-8.53609,-108.717 +NC_045512.2 9104 . A C 4.09133E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=23.7032;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.7304;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1270;RO=34;RPL=1;RPP=5.18177;RPPR=19.3602;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8839A>C|p.Ser2947Arg|8839/21291|8839/21291|2947/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1270:1:11:0,-9.43605,-113.497 +NC_045512.2 9113 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=9.39698;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.9607;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1264;RO=34;RPL=1;RPP=5.18177;RPPR=39.7976;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8848C>G|p.Pro2950Ala|8848/21291|8848/21291|2950/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1264:1:10:0,-9.53605,-113.058 +NC_045512.2 9134 . A C 4.09133E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.7304;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1230;RO=34;RPL=1;RPP=5.18177;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8869A>C|p.Met2957Leu|8869/21291|8869/21291|2957/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1230:1:11:0,-9.43605,-109.889 +NC_045512.2 9161 . A C 4.09133E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.7304;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1202;RO=34;RPL=1;RPP=5.18177;RPPR=76.8404;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8896A>C|p.Asn2966His|8896/21291|8896/21291|2966/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1202:1:11:0,-9.43605,-107.369 +NC_045512.2 9163 . C A 6.40845E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=7.35324;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.7908;PAIRED=0.5;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1195;RO=33;RPL=2;RPP=7.35324;RPPR=74.6689;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8898C>A|p.Asn2966Lys|8898/21291|8898/21291|2966/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1195:2:17:0,-8.92105,-106.229 +NC_045512.2 9170 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.4212;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1233;RO=34;RPL=1;RPP=5.18177;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8905C>A|p.Leu2969Ile|8905/21291|8905/21291|2969/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1233:1:8:0,-9.73605,-110.464 +NC_045512.2 9171 . T G 4.09133E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=47.7304;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1247;RO=34;RPL=1;RPP=5.18177;RPPR=76.8404;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8906T>G|p.Leu2969Arg|8906/21291|8906/21291|2969/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1247:1:11:0,-9.43605,-111.426 +NC_045512.2 9214 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=97.7145;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.7286;PAIRED=1;PAIREDR=0.919355;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=2292;RO=62;RPL=0;RPP=5.18177;RPPR=30.4689;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=40;SRP=14.358;SRR=22;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8949C>G|p.Tyr2983*|8949/21291|8949/21291|2983/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2292:1:12:0,-17.7649,-205.308 +NC_045512.2 9225 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=75;DPB=75;DPRA=0;EPP=5.18177;EPPR=123.204;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=97.8161;PAIRED=0;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=2751;RO=74;RPL=0;RPP=5.18177;RPPR=49.9611;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=52;SRP=29.4201;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8960G>T|p.Gly2987Val|8960/21291|8960/21291|2987/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:75:74,1:74:2751:1:31:0,-19.4778,-244.701 +NC_045512.2 9236 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=5.18177;EPPR=128.688;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.8365;PAIRED=1;PAIREDR=0.931507;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2729;RO=73;RPL=0;RPP=5.18177;RPPR=48.2543;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=52;SRP=31.5964;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8971A>G|p.Arg2991Gly|8971/21291|8971/21291|2991/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:74:73,1:73:2729:1:38:0,-18.4789,-242.017 +NC_045512.2 9246 . C G 2.28425E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=75;DPB=75;DPRA=0;EPP=5.18177;EPPR=130.834;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.808;PAIRED=1;PAIREDR=0.932432;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=2780;RO=74;RPL=0;RPP=5.18177;RPPR=49.9611;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=33.0588;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8981C>G|p.Ala2994Gly|8981/21291|8981/21291|2994/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:75:74,1:74:2780:1:18:0,-20.7773,-248.606 +NC_045512.2 9274 . A T 1.88948E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=46.0936;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=96.4786;PAIRED=1;PAIREDR=0.927536;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2555;RO=69;RPL=0;RPP=5.18177;RPPR=152.842;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=46.0936;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9009A>T|p.Arg3003Ser|9009/21291|9009/21291|3003/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2555:1:7:0,-20.3721,-229.472 +NC_045512.2 9279 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=73;DPB=73;DPRA=0;EPP=5.18177;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6745;PAIRED=1;PAIREDR=0.930556;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2691;RO=72;RPL=0;RPP=5.18177;RPPR=159.356;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=52;SRP=33.8935;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9014T>G|p.Val3005Gly|9014/21291|9014/21291|3005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:73:72,1:72:2691:1:11:0,-20.8752,-241.302 +NC_045512.2 9280 . A G,T 1.90158E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=76;DPB=76;DPRA=0,0;EPP=5.18177,5.18177;EPPR=29.4201;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=102.65;PAIRED=1,1;PAIREDR=0.932432;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,9;QR=2746;RO=74;RPL=0,0;RPP=5.18177,5.18177;RPPR=163.699;RPR=1,1;RUN=1,1;SAF=1,0;SAP=5.18177,5.18177;SAR=0,1;SRF=52;SRP=29.4201;SRR=22;TYPE=snp,snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9015A>G|p.Val3005Val|9015/21291|9015/21291|3005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:74,1,1:74:2746:1,1:11,9:0,-21.5773,-246.257,-21.7773,-246.053,-246.437 +NC_045512.2 9285 . A T 1.84432E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=4.82359;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=134.037;PAIRED=1;PAIREDR=0.927835;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3475;RO=97;RPL=0;RPP=5.18177;RPPR=213.643;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=4.82359;SRR=44;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9020A>T|p.Asn3007Ile|9020/21291|9020/21291|3007/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3475:1:11:0,-28.4009,-311.823 +NC_045512.2 9287 . A G 1.33202E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=4.82359;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=134.268;PAIRED=1;PAIREDR=0.927835;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3456;RO=97;RPL=0;RPP=5.18177;RPPR=213.643;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=4.82359;SRR=44;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9022A>G|p.Asn3008Asp|9022/21291|9022/21291|3008/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3456:1:10:0,-28.5009,-310.204 +NC_045512.2 9303 . CTTTAC CTTAC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D4M;DP=102;DPB=101.667;DPRA=0;EPP=3.0103;EPPR=3.35774;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.409;PAIRED=1;PAIREDR=0.91;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3649;RO=100;RPL=0;RPP=7.35324;RPPR=220.158;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=52;SRP=3.35774;SRR=48;TYPE=del;ANN=CTTAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9041delT|p.Leu3014fs|9041/21291|9041/21291|3014/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:102:100,2:100:3649:2:34:0,-27.4752,-325.352 +NC_045512.2 9331 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=4.4284;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.35;PAIRED=1;PAIREDR=0.918367;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=3644;RO=98;RPL=0;RPP=5.18177;RPPR=215.815;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=4.4284;SRR=45;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9066T>G|p.Asp3022Glu|9066/21291|9066/21291|3022/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3644:1:33:0,-26.5028,-324.813 +NC_045512.2 9332 . G T 1.68157E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=4.4284;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=135.644;PAIRED=0;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3670;RO=98;RPL=0;RPP=5.18177;RPPR=215.815;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=4.4284;SRR=45;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9067G>T|p.Ala3023Ser|9067/21291|9067/21291|3023/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3670:1:10:0,-28.802,-329.452 +NC_045512.2 9340 . T C 401.577 . AB=0.259615;ABP=55.2092;AC=1;AF=0.5;AN=2;AO=27;CIGAR=1X;DP=104;DPB=104;DPRA=0;EPP=3.09072;EPPR=3.26411;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=92.4666;PAIRED=0.962963;PAIREDR=0.896104;PAO=0;PQA=0;PQR=0;PRO=0;QA=987;QR=2796;RO=77;RPL=0;RPP=61.6401;RPPR=170.214;RPR=27;RUN=1;SAF=13;SAP=3.09072;SAR=14;SRF=40;SRP=3.26411;SRR=37;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9075T>C|p.Asn3025Asn|9075/21291|9075/21291|3025/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:104:77,27:77:2796:27:987:-57.8278,0,-220.535 +NC_045512.2 9341 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=4.4284;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.661;PAIRED=0;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=3639;RO=98;RPL=0;RPP=5.18177;RPPR=215.815;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=4.4284;SRR=45;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9076T>G|p.Leu3026Val|9076/21291|9076/21291|3026/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3639:1:36:0,-26.2037,-324.063 +NC_045512.2 9355 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=104;DPB=104;DPRA=0;EPP=3.0103;EPPR=65.0889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=124.967;PAIRED=1;PAIREDR=0.911765;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3801;RO=102;RPL=2;RPP=7.35324;RPPR=22.1704;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=52;SRP=3.09546;SRR=50;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9090G>A|p.Met3030Ile|9090/21291|9090/21291|3030/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:104:102,2:102:3801:2:76:0,-24.0923,-335.018 +NC_045512.2 9380 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=104;DPB=104;DPRA=0;EPP=7.35324;EPPR=183.2;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=124.967;PAIRED=1;PAIREDR=0.911765;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3840;RO=102;RPL=1;RPP=3.0103;RPPR=6.07591;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=52;SRP=3.09546;SRR=50;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9115G>C|p.Gly3039Arg|9115/21291|9115/21291|3039/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:104:102,2:102:3840:2:76:0,-24.0923,-338.526 +NC_045512.2 9391 . C T 6.5635E-14 . AB=0.105769;ABP=143.404;AC=1;AF=0.5;AN=2;AO=11;CIGAR=1X;DP=104;DPB=104;DPRA=0;EPP=26.8965;EPPR=163.863;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.5225;PAIRED=0.909091;PAIREDR=0.913978;PAO=0;PQA=0;PQR=0;PRO=0;QA=418;QR=3482;RO=93;RPL=6;RPP=3.20771;RPPR=5.83555;RPR=5;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=47;SRP=3.03365;SRR=46;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9126C>T|p.Asp3042Asp|9126/21291|9126/21291|3042/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:104:93,11:93:3482:11:418:-6.66557,0,-282.23 +NC_045512.2 9474 . CTTTTGGTGA CTTTGGTGA 2.20289E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D8M;DP=100;DPB=99.8;DPRA=0;EPP=3.0103;EPPR=3.03269;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=118.778;PAIRED=1;PAIREDR=0.907216;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=3520;RO=97;RPL=2;RPP=7.35324;RPPR=213.643;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=48;SRP=3.03269;SRR=49;TYPE=del;ANN=CTTTGGTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9213delT|p.Phe3071fs|9213/21291|9213/21291|3071/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:100:97,2:97:3520:2:75:0,-22.8665,-309.952 +NC_045512.2 9514 . A T 4.08356E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=137.819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.203;PAIRED=1;PAIREDR=0.94898;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3695;RO=98;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=52;SRP=3.80798;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9249A>T|p.Leu3083Phe|9249/21291|9249/21291|3083/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3695:1:38:0,-26.0047,-328.901 +NC_045512.2 9519 . T G 1.3938E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=155.104;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.129;PAIRED=1;PAIREDR=0.947917;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=3613;RO=96;RPL=1;RPP=5.18177;RPPR=5.27225;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=50;SRP=3.37221;SRR=46;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9254T>G|p.Phe3085Cys|9254/21291|9254/21291|3085/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3613:1:22:0,-27,-323.124 +NC_045512.2 9527 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=194.1;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=115.446;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3331;RO=88;RPL=0;RPP=5.18177;RPPR=3.40511;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=3.40511;SRR=46;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9262T>C|p.Ser3088Pro|9262/21291|9262/21291|3088/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3331:1:38:0,-22.9944,-296.16 +NC_045512.2 9536 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=194.1;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=115.446;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3334;RO=88;RPL=1;RPP=5.18177;RPPR=3.109;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.109;SRR=45;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9271G>A|p.Val3091Ile|9271/21291|9271/21291|3091/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3334:1:38:0,-22.9944,-296.43 +NC_045512.2 9539 . C T 9.58348E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=7.35324;EPPR=179.29;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=113.114;PAIRED=1;PAIREDR=0.94382;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=3325;RO=89;RPL=1;RPP=3.0103;RPPR=3.0347;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=42;SRP=3.62026;SRR=47;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9274C>T|p.Leu3092Phe|9274/21291|9274/21291|3092/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:89,2:89:3325:2:49:0,-22.7413,-294.763 +NC_045512.2 9543 . G T 8.25729E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=166.009;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.91;PAIRED=1;PAIREDR=0.946809;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3521;RO=94;RPL=0;RPP=5.18177;RPPR=3.1027;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=4.48875;SRR=51;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9278G>T|p.Cys3093Phe|9278/21291|9278/21291|3093/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3521:1:11:0,-27.4979,-315.945 +NC_045512.2 9584 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=112;DPB=112;DPRA=0;EPP=3.0103;EPPR=9.40627;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=143.555;PAIRED=1;PAIREDR=0.918182;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=3971;RO=110;RPL=1;RPP=3.0103;RPPR=94.2911;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=43;SRP=14.3809;SRR=67;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9319G>T|p.Val3107Phe|9319/21291|9319/21291|3107/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:112:110,2:110:3971:2:41:0,-29.8214,-353.644 +NC_045512.2 9592 . C T 1.61525E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=3.109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=122.118;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3259;RO=88;RPL=0;RPP=5.18177;RPPR=194.1;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.109;SRR=45;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9327C>T|p.Tyr3109Tyr|9327/21291|9327/21291|3109/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3259:1:9:0,-25.8917,-292.586 +NC_045512.2 9596 . T G 8.44493E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=3.22989;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=117.05;PAIRED=1;PAIREDR=0.94382;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=3306;RO=89;RPL=0;RPP=5.18177;RPPR=196.271;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.22989;SRR=46;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9331T>G|p.Tyr3111Asp|9331/21291|9331/21291|3111/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3306:1:37:0,-23.3949,-294.017 +NC_045512.2 9605 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=5.18177;EPPR=3.03585;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=112.239;PAIRED=1;PAIREDR=0.952941;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3179;RO=85;RPL=0;RPP=5.18177;RPPR=187.585;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.03585;SRR=42;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9340T>G|p.Phe3114Val|9340/21291|9340/21291|3114/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:85,1:85:3179:1:34:0,-22.4897,-282.892 +NC_045512.2 9623 . GTTTC TTTTA 1.23408E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=4.98658;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=121.42;PAIRED=1;PAIREDR=0.94382;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=3325;RO=89;RPL=0;RPP=5.18177;RPPR=171.092;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.22989;SRR=46;TYPE=complex;ANN=TTTTA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9358_9362delGTTTCinsTTTTA|p.ValSer3120PheTyr|9358/21291|9358/21291|3120/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3325:1:18:0,-25.2927,-297.627 +NC_045512.2 9636 . C T 6.58455E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=7.35324;EPPR=74.965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.85;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3244;RO=88;RPL=1;RPP=3.0103;RPPR=38.6422;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=42;SRP=3.40511;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9371C>T|p.Ala3124Val|9371/21291|9371/21291|3124/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:88,2:88:3244:2:76:0,-19.8779,-284.918 +NC_045512.2 9685 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=196.271;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.032;PAIRED=0;PAIREDR=0.955056;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3339;RO=89;RPL=0;RPP=5.18177;RPPR=3.22989;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.22989;SRR=46;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9420A>T|p.Ile3140Ile|9420/21291|9420/21291|3140/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3339:1:11:0,-25.9927,-299.578 +NC_045512.2 9695 . TAT TT 6.56972E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D1M;DP=90;DPB=89.3333;DPRA=0;EPP=3.0103;EPPR=123.922;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.85;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3315;RO=88;RPL=2;RPP=7.35324;RPPR=7.84676;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=42;SRP=3.40511;SRR=46;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9431delA|p.Tyr3144fs|9431/21291|9431/21291|3144/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:88,2:88:3315:2:76:0,-19.8779,-291.306 +NC_045512.2 9702 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=87.9417;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.032;PAIRED=1;PAIREDR=0.94382;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3336;RO=89;RPL=1;RPP=5.18177;RPPR=18.2594;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=3.62026;SRR=47;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9437T>G|p.Ile3146Ser|9437/21291|9437/21291|3146/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3336:1:11:0,-25.9927,-299.311 +NC_045512.2 9705 . G A 6.56972E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=3.0103;EPPR=80.3937;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.85;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3310;RO=88;RPL=2;RPP=7.35324;RPPR=22.3561;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=42;SRP=3.40511;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9440G>A|p.Cys3147Tyr|9440/21291|9440/21291|3147/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:88,2:88:3310:2:76:0,-19.8779,-290.854 +NC_045512.2 9725 . T A 1.23858E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=3.0103;EPPR=3.63429;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=110.818;PAIRED=1;PAIREDR=0.942529;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=3249;RO=87;RPL=2;RPP=7.35324;RPPR=191.928;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=41;SRP=3.63429;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9460T>A|p.Tyr3154Asn|9460/21291|9460/21291|3154/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:87,2:87:3249:2:47:0,-22.3269,-288.122 +NC_045512.2 9746 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=3.89863;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=121.887;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3195;RO=88;RPL=1;RPP=5.18177;RPPR=194.1;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=3.89863;SRR=47;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9481C>T|p.Leu3161Leu|9481/21291|9481/21291|3161/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3195:1:10:0,-25.7917,-286.734 +NC_045512.2 9753 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=88;DPB=88;DPRA=0;EPP=5.18177;EPPR=4.23331;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=120.512;PAIRED=1;PAIREDR=0.942529;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3145;RO=87;RPL=1;RPP=5.18177;RPPR=191.928;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=40;SRP=4.23331;SRR=47;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9488G>A|p.Arg3163Lys|9488/21291|9488/21291|3163/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:88:87,1:87:3145:1:10:0,-25.4906,-282.236 +NC_045512.2 9760 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=3.0103;EPPR=3.40511;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=106.067;PAIRED=1;PAIREDR=0.943182;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=3231;RO=88;RPL=2;RPP=7.35324;RPPR=194.1;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=42;SRP=3.40511;SRR=46;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9495A>G|p.Val3165Val|9495/21291|9495/21291|3165/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:88,2:88:3231:2:75:0,-19.9724,-283.853 +NC_045512.2 9762 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=3.22989;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.032;PAIRED=1;PAIREDR=0.94382;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3245;RO=89;RPL=1;RPP=5.18177;RPPR=196.271;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=43;SRP=3.22989;SRR=46;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9497T>C|p.Val3166Ala|9497/21291|9497/21291|3166/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3245:1:11:0,-25.9927,-291.133 +NC_045512.2 9773 . G T 9.34239E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=87;DPB=87;DPRA=0;EPP=5.18177;EPPR=4.62628;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=119.368;PAIRED=1;PAIREDR=0.94186;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3083;RO=86;RPL=1;RPP=5.18177;RPPR=189.757;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=4.62628;SRR=47;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9508G>T|p.Val3170Phe|9508/21291|9508/21291|3170/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:87:86,1:86:3083:1:9:0,-25.2896,-276.761 +NC_045512.2 9779 . T G 1.30639E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=22.6794;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=96.0181;PAIRED=1;PAIREDR=0.942029;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2558;RO=69;RPL=1;RPP=5.18177;RPPR=152.842;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=22.6794;SRR=47;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9514T>G|p.Phe3172Val|9514/21291|9514/21291|3172/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2558:1:9:0,-20.1721,-229.542 +NC_045512.2 9781 . T C 1.83222E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=5.18177;EPPR=25.2514;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.2318;PAIRED=1;PAIREDR=0.939394;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2420;RO=66;RPL=1;RPP=5.18177;RPPR=146.327;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=25.2514;SRR=46;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9516T>C|p.Phe3172Phe|9516/21291|9516/21291|3172/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:66,1:66:2420:1:38:0,-16.3717,-214.23 +NC_045512.2 9785 . A G,T 9.88459E-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=70;DPB=70;DPRA=0,0;EPP=5.18177,5.18177;EPPR=44.396;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=94.4275;PAIRED=1,1;PAIREDR=0.941176;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,10;QR=2494;RO=68;RPL=1,1;RPP=5.18177,5.18177;RPPR=103.153;RPR=0,0;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=22;SRP=21.4039;SRR=46;TYPE=snp,snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9520A>G|p.Thr3174Ala|9520/21291|9520/21291|3174/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:68,1,1:68:2494:1,1:11,10:0,-19.7761,-223.588,-19.8761,-223.294,-223.678 +NC_045512.2 9789 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=57.7314;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=91.6363;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2600;RO=70;RPL=0;RPP=5.18177;RPPR=86.8912;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=20.8784;SRR=47;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9524T>C|p.Phe3175Ser|9524/21291|9524/21291|3175/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2600:1:34:0,-17.9742,-230.824 +NC_045512.2 9807 . G A,T 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=76;DPB=76;DPRA=0,0;EPP=5.18177,5.18177;EPPR=163.699;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=97.0034;PAIRED=1,1;PAIREDR=0.932432;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,31;QR=2777;RO=74;RPL=0,0;RPP=5.18177,5.18177;RPPR=14.748;RPR=1,1;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=27;SRP=14.748;SRR=47;TYPE=snp,snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9542G>A|p.Cys3181Tyr|9542/21291|9542/21291|3181/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:74,1,1:74:2777:1,1:38,31:0,-19.1248,-246.373,-19.8226,-244.187,-247.002 +NC_045512.2 9820 . A G 1.48268E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=5.18177;EPPR=165.871;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=97.8114;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=2811;RO=75;RPL=0;RPP=5.18177;RPPR=13.4623;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=13.4623;SRR=47;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9555A>G|p.Leu3185Leu|9555/21291|9555/21291|3185/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:75,1:75:2811:1:37:0,-19.1804,-249.493 +NC_045512.2 9843 . T G 7.00668E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=150.67;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.4159;PAIRED=1;PAIREDR=0.926471;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2533;RO=68;RPL=1;RPP=5.18177;RPPR=6.20364;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=29;SRP=6.20364;SRR=39;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9578T>G|p.Leu3193Trp|9578/21291|9578/21291|3193/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2533:1:10:0,-19.7711,-227.195 +NC_045512.2 9856 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=114.344;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.6381;PAIRED=1;PAIREDR=0.915254;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2065;RO=59;RPL=0;RPP=5.18177;RPPR=3.0471;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.34154;SRR=31;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9591G>A|p.Val3197Val|9591/21291|9591/21291|3197/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2065:1:38:0,-14.2645,-182.312 +NC_045512.2 9872 . C A 4.67332E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=7.5342;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.0323;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1749;RO=48;RPL=0;RPP=5.18177;RPPR=107.241;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=29;SRP=7.5342;SRR=19;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9607C>A|p.Gln3203Lys|9607/21291|9607/21291|3203/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1749:1:10:0,-13.7505,-156.68 +NC_045512.2 9879 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.17115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.0043;PAIRED=1;PAIREDR=0.981481;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1949;RO=54;RPL=0;RPP=5.18177;RPPR=120.27;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.17115;SRR=26;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9614A>G|p.Asn3205Ser|9614/21291|9614/21291|3205/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:1949:1:11:0,-15.4567,-174.565 +NC_045512.2 9960 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=7.35324;EPPR=122.441;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.0223;PAIRED=1;PAIREDR=0.981818;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2030;RO=55;RPL=1;RPP=3.0103;RPPR=3.04978;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=28;SRP=3.04978;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9695G>A|p.Cys3232Tyr|9695/21291|9695/21291|3232/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:55,2:55:2030:2:76:0,-9.9439,-175.734 +NC_045512.2 9981 . A C 1.98916E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=124.613;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.7412;PAIRED=1;PAIREDR=0.982143;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2063;RO=56;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9716A>C|p.Asn3239Thr|9716/21291|9716/21291|3239/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2063:1:11:0,-16.0587,-184.816 +NC_045512.2 10027 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.2017;PAIRED=1;PAIREDR=0.982143;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2069;RO=56;RPL=1;RPP=5.18177;RPPR=116.082;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9762A>C|p.Gln3254His|9762/21291|9762/21291|3254/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2069:1:9:0,-16.2587,-185.558 +NC_045512.2 10040 . T C 1.18288E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=56;DPB=56;DPRA=0;EPP=7.35324;EPPR=3.17115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.7333;PAIRED=1;PAIREDR=0.981481;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1785;RO=54;RPL=2;RPP=7.35324;RPPR=120.27;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=26;SRP=3.17115;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9775T>C|p.Ser3259Pro|9775/21291|9775/21291|3259/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:56:54,2:54:1785:2:18:0,-15.1477,-159.18 +NC_045512.2 10041 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.67845;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.2688;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1863;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=3.67845;SRR=28;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9776C>A|p.Ser3259*|9776/21291|9776/21291|3259/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1863:1:11:0,-14.8546,-166.823 +NC_045512.2 10048 . T C 605.572 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=27;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=3.09072;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=133.211;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=985;QR=955;RO=27;RPL=27;RPP=61.6401;RPPR=61.6401;RPR=0;RUN=1;SAF=13;SAP=3.09072;SAR=14;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9783T>C|p.Val3261Val|9783/21291|9783/21291|3261/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:54:27,27:27:955:27:985:-72.7003,0,-69.9958 +NC_045512.2 10050 . TG AA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=3.37904;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.1759;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1912;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.37904;SRR=28;TYPE=complex;ANN=AA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9785_9786delTGinsAA|p.Leu3262*|9785/21291|9785/21291|3262/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1912:1:13:0,-14.9556,-171.034 +NC_045512.2 10053 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=3.37904;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.0969;PAIRED=1;PAIREDR=0.981132;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1902;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.37904;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9788A>C|p.Gln3263Pro|9788/21291|9788/21291|3263/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1902:1:9:0,-15.3556,-170.532 +NC_045512.2 10067 . A G 1.05626E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=3.0103;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.3218;PAIRED=1;PAIREDR=0.981132;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1929;RO=53;RPL=2;RPP=7.35324;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9802A>G|p.Lys3268Glu|9802/21291|9802/21291|3268/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:53,2:53:1929:2:76:0,-9.34184,-166.654 +NC_045512.2 10076 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.67845;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.7293;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1910;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=3.67845;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9811T>A|p.Phe3271Ile|9811/21291|9811/21291|3271/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:52,1:52:1910:1:9:0,-15.0546,-171.259 +NC_045512.2 10082 . T A 6.09509E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=19.4678;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.627;PAIRED=1;PAIREDR=0.921053;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2749;RO=76;RPL=1;RPP=5.18177;RPPR=25.4108;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=46;SRP=10.3247;SRR=30;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9817T>A|p.Ser3273Thr|9817/21291|9817/21291|3273/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2749:1:9:0,-22.2793,-246.723 +NC_045512.2 10084 . T G 4.42258E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=19.4678;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.483;PAIRED=1;PAIREDR=0.921053;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=2776;RO=76;RPL=1;RPP=5.18177;RPPR=25.4108;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=46;SRP=10.3247;SRR=30;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9819T>G|p.Ser3273Ser|9819/21291|9819/21291|3273/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2776:1:27:0,-20.4795,-247.347 +NC_045512.2 10099 . T C 3.63883E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=81.6461;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=84.5886;PAIRED=0;PAIREDR=0.918033;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2227;RO=61;RPL=0;RPP=5.18177;RPPR=3.90025;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.0459;SRR=30;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9834T>C|p.Gly3278Gly|9834/21291|9834/21291|3278/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2227:1:11:0,-17.5639,-199.57 +NC_045512.2 10144 . T C 1.32619E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=102.098;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.4265;PAIRED=1;PAIREDR=0.894737;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=2138;RO=57;RPL=0;RPP=5.18177;RPPR=3.0484;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.9627;SRR=31;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9879T>C|p.Leu3293Leu|9879/21291|9879/21291|3293/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2138:1:27:0,-14.76,-189.966 +NC_045512.2 10157 . G T 4.61093E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=70.8163;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.4194;PAIRED=1;PAIREDR=0.903226;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2306;RO=62;RPL=0;RPP=5.18177;RPPR=6.51267;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=5.25182;SRR=35;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9892G>T|p.Val3298Leu|9892/21291|9892/21291|3298/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2306:1:9:0,-18.0649,-206.877 +NC_045512.2 10176 . A G 1.23858E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.18402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.5347;PAIRED=1;PAIREDR=0.82;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1853;RO=50;RPL=0;RPP=5.18177;RPPR=111.584;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9911A>G|p.His3304Arg|9911/21291|9911/21291|3304/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1853:1:11:0,-14.2525,-165.936 +NC_045512.2 10208 . C A 6.7955E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.5415;PAIRED=0;PAIREDR=0.82;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=1807;RO=50;RPL=1;RPP=5.18177;RPPR=103.072;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9943C>A|p.Pro3315Thr|9943/21291|9943/21291|3315/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1807:1:24:0,-12.9526,-160.485 +NC_045512.2 10212 . A T 1.07135E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=3.05288;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.1318;PAIRED=1;PAIREDR=0.803922;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1871;RO=51;RPL=0;RPP=5.18177;RPPR=97.0649;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.3935;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9947A>T|p.Asn3316Ile|9947/21291|9947/21291|3316/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1871:1:10:0,-14.6536,-167.65 +NC_045512.2 10215 . A G 9.96017E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.9952;PAIRED=0;PAIREDR=0.84;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1867;RO=50;RPL=0;RPP=5.18177;RPPR=94.907;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.70517;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9950A>G|p.Tyr3317Cys|9950/21291|9950/21291|3317/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1867:1:9:0,-14.4525,-167.39 +NC_045512.2 10233 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=61.2994;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.0677;PAIRED=0;PAIREDR=0.823529;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1902;RO=51;RPL=1;RPP=5.18177;RPPR=4.07475;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05288;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9968G>A|p.Arg3323His|9968/21291|9968/21291|3323/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1902:1:32:0,-12.4542,-168.239 +NC_045512.2 10244 . C T 3.76926E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=74.5837;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.9015;PAIRED=1;PAIREDR=0.803922;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1869;RO=51;RPL=1;RPP=5.18177;RPPR=3.05288;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05288;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9979C>T|p.His3327Tyr|9979/21291|9979/21291|3327/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1869:1:11:0,-14.5536,-167.362 +NC_045512.2 10278 . TCA ACC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=97.0649;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.52;PAIRED=1;PAIREDR=0.803922;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1891;RO=51;RPL=1;RPP=5.18177;RPPR=4.07475;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05288;SRR=25;TYPE=complex;ANN=ACC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10013_10015delTCAinsACC|p.Leu3338His|10013/21291|10013/21291|3338/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1891:1:17:0,-13.9536,-168.752 +NC_045512.2 10291 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=89.2305;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.9015;PAIRED=0;PAIREDR=0.823529;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1882;RO=51;RPL=1;RPP=5.18177;RPPR=5.09662;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05288;SRR=25;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10026A>C|p.Gly3342Gly|10026/21291|10026/21291|3342/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1882:1:11:0,-14.5536,-168.54 +NC_045512.2 10298 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=67.7713;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.9084;PAIRED=0;PAIREDR=0.823529;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=1881;RO=51;RPL=1;RPP=5.18177;RPPR=10.206;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.05288;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10033A>C|p.Met3345Leu|10033/21291|10033/21291|3345/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1881:1:24:0,-13.2537,-167.146 +NC_045512.2 10300 . G A 3.31723E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=7.35324;EPPR=65.7224;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.2761;PAIRED=1;PAIREDR=0.8;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1817;RO=50;RPL=1;RPP=3.0103;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10035G>A|p.Met3345Ile|10035/21291|10035/21291|3345/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:50,2:50:1817:2:76:0,-8.43875,-156.572 +NC_045512.2 10331 . A C 1.35159E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=3.76559;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.7687;PAIRED=0;PAIREDR=0.847826;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1692;RO=46;RPL=1;RPP=5.18177;RPPR=102.898;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.76559;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10066A>C|p.Thr3356Pro|10066/21291|10066/21291|3356/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:47:46,1:46:1692:1:21:0,-12.0485,-150.448 +NC_045512.2 10339 . T A 9.01067E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=3.05462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.1682;PAIRED=1;PAIREDR=0.816327;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1797;RO=49;RPL=1;RPP=5.18177;RPPR=109.412;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=3.05462;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10074T>A|p.Asn3358Lys|10074/21291|10074/21291|3358/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:49,1:49:1797:1:11:0,-13.9515,-160.896 +NC_045512.2 10364 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=3.70517;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.3908;PAIRED=0;PAIREDR=0.84;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1838;RO=50;RPL=1;RPP=5.18177;RPPR=87.0897;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.18402;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10099G>T|p.Val3367Phe|10099/21291|10099/21291|3367/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1838:1:29:0,-12.4529,-162.787 +NC_045512.2 10485 . C T 2.52656E-4 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.752;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=160;RO=5;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10220C>T|p.Ser3407Leu|10220/21291|10220/21291|3407/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:6:5,1:5:160:1:9:0,-0.906183,-13.8105 +NC_045512.2 10618 . G A 21.7937 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.01154;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=152;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.0103;SRR=2;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10353G>A|p.Arg3451Arg|10353/21291|10353/21291|3451/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:152:2:76:-5.40863,0,-12.2437 +NC_045512.2 10693 . A G 8.04159E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.3403;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=946;RO=25;RPL=0;RPP=5.18177;RPPR=34.3664;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=34.3664;SRR=3;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10428A>G|p.Ile3476Met|10428/21291|10428/21291|3476/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:946:1:38:0,-4.02951,-81.6613 +NC_045512.2 10821 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=7.35324;EPPR=81.9729;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.4237;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1653;RO=44;RPL=1;RPP=3.0103;RPPR=3.20771;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=23;SRP=3.20771;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10556A>G|p.Gln3519Arg|10556/21291|10556/21291|3519/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:44,2:44:1653:2:75:0,-6.72704,-141.925 +NC_045512.2 10846 . GT TG 2.1549E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=96.5684;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.4364;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1761;RO=47;RPL=0;RPP=5.18177;RPPR=3.0565;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=24;SRP=3.0565;SRR=23;TYPE=complex;ANN=TG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10581_10582delGTinsTG|p.MetCys3527IleGly|10581/21291|10581/21291|3527/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1761:1:11:0,-13.3494,-157.657 +NC_045512.2 10942 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=3.0565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.8969;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1726;RO=47;RPL=1;RPP=5.18177;RPPR=96.5684;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.0565;SRR=24;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10677T>G|p.Val3559Val|10677/21291|10677/21291|3559/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1726:1:9:0,-13.5494,-154.708 +NC_045512.2 10947 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=3.0565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.8969;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1748;RO=47;RPL=1;RPP=5.18177;RPPR=105.07;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.0565;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10682G>T|p.Arg3561Ile|10682/21291|10682/21291|3561/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1748:1:9:0,-13.5494,-156.691 +NC_045512.2 10963 . T G 1.07585E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=7.35324;EPPR=3.79993;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.4242;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1580;RO=44;RPL=2;RPP=7.35324;RPPR=98.5551;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=3.79993;SRR=24;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10698T>G|p.Val3566Val|10698/21291|10698/21291|3566/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:44,2:44:1580:2:31:0,-10.9024,-139.527 +NC_045512.2 10969 . C T 2.98944E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=28.1373;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6007;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1026;RO=28;RPL=1;RPP=5.18177;RPPR=63.8115;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=28.1373;SRR=23;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10704C>T|p.Phe3568Phe|10704/21291|10704/21291|3568/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:28,1:28:1026:1:11:0,-7.62987,-91.5462 +NC_045512.2 11069 . T A 4.67332E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=82.8119;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.0323;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1771;RO=48;RPL=0;RPP=5.18177;RPPR=24.906;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=14.5915;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10804T>A|p.Leu3602Met|10804/21291|10804/21291|3602/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1771:1:10:0,-13.7505,-158.659 +NC_045512.2 11074 . CTTTTTTTTGTATGA CTTTTTTTTTGTATGA 7.70002E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I14M;DP=39;DPB=39.0667;DPRA=0;EPP=5.18177;EPPR=39.6906;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.3674;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1356;RO=37;RPL=0;RPP=5.18177;RPPR=83.3548;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=39.6906;SRR=6;TYPE=ins;ANN=CTTTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817dupT|p.Leu3606fs|10818/21291|10818/21291|3606/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:37,1:37:1356:1:38:0,-7.97672,-118.581 +NC_045512.2 11094 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=3.15039;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.8799;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2201;RO=62;RPL=0;RPP=5.18177;RPPR=137.642;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.15039;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10829C>T|p.Ala3610Val|10829/21291|10829/21291|3610/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2201:1:7:0,-18.2649,-197.634 +NC_045512.2 11111 . A T 9.59854E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=7.35324;EPPR=3.15039;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.2106;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=2218;RO=62;RPL=0;RPP=7.35324;RPPR=137.642;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=32;SRP=3.15039;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10846A>T|p.Met3616Leu|10846/21291|10846/21291|3616/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,2:62:2218:2:15:0,-17.8409,-198.431 +NC_045512.2 11113 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.79;PAIRED=1;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2177;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10848G>T|p.Met3616Ile|10848/21291|10848/21291|3616/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2177:1:9:0,-18.3659,-195.256 +NC_045512.2 11120 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=89.1607;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2359;RO=64;RPL=0;RPP=5.18177;RPPR=141.985;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10855A>T|p.Ile3619Phe|10855/21291|10855/21291|3619/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2359:1:9:0,-18.667,-211.643 +NC_045512.2 11122 . T G 1.14971E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.4895;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2381;RO=64;RPL=0;RPP=5.18177;RPPR=141.985;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10857T>G|p.Ile3619Met|10857/21291|10857/21291|3619/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2381:1:38:0,-15.7697,-210.722 +NC_045512.2 11130 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.7177;PAIRED=1;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=2343;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10865C>T|p.Ser3622Phe|10865/21291|10865/21291|3622/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2343:1:18:0,-17.4659,-209.3 +NC_045512.2 11133 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=89.1607;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2407;RO=64;RPL=0;RPP=5.18177;RPPR=141.985;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10868C>T|p.Ala3623Val|10868/21291|10868/21291|3623/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2407:1:9:0,-18.667,-215.959 +NC_045512.2 11144 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=9.66043;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=89.1607;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2367;RO=64;RPL=0;RPP=5.18177;RPPR=87.8334;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10879A>C|p.Met3627Leu|10879/21291|10879/21291|3627/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2367:1:9:0,-18.667,-212.362 +NC_045512.2 11192 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=125.156;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.7002;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2335;RO=64;RPL=1;RPP=5.18177;RPPR=3.14602;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.14602;SRR=33;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10927T>G|p.Ser3643Ala|10927/21291|10927/21291|3643/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2335:1:11:0,-18.467,-209.277 +NC_045512.2 11213 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=133.434;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.7002;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2381;RO=64;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.14602;SRR=33;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10948T>G|p.Phe3650Val|10948/21291|10948/21291|3650/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2381:1:11:0,-18.467,-213.42 +NC_045512.2 11240 . T C 1.38474E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.0103;EPPR=10.7656;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.8478;PAIRED=1;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2329;RO=63;RPL=2;RPP=7.35324;RPPR=79.1497;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10975T>C|p.Trp3659Arg|10975/21291|10975/21291|3659/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:63,2:63:2329:2:76:0,-12.3521,-202.627 +NC_045512.2 11243 . G T 8.97432E-14 . AB=0.09375;ABP=94.755;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.0103;EPPR=3.16006;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.6248;PAIRED=1;PAIREDR=0.982759;PAO=0;PQA=0;PQR=0;PRO=0;QA=226;QR=2109;RO=58;RPL=6;RPP=16.0391;RPPR=112.183;RPR=0;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=28;SRP=3.16006;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10978G>T|p.Val3660Leu|10978/21291|10978/21291|3660/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:64:58,6:58:2109:6:226:-1.43665,0,-170.792 +NC_045512.2 11246 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=89.1607;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2231;RO=64;RPL=1;RPP=5.18177;RPPR=133.434;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.14602;SRR=33;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10981A>G|p.Met3661Val|10981/21291|10981/21291|3661/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2231:1:9:0,-18.667,-200.121 +NC_045512.2 11248 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.14602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.9305;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2311;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.14602;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10983G>T|p.Met3661Ile|10983/21291|10983/21291|3661/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2311:1:10:0,-18.567,-207.222 +NC_045512.2 11255 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.79;PAIRED=1;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2244;RO=63;RPL=1;RPP=5.18177;RPPR=139.813;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=30;SRP=3.32051;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10990A>T|p.Met3664Leu|10990/21291|10990/21291|3664/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2244:1:9:0,-18.3659,-201.283 +NC_045512.2 11270 . A C 4.38491E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.14602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9373;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=2296;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.14602;SRR=33;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11005A>C|p.Met3669Leu|11005/21291|11005/21291|3669/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2296:1:23:0,-17.267,-204.573 +NC_045512.2 11287 . GTCTGGTTTTA GA 1435.06 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=57;CIGAR=1M9D1M;DP=57;DPB=10.3636;DPRA=0;EPP=6.09608;EPPR=0;GTI=0;LEN=9;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=82.2377;PAIRED=0.982456;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1811;QR=0;RO=0;RPL=57;RPP=126.784;RPPR=0;RPR=0;RUN=1;SAF=24;SAP=6.09608;SAR=33;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=GA|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11023_11031delTCTGGTTTT|p.Ser3675_Phe3677del|11023/21291|11023/21291|3675/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:57:0,57:0:0:57:1811:-163.229,-17.1587,0 +NC_045512.2 11326 . A C 1.85355E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=5.18177;EPPR=127.319;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0713;PAIRED=1;PAIREDR=0.938462;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2424;RO=65;RPL=1;RPP=5.18177;RPPR=3.04371;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.04371;SRR=33;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11061A>C|p.Ser3687Ser|11061/21291|11061/21291|3687/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:65,1:65:2424:1:11:0,-18.768,-217.291 +NC_045512.2 11332 . A T 4.52052E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=132.228;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8873;NS=1;NUMALT=1;ODDS=92.0913;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2636;RO=71;RPL=0;RPP=5.18177;RPPR=3.7749;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=37;SRP=3.28556;SRR=34;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11067A>T|p.Val3689Val|11067/21291|11067/21291|3689/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2636:1:38:0,-17.8769,-233.655 +NC_045512.2 11382 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=93.4676;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8857;NS=1;NUMALT=1;ODDS=96.9297;PAIRED=1;PAIREDR=0.942857;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2553;RO=70;RPL=0;RPP=5.18177;RPPR=20.8784;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=4.99565;SRR=31;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11117G>A|p.Arg3706Lys|11117/21291|11117/21291|3706/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2553:1:11:0,-20.2731,-228.872 +NC_045512.2 11384 . A G 1.13914E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=91.4113;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8841;NS=1;NUMALT=1;ODDS=91.8739;PAIRED=1;PAIREDR=0.942029;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=2521;RO=69;RPL=0;RPP=5.18177;RPPR=25.9524;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=6.81824;SRR=29;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11119A>G|p.Arg3707Gly|11119/21291|11119/21291|3707/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2521:1:27:0,-18.3723,-224.404 +NC_045512.2 11392 . G T 1.43295E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=7.35324;EPPR=50.8771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8841;NS=1;NUMALT=1;ODDS=83.1167;PAIRED=1;PAIREDR=0.942029;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=2433;RO=69;RPL=0;RPP=7.35324;RPPR=46.0936;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=38;SRP=4.55236;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11127G>T|p.Trp3709Cys|11127/21291|11127/21291|3709/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:69,2:69:2433:2:68:0,-14.9152,-212.733 +NC_045512.2 11395 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=5.48761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8873;NS=1;NUMALT=1;ODDS=98.9928;PAIRED=1;PAIREDR=0.929577;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2573;RO=71;RPL=0;RPP=5.18177;RPPR=157.185;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=5.48761;SRR=31;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11130A>T|p.Thr3710Thr|11130/21291|11130/21291|3710/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2573:1:8:0,-20.8742,-230.983 +NC_045512.2 11409 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=3.0385;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7403;NS=1;NUMALT=1;ODDS=100.329;PAIRED=1;PAIREDR=0.935065;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2836;RO=77;RPL=0;RPP=5.18177;RPPR=170.214;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=3.0385;SRR=38;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11144T>C|p.Leu3715Ser|11144/21291|11144/21291|3715/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2836:1:38:0,-19.6831,-251.618 +NC_045512.2 11415 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=3.26411;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7403;NS=1;NUMALT=1;ODDS=100.787;PAIRED=1;PAIREDR=0.935065;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=2748;RO=77;RPL=0;RPP=5.18177;RPPR=170.214;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=3.26411;SRR=37;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11150T>G|p.Leu3717Arg|11150/21291|11150/21291|3717/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2748:1:36:0,-19.8821,-243.911 +NC_045512.2 11417 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=3.26411;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7403;NS=1;NUMALT=1;ODDS=105.849;PAIRED=1;PAIREDR=0.935065;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2847;RO=77;RPL=0;RPP=5.18177;RPPR=170.214;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=3.26411;SRR=37;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11152G>T|p.Val3718Phe|11152/21291|11152/21291|3718/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2847:1:14:0,-22.0803,-255.022 +NC_045512.2 11421 . A T 1.02766E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=3.12166;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7436;NS=1;NUMALT=1;ODDS=108.144;PAIRED=1;PAIREDR=0.935897;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2806;RO=78;RPL=0;RPP=5.18177;RPPR=172.385;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=3.12166;SRR=38;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11156A>T|p.Tyr3719Phe|11156/21291|11156/21291|3719/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2806:1:10:0,-22.7814,-251.725 +NC_045512.2 11435 . G C,T 6.31357E-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=78;DPB=78;DPRA=0,0;EPP=5.18177,5.18177;EPPR=3.12459;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=59.7368;NS=1;NUMALT=2;ODDS=105.408;PAIRED=0,0;PAIREDR=0.960526;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,10;QR=2731;RO=76;RPL=0,0;RPP=5.18177,5.18177;RPPR=168.042;RPR=1,1;RUN=1,1;SAF=1,0;SAP=5.18177,5.18177;SAR=0,1;SRF=39;SRP=3.12459;SRR=37;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11170G>C|p.Gly3724Arg|11170/21291|11170/21291|3724/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:76,1,1:76:2731:1,1:11,10:0,-22.1843,-244.876,-22.2843,-244.582,-244.966 +NC_045512.2 11449 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8933;NS=1;NUMALT=1;ODDS=102.872;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=2759;RO=75;RPL=0;RPP=5.18177;RPPR=132.98;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=3.73412;SRR=35;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11184T>G|p.Asp3728Glu|11184/21291|11184/21291|3728/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:76:75,1:75:2759:1:15:0,-21.3783,-247.006 +NC_045512.2 11480 . T C 1.5384E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=124.279;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7436;NS=1;NUMALT=1;ODDS=107.913;PAIRED=0;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2924;RO=78;RPL=1;RPP=5.18177;RPPR=3.45573;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=3.0103;SRR=39;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11215T>C|p.Ser3739Pro|11215/21291|11215/21291|3739/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2924:1:11:0,-22.6814,-262.211 +NC_045512.2 11508 . T A 1.53544E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=131.74;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7436;NS=1;NUMALT=1;ODDS=107.913;PAIRED=1;PAIREDR=0.935897;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2914;RO=78;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=3.12166;SRR=38;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11243T>A|p.Val3748Asp|11243/21291|11243/21291|3748/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2914:1:11:0,-22.6814,-261.309 +NC_045512.2 11522 . T G 1547.79 . AB=0.759494;ABP=49.2159;AC=1;AF=0.5;AN=2;AO=60;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=79.5909;EPPR=36.0395;GTI=0;LEN=1;MEANALT=1;MQM=59.6667;MQMR=60;NS=1;NUMALT=1;ODDS=57.5974;PAIRED=0.966667;PAIREDR=0.842105;PAO=0;PQA=0;PQR=0;PRO=0;QA=2191;QR=686;RO=19;RPL=33;RPP=4.31318;RPPR=4.03889;RPR=27;RUN=1;SAF=30;SAP=3.0103;SAR=30;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11257T>G|p.Phe3753Val|11257/21291|11257/21291|3753/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:79:19,60:19:686:60:2191:-173.593,0,-38.2831 +NC_045512.2 11529 . C T 1.37268E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=7.35324;EPPR=107.946;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7403;NS=1;NUMALT=1;ODDS=91.0805;PAIRED=1;PAIREDR=0.935065;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=2823;RO=77;RPL=1;RPP=3.0103;RPPR=11.1604;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=39;SRP=3.0385;SRR=38;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11264C>T|p.Ala3755Val|11264/21291|11264/21291|3755/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:77,2:77:2823:2:75:0,-16.661,-247.129 +NC_045512.2 11533 . A C 1.02462E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=103.232;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7436;NS=1;NUMALT=1;ODDS=108.144;PAIRED=0;PAIREDR=0.948718;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2774;RO=78;RPL=1;RPP=5.18177;RPPR=12.0303;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=3.0103;SRR=39;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11268A>C|p.Arg3756Ser|11268/21291|11268/21291|3756/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2774:1:10:0,-22.7814,-248.813 +NC_045512.2 11536 . T G 1.02766E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=96.662;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7436;NS=1;NUMALT=1;ODDS=108.144;PAIRED=1;PAIREDR=0.935897;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2907;RO=78;RPL=1;RPP=5.18177;RPPR=14.1461;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=3.0103;SRR=39;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11271T>G|p.Gly3757Gly|11271/21291|11271/21291|3757/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2907:1:10:0,-22.7814,-260.785 +NC_045512.2 11549 . T A 1.02766E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=4.01252;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7436;NS=1;NUMALT=1;ODDS=108.144;PAIRED=1;PAIREDR=0.935897;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2896;RO=78;RPL=1;RPP=5.18177;RPPR=147.33;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=3.0103;SRR=39;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11284T>A|p.Cys3762Ser|11284/21291|11284/21291|3762/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2896:1:10:0,-22.7814,-259.795 +NC_045512.2 11559 . A T 9.96017E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=10.339;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7917;NS=1;NUMALT=1;ODDS=132.892;PAIRED=1;PAIREDR=0.947917;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3393;RO=96;RPL=1;RPP=5.18177;RPPR=84.4405;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=57;SRP=10.339;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11294A>T|p.Tyr3765Phe|11294/21291|11294/21291|3765/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3393:1:10:0,-28.1999,-304.5 +NC_045512.2 11562 . G T 6.18243E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=9.52472;EPPR=13.0905;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7895;NS=1;NUMALT=1;ODDS=126.935;PAIRED=0.666667;PAIREDR=0.957895;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=3330;RO=95;RPL=3;RPP=9.52472;RPPR=77.2747;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=56;SRP=9.61615;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11297G>T|p.Cys3766Phe|11297/21291|11297/21291|3766/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:95,3:95:3330:3:30:0,-26.7009,-297.023 +NC_045512.2 11565 . C A,T 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=98;DPB=98;DPRA=0,0;EPP=5.18177,5.18177;EPPR=13.9581;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=59.7917;NS=1;NUMALT=2;ODDS=133.122;PAIRED=1,0;PAIREDR=0.958333;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=10,10;QR=3383;RO=96;RPL=1,1;RPP=5.18177,5.18177;RPPR=73.9451;RPR=0,0;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=57;SRP=10.339;SRR=39;TYPE=snp,snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11300C>A|p.Pro3767His|11300/21291|11300/21291|3767/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:96,1,1:96:3383:1,1:10,10:0,-28.2999,-303.6,-28.2999,-303.305,-303.6 +NC_045512.2 11567 . A C,G,T 1.05476E-14 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=1,2,1;CIGAR=1X,1X,1X;DP=99;DPB=99;DPRA=0,0,0;EPP=5.18177,3.0103,5.18177;EPPR=13.0905;GTI=0;LEN=1,1,1;MEANALT=3,3,3;MQM=60,60,60;MQMR=59.7895;NS=1;NUMALT=3;ODDS=116.025;PAIRED=1,1,1;PAIREDR=0.947368;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=23,76,9;QR=3352;RO=95;RPL=1,2,1;RPP=5.18177,7.35324,5.18177;RPPR=72.1546;RPR=0,0,0;RUN=1,1,1;SAF=1,1,1;SAP=5.18177,3.0103,5.18177;SAR=0,1,0;SRF=57;SRP=11.2619;SRR=38;TYPE=snp,snp,snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11302A>C|p.Ile3768Leu|11302/21291|11302/21291|3768/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:95,1,2,1:95:3352:1,2,1:23,76,9:0,-26.8422,-299.463,-22.255,-293.53,-294.696,-28.1488,-299.257,-294.791,-300.724 +NC_045512.2 11578 . A T 6.55441E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=15.102;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8737;NS=1;NUMALT=1;ODDS=131.516;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3411;RO=95;RPL=1;RPP=5.18177;RPPR=62.4629;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=58;SRP=13.0905;SRR=37;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11313A>T|p.Ile3771Ile|11313/21291|11313/21291|3771/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3411:1:10:0,-27.8989,-306.125 +NC_045512.2 11583 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=7.35324;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.875;NS=1;NUMALT=1;ODDS=129.518;PAIRED=1;PAIREDR=0.947917;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=3520;RO=96;RPL=2;RPP=7.35324;RPPR=59.5591;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=59;SRP=13.9581;SRR=37;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11318G>T|p.Gly3773Val|11318/21291|11318/21291|3773/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:96,2:96:3520:2:24:0,-27.221,-314.642 +NC_045512.2 11584 . T C 3.02883E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=3.0103;EPPR=13.9581;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.875;NS=1;NUMALT=1;ODDS=116.769;PAIRED=1;PAIREDR=0.947917;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3547;RO=96;RPL=2;RPP=7.35324;RPPR=59.5591;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=60;SRP=16.0391;SRR=36;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11319T>C|p.Gly3773Gly|11319/21291|11319/21291|3773/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:96,2:96:3547:2:76:0,-22.2861,-312.14 +NC_045512.2 11595 . A T 6.53205E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=17.2963;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8737;NS=1;NUMALT=1;ODDS=131.516;PAIRED=1;PAIREDR=0.957895;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3476;RO=95;RPL=1;RPP=5.18177;RPPR=49.2969;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=9.61615;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11330A>T|p.Gln3777Leu|11330/21291|11330/21291|3777/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3476:1:10:0,-27.8989,-311.97 +NC_045512.2 11598 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=17.2963;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8737;NS=1;NUMALT=1;ODDS=131.746;PAIRED=1;PAIREDR=0.957895;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3459;RO=95;RPL=1;RPP=5.18177;RPPR=49.2969;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=9.61615;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11333G>T|p.Cys3778Phe|11333/21291|11333/21291|3778/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3459:1:9:0,-27.9989,-310.536 +NC_045512.2 11601 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=18.6264;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8723;NS=1;NUMALT=1;ODDS=129.91;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3455;RO=94;RPL=1;RPP=5.18177;RPPR=47.7334;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=55;SRP=8.9241;SRR=39;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11336T>C|p.Ile3779Thr|11336/21291|11336/21291|3779/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3455:1:11:0,-27.4979,-309.977 +NC_045512.2 11613 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=53.4113;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8421;NS=1;NUMALT=1;ODDS=98.9556;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2806;RO=76;RPL=1;RPP=5.18177;RPPR=22.325;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=38;SRP=3.0103;SRR=38;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11348A>G|p.Tyr3783Cys|11348/21291|11348/21291|3783/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2806:1:38:0,-19.382,-248.907 +NC_045512.2 11618 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=73;DPB=73;DPRA=0;EPP=5.18177;EPPR=66.8275;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8333;NS=1;NUMALT=1;ODDS=99.6745;PAIRED=1;PAIREDR=0.972222;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2694;RO=72;RPL=1;RPP=5.18177;RPPR=17.6074;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.49285;SRR=38;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11353T>C|p.Phe3785Leu|11353/21291|11353/21291|3785/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:73:72,1:72:2694:1:11:0,-20.8752,-241.536 +NC_045512.2 11636 . A T 4.53559E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=70.5706;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.831;NS=1;NUMALT=1;ODDS=92.0913;PAIRED=1;PAIREDR=0.971831;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2613;RO=71;RPL=1;RPP=5.18177;RPPR=4.50892;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=14.0512;SRR=45;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11371A>T|p.Thr3791Ser|11371/21291|11371/21291|3791/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2613:1:38:0,-17.8769,-231.554 +NC_045512.2 11650 . C T 1.5522E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=83;DPB=83;DPRA=0;EPP=5.18177;EPPR=41.2494;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8537;NS=1;NUMALT=1;ODDS=114.33;PAIRED=1;PAIREDR=0.963415;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2984;RO=82;RPL=0;RPP=5.18177;RPPR=3.11623;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=26.8435;SRR=56;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11385C>T|p.Gly3795Gly|11385/21291|11385/21291|3795/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:83:82,1:82:2984:1:7:0,-24.2855,-268.018 +NC_045512.2 11651 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=83;DPB=83;DPRA=0;EPP=5.18177;EPPR=41.2494;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8537;NS=1;NUMALT=1;ODDS=114.1;PAIRED=1;PAIREDR=0.963415;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=3073;RO=82;RPL=1;RPP=5.18177;RPPR=3.434;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=30.1272;SRR=57;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11386C>T|p.Leu3796Phe|11386/21291|11386/21291|3796/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:83:82,1:82:3073:1:8:0,-24.1855,-275.927 +NC_045512.2 11652 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=5.18177;EPPR=38.8265;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8554;NS=1;NUMALT=1;ODDS=111.1;PAIRED=1;PAIREDR=0.963855;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=3087;RO=83;RPL=0;RPP=5.18177;RPPR=3.24576;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=28.1523;SRR=57;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11387T>G|p.Leu3796Arg|11387/21291|11387/21291|3796/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:84:83,1:83:3087:1:27:0,-22.5867,-275.283 +NC_045512.2 11705 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=59.6072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.6839;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1759;RO=47;RPL=0;RPP=5.18177;RPPR=8.60069;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=24;SRP=3.0565;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11440T>G|p.Leu3814Val|11440/21291|11440/21291|3814/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:48:47,1:47:1759:1:36:0,-10.8512,-154.976 +NC_045512.2 11743 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=7.35324;EPPR=80.6751;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.2373;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1756;RO=47;RPL=1;RPP=3.0103;RPPR=3.0565;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=23;SRP=3.0565;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11478G>T|p.Gln3826His|11478/21291|11478/21291|3826/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:47,2:47:1756:2:76:0,-7.53566,-151.095 +NC_045512.2 11782 . A G 3.27407E-5 . AB=0.122449;ABP=63.6786;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=4.45795;EPPR=51.5402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7954;PAIRED=1;PAIREDR=0.976744;PAO=0;PQA=0;PQR=0;PRO=0;QA=227;QR=1573;RO=43;RPL=5;RPP=8.80089;RPPR=5.48477;RPR=1;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11517A>G|p.Lys3839Lys|11517/21291|11517/21291|3839/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:49:43,6:43:1573:6:227:-6.04336,0,-127.096 +NC_045512.2 11783 . C A 4.52028E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=43.7254;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.0323;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1798;RO=48;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.19126;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11518C>A|p.Leu3840Ile|11518/21291|11518/21291|3840/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1798:1:10:0,-13.7505,-161.085 +NC_045512.2 11791 . T C 5.56748E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.8021;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1779;RO=48;RPL=1;RPP=5.18177;RPPR=17.6677;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.19126;SRR=25;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11526T>C|p.Ile3842Ile|11526/21291|11526/21291|3842/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:48,1:48:1779:1:11:0,-13.6505,-159.274 +NC_045512.2 11806 . TGGT GGGA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=4.78696;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.1908;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1616;RO=44;RPL=1;RPP=5.18177;RPPR=81.9729;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=4.78696;SRR=25;TYPE=complex;ANN=GGGA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11541_11544delTGGTinsGGGA|p.3849|11541/21291|11541/21291|3847/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:45:44,1:44:1616:1:16:0,-11.9464,-144.118 +NC_045512.2 11812 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=3.0103;EPPR=3.0565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.6939;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1661;RO=47;RPL=2;RPP=7.35324;RPPR=105.07;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=23;SRP=3.0565;SRR=24;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11547C>G|p.Gly3849Gly|11547/21291|11547/21291|3849/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:47,2:47:1661:2:19:0,-12.9455,-147.941 +NC_045512.2 11828 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=9.52472;EPPR=3.76559;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.9021;PAIRED=1;PAIREDR=0.978261;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1617;RO=46;RPL=3;RPP=9.52472;RPPR=102.898;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=21;SRP=3.76559;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11563G>A|p.Val3855Ile|11563/21291|11563/21291|3855/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:49:46,3:46:1617:3:31:0,-11.8571,-142.895 +NC_045512.2 11847 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=4.21667;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.7064;PAIRED=1;PAIREDR=0.977778;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1661;RO=45;RPL=1;RPP=5.18177;RPPR=100.727;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=4.21667;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11582A>C|p.Lys3861Thr|11582/21291|11582/21291|3861/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:46:45,1:45:1661:1:11:0,-12.7474,-148.666 +NC_045512.2 11874 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=102;DPB=102;DPRA=0;EPP=3.0103;EPPR=103.419;GTI=0;LEN=1;MEANALT=1;MQM=58;MQMR=59.27;NS=1;NUMALT=1;ODDS=134.472;PAIRED=1;PAIREDR=0.9;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=3708;RO=100;RPL=1;RPP=3.0103;RPPR=53.041;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=62;SRP=15.518;SRR=38;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11609T>G|p.Val3870Gly|11609/21291|11609/21291|3870/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:102:100,2:100:3708:2:20:0,-28.8051,-331.821 +NC_045512.2 11960 . C A 4.82166E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=169;DPB=169;DPRA=0;EPP=7.35324;EPPR=4.89399;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.4639;NS=1;NUMALT=1;ODDS=218.402;PAIRED=0.5;PAIREDR=0.891566;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=6005;RO=166;RPL=0;RPP=7.35324;RPPR=363.475;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=89;SRP=4.89399;SRR=77;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11695C>A|p.Leu3899Ile|11695/21291|11695/21291|3899/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:169:166,2:166:6005:2:58:0,-45.2208,-534.821 +NC_045512.2 11966 . G A 1.13914E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=177;DPB=177;DPRA=0;EPP=3.0103;EPPR=3.06022;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.4885;NS=1;NUMALT=1;ODDS=229.978;PAIRED=1;PAIREDR=0.87931;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=6182;RO=174;RPL=0;RPP=7.35324;RPPR=380.846;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=88;SRP=3.06022;SRR=86;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11701G>A|p.Ala3901Thr|11701/21291|11701/21291|3901/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:177:174,2:174:6182:2:49:0,-48.4826,-551.596 +NC_045512.2 11997 . T C 2.1728E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=181;DPB=181;DPRA=0;EPP=3.0103;EPPR=3.31358;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5028;NS=1;NUMALT=1;ODDS=234.969;PAIRED=1;PAIREDR=0.871508;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=6472;RO=179;RPL=0;RPP=7.35324;RPPR=204.884;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=88;SRP=3.11948;SRR=91;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11732T>C|p.Met3911Thr|11732/21291|11732/21291|3911/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:181:179,2:179:6472:2:56:0,-49.169,-576.957 +NC_045512.2 12002 . T G 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=174;DPB=174;DPRA=0;EPP=7.35324;EPPR=3.46479;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4826;NS=1;NUMALT=1;ODDS=227.601;PAIRED=0.5;PAIREDR=0.883721;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=6264;RO=172;RPL=0;RPP=7.35324;RPPR=161.376;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=89;SRP=3.46479;SRR=83;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11737T>G|p.Ser3913Ala|11737/21291|11737/21291|3913/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:174:172,2:172:6264:2:52:0,-47.4403,-558.645 +NC_045512.2 12003 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=178;DPB=178;DPRA=0;EPP=7.35324;EPPR=3.05965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4943;NS=1;NUMALT=1;ODDS=240.098;PAIRED=0;PAIREDR=0.892045;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=6464;RO=176;RPL=0;RPP=7.35324;RPPR=169.029;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=89;SRP=3.05965;SRR=87;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11738C>T|p.Ser3913Leu|11738/21291|11738/21291|3913/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:178:176,2:176:6464:2:20:0,-51.6833,-579.669 +NC_045512.2 12060 . A G 8.52851E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=181;DPB=181;DPRA=0;EPP=3.0103;EPPR=237.396;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5028;NS=1;NUMALT=1;ODDS=230.6;PAIRED=1;PAIREDR=0.871508;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6612;RO=179;RPL=0;RPP=7.35324;RPPR=6.5162;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=88;SRP=3.11948;SRR=91;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11795A>G|p.Glu3932Gly|11795/21291|11795/21291|3932/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:181:179,2:179:6612:2:76:0,-47.2716,-587.675 +NC_045512.2 12064 . A G 8.52851E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=181;DPB=181;DPRA=0;EPP=3.0103;EPPR=237.396;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5028;NS=1;NUMALT=1;ODDS=230.6;PAIRED=1;PAIREDR=0.871508;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6635;RO=179;RPL=2;RPP=7.35324;RPPR=5.06046;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=88;SRP=3.11948;SRR=91;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11799A>G|p.Glu3933Glu|11799/21291|11799/21291|3933/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:181:179,2:179:6635:2:76:0,-47.2716,-589.733 +NC_045512.2 12086 . T A 8.52851E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=181;DPB=181;DPRA=0;EPP=7.35324;EPPR=258.067;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5028;NS=1;NUMALT=1;ODDS=230.6;PAIRED=1;PAIREDR=0.871508;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6628;RO=179;RPL=1;RPP=3.0103;RPPR=9.42767;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=88;SRP=3.11948;SRR=91;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11821T>A|p.Leu3941Ile|11821/21291|11821/21291|3941/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:181:179,2:179:6628:2:76:0,-47.2716,-589.134 +NC_045512.2 12186 . A C 7.62492E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=190;DPB=190;DPRA=0;EPP=7.35324;EPPR=147.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9362;NS=1;NUMALT=1;ODDS=256.166;PAIRED=0.5;PAIREDR=0.87234;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=6986;RO=188;RPL=0;RPP=7.35324;RPPR=7.63045;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=80;SRP=12.0658;SRR=108;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11921A>C|p.Glu3974Ala|11921/21291|11921/21291|3974/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:190:188,2:188:6986:2:22:0,-55.1057,-626.578 +NC_045512.2 12205 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=14;CIGAR=1X;DP=241;DPB=241;DPRA=0;EPP=3.63072;EPPR=38.6052;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9471;NS=1;NUMALT=1;ODDS=190.238;PAIRED=0.571429;PAIREDR=0.85022;PAO=0;PQA=0;PQR=0;PRO=0;QA=522;QR=8436;RO=227;RPL=0;RPP=33.4109;RPPR=38.6052;RPR=14;RUN=1;SAF=8;SAP=3.63072;SAR=6;SRF=73;SRP=65.7725;SRR=154;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11940G>T|p.Leu3980Phe|11940/21291|11940/21291|3980/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:241:227,14:227:8436:14:522:0,-25.2255,-711.766 +NC_045512.2 12332 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=174;DPB=174;DPRA=0;EPP=3.0103;EPPR=155.771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6163;NS=1;NUMALT=1;ODDS=220.975;PAIRED=1;PAIREDR=0.848837;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6314;RO=172;RPL=2;RPP=7.35324;RPPR=9.12072;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=82;SRP=3.81829;SRR=90;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12067G>A|p.Ala4023Thr|12067/21291|12067/21291|4023/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:174:172,2:172:6314:2:76:0,-45.1644,-560.914 +NC_045512.2 12370 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=172;DPB=172;DPRA=0;EPP=3.0103;EPPR=4.56502;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.6095;NS=1;NUMALT=1;ODDS=217.28;PAIRED=1;PAIREDR=0.852071;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6236;RO=169;RPL=2;RPP=7.35324;RPPR=352.823;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=79;SRP=4.56502;SRR=90;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12105T>C|p.Thr4035Thr|12105/21291|12105/21291|4035/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:172:169,2:169:6236:2:76:0,-44.4479,-553.974 +NC_045512.2 12393 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=174;DPB=174;DPRA=0;EPP=3.0103;EPPR=3.81829;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6163;NS=1;NUMALT=1;ODDS=222.283;PAIRED=1;PAIREDR=0.848837;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=6269;RO=172;RPL=2;RPP=7.35324;RPPR=376.504;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=82;SRP=3.81829;SRR=90;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12128A>T|p.Asp4043Val|12128/21291|12128/21291|4043/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:174:172,2:172:6269:2:70:0,-45.7325,-557.441 +NC_045512.2 12408 . T A 1.59116E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=167;DPB=167;DPRA=0;EPP=9.52472;EPPR=7.30028;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5976;NS=1;NUMALT=1;ODDS=221.622;PAIRED=0.666667;PAIREDR=0.871951;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=5960;RO=164;RPL=3;RPP=9.52472;RPPR=359.132;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=73;SRP=7.30028;SRR=91;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12143T>A|p.Ile4048Asn|12143/21291|12143/21291|4048/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:167:164,3:164:5960:3:27:0,-47.752,-533.77 +NC_045512.2 12459 . C T 0.00770109 . AB=0.161677;ABP=169.043;AC=1;AF=0.5;AN=2;AO=27;CIGAR=1X;DP=167;DPB=167;DPRA=0;EPP=61.6401;EPPR=211.72;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5286;NS=1;NUMALT=1;ODDS=6.33406;PAIRED=0.962963;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=1025;QR=5242;RO=140;RPL=0;RPP=61.6401;RPPR=41.7866;RPR=27;RUN=1;SAF=27;SAP=61.6401;SAR=0;SRF=49;SRP=30.3709;SRR=91;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12194C>T|p.Thr4065Ile|12194/21291|12194/21291|4065/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:167:140,27:140:5242:27:1025:-42.2915,0,-421.415 +NC_045512.2 12485 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=152;DPB=152;DPRA=0;EPP=3.0103;EPPR=197.806;GTI=0;LEN=1;MEANALT=1;MQM=54;MQMR=59.64;NS=1;NUMALT=1;ODDS=194.764;PAIRED=1;PAIREDR=0.893333;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=5555;RO=150;RPL=2;RPP=7.35324;RPPR=5.09491;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=78;SRP=3.53145;SRR=72;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12220A>G|p.Ile4074Val|12220/21291|12220/21291|4074/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:152:150,2:150:5555:2:58:0,-40.2859,-494.422 +NC_045512.2 12545 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=142;DPB=142;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=177.239;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5149;RO=140;RPL=0;RPP=7.35324;RPPR=307.016;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=70;SRP=3.0103;SRR=70;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12280G>A|p.Ala4094Thr|12280/21291|12280/21291|4094/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:142:140,2:140:5149:2:75:0,-35.6259,-456.349 +NC_045512.2 12548 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=140;DPB=140;DPRA=0;EPP=7.35324;EPPR=3.26206;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=182.001;PAIRED=0.5;PAIREDR=0.978261;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=5135;RO=138;RPL=0;RPP=7.35324;RPPR=302.673;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=71;SRP=3.26206;SRR=67;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12283T>G|p.Leu4095Val|12283/21291|12283/21291|4095/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:140:138,2:138:5135:2:47:0,-37.6818,-457.749 +NC_045512.2 12583 . TAAAATTG TAAATTG 2.29004E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D6M;DP=143;DPB=142.75;DPRA=0;EPP=3.0103;EPPR=206.682;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.393;PAIRED=1;PAIREDR=0.964539;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5273;RO=141;RPL=0;RPP=7.35324;RPPR=4.87376;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=70;SRP=3.0257;SRR=71;TYPE=del;ANN=TAAATTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12322delA|p.Ile4108fs|12322/21291|12322/21291|4108/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5273:2:76:0,-35.8325,-467.418 +NC_045512.2 12617 . A T 2.26038E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=3.0103;EPPR=275.43;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.393;PAIRED=1;PAIREDR=0.964539;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5314;RO=141;RPL=2;RPP=7.35324;RPPR=3.1489;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=70;SRP=3.0257;SRR=71;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12352A>T|p.Asn4118Tyr|12352/21291|12352/21291|4118/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5314:2:76:0,-35.8325,-471.092 +NC_045512.2 12757 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=165;DPB=165;DPRA=0;EPP=3.0103;EPPR=253.049;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=208.822;PAIRED=1;PAIREDR=0.907975;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=6169;RO=163;RPL=0;RPP=7.35324;RPPR=10.0576;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=84;SRP=3.34335;SRR=79;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12492T>C|p.Thr4164Thr|12492/21291|12492/21291|4164/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:165:163,2:163:6169:2:75:0,-42.5496,-548.078 +NC_045512.2 12798 . G T 0.0 . AB=0.0963303;ABP=311.559;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=218;DPB=218;DPRA=0;EPP=3.1137;EPPR=19.7758;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=93.4196;PAIRED=0.809524;PAIREDR=0.873096;PAO=0;PQA=0;PQR=0;PRO=0;QA=785;QR=7052;RO=197;RPL=0;RPP=48.6112;RPPR=159.103;RPR=21;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=79;SRP=19.7758;SRR=118;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12533G>T|p.Gly4178Val|12533/21291|12533/21291|4178/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:218:197,21:197:7052:21:785:-5.35376,0,-569.054 +NC_045512.2 12883 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=186;DPB=186;DPRA=0;EPP=11.6962;EPPR=257.335;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=215.76;PAIRED=0.5;PAIREDR=0.862637;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=6828;RO=182;RPL=2;RPP=3.0103;RPPR=3.05802;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=88;SRP=3.43982;SRR=94;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12618T>C|p.Tyr4206Tyr|12618/21291|12618/21291|4206/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:186:182,4:182:6828:4:152:0,-41.9417,-600.419 +NC_045512.2 12892 . G A 2.55853E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=186;DPB=186;DPRA=0;EPP=7.35324;EPPR=254.571;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=237.477;PAIRED=1;PAIREDR=0.853261;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=6886;RO=184;RPL=1;RPP=3.0103;RPPR=3.19912;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=89;SRP=3.43515;SRR=95;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12627G>A|p.Leu4209Leu|12627/21291|12627/21291|4209/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:186:184,2:184:6886:2:76:0,-48.7768,-612.475 +NC_045512.2 12903 . G T 208.9 . AB=0.166667;ABP=182.519;AC=1;AF=0.5;AN=2;AO=31;CIGAR=1X;DP=186;DPB=186;DPRA=0;EPP=33.9012;EPPR=228.97;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.101;PAIRED=0.967742;PAIREDR=0.832258;PAO=0;PQA=0;PQR=0;PRO=0;QA=1161;QR=5829;RO=155;RPL=16;RPP=3.08035;RPPR=3.13639;RPR=15;RUN=1;SAF=15;SAP=3.08035;SAR=16;SRF=75;SRP=3.36054;SRR=80;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12638G>T|p.Cys4213Phe|12638/21291|12638/21291|4213/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:186:155,31:155:5829:31:1161:-48.7999,0,-468.631 +NC_045512.2 12935 . A G 1.81416E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=186;DPB=186;DPRA=0;EPP=7.35324;EPPR=145.808;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=238.13;PAIRED=1;PAIREDR=0.853261;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=6850;RO=184;RPL=1;RPP=3.0103;RPPR=40.0197;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=89;SRP=3.43515;SRR=95;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12670A>G|p.Lys4224Glu|12670/21291|12670/21291|4224/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:186:184,2:184:6850:2:73:0,-49.0605,-609.52 +NC_045512.2 13117 . A G 4.84575E-14 . AB=0.12381;ABP=261.147;AC=1;AF=0.5;AN=2;AO=26;CIGAR=1X;DP=210;DPB=210;DPRA=0;EPP=3.0103;EPPR=4.19045;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.9351;PAIRED=1;PAIREDR=0.907609;PAO=0;PQA=0;PQR=0;PRO=0;QA=928;QR=6700;RO=184;RPL=0;RPP=59.4686;RPPR=402.561;RPR=26;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=87;SRP=4.19045;SRR=97;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12852A>G|p.Leu4284Leu|12852/21291|12852/21291|4284/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:210:184,26:184:6700:26:928:-20.6058,0,-539.756 +NC_045512.2 13142 . A G 3.23054E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=210;DPB=210;DPRA=0;EPP=3.73412;EPPR=3.86001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=274.476;PAIRED=0.666667;PAIREDR=0.922705;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=7721;RO=207;RPL=0;RPP=9.52472;RPPR=452.505;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=99;SRP=3.86001;SRR=108;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12877A>G|p.Asn4293Asp|12877/21291|12877/21291|4293/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:210:207,3:207:7721:3:45:0,-59.0165,-690.597 +NC_045512.2 13156 . G T 559.893 . AB=0.21327;ABP=153.686;AC=1;AF=0.5;AN=2;AO=45;CIGAR=1X;DP=211;DPB=211;DPRA=0;EPP=8.84915;EPPR=42.8206;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=128.92;PAIRED=0.911111;PAIREDR=0.921212;PAO=0;PQA=0;PQR=0;PRO=0;QA=1637;QR=6122;RO=165;RPL=5;RPP=62.1226;RPPR=189.375;RPR=40;RUN=1;SAF=22;SAP=3.05855;SAR=23;SRF=78;SRP=4.0763;SRR=87;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12891G>T|p.Met4297Ile|12891/21291|12891/21291|4297/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:211:165,45:165:6122:45:1637:-84.286,0,-487.677 +NC_045512.2 13378 . C A 1.31693E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=174;DPB=174;DPRA=0;EPP=3.0103;EPPR=184.808;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=227.531;PAIRED=1;PAIREDR=0.912791;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=6414;RO=172;RPL=0;RPP=7.35324;RPPR=7.10075;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=73;SRP=11.5447;SRR=99;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13113C>A|p.Thr4371Thr|13113/21291|13113/21291|4371/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:174:172,2:172:6414:2:46:0,-48.0118,-572.885 +NC_045512.2 13395 . A T 1.80211E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=144;DPB=144;DPRA=0;EPP=3.0103;EPPR=4.25774;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=179.067;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5131;RO=141;RPL=0;RPP=7.35324;RPPR=267.299;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=70;SRP=3.0257;SRR=71;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13130A>T|p.Lys4377Ile|13130/21291|13130/21291|4377/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:144:141,2:141:5131:2:75:0,-36.1252,-454.827 +NC_045512.2 13416 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=141;DPB=141;DPRA=0;EPP=7.35324;EPPR=3.40085;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=184.244;PAIRED=1;PAIREDR=0.992806;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=5041;RO=139;RPL=0;RPP=7.35324;RPPR=304.845;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=72;SRP=3.40085;SRR=67;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13151A>C|p.Asp4384Ala|13151/21291|13151/21291|4384/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:141:139,2:139:5041:2:43:0,-38.3613,-449.674 +NC_045512.2 13453 . A T 1.1542E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=142;DPB=142;DPRA=0;EPP=3.0103;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=186.415;PAIRED=1;PAIREDR=0.992857;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=5228;RO=140;RPL=0;RPP=7.35324;RPPR=307.016;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.07234;SRR=69;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13188A>T|p.Ala4396Ala|13188/21291|13188/21291|4396/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:142:140,2:140:5228:2:33:0,-39.6114,-467.438 +NC_045512.2 13474 . T C 2.26038E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=7.35324;EPPR=109.104;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.393;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5247;RO=141;RPL=1;RPP=3.0103;RPPR=46.2703;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13210T>C|p.Cys4404Arg|13210/21291|13210/21291|4404/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5247:2:76:0,-35.8325,-465.07 +NC_045512.2 13501 . C T 2.26038E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=7.35324;EPPR=283.685;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.393;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5314;RO=141;RPL=1;RPP=3.0103;RPPR=3.1489;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13237C>T|p.Pro4413Ser|13237/21291|13237/21291|4413/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5314:2:76:0,-35.8325,-471.089 +NC_045512.2 13524 . T C 2.29004E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=7.35324;EPPR=153.951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.393;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5296;RO=141;RPL=1;RPP=3.0103;RPPR=31.4858;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13260T>C|p.Thr4420Thr|13260/21291|13260/21291|4420/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5296:2:76:0,-35.8325,-469.474 +NC_045512.2 13535 . A G 2.29004E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=3.0103;EPPR=104.053;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.393;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5295;RO=141;RPL=2;RPP=7.35324;RPPR=60.3156;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13271A>G|p.Tyr4424Cys|13271/21291|13271/21291|4424/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5295:2:76:0,-35.8325,-469.38 +NC_045512.2 13547 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=3.0103;EPPR=3.39531;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.829;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=5252;RO=141;RPL=2;RPP=7.35324;RPPR=292.063;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13283A>G|p.Asp4428Gly|13283/21291|13283/21291|4428/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5252:2:74:0,-36.0215,-465.712 +NC_045512.2 13569 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=3.0103;EPPR=3.1489;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=190.85;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=5236;RO=141;RPL=2;RPP=7.35324;RPPR=300.564;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13305T>C|p.Ala4435Ala|13305/21291|13305/21291|4435/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5236:2:19:0,-41.2423,-469.494 +NC_045512.2 13584 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=143;DPB=143;DPRA=0;EPP=3.0103;EPPR=3.0257;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.611;PAIRED=1;PAIREDR=0.992908;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5161;RO=141;RPL=2;RPP=7.35324;RPPR=309.188;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.0257;SRR=70;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13320C>T|p.Phe4440Phe|13320/21291|13320/21291|4440/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:143:141,2:141:5161:2:75:0,-35.9269,-457.434 +NC_045512.2 13595 . A C 2.5316E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=142;DPB=142;DPRA=0;EPP=7.35324;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=180.152;PAIRED=1;PAIREDR=0.992857;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=5090;RO=140;RPL=2;RPP=7.35324;RPPR=307.016;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=69;SRP=3.07234;SRR=71;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13331A>C|p.Asn4444Thr|13331/21291|13331/21291|4444/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:142:140,2:140:5090:2:68:0,-36.2893,-451.715 +NC_045512.2 13687 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=199;DPB=199;DPRA=0;EPP=3.0103;EPPR=27.3594;GTI=0;LEN=1;MEANALT=1;MQM=54;MQMR=60;NS=1;NUMALT=1;ODDS=261.96;PAIRED=1;PAIREDR=0.984772;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=7171;RO=197;RPL=0;RPP=7.35324;RPPR=164.394;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=84;SRP=12.2804;SRR=113;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13423G>A|p.Glu4475Lys|13423/21291|13423/21291|4475/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:199:197,2:197:7171:2:46:0,-55.5551,-641.031 +NC_045512.2 13844 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=164;DPB=164;DPRA=0;EPP=7.35324;EPPR=3.06392;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8519;NS=1;NUMALT=1;ODDS=214.73;PAIRED=1;PAIREDR=0.987654;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=6037;RO=162;RPL=2;RPP=7.35324;RPPR=354.789;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=80;SRP=3.06392;SRR=82;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13580A>C|p.Asp4527Ala|13580/21291|13580/21291|4527/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:164:162,2:162:6037:2:48:0,-44.8091,-538.717 +NC_045512.2 13847 . A C 7.68496E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=163;DPB=163;DPRA=0;EPP=7.35324;EPPR=3.13169;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8509;NS=1;NUMALT=1;ODDS=213.58;PAIRED=1;PAIREDR=0.981366;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=5969;RO=161;RPL=2;RPP=7.35324;RPPR=352.617;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=79;SRP=3.13169;SRR=82;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13583A>C|p.Glu4528Ala|13583/21291|13583/21291|4528/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:163:161,2:161:5969:2:47:0,-44.6055,-532.709 +NC_045512.2 13893 . TTGT TT 5.9668E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M2D1M;DP=153;DPB=152;DPRA=0;EPP=3.0103;EPPR=5.09491;GTI=0;LEN=2;MEANALT=2;MQM=60;MQMR=59.84;NS=1;NUMALT=1;ODDS=192.416;PAIRED=1;PAIREDR=0.993333;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=5478;RO=150;RPL=2;RPP=7.35324;RPPR=328.731;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=69;SRP=5.09491;SRR=81;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13632_13633delTG|p.Cys4544fs|13632/21291|13632/21291|4544/7096||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:153:150,2:150:5478:2:71:0,-39.2666,-486.331 +NC_045512.2 13899 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=152;DPB=152;DPRA=0;EPP=7.35324;EPPR=5.84769;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.84;NS=1;NUMALT=1;ODDS=199.778;PAIRED=1;PAIREDR=0.993333;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=5539;RO=150;RPL=2;RPP=7.35324;RPPR=328.731;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=68;SRP=5.84769;SRR=82;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13635T>G|p.Asp4545Glu|13635/21291|13635/21291|4545/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:152:150,2:150:5539:2:41:0,-41.8617,-494.595 +NC_045512.2 13900 . G A 1.25664E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=146;DPB=146;DPRA=0;EPP=3.0103;EPPR=7.89611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8333;NS=1;NUMALT=1;ODDS=182.511;PAIRED=1;PAIREDR=0.993056;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5198;RO=144;RPL=2;RPP=7.35324;RPPR=315.702;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=63;SRP=7.89611;SRR=81;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13636G>A|p.Asp4546Asn|13636/21291|13636/21291|4546/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:146:144,2:144:5198:2:76:0,-36.7356,-460.615 +NC_045512.2 13909 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=103;DPB=103;DPRA=0;EPP=7.35324;EPPR=77.8508;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7624;NS=1;NUMALT=1;ODDS=136.787;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=3780;RO=101;RPL=2;RPP=7.35324;RPPR=222.329;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=21;SRP=77.8508;SRR=80;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13645T>C|p.Phe4549Leu|13645/21291|13645/21291|4549/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:103:101,2:101:3780:2:22:0,-28.9161,-338.201 +NC_045512.2 13995 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=91.8433;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8636;NS=1;NUMALT=1;ODDS=115.446;PAIRED=1;PAIREDR=0.988636;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3247;RO=88;RPL=0;RPP=5.18177;RPPR=194.1;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=74;SRP=91.8433;SRR=14;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13731T>G|p.Ala4577Ala|13731/21291|13731/21291|4577/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3247:1:38:0,-22.9944,-288.607 +NC_045512.2 14045 . T G 1.69965E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=141;DPB=141;DPRA=0;EPP=11.6962;EPPR=4.92817;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9124;NS=1;NUMALT=1;ODDS=158.079;PAIRED=1;PAIREDR=0.992701;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=5141;RO=137;RPL=0;RPP=11.6962;RPPR=300.502;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=74;SRP=4.92817;SRR=63;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13781T>G|p.Val4594Gly|13781/21291|13781/21291|4594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:141:137,4:137:5141:4:152:0,-28.3953,-448.67 +NC_045512.2 14088 . G A 1.59116E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=3.0103;EPPR=155.777;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9172;NS=1;NUMALT=1;ODDS=183.883;PAIRED=1;PAIREDR=0.986207;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5436;RO=145;RPL=0;RPP=7.35324;RPPR=17.4019;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=73;SRP=3.02528;SRR=72;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13824G>A|p.Trp4608*|13824/21291|13824/21291|4608/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:147:145,2:145:5436:2:76:0,-37.0366,-482.057 +NC_045512.2 14204 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=3.0103;EPPR=3.02528;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9172;NS=1;NUMALT=1;ODDS=184.101;PAIRED=1;PAIREDR=0.986207;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5297;RO=145;RPL=2;RPP=7.35324;RPPR=317.874;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=73;SRP=3.02528;SRR=72;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13940C>A|p.Ser4647*|13940/21291|13940/21291|4647/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:147:145,2:145:5297:2:75:0,-37.1311,-469.67 +NC_045512.2 14251 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=121;DPB=121;DPRA=0;EPP=7.35324;EPPR=252.803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7983;NS=1;NUMALT=1;ODDS=148.23;PAIRED=1;PAIREDR=0.991597;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4437;RO=119;RPL=1;RPP=3.0103;RPPR=11.0575;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=50;SRP=9.59771;SRR=69;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13987T>A|p.Leu4663Ile|13987/21291|13987/21291|4663/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:121:119,2:119:4437:2:76:0,-29.2098,-392.183 +NC_045512.2 14332 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=107;DPB=107;DPRA=0;EPP=3.0103;EPPR=3.19643;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7714;NS=1;NUMALT=1;ODDS=130.377;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=3825;RO=105;RPL=0;RPP=7.35324;RPPR=231.015;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=51;SRP=3.19643;SRR=54;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14068T>C|p.Cys4690Arg|14068/21291|14068/21291|4690/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:107:105,2:105:3825:2:70:0,-25.5635,-337.68 +NC_045512.2 14380 . A C 1.35656E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=7.35324;EPPR=199.754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7736;NS=1;NUMALT=1;ODDS=140.999;PAIRED=1;PAIREDR=0.971698;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3978;RO=106;RPL=0;RPP=7.35324;RPPR=5.05886;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=52;SRP=3.09224;SRR=54;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14116A>C|p.Asn4706His|14116/21291|14116/21291|4706/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:106,2:106:3978:2:34:0,-29.2813,-354.884 +NC_045512.2 14408 . C T 3305.45 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=108;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=220.479;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.7778;MQMR=0;NS=1;NUMALT=1;ODDS=152.939;PAIRED=0.972222;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4018;QR=0;RO=0;RPL=50;RPP=4.2971;RPPR=0;RPR=58;RUN=1;SAF=52;SAP=3.332;SAR=56;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144C>T|p.Pro4715Leu|14144/21291|14144/21291|4715/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:108:0,108:0:0:108:4018:-361.685,-32.5112,0 +NC_045512.2 14442 . T C 2.41084E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=8.80089;EPPR=79.6505;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=88.4581;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=228;QR=3832;RO=102;RPL=4;RPP=4.45795;RPPR=33.7515;RPR=2;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=49;SRP=3.35092;SRR=53;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14178T>C|p.Phe4726Phe|14178/21291|14178/21291|4726/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:102,6:102:3832:6:228:0,-11.6263,-324.08 +NC_045512.2 14505 . T A 4.30981E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=104;DPB=104;DPRA=0;EPP=7.35324;EPPR=5.13919;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=139.248;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=3747;RO=102;RPL=2;RPP=7.35324;RPPR=224.5;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=46;SRP=5.13919;SRR=56;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14241T>A|p.His4747Gln|14241/21291|14241/21291|4747/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:104:102,2:102:3747:2:17:0,-29.6921,-335.766 +NC_045512.2 14509 . C T 1.78702E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=37.5565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=103.777;PAIRED=1;PAIREDR=0.961039;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=2786;RO=77;RPL=1;RPP=5.18177;RPPR=170.214;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=37.5565;SRR=56;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14245C>T|p.Gln4749*|14245/21291|14245/21291|4749/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2786:1:23:0,-21.1804,-248.639 +NC_045512.2 14521 . T G 4.33994E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=64.8334;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.2719;PAIRED=1;PAIREDR=0.955882;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=2561;RO=68;RPL=1;RPP=5.18177;RPPR=150.67;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=64.8334;SRR=56;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14257T>G|p.Leu4753Val|14257/21291|14257/21291|4753/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2561:1:28:0,-17.9713,-227.91 +NC_045512.2 14547 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=185.513;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=116.364;PAIRED=1;PAIREDR=0.931818;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3165;RO=88;RPL=0;RPP=5.18177;RPPR=19.6912;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=17.2236;SRR=56;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14283G>A|p.Lys4761Lys|14283/21291|14283/21291|4761/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3165:1:34:0,-23.3928,-281.65 +NC_045512.2 14549 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=192.294;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=125.075;PAIRED=1;PAIREDR=0.936842;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3436;RO=95;RPL=1;RPP=5.18177;RPPR=11.2619;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=40;SRP=8.15326;SRR=55;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14285A>G|p.Glu4762Gly|14285/21291|14285/21291|4762/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3436:1:38:0,-25.1016,-305.634 +NC_045512.2 14593 . G C 4.06826E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=215.815;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.203;PAIRED=1;PAIREDR=0.94898;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3690;RO=98;RPL=1;RPP=5.18177;RPPR=38.4629;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=69;SRP=38.4629;SRR=29;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14329G>C|p.Gly4777Arg|14329/21291|14329/21291|4777/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3690:1:38:0,-26.0047,-328.452 +NC_045512.2 14612 . A C 2.29028E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=81;DPB=81;DPRA=0;EPP=5.18177;EPPR=100.727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.367;PAIRED=1;PAIREDR=0.9625;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2988;RO=80;RPL=0;RPP=5.18177;RPPR=176.728;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=70;SRP=100.727;SRR=10;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14348A>C|p.Lys4783Thr|14348/21291|14348/21291|4783/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:81:80,1:80:2988:1:34:0,-20.9845,-265.714 +NC_045512.2 14623 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=92;DPB=92;DPRA=0;EPP=5.18177;EPPR=60.3038;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=125.783;PAIRED=1;PAIREDR=0.967033;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3394;RO=91;RPL=0;RPP=5.18177;RPPR=200.614;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=70;SRP=60.3038;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14359T>A|p.Cys4787Ser|14359/21291|14359/21291|4787/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:92:91,1:91:3394:1:11:0,-26.5948,-304.53 +NC_045512.2 14626 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=5.18177;EPPR=50.2924;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=122.323;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3417;RO=93;RPL=0;RPP=5.18177;RPPR=204.957;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=69;SRP=50.2924;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14362T>C|p.Phe4788Leu|14362/21291|14362/21291|4788/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:94:93,1:93:3417:1:38:0,-24.4995,-303.902 +NC_045512.2 14631 . A G 1.69061E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=134;DPB=134;DPRA=0;EPP=7.35324;EPPR=4.35297;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=177.425;PAIRED=1;PAIREDR=0.977099;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=4805;RO=131;RPL=0;RPP=7.35324;RPPR=287.473;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=70;SRP=4.35297;SRR=61;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14367A>G|p.Ser4789Ser|14367/21291|14367/21291|4789/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:134:131,2:131:4805:2:26:0,-37.757,-430.04 +NC_045512.2 14637 . T C 2.92015E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=135;DPB=135;DPRA=0;EPP=3.0103;EPPR=3.41847;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=168.072;PAIRED=1;PAIREDR=0.977444;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=4908;RO=133;RPL=0;RPP=7.35324;RPPR=291.816;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=69;SRP=3.41847;SRR=64;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14373T>C|p.Ala4791Ala|14373/21291|14373/21291|4791/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:135:133,2:133:4908:2:73:0,-33.7079,-434.881 +NC_045512.2 14660 . T A 1.92889E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=136;DPB=136;DPRA=0;EPP=3.0103;EPPR=3.15724;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=167.879;PAIRED=1;PAIREDR=0.977444;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4930;RO=133;RPL=0;RPP=7.35324;RPPR=291.816;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=68;SRP=3.15724;SRR=65;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14396T>A|p.Phe4799Tyr|14396/21291|14396/21291|4799/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:136:133,2:133:4930:2:76:0,-33.6241,-436.651 +NC_045512.2 14676 . C T 4105.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=136;CIGAR=1X;DP=136;DPB=136;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=191.755;PAIRED=0.977941;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5042;QR=0;RO=0;RPL=0;RPP=298.331;RPPR=0;RPR=136;RUN=1;SAF=70;SAP=3.26577;SAR=66;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14412C>T|p.Pro4804Pro|14412/21291|14412/21291|4804/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:136:0,136:0:0:136:5042:-453.852,-40.9401,0 +NC_045512.2 14711 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=136;DPB=136;DPRA=0;EPP=3.0103;EPPR=185.09;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=168.79;PAIRED=1;PAIREDR=0.977612;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5036;RO=134;RPL=0;RPP=7.35324;RPPR=12.3444;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=69;SRP=3.26958;SRR=65;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14447T>C|p.Val4816Ala|14447/21291|14447/21291|4816/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:136:134,2:134:5036:2:76:0,-33.7253,-446.089 +NC_045512.2 14750 . TAAAACACT TAAACACT,TAAAGCACT 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=2,2;CIGAR=1M1D7M,4M1X4M;DP=136;DPB=135.778;DPRA=0,0;EPP=7.35324,7.35324;EPPR=255.954;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=166.916;PAIRED=1,1;PAIREDR=0.977273;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,75;QR=4880;RO=132;RPL=1,1;RPP=3.0103,3.0103;RPPR=5.37918;RPR=1,1;RUN=1,1;SAF=1,1;SAP=3.0103,3.0103;SAR=1,1;SRF=68;SRP=3.27351;SRR=64;TYPE=del,snp;ANN=TAAACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14490delA|p.Lys4830fs|14490/21291|14490/21291|4830/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:136:132,2,2:132:4880:2,2:76,75:0,-33.5004,-432.088,-33.5949,-426.546,-432.177 +NC_045512.2 14816 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=136;DPB=136;DPRA=0;EPP=3.0103;EPPR=3.26958;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=168.79;PAIRED=1;PAIREDR=0.977612;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4965;RO=134;RPL=2;RPP=7.35324;RPPR=293.988;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=69;SRP=3.26958;SRR=65;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14552A>G|p.Asn4851Ser|14552/21291|14552/21291|4851/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:136:134,2:134:4965:2:76:0,-33.7253,-439.712 +NC_045512.2 14846 . T C 9.52344E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=120;DPB=120;DPRA=0;EPP=3.73412;EPPR=6.14687;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=138.945;PAIRED=1;PAIREDR=0.991453;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=4231;RO=117;RPL=3;RPP=9.52472;RPPR=257.073;RPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=52;SRP=6.14687;SRR=65;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14582T>C|p.Leu4861Pro|14582/21291|14582/21291|4861/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:120:117,3:117:4231:3:103:0,-26.5151,-371.306 +NC_045512.2 14849 . T G 2.01906E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=32.3252;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.819;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=3509;RO=96;RPL=1;RPP=5.18177;RPPR=211.472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=30;SRP=32.3252;SRR=66;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14585T>G|p.Leu4862Arg|14585/21291|14585/21291|4862/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3509:1:19:0,-27.2999,-314.077 +NC_045512.2 14885 . G T 6.48577E-10 . AB=0.132653;ABP=117.877;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=23.2217;EPPR=187.585;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.6249;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=489;QR=3178;RO=85;RPL=13;RPP=31.2394;RPPR=16.5245;RPR=0;RUN=1;SAF=1;SAP=23.2217;SAR=12;SRF=31;SRP=16.5245;SRR=54;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14621G>T|p.Cys4874Phe|14621/21291|14621/21291|4874/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:98:85,13:85:3178:13:489:-14.855,0,-256.701 +NC_045512.2 14937 . C A 1.45254E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=61;DPB=61;DPRA=0;EPP=5.18177;EPPR=40.0701;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.6859;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=2217;RO=60;RPL=0;RPP=5.18177;RPPR=133.299;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=40.0701;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14673C>A|p.Asp4891Glu|14673/21291|14673/21291|4891/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:61:60,1:60:2217:1:22:0,-16.1629,-197.569 +NC_045512.2 14950 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=3.40511;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=120.736;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=3214;RO=88;RPL=0;RPP=5.18177;RPPR=194.1;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.40511;SRR=42;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14686T>G|p.Phe4896Val|14686/21291|14686/21291|4896/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3214:1:15:0,-25.2917,-287.946 +NC_045512.2 14980 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.389;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3375;RO=92;RPL=0;RPP=5.18177;RPPR=202.786;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14716C>T|p.Leu4906Phe|14716/21291|14716/21291|4906/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3375:1:10:0,-26.9958,-302.921 +NC_045512.2 14984 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.389;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3450;RO=92;RPL=0;RPP=5.18177;RPPR=202.786;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14720A>T|p.Tyr4907Phe|14720/21291|14720/21291|4907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3450:1:10:0,-26.9958,-309.667 +NC_045512.2 14992 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=5.18177;EPPR=3.40511;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=121.657;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3242;RO=88;RPL=0;RPP=5.18177;RPPR=194.1;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.40511;SRR=42;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14728T>G|p.Ser4910Ala|14728/21291|14728/21291|4910/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:89:88,1:88:3242:1:11:0,-25.6917,-290.852 +NC_045512.2 14998 . A G 2.98042E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.619;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3414;RO=92;RPL=0;RPP=5.18177;RPPR=202.786;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14734A>G|p.Ser4912Gly|14734/21291|14734/21291|4912/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3414:1:9:0,-27.0958,-306.526 +NC_045512.2 15024 . CGCAT AGCAG 1.07585E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=125.777;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=3417;RO=92;RPL=0;RPP=5.18177;RPPR=52.9542;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=complex;ANN=AGCAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14760_14764delCGCATinsAGCAG|p.PheAlaTyr4920LeuAlaAsp|14760/21291|14760/21291|4920/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3417:1:17:0,-26.2958,-306.004 +NC_045512.2 15036 . A G,T 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=2,1;CIGAR=1X,1X;DP=93;DPB=93;DPRA=0,0;EPP=7.35324,5.18177;EPPR=114.576;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=109.023;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,10;QR=3323;RO=90;RPL=1,0;RPP=3.0103,5.18177;RPPR=14.688;RPR=1,1;RUN=1,1;SAF=1,0;SAP=3.0103,5.18177;SAR=1,1;SRF=45;SRP=3.0103;SRR=45;TYPE=snp,snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14772A>T|p.Lys4924Asn|14772/21291|14772/21291|4924/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:90,2,1:90:3323:2,1:76,10:0,-20.6732,-292.121,-26.587,-292.127,-298.059 +NC_045512.2 15063 . A G 1.68157E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=7.35324;EPPR=192.024;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.943;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3428;RO=91;RPL=1;RPP=3.0103;RPPR=3.03416;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=45;SRP=3.03416;SRR=46;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14799A>G|p.Gln4933Gln|14799/21291|14799/21291|4933/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:91,2:91:3428:2:76:0,-20.781,-301.469 +NC_045512.2 15073 . A G 1.68157E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=7.35324;EPPR=192.024;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.943;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3420;RO=91;RPL=1;RPP=3.0103;RPPR=3.03416;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=45;SRP=3.03416;SRR=46;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14809A>G|p.Lys4937Glu|14809/21291|14809/21291|4937/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:91,2:91:3420:2:76:0,-20.781,-300.751 +NC_045512.2 15104 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.389;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3451;RO=92;RPL=1;RPP=5.18177;RPPR=202.786;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14840G>T|p.Arg4947Leu|14840/21291|14840/21291|4947/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3451:1:10:0,-26.9958,-309.753 +NC_045512.2 15107 . C A 1.38669E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.158;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3429;RO=92;RPL=1;RPP=5.18177;RPPR=202.786;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14843C>A|p.Thr4948Asn|14843/21291|14843/21291|4948/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3429:1:11:0,-26.8958,-307.676 +NC_045512.2 15118 . G T 2.66395E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=3.10471;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=124.165;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=3383;RO=92;RPL=1;RPP=5.18177;RPPR=202.786;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=45;SRP=3.10471;SRR=47;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14854G>T|p.Val4952Phe|14854/21291|14854/21291|4952/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3383:1:24:0,-25.5959,-302.24 +NC_045512.2 15130 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=92;DPB=92;DPRA=0;EPP=5.18177;EPPR=3.22506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=124.862;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=3358;RO=91;RPL=1;RPP=5.18177;RPPR=200.614;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=44;SRP=3.22506;SRR=47;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14866A>C|p.Ser4956Arg|14866/21291|14866/21291|4956/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:92:91,1:91:3358:1:15:0,-26.1948,-300.892 +NC_045512.2 15138 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=3.62026;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.262;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3246;RO=89;RPL=1;RPP=5.18177;RPPR=196.271;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=3.62026;SRR=47;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14874G>T|p.Met4958Ile|14874/21291|14874/21291|4958/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3246:1:10:0,-26.0927,-291.315 +NC_045512.2 15163 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=3.62026;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=122.572;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=3182;RO=89;RPL=1;RPP=5.18177;RPPR=196.271;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=3.62026;SRR=47;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14899T>A|p.Leu4967Ile|14899/21291|14899/21291|4967/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3182:1:13:0,-25.7927,-285.262 +NC_045512.2 15164 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=3.62026;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.032;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3238;RO=89;RPL=1;RPP=5.18177;RPPR=196.271;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=3.62026;SRR=47;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14900T>G|p.Leu4967*|14900/21291|14900/21291|4967/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3238:1:11:0,-25.9927,-290.506 +NC_045512.2 15246 . A T 1.92265E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=135.739;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=128.744;PAIRED=1;PAIREDR=0.927835;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3543;RO=97;RPL=1;RPP=5.18177;RPPR=61.2371;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=64;SRP=24.5235;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14982A>T|p.Leu4994Phe|14982/21291|14982/21291|4994/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3543:1:34:0,-26.102,-315.649 +NC_045512.2 15247 . A C 1.68781E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=75;DPB=75;DPRA=0;EPP=5.18177;EPPR=82.3571;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=102.42;PAIRED=1;PAIREDR=0.905405;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2753;RO=74;RPL=0;RPP=5.18177;RPPR=163.699;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=63;SRP=82.3571;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14983A>C|p.Lys4995Gln|14983/21291|14983/21291|4995/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:75:74,1:74:2753:1:11:0,-21.4773,-246.876 +NC_045512.2 15257 . A T 1.5369E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=83;DPB=83;DPRA=0;EPP=5.18177;EPPR=59.0449;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=114.33;PAIRED=1;PAIREDR=0.914634;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3037;RO=82;RPL=0;RPP=5.18177;RPPR=181.071;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=64;SRP=59.0449;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14993A>T|p.Tyr4998Phe|14993/21291|14993/21291|4998/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:83:82,1:82:3037:1:7:0,-24.2855,-272.818 +NC_045512.2 15259 . A G,T 2.93823E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=2,1;CIGAR=1X,1X;DP=93;DPB=93;DPRA=0,0;EPP=3.0103,5.18177;EPPR=34.2795;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=120.632;PAIRED=1,1;PAIREDR=0.922222;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=22,11;QR=3285;RO=90;RPL=0,0;RPP=7.35324,5.18177;RPPR=198.443;RPR=2,1;RUN=1,1;SAF=1,0;SAP=3.0103,5.18177;SAR=1,1;SRF=63;SRP=34.2795;SRR=27;TYPE=snp,snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14995A>G|p.Ser4999Gly|14995/21291|14995/21291|4999/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:90,2,1:90:3285:2,1:22,11:0,-25.7148,-293.737,-26.4037,-293.653,-294.724 +NC_045512.2 15270 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=127;DPB=127;DPRA=0;EPP=3.73412;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=165.23;PAIRED=0.333333;PAIREDR=0.895161;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=4314;RO=124;RPL=0;RPP=9.52472;RPPR=272.273;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=63;SRP=3.08035;SRR=61;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15006A>C|p.Glu5002Asp|15006/21291|15006/21291|5002/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:127:124,3:124:4314:3:25:0,-35.8975,-386.049 +NC_045512.2 15279 . C T 3718.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=128;CIGAR=1X;DP=129;DPB=129;DPRA=0;EPP=3.07816;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=180.665;PAIRED=0.890625;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4586;QR=0;RO=0;RPL=0;RPP=280.959;RPPR=0;RPR=128;RUN=1;SAF=63;SAP=3.07816;SAR=65;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15015C>T|p.His5005His|15015/21291|15015/21291|5005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:129:0,128:0:0:128:4586:-412.73,-38.5318,0 +NC_045512.2 15285 . G T 2.09744E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=130;DPB=130;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=172.218;PAIRED=1;PAIREDR=0.875;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=4480;RO=128;RPL=0;RPP=7.35324;RPPR=280.959;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=64;SRP=3.0103;SRR=64;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15021G>T|p.Met5007Ile|15021/21291|15021/21291|5007/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:130:128,2:128:4480:2:29:0,-36.3789,-400.544 +NC_045512.2 15341 . C T 2.30236E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=131;DPB=131;DPRA=0;EPP=7.35324;EPPR=266.028;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=161.934;PAIRED=1;PAIREDR=0.868217;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4724;RO=129;RPL=1;RPP=3.0103;RPPR=3.83512;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=63;SRP=3.1618;SRR=66;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15077C>T|p.Ala5026Val|15077/21291|15077/21291|5026/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:131:129,2:129:4724:2:76:0,-32.2201,-418.034 +NC_045512.2 15364 . C T 2.30236E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=131;DPB=131;DPRA=0;EPP=7.35324;EPPR=257.679;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=161.934;PAIRED=1;PAIREDR=0.868217;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4780;RO=129;RPL=1;RPP=3.0103;RPPR=3.43113;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=63;SRP=3.1618;SRR=66;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15100C>T|p.His5034Tyr|15100/21291|15100/21291|5034/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:131:129,2:129:4780:2:76:0,-32.2201,-423.066 +NC_045512.2 15422 . A C 2.88698E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=129;DPB=129;DPRA=0;EPP=3.0103;EPPR=3.16418;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=168.586;PAIRED=1;PAIREDR=0.88189;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=4648;RO=127;RPL=2;RPP=7.35324;RPPR=270.17;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=61;SRP=3.43776;SRR=66;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15158A>C|p.Gln5053Pro|15158/21291|15158/21291|5053/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:129:127,2:127:4648:2:33:0,-35.698,-415.285 +NC_045512.2 15442 . A G 1.2778E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=128;DPB=128;DPRA=0;EPP=3.0103;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=157.821;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4631;RO=126;RPL=2;RPP=7.35324;RPPR=276.616;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=60;SRP=3.63072;SRR=66;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15178A>G|p.Met5060Val|15178/21291|15178/21291|5060/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:128:126,2:126:4631:2:76:0,-31.317,-409.678 +NC_045512.2 15488 . G T 1.66952E-14 . AB=0.105263;ABP=157.299;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=14.5915;EPPR=160.463;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.6941;PAIRED=0.916667;PAIREDR=0.892157;PAO=0;PQA=0;PQR=0;PRO=0;QA=454;QR=3762;RO=102;RPL=12;RPP=29.068;RPPR=19.7008;RPR=0;RUN=1;SAF=2;SAP=14.5915;SAR=10;SRF=45;SRP=6.07591;SRR=57;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15224G>T|p.Gly5075Val|15224/21291|15224/21291|5075/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:114:102,12:102:3762:12:454:-6.89216,0,-304.41 +NC_045512.2 15577 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=23.9805;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=96.9297;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2626;RO=70;RPL=0;RPP=5.18177;RPPR=155.013;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=48;SRP=23.9805;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15313A>C|p.Asn5105His|15313/21291|15313/21291|5105/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2626:1:11:0,-20.2731,-235.457 +NC_045512.2 15610 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=3.21602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.746;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3384;RO=95;RPL=0;RPP=5.18177;RPPR=209.3;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.21602;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15346C>A|p.Gln5116Lys|15346/21291|15346/21291|5116/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3384:1:9:0,-27.9989,-303.821 +NC_045512.2 15613 . C T 8.19702E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=3.37991;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.91;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3452;RO=94;RPL=0;RPP=5.18177;RPPR=207.129;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.37991;SRR=45;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15349C>T|p.His5117Tyr|15349/21291|15349/21291|5117/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3452:1:11:0,-27.4979,-309.743 +NC_045512.2 15626 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=5.18177;EPPR=3.59403;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=128.994;PAIRED=1;PAIREDR=0.978495;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3443;RO=93;RPL=0;RPP=5.18177;RPPR=204.957;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.59403;SRR=44;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15362A>G|p.Glu5121Gly|15362/21291|15362/21291|5121/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:94:93,1:93:3443:1:9:0,-27.3968,-309.137 +NC_045512.2 15631 . C T 6.55441E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=93.7321;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.516;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3443;RO=95;RPL=0;RPP=5.18177;RPPR=22.2335;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.21602;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15367C>T|p.Leu5123Phe|15367/21291|15367/21291|5123/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3443:1:10:0,-27.8989,-309.029 +NC_045512.2 15634 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=7.35324;EPPR=109.828;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=114.038;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3458;RO=94;RPL=1;RPP=3.0103;RPPR=16.3163;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=48;SRP=3.1027;SRR=46;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15370T>C|p.Tyr5124His|15370/21291|15370/21291|5124/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:94,2:94:3458:2:76:0,-21.6841,-304.168 +NC_045512.2 15642 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=5.18177;EPPR=127.438;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=126.922;PAIRED=1;PAIREDR=0.978495;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=3510;RO=93;RPL=0;RPP=5.18177;RPPR=8.26386;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.59403;SRR=44;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15378T>G|p.Asn5126Lys|15378/21291|15378/21291|5126/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:94:93,1:93:3510:1:18:0,-26.4968,-314.258 +NC_045512.2 15644 . G C 1.16776E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=145.665;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.285;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3541;RO=95;RPL=1;RPP=5.18177;RPPR=8.15326;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=48;SRP=3.03316;SRR=47;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15380G>C|p.Arg5127Thr|15380/21291|15380/21291|5127/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3541:1:11:0,-27.7989,-317.744 +NC_045512.2 15726 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=66.8327;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=121.406;PAIRED=1;PAIREDR=0.978261;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=3438;RO=92;RPL=0;RPP=5.18177;RPPR=40.775;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=46;SRP=3.0103;SRR=46;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15462T>C|p.Ala5154Ala|15462/21291|15462/21291|5154/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3438:1:36:0,-24.3975,-305.984 +NC_045512.2 15756 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.831;PAIRED=0;PAIREDR=0.989362;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3391;RO=94;RPL=1;RPP=5.18177;RPPR=207.129;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=3.0103;SRR=47;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15492T>C|p.Ser5164Ser|15492/21291|15492/21291|5164/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3391:1:7:0,-27.8979,-304.655 +NC_045512.2 15761 . G T 6.56972E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=3.03316;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.516;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3349;RO=95;RPL=1;RPP=5.18177;RPPR=209.3;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=48;SRP=3.03316;SRR=47;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15497G>T|p.Gly5166Val|15497/21291|15497/21291|5166/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3349:1:10:0,-27.8989,-300.572 +NC_045512.2 15767 . TG GT 1.16929E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=3.03316;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.285;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3445;RO=95;RPL=1;RPP=5.18177;RPPR=209.3;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=48;SRP=3.03316;SRR=47;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15503_15504delTGinsGT|p.Val5168Gly|15503/21291|15503/21291|5168/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3445:1:11:0,-27.7989,-309.127 +NC_045512.2 15771 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.831;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3408;RO=94;RPL=1;RPP=5.18177;RPPR=207.129;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=3.0103;SRR=47;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15507T>C|p.Ala5169Ala|15507/21291|15507/21291|5169/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3408:1:7:0,-27.8979,-306.194 +NC_045512.2 15780 . G A 2.24811E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=38.8746;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9589;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2263;RO=62;RPL=1;RPP=5.18177;RPPR=137.642;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=38.8746;SRR=47;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15516G>A|p.Lys5172Lys|15516/21291|15516/21291|5172/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2263:1:11:0,-17.8649,-202.803 +NC_045512.2 15790 . T C 5.42434E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=49.6779;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.1101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2110;RO=57;RPL=1;RPP=5.18177;RPPR=126.784;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=49.6779;SRR=46;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15526T>C|p.Ser5176Pro|15526/21291|15526/21291|5176/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2110:1:11:0,-16.3597,-189.043 +NC_045512.2 15797 . T C 1.4887E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=71.8828;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.4131;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=1968;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=71.8828;SRR=47;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15533T>C|p.Leu5178Pro|15533/21291|15533/21291|5178/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:1968:1:25:0,-13.7558,-174.872 +NC_045512.2 15823 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2373;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1745;RO=46;RPL=1;RPP=5.18177;RPPR=102.898;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=102.898;SRR=46;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15559T>C|p.Ser5187Pro|15559/21291|15559/21291|5187/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:47:46,1:46:1745:1:32:0,-10.9491,-154.118 +NC_045512.2 15891 . A C 2.26014E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=139.341;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=125.546;PAIRED=1;PAIREDR=0.793478;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=3428;RO=92;RPL=0;RPP=5.18177;RPPR=202.786;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=84;SRP=139.341;SRR=8;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15627A>C|p.Thr5209Thr|15627/21291|15627/21291|5209/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3428:1:18:0,-26.1958,-306.881 +NC_045512.2 15918 . T C 4.66498E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=156;DPB=156;DPRA=0;EPP=3.0103;EPPR=5.04077;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=196.241;PAIRED=1;PAIREDR=0.805195;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5656;RO=154;RPL=0;RPP=7.35324;RPPR=337.417;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=83;SRP=5.04077;SRR=71;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15654T>C|p.Tyr5218Tyr|15654/21291|15654/21291|5218/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:156:154,2:154:5656:2:76:0,-39.7459,-501.867 +NC_045512.2 15934 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=159;DPB=159;DPRA=0;EPP=3.0103;EPPR=4.13061;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=200.796;PAIRED=1;PAIREDR=0.802548;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=5691;RO=157;RPL=0;RPP=7.35324;RPPR=343.931;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=83;SRP=4.13061;SRR=74;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15670C>G|p.Pro5224Ala|15670/21291|15670/21291|5224/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:159:157,2:157:5691:2:74:0,-40.8379,-505.206 +NC_045512.2 15965 . G T 3.91758E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=155;DPB=155;DPRA=0;EPP=7.35324;EPPR=4.72761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=205.21;PAIRED=0.5;PAIREDR=0.816993;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=5729;RO=153;RPL=0;RPP=7.35324;RPPR=318.101;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=84;SRP=6.20364;SRR=69;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15701G>T|p.Cys5234Phe|15701/21291|15701/21291|5234/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:155:153,2:153:5729:2:35:0,-43.3348,-512.307 +NC_045512.2 15983 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=161;DPB=161;DPRA=0;EPP=7.35324;EPPR=157.432;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=202.364;PAIRED=1;PAIREDR=0.797468;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5904;RO=158;RPL=1;RPP=3.0103;RPPR=32.0915;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=82;SRP=3.50507;SRR=76;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15719T>A|p.Val5240Glu|15719/21291|15719/21291|5240/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:161:158,2:158:5904:2:76:0,-41.2232,-524.212 +NC_045512.2 16109 . A C 1.57612E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=157;DPB=157;DPRA=0;EPP=7.35324;EPPR=3.02431;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=211.894;PAIRED=0.5;PAIREDR=0.825806;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=5604;RO=155;RPL=2;RPP=7.35324;RPPR=339.589;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=78;SRP=3.02431;SRR=77;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15845A>C|p.Lys5282Thr|15845/21291|15845/21291|5282/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:157:155,2:155:5604:2:17:0,-45.6467,-502.796 +NC_045512.2 16112 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=157;DPB=157;DPRA=0;EPP=3.0103;EPPR=3.13639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=200.889;PAIRED=1;PAIREDR=0.819355;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=5586;RO=155;RPL=2;RPP=7.35324;RPPR=339.589;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=79;SRP=3.13639;SRR=76;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15848T>C|p.Leu5283Pro|15848/21291|15848/21291|5283/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:157:155,2:155:5586:2:61:0,-41.4694,-496.999 +NC_045512.2 16119 . T A 9.07071E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=172;DPB=172;DPRA=0;EPP=7.35324;EPPR=7.14887;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=232.724;PAIRED=1;PAIREDR=0.835294;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=6148;RO=170;RPL=2;RPP=7.35324;RPPR=239.266;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=93;SRP=6.28028;SRR=77;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15855T>A|p.Asp5285Glu|15855/21291|15855/21291|5285/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:172:170,2:170:6148:2:16:0,-50.2572,-551.828 +NC_045512.2 16124 . T G 1.09692E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=1X;DP=170;DPB=170;DPRA=0;EPP=13.8677;EPPR=15.6575;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=201.978;PAIRED=0.8;PAIREDR=0.848485;PAO=0;PQA=0;PQR=0;PRO=0;QA=125;QR=6023;RO=165;RPL=5;RPP=13.8677;RPPR=202.115;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=88;SRP=4.60271;SRR=77;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15860T>G|p.Leu5287*|15860/21291|15860/21291|5287/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:170:165,5:165:6023:5:125:0,-39.6768,-530.595 +NC_045512.2 16176 . T C 3512.61 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=115;CIGAR=1X;DP=115;DPB=115;DPRA=0;EPP=235.66;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=162.643;PAIRED=0.878261;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4327;QR=0;RO=0;RPL=76;RPP=28.8603;RPPR=0;RPR=39;RUN=1;SAF=39;SAP=28.8603;SAR=76;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15912T>C|p.Thr5304Thr|15912/21291|15912/21291|5304/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:115:0,115:0:0:115:4327:-389.537,-34.6185,0 +NC_045512.2 16218 . A C,G 1.45857E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,2;CIGAR=1X,1X;DP=82;DPB=82;DPRA=0,0;EPP=5.18177,3.0103;EPPR=3.25768;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=93.9842;PAIRED=1,1;PAIREDR=0.974684;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=7,76;QR=2833;RO=79;RPL=0,0;RPP=5.18177,7.35324;RPPR=174.557;RPR=1,2;RUN=1,1;SAF=0,1;SAP=5.18177,3.0103;SAR=1,1;SRF=41;SRP=3.25768;SRR=38;TYPE=snp,snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15954A>C|p.Thr5318Thr|15954/21291|15954/21291|5318/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:82:79,1,2:79:2833:1,2:7,76:0,-23.5556,-254.264,-17.3419,-248.331,-248.054 +NC_045512.2 16233 . AC CA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=83;DPB=83;DPRA=0;EPP=5.18177;EPPR=3.11623;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=114.1;PAIRED=1;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2970;RO=82;RPL=0;RPP=5.18177;RPPR=181.071;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=42;SRP=3.11623;SRR=40;TYPE=complex;ANN=CA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15969_15970delACinsCA|p.LeuGln5323PheLys|15969/21291|15969/21291|5323/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:83:82,1:82:2970:1:8:0,-24.1855,-266.694 +NC_045512.2 16246 . G T 3.04368E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=116.849;PAIRED=1;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=3010;RO=84;RPL=0;RPP=5.18177;RPPR=185.414;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=42;SRP=3.0103;SRR=42;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15982G>T|p.Ala5328Ser|15982/21291|15982/21291|5328/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3010:1:8:0,-24.7876,-270.287 +NC_045512.2 16247 . C G 8.85976E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=115.928;PAIRED=1;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=3114;RO=84;RPL=0;RPP=5.18177;RPPR=185.414;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=42;SRP=3.0103;SRR=42;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15983C>G|p.Ala5328Gly|15983/21291|15983/21291|5328/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3114:1:12:0,-24.3876,-279.243 +NC_045512.2 16255 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=7.35324;EPPR=3.11623;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=111.733;PAIRED=1;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=3059;RO=82;RPL=0;RPP=7.35324;RPPR=181.071;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=42;SRP=3.11623;SRR=40;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15991C>T|p.Leu5331Phe|15991/21291|15991/21291|5331/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:84:82,2:82:3059:2:18:0,-23.5765,-273.79 +NC_045512.2 16259 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=3.0103;EPPR=3.03646;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.0334;PAIRED=1;PAIREDR=0.975904;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3066;RO=83;RPL=0;RPP=7.35324;RPPR=183.243;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=41;SRP=3.03646;SRR=42;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15995G>A|p.Cys5332Tyr|15995/21291|15995/21291|5332/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:83,2:83:3066:2:76:0,-18.3727,-268.908 +NC_045512.2 16260 . C A 3.07384E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=116.388;PAIRED=1;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3141;RO=84;RPL=0;RPP=5.18177;RPPR=185.414;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=42;SRP=3.0103;SRR=42;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15996C>A|p.Cys5332*|15996/21291|15996/21291|5332/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3141:1:10:0,-24.5876,-281.874 +NC_045512.2 16270 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=5.18177;EPPR=41.8669;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=111.322;PAIRED=1;PAIREDR=0.964706;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3102;RO=85;RPL=0;RPP=5.18177;RPPR=59.443;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=42;SRP=3.03585;SRR=43;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16006A>G|p.Thr5336Ala|16006/21291|16006/21291|5336/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:85,1:85:3102:1:38:0,-22.0913,-275.572 +NC_045512.2 16293 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=7.35324;EPPR=152.325;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.614;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=3142;RO=84;RPL=1;RPP=3.0103;RPPR=5.59539;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=41;SRP=3.1137;SRR=43;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16029C>T|p.Cys5343Cys|16029/21291|16029/21291|5343/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:84,2:84:3142:2:75:0,-18.7682,-275.838 +NC_045512.2 16302 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=5.18177;EPPR=146.711;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=112.009;PAIRED=1;PAIREDR=0.964706;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=3119;RO=85;RPL=1;RPP=5.18177;RPPR=5.07959;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=3.24022;SRR=44;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16038A>C|p.Arg5346Ser|16038/21291|16038/21291|5346/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:85,1:85:3119:1:35:0,-22.3899,-277.394 +NC_045512.2 16306 . T A 9.10108E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=5.18177;EPPR=146.711;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=112.239;PAIRED=0;PAIREDR=0.976471;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3160;RO=85;RPL=1;RPP=5.18177;RPPR=5.07959;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=3.24022;SRR=44;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16042T>A|p.Phe5348Ile|16042/21291|16042/21291|5348/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:85,1:85:3160:1:34:0,-22.4897,-281.179 +NC_045512.2 16315 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=7.35324;EPPR=144.57;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=100.396;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3145;RO=84;RPL=1;RPP=3.0103;RPPR=4.66476;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=41;SRP=3.1137;SRR=43;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16051T>C|p.Cys5351Arg|16051/21291|16051/21291|5351/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:84,2:84:3145:2:76:0,-18.6738,-276.016 +NC_045512.2 16348 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=3.0103;EPPR=115.617;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.049;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=3146;RO=84;RPL=2;RPP=7.35324;RPPR=9.62812;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=41;SRP=3.1137;SRR=43;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16084T>C|p.Ser5362Pro|16084/21291|16084/21291|5362/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:84,2:84:3146:2:73:0,-18.9575,-276.39 +NC_045512.2 16355 . A G 8.3929E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=5.18177;EPPR=98.0697;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=117.532;PAIRED=1;PAIREDR=0.964706;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3140;RO=85;RPL=0;RPP=5.18177;RPPR=16.5245;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=42;SRP=3.03585;SRR=43;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16091A>G|p.Lys5364Arg|16091/21291|16091/21291|5364/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:85,1:85:3140:1:11:0,-24.7886,-281.689 +NC_045512.2 16373 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=83;DPB=83;DPRA=0;EPP=5.18177;EPPR=3.11623;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=108.345;PAIRED=1;PAIREDR=0.963415;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=2934;RO=82;RPL=1;RPP=5.18177;RPPR=164.123;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=38;SRP=3.96363;SRR=44;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16109A>C|p.Asn5370Thr|16109/21291|16109/21291|5370/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:83:82,1:82:2934:1:33:0,-21.6864,-260.952 +NC_045512.2 16376 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=115.237;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=3001;RO=84;RPL=1;RPP=5.18177;RPPR=176.831;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=40;SRP=3.42391;SRR=44;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16112C>A|p.Pro5371Gln|16112/21291|16112/21291|5371/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3001:1:15:0,-24.0876,-268.779 +NC_045512.2 16384 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=116.388;PAIRED=0;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3116;RO=84;RPL=1;RPP=5.18177;RPPR=176.831;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=40;SRP=3.42391;SRR=44;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16120T>G|p.Cys5374Gly|16120/21291|16120/21291|5374/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3116:1:10:0,-24.5876,-279.627 +NC_045512.2 16409 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=7.35324;EPPR=3.96363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.326;PAIRED=1;PAIREDR=0.963415;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=2966;RO=82;RPL=2;RPP=7.35324;RPPR=181.071;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=38;SRP=3.96363;SRR=44;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16145C>A|p.Thr5382Lys|16145/21291|16145/21291|5382/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:84:82,2:82:2966:2:29:0,-22.5315,-264.381 +NC_045512.2 16415 . T G 5.12323E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=82;DPB=82;DPRA=0;EPP=9.52472;EPPR=5.23675;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=97.5596;PAIRED=1;PAIREDR=0.962025;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=2877;RO=79;RPL=3;RPP=9.52472;RPPR=174.557;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=35;SRP=5.23675;SRR=44;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16151T>G|p.Val5384Gly|16151/21291|16151/21291|5384/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:82:79,3:79:2877:3:66:0,-18.5252,-252.971 +NC_045512.2 16420 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=27.3308;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=96.9297;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2503;RO=70;RPL=1;RPP=5.18177;RPPR=107.365;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=10.9517;SRR=43;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16156C>T|p.Gln5386*|16156/21291|16156/21291|5386/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2503:1:11:0,-20.2731,-224.397 +NC_045512.2 16437 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=72.8076;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8095;NS=1;NUMALT=1;ODDS=83.4157;PAIRED=1;PAIREDR=0.968254;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=2359;RO=63;RPL=1;RPP=5.18177;RPPR=66.7413;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=24.5527;SRR=44;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16173T>G|p.Gly5391Gly|16173/21291|16173/21291|5391/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2359:1:28:0,-16.4662,-209.729 +NC_045512.2 16485 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=105.14;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8065;NS=1;NUMALT=1;ODDS=85.9589;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2324;RO=62;RPL=1;RPP=5.18177;RPPR=34.5317;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=19.9618;SRR=42;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16221G>A|p.Leu5407Leu|16221/21291|16221/21291|5407/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2324:1:11:0,-17.8649,-208.258 +NC_045512.2 16495 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=105.24;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=70.9015;PAIRED=1;PAIREDR=0.980392;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1910;RO=51;RPL=0;RPP=5.18177;RPPR=21.7871;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=18.3809;SRR=35;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16231G>C|p.Gly5411Arg|16231/21291|16231/21291|5411/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1910:1:11:0,-14.5536,-171.024 +NC_045512.2 16536 . C T 5.40649E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5714;NS=1;NUMALT=1;ODDS=25.1098;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1036;RO=28;RPL=0;RPP=7.35324;RPPR=63.8115;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.32051;SRR=13;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16272C>T|p.Ser5424Ser|16272/21291|16272/21291|5424/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:28,2:28:1036:2:75:0,-1.91056,-86.3969 +NC_045512.2 16553 . T G 6.83316E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=44.1217;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1138;RO=31;RPL=0;RPP=5.18177;RPPR=70.3259;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16289T>G|p.Phe5430Cys|16289/21291|16289/21291|5430/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1138:1:9:0,-8.73296,-101.784 +NC_045512.2 16565 . C T 3.86495E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=3.0103;EPPR=3.29983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6;NS=1;NUMALT=1;ODDS=27.7511;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1111;RO=30;RPL=0;RPP=7.35324;RPPR=59.7581;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16301C>T|p.Ala5434Val|16301/21291|16301/21291|5434/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1111:2:75:0,-2.51262,-93.139 +NC_045512.2 16610 . C A 4.1589E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=43.8914;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1164;RO=31;RPL=0;RPP=5.18177;RPPR=3.08035;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16346C>A|p.Thr5449Asn|16346/21291|16346/21291|5449/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1164:1:10:0,-8.63296,-104.029 +NC_045512.2 16693 . A C 2.23154E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=37.4505;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1129;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16429A>C|p.Thr5477Pro|16429/21291|16429/21291|5477/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1129:1:38:0,-5.83569,-98.0837 +NC_045512.2 16706 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=44.5822;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1094;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16442T>G|p.Val5481Gly|16442/21291|16442/21291|5481/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1094:1:7:0,-8.93296,-98.0505 +NC_045512.2 16708 . C A 4.1589E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=43.8914;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1111;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16444C>A|p.Leu5482Met|16444/21291|16444/21291|5482/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1111:1:10:0,-8.63296,-99.2727 +NC_045512.2 16735 . T A 1.32852E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=15.5221;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.0939;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=786;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=15.5221;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16471T>A|p.Trp5491Arg|16471/21291|16471/21291|5491/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:786:1:7:0,-5.92266,-70.3665 +NC_045512.2 16908 . T G 3.03321E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=18.5208;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.7796;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=522;RO=14;RPL=0;RPP=5.18177;RPPR=3.63072;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=3.63072;SRR=6;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16644T>G|p.Tyr5548*|16644/21291|16644/21291|5548/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:522:1:20:0,-2.51549,-45.3221 +NC_045512.2 17027 . G T 8.08935E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.4039;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=547;RO=15;RPL=1;RPP=5.18177;RPPR=35.5824;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16763G>T|p.Ser5588Ile|16763/21291|16763/21291|5588/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:547:1:10:0,-3.81648,-48.5652 +NC_045512.2 17030 . A C 1.01839E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1736;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=519;RO=15;RPL=1;RPP=5.18177;RPPR=35.5824;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=3.15506;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16766A>C|p.Asn5589Thr|16766/21291|16766/21291|5589/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:15,1:15:519:1:11:0,-3.71648,-45.9273 +NC_045512.2 17067 . T A 1.22354E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=9.52472;EPPR=118.668;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=65.6291;PAIRED=1;PAIREDR=0.786885;PAO=0;PQA=0;PQR=0;PRO=0;QA=102;QR=2110;RO=61;RPL=0;RPP=9.52472;RPPR=62.8504;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=53;SRP=75.0961;SRR=8;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16803T>A|p.Tyr5601*|16803/21291|16803/21291|5601/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:61,3:61:2110:3:102:0,-9.74897,-180.656 +NC_045512.2 17072 . CAC CC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=71;DPB=70.6667;DPRA=0;EPP=5.18177;EPPR=155.013;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.719;PAIRED=1;PAIREDR=0.814286;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2623;RO=70;RPL=0;RPP=5.18177;RPPR=93.4676;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=62;SRP=93.4676;SRR=8;TYPE=del;ANN=CC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16809delA|p.Leu5604fs|16809/21291|16809/21291|5603/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2623:1:38:0,-17.5759,-232.489 +NC_045512.2 17080 . G T 1.18434E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=172.385;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=103.309;PAIRED=1;PAIREDR=0.833333;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=2897;RO=78;RPL=0;RPP=5.18177;RPPR=110.025;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=70;SRP=110.025;SRR=8;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16816G>T|p.Gly5606*|16816/21291|16816/21291|5606/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2897:1:31:0,-20.6819,-257.826 +NC_045512.2 17089 . G T 3.52585E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=82;DPB=82;DPRA=0;EPP=5.18177;EPPR=178.9;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=106.053;PAIRED=1;PAIREDR=0.839506;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=3046;RO=81;RPL=0;RPP=5.18177;RPPR=116.275;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=73;SRP=116.275;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16825G>T|p.Gly5609Cys|16825/21291|16825/21291|5609/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:82:81,1:81:3046:1:37:0,-20.9866,-270.629 +NC_045512.2 17096 . G T 1.80211E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=160.287;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.947;PAIRED=1;PAIREDR=0.845238;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3151;RO=84;RPL=0;RPP=5.18177;RPPR=122.545;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=73;SRP=102.381;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16832G>T|p.Gly5611Val|16832/21291|16832/21291|5611/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3151:1:38:0,-21.7903,-279.972 +NC_045512.2 17113 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=5.18177;EPPR=133.03;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=116.821;PAIRED=1;PAIREDR=0.853933;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3321;RO=89;RPL=1;RPP=5.18177;RPPR=140.252;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=74;SRP=87.9417;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16849A>G|p.Ile5617Val|16849/21291|16849/21291|5617/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:89,1:89:3321:1:38:0,-23.2954,-295.264 +NC_045512.2 17134 . C T 5.54488E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=5.18177;EPPR=114.176;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.24;PAIRED=1;PAIREDR=0.860215;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3493;RO=93;RPL=0;RPP=5.18177;RPPR=148.732;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=74;SRP=73.6415;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16870C>T|p.Pro5624Ser|16870/21291|16870/21291|5624/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:94:93,1:93:3493:1:34:0,-24.8979,-311.131 +NC_045512.2 17171 . C T 1.98916E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=161;DPB=161;DPRA=0;EPP=3.0103;EPPR=3.02396;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=203.109;PAIRED=1;PAIREDR=0.842767;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5720;RO=159;RPL=0;RPP=7.35324;RPPR=348.274;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=80;SRP=3.02396;SRR=79;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16907C>T|p.Ala5636Val|16907/21291|16907/21291|5636/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:161:159,2:159:5720:2:76:0,-41.251,-507.629 +NC_045512.2 17180 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=160;DPB=160;DPRA=0;EPP=7.35324;EPPR=3.2302;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=213.172;PAIRED=0.5;PAIREDR=0.848101;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=5795;RO=158;RPL=0;RPP=7.35324;RPPR=346.103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=81;SRP=3.2302;SRR=77;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16916A>T|p.Asp5639Val|16916/21291|16916/21291|5639/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:160:158,2:158:5795:2:30:0,-45.3149,-518.726 +NC_045512.2 17185 . C T 4.50825E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=161;DPB=161;DPRA=0;EPP=3.0103;EPPR=3.06527;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=202.378;PAIRED=1;PAIREDR=0.848101;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5794;RO=158;RPL=0;RPP=7.35324;RPPR=346.103;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=80;SRP=3.06527;SRR=78;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16921C>T|p.Leu5641Leu|16921/21291|16921/21291|5641/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:161:158,2:158:5794:2:75:0,-41.2294,-514.457 +NC_045512.2 17195 . A T 1.95879E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=161;DPB=161;DPRA=0;EPP=3.0103;EPPR=3.02396;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=203.109;PAIRED=1;PAIREDR=0.842767;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5867;RO=159;RPL=0;RPP=7.35324;RPPR=339.643;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=80;SRP=3.02396;SRR=79;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16931A>T|p.Lys5644Met|16931/21291|16931/21291|5644/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:161:159,2:159:5867:2:76:0,-41.251,-520.839 +NC_045512.2 17208 . T G 4.36358E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=157;DPB=157;DPRA=0;EPP=11.6962;EPPR=3.70574;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=185.996;PAIRED=0.5;PAIREDR=0.862745;PAO=0;PQA=0;PQR=0;PRO=0;QA=123;QR=5731;RO=153;RPL=0;RPP=11.6962;RPPR=326.616;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=81;SRP=4.1599;SRR=72;TYPE=snp;ANN=G|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16944T>G|p.Tyr5648*|16944/21291|16944/21291|5648/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:157:153,4:153:5731:4:123:0,-35.8918,-504.441 +NC_045512.2 17211 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=162;DPB=162;DPRA=0;EPP=3.0103;EPPR=3.06459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=204.483;PAIRED=1;PAIREDR=0.8375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5965;RO=160;RPL=0;RPP=7.35324;RPPR=341.814;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=80;SRP=3.0103;SRR=80;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16947G>T|p.Leu5649Phe|16947/21291|16947/21291|5649/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:162:160,2:160:5965:2:76:0,-41.552,-529.651 +NC_045512.2 17278 . G T 1.78403E-14 . AB=0.111111;ABP=215.815;AC=1;AF=0.5;AN=2;AO=18;CIGAR=1X;DP=162;DPB=162;DPRA=0;EPP=20.3821;EPPR=220.158;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.5327;PAIRED=0.888889;PAIREDR=0.833333;PAO=0;PQA=0;PQR=0;PRO=0;QA=683;QR=5422;RO=144;RPL=10;RPP=3.49285;RPPR=3.0103;RPR=8;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=72;SRP=3.0103;SRR=72;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17014G>T|p.Val5672Leu|17014/21291|17014/21291|5672/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:162:144,18:144:5422:18:683:-13.0386,0,-439.253 +NC_045512.2 17331 . G T 6.02707E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=160;DPB=160;DPRA=0;EPP=3.0103;EPPR=3.06527;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=201.735;PAIRED=1;PAIREDR=0.841772;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5801;RO=158;RPL=2;RPP=7.35324;RPPR=346.103;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=78;SRP=3.06527;SRR=80;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17067G>T|p.Glu5689Asp|17067/21291|17067/21291|5689/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:160:158,2:158:5801:2:76:0,-40.95,-514.905 +NC_045512.2 17363 . T A 9.16135E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=156;DPB=156;DPRA=0;EPP=9.52472;EPPR=4.1599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=203.999;PAIRED=0.333333;PAIREDR=0.849673;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=5662;RO=153;RPL=3;RPP=9.52472;RPPR=335.246;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=72;SRP=4.1599;SRR=81;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17099T>A|p.Ile5700Asn|17099/21291|17099/21291|5700/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:156:153,3:153:5662:3:39:0,-43.3207,-505.983 +NC_045512.2 17365 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=158;DPB=158;DPRA=0;EPP=3.0103;EPPR=3.23302;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=200.732;PAIRED=1;PAIREDR=0.839744;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=5723;RO=156;RPL=2;RPP=7.35324;RPPR=341.76;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=76;SRP=3.23302;SRR=80;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17101T>C|p.Ser5701Pro|17101/21291|17101/21291|5701/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:158:156,2:156:5723:2:68:0,-41.1053,-508.646 +NC_045512.2 17484 . A T 1.59415E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=3.0103;EPPR=3.14508;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8069;NS=1;NUMALT=1;ODDS=183.883;PAIRED=1;PAIREDR=0.97931;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5327;RO=145;RPL=0;RPP=7.35324;RPPR=317.874;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.14508;SRR=74;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17220A>T|p.Thr5740Thr|17220/21291|17220/21291|5740/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:147:145,2:145:5327:2:76:0,-37.0366,-472.245 +NC_045512.2 17500 . T C 1.59415E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=3.0103;EPPR=3.14508;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8069;NS=1;NUMALT=1;ODDS=183.883;PAIRED=1;PAIREDR=0.97931;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5302;RO=145;RPL=0;RPP=7.35324;RPPR=317.874;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.14508;SRR=74;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17236T>C|p.Phe5746Leu|17236/21291|17236/21291|5746/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:147:145,2:145:5302:2:76:0,-37.0366,-469.985 +NC_045512.2 17523 . G T 1.59415E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=3.0103;EPPR=3.38469;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8069;NS=1;NUMALT=1;ODDS=183.883;PAIRED=1;PAIREDR=0.97931;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5464;RO=145;RPL=0;RPP=7.35324;RPPR=309.248;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=71;SRP=3.14508;SRR=74;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17259G>T|p.Met5753Ile|17259/21291|17259/21291|5753/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:147:145,2:145:5464:2:76:0,-37.0366,-484.528 +NC_045512.2 17661 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=146;DPB=146;DPRA=0;EPP=3.0103;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8889;NS=1;NUMALT=1;ODDS=182.728;PAIRED=1;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5377;RO=144;RPL=2;RPP=7.35324;RPPR=315.702;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=70;SRP=3.25157;SRR=74;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17397T>A|p.Phe5799Leu|17397/21291|17397/21291|5799/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:146:144,2:144:5377:2:75:0,-36.83,-476.824 +NC_045512.2 17679 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=182;DPB=182;DPRA=0;EPP=7.35324;EPPR=33.1696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9111;NS=1;NUMALT=1;ODDS=244.068;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=6425;RO=180;RPL=2;RPP=7.35324;RPPR=123.648;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=105;SRP=13.8677;SRR=75;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17415G>C|p.Thr5805Thr|17415/21291|17415/21291|5805/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:182:180,2:180:6425:2:27:0,-52.2225,-575.707 +NC_045512.2 17681 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=171;DPB=171;DPRA=0;EPP=3.0103;EPPR=50.8212;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9053;NS=1;NUMALT=1;ODDS=218.814;PAIRED=1;PAIREDR=0.964497;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=6211;RO=169;RPL=2;RPP=7.35324;RPPR=95.844;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=96;SRP=9.80739;SRR=73;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17417A>G|p.His5806Arg|17417/21291|17417/21291|5806/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:171:169,2:169:6211:2:67:0,-45.114,-552.597 +NC_045512.2 17807 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=121;DPB=121;DPRA=0;EPP=3.0103;EPPR=3.02855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=148.23;PAIRED=1;PAIREDR=0.94958;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4364;RO=119;RPL=0;RPP=7.35324;RPPR=261.416;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=60;SRP=3.02855;SRR=59;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17543A>G|p.Lys5848Arg|17543/21291|17543/21291|5848/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:121:119,2:119:4364:2:76:0,-29.2098,-385.653 +NC_045512.2 17809 . A T 2.33852E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=118;DPB=118;DPRA=0;EPP=3.0103;EPPR=3.30981;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=144.339;PAIRED=1;PAIREDR=0.948276;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=4331;RO=116;RPL=0;RPP=7.35324;RPPR=254.901;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=60;SRP=3.30981;SRR=56;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17545A>T|p.Ile5849Phe|17545/21291|17545/21291|5849/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:118:116,2:116:4331:2:75:0,-28.4012,-382.783 +NC_045512.2 17813 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=122;DPB=122;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=149.6;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4429;RO=120;RPL=0;RPP=7.35324;RPPR=263.587;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=60;SRP=3.0103;SRR=60;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17549T>G|p.Leu5850Trp|17549/21291|17549/21291|5850/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:122:120,2:120:4429:2:76:0,-29.5108,-391.499 +NC_045512.2 17842 . TCAC TC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M2D1M;DP=122;DPB=121;DPRA=0;EPP=7.35324;EPPR=204.191;GTI=0;LEN=2;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=148.675;PAIRED=1;PAIREDR=0.94958;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4473;RO=119;RPL=1;RPP=3.0103;RPPR=3.46649;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=60;SRP=3.02855;SRR=59;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17581_17582delCA|p.Gln5861fs|17581/21291|17581/21291|5861/7096||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:122:119,2:119:4473:2:76:0,-29.4031,-395.549 +NC_045512.2 17964 . G T 1.45857E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=119;DPB=119;DPRA=0;EPP=3.0103;EPPR=3.1896;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.5179;PAIRED=1;PAIREDR=0.944954;PAO=0;PQA=0;PQR=0;PRO=0;QA=373;QR=3977;RO=109;RPL=10;RPP=24.725;RPPR=239.701;RPR=0;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=53;SRP=3.1896;SRR=56;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17700G>T|p.Met5900Ile|17700/21291|17700/21291|5900/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:119:109,10:109:3977:10:373:0,-1.90096,-324.147 +NC_045512.2 18045 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=7.35324;EPPR=131.69;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=145.484;PAIRED=1;PAIREDR=0.953704;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=4069;RO=108;RPL=0;RPP=7.35324;RPPR=8.15749;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=48;SRP=5.9056;SRR=60;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17781A>C|p.Glu5927Asp|17781/21291|17781/21291|5927/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:110:108,2:108:4069:2:26:0,-30.6433,-363.866 +NC_045512.2 18052 . A C 4.74677E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=134;DPB=134;DPRA=0;EPP=7.35324;EPPR=40.9124;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=175.734;PAIRED=1;PAIREDR=0.94697;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=4910;RO=132;RPL=0;RPP=7.35324;RPPR=44.1367;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=49;SRP=22.0271;SRR=83;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17788A>C|p.Thr5930Pro|17788/21291|17788/21291|5930/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:134:132,2:132:4910:2:38:0,-36.7282,-438.375 +NC_045512.2 18054 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=134;DPB=134;DPRA=0;EPP=3.0103;EPPR=34.8586;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=166.265;PAIRED=1;PAIREDR=0.94697;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=4921;RO=132;RPL=0;RPP=7.35324;RPPR=47.4926;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=48;SRP=24.3302;SRR=84;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17790A>T|p.Thr5930Thr|17790/21291|17790/21291|5930/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:134:132,2:132:4921:2:75:0,-33.2177,-435.853 +NC_045512.2 18066 . A T 2.36865E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=100;DPB=100;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=119.719;PAIRED=1;PAIREDR=0.959184;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=3563;RO=98;RPL=0;RPP=7.35324;RPPR=215.815;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=49;SRP=3.0103;SRR=49;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17802A>T|p.Lys5934Asn|17802/21291|17802/21291|5934/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:100:98,2:98:3563:2:75:0,-22.9827,-313.709 +NC_045512.2 18094 . C T 6.2686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=3.58174;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=131.976;PAIRED=0;PAIREDR=0.957895;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=3541;RO=95;RPL=0;RPP=5.18177;RPPR=209.3;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=50;SRP=3.58174;SRR=45;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17830C>T|p.His5944Tyr|17830/21291|17830/21291|5944/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3541:1:8:0,-28.0989,-318.046 +NC_045512.2 18104 . A T 1.84432E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=3.03269;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=134.037;PAIRED=1;PAIREDR=0.958763;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3607;RO=97;RPL=0;RPP=5.18177;RPPR=205.047;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=50;SRP=3.21178;SRR=47;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17840A>T|p.Gln5947Leu|17840/21291|17840/21291|5947/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3607:1:11:0,-28.4009,-323.684 +NC_045512.2 18140 . A G 1.24765E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=101;DPB=101;DPRA=0;EPP=7.35324;EPPR=161.484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=132.668;PAIRED=1;PAIREDR=0.949495;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=3697;RO=99;RPL=1;RPP=3.0103;RPPR=7.94546;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=49;SRP=3.03223;SRR=50;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17876A>G|p.Lys5959Arg|17876/21291|17876/21291|5959/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:101:99,2:99:3697:2:22:0,-28.314,-330.791 +NC_045512.2 18211 . A C 1.39225E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=3.37221;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.129;PAIRED=1;PAIREDR=0.947917;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=3550;RO=96;RPL=1;RPP=5.18177;RPPR=202.876;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=45;SRP=3.8246;SRR=51;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17947A>C|p.Met5983Leu|17947/21291|17947/21291|5983/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3550:1:22:0,-27,-317.461 +NC_045512.2 18221 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=4.48875;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=123.699;PAIRED=1;PAIREDR=0.946809;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3535;RO=94;RPL=1;RPP=5.18177;RPPR=207.129;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=4.48875;SRR=51;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17957A>C|p.Lys5986Thr|17957/21291|17957/21291|5986/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3535:1:38:0,-24.8006,-314.511 +NC_045512.2 18242 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=3.36483;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=135.874;PAIRED=1;PAIREDR=0.959184;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3654;RO=98;RPL=1;RPP=5.18177;RPPR=215.815;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=3.36483;SRR=51;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17978G>T|p.Gly5993Val|17978/21291|17978/21291|5993/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3654:1:9:0,-28.902,-328.11 +NC_045512.2 18277 . A T 3.05896E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=103;DPB=103;DPRA=0;EPP=3.0103;EPPR=83.0108;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8812;NS=1;NUMALT=1;ODDS=123.818;PAIRED=1;PAIREDR=0.960396;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=3754;RO=101;RPL=2;RPP=7.35324;RPPR=35.7114;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=51;SRP=3.0318;SRR=50;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18013A>T|p.Ile6005Leu|18013/21291|18013/21291|6005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:103:101,2:101:3754:2:75:0,-23.8857,-330.869 +NC_045512.2 18288 . A T 7.65482E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=5.18177;EPPR=128.087;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8667;NS=1;NUMALT=1;ODDS=118.197;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3377;RO=90;RPL=0;RPP=5.18177;RPPR=24.725;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=6.48466;SRR=51;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18024A>T|p.Val6008Val|18024/21291|18024/21291|6008/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:90,1:90:3377:1:38:0,-23.5965,-300.268 +NC_045512.2 18335 . A C 8.28742E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=129.604;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=60;NS=1;NUMALT=1;ODDS=106.54;PAIRED=1;PAIREDR=0.961039;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2864;RO=77;RPL=0;RPP=5.18177;RPPR=5.29458;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=6.42261;SRR=44;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18071A>C|p.Glu6024Ala|18071/21291|18071/21291|6024/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2864:1:11:0,-22.3804,-256.86 +NC_045512.2 18354 . A C 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=37.8095;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6923;NS=1;NUMALT=1;ODDS=54.9889;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1432;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=37.8095;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18090A>C|p.Leu6030Phe|18090/21291|18090/21291|6030/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1432:1:9:0,-11.1412,-128.225 +NC_045512.2 18388 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=59.8095;NS=1;NUMALT=1;ODDS=87.3296;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2275;RO=63;RPL=0;RPP=5.18177;RPPR=131.265;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18124C>T|p.Leu6042Leu|18124/21291|18124/21291|6042/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2275:1:11:0,-18.166,-203.846 +NC_045512.2 18471 . TCA TA,TAA,ACA 0.0 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=2,2,1;CIGAR=1M1D1M,1M1X1M,1X2M;DP=64;DPB=63.3333;DPRA=0,0,0;EPP=3.0103,7.35324,5.18177;EPPR=106.394;GTI=0;LEN=1,1,1;MEANALT=3,3,3;MQM=60,60,48;MQMR=59.7966;NS=1;NUMALT=3;ODDS=67.2222;PAIRED=1,1,1;PAIREDR=1;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=76,76,11;QR=2194;RO=59;RPL=2,1,1;RPP=7.35324,3.0103,5.18177;RPPR=3.0471;RPR=0,1,0;RUN=1,1,1;SAF=1,1,1;SAP=3.0103,3.0103,5.18177;SAR=1,1,0;SRF=29;SRP=3.0471;SRR=30;TYPE=del,snp,snp;ANN=TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18208delC|p.Gln6070fs|18208/21291|18208/21291|6070/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:59,2,2,1:59:2194:2,2,1:76,76,11:0,-11.4918,-190.518,-11.4918,-184.887,-190.518,-17.1258,-190.436,-190.436,-196.368 +NC_045512.2 18492 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=114.996;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=87.79;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2286;RO=63;RPL=1;RPP=5.18177;RPPR=3.872;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18228A>C|p.Pro6076Pro|18228/21291|18228/21291|6076/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2286:1:9:0,-18.3659,-205.039 +NC_045512.2 18496 . A C,T 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=64;DPB=64;DPRA=0,0;EPP=5.18177,5.18177;EPPR=112.845;GTI=0;LEN=1,1;MEANALT=2,2;MQM=48,60;MQMR=59.8065;NS=1;NUMALT=2;ODDS=86.408;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=10,9;QR=2325;RO=62;RPL=1,1;RPP=5.18177,5.18177;RPPR=3.57068;RPR=0,0;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=30;SRP=3.15039;SRR=32;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18232A>C|p.Met6078Leu|18232/21291|18232/21291|6078/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:62,1,1:62:2325:1,1:10,9:0,-18.0599,-208.451,-18.1599,-208.247,-208.541 +NC_045512.2 18504 . A C 5.05542E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=79.1497;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=88.0202;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2308;RO=63;RPL=1;RPP=5.18177;RPPR=10.7656;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18240A>C|p.Lys6080Asn|18240/21291|18240/21291|6080/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2308:1:8:0,-18.4659,-207.112 +NC_045512.2 18511 . C A 5.05542E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=45.2334;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=88.0202;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2336;RO=63;RPL=1;RPP=5.18177;RPPR=28.1373;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18247C>A|p.Pro6083Thr|18247/21291|18247/21291|6083/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2336:1:8:0,-18.4659,-209.638 +NC_045512.2 18525 . G T 1.10902E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=61;DPB=61;DPRA=0;EPP=7.35324;EPPR=3.34154;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7966;NS=1;NUMALT=1;ODDS=78.7423;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=2146;RO=59;RPL=2;RPP=7.35324;RPPR=98.7391;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=27;SRP=3.93042;SRR=32;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18261G>T|p.Val6087Val|18261/21291|18261/21291|6087/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:61:59,2:59:2146:2:26:0,-15.8929,-190.879 +NC_045512.2 18545 . T A 1.11206E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=3.93042;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7966;NS=1;NUMALT=1;ODDS=79.3161;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=2143;RO=59;RPL=1;RPP=5.18177;RPPR=131.127;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=27;SRP=3.93042;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18281T>A|p.Met6094Lys|18281/21291|18281/21291|6094/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2143:1:22:0,-15.8619,-190.881 +NC_045512.2 18566 . A G 116.835 . AB=0.294118;ABP=15.5282;AC=1;AF=0.5;AN=2;AO=10;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=24.725;EPPR=39.2015;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5;NS=1;NUMALT=1;ODDS=26.9022;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=379;QR=905;RO=24;RPL=10;RPP=24.725;RPPR=55.1256;RPR=0;RUN=1;SAF=0;SAP=24.725;SAR=10;SRF=2;SRP=39.2015;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18302A>G|p.Asn6101Ser|18302/21291|18302/21291|6101/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:34:24,10:24:905:10:379:-24.2296,0,-71.5009 +NC_045512.2 18604 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=142.112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8235;NS=1;NUMALT=1;ODDS=87.975;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2553;RO=68;RPL=0;RPP=5.18177;RPPR=3.13803;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=3.52123;SRR=32;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18340G>T|p.Gly6114Cys|18340/21291|18340/21291|6114/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2553:1:38:0,-16.9738,-226.156 +NC_045512.2 18617 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=144.57;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8571;NS=1;NUMALT=1;ODDS=109.947;PAIRED=1;PAIREDR=0.97619;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3131;RO=84;RPL=0;RPP=5.18177;RPPR=15.5221;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=50;SRP=9.62812;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18353C>T|p.Thr6118Ile|18353/21291|18353/21291|6118/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3131:1:38:0,-21.7903,-278.144 +NC_045512.2 18648 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=3.0103;EPPR=155.967;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8537;NS=1;NUMALT=1;ODDS=98.7606;PAIRED=1;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=3078;RO=82;RPL=0;RPP=7.35324;RPPR=18.2636;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=50;SRP=11.5903;SRR=32;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18384T>C|p.Pro6128Pro|18384/21291|18384/21291|6128/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:84:82,2:82:3078:2:71:0,-18.5449,-270.441 +NC_045512.2 18675 . A C 8.52851E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=5.18177;EPPR=28.7251;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.166;PAIRED=0;PAIREDR=0.986842;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2787;RO=76;RPL=0;RPP=5.18177;RPPR=168.042;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=53;SRP=28.7251;SRR=23;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18411A>C|p.Arg6137Ser|18411/21291|18411/21291|6137/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:77:76,1:76:2787:1:11:0,-22.0793,-249.937 +NC_045512.2 18701 . C T 774.651 . AB=0.35514;ABP=22.513;AC=1;AF=0.5;AN=2;AO=38;CIGAR=1X;DP=107;DPB=107;DPRA=0;EPP=3.0103;EPPR=3.04177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=178.37;PAIRED=0.947368;PAIREDR=0.971014;PAO=0;PQA=0;PQR=0;PRO=0;QA=1412;QR=2519;RO=69;RPL=0;RPP=85.5263;RPPR=152.842;RPR=38;RUN=1;SAF=19;SAP=3.0103;SAR=19;SRF=35;SRP=3.04177;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18437C>T|p.Ser6146Leu|18437/21291|18437/21291|6146/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:107:69,38:69:2519:38:1412:-95.1572,0,-194.722 +NC_045512.2 18717 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=3.73412;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.176;PAIRED=0.666667;PAIREDR=0.971154;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=3843;RO=104;RPL=0;RPP=9.52472;RPPR=228.843;RPR=3;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=52;SRP=3.0103;SRR=52;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18453T>C|p.Cys6151Cys|18453/21291|18453/21291|6151/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:104,3:104:3843:3:68:0,-26.0348,-339.681 +NC_045512.2 18769 . G A 6.2686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=7.35324;EPPR=176.4;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.437;PAIRED=1;PAIREDR=0.962264;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3981;RO=106;RPL=1;RPP=3.0103;RPPR=3.09224;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=53;SRP=3.0103;SRR=53;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18505G>A|p.Val6169Ile|18505/21291|18505/21291|6169/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:106,2:106:3981:2:76:0,-25.2964,-351.204 +NC_045512.2 18798 . A G 1.54596E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=3.0103;EPPR=184.021;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=136.769;PAIRED=1;PAIREDR=0.962264;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=3983;RO=106;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=53;SRP=3.0103;SRR=53;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18534A>G|p.Leu6178Leu|18534/21291|18534/21291|6178/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:106,2:106:3983:2:47:0,-28.0464,-354.133 +NC_045512.2 18842 . A G 6.23846E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=3.0103;EPPR=3.09224;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.437;PAIRED=1;PAIREDR=0.962264;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3930;RO=106;RPL=2;RPP=7.35324;RPPR=224.582;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=53;SRP=3.0103;SRR=53;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18578A>G|p.His6193Arg|18578/21291|18578/21291|6193/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:106,2:106:3930:2:76:0,-25.2964,-346.618 +NC_045512.2 18883 . G A 2.27822E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=133.055;PAIRED=1;PAIREDR=0.962264;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=3924;RO=106;RPL=2;RPP=7.35324;RPPR=233.186;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=53;SRP=3.0103;SRR=53;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18619G>A|p.Val6207Ile|18619/21291|18619/21291|6207/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:108:106,2:106:3924:2:64:0,-26.4335,-347.227 +NC_045512.2 18896 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=106;DPB=106;DPRA=0;EPP=3.0103;EPPR=3.09382;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=130.977;PAIRED=1;PAIREDR=0.971154;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=3802;RO=104;RPL=2;RPP=7.35324;RPPR=228.843;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=51;SRP=3.09382;SRR=53;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18632T>C|p.Phe6211Ser|18632/21291|18632/21291|6211/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:106:104,2:104:3802:2:61:0,-26.1169,-336.541 +NC_045512.2 18902 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=67.6375;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=113.165;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=3136;RO=84;RPL=1;RPP=5.18177;RPPR=89.9726;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=30;SRP=17.9004;SRR=54;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18638A>T|p.Lys6213Met|18638/21291|18638/21291|6213/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3136:1:24:0,-23.1877,-280.025 +NC_045512.2 18936 . T C 6.9528E-13 . AB=0.113924;ABP=105.289;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=14.8328;EPPR=138.138;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.5181;PAIRED=1;PAIREDR=0.957143;PAO=0;PQA=0;PQR=0;PRO=0;QA=341;QR=2657;RO=70;RPL=9;RPP=22.5536;RPPR=13.0611;RPR=0;RUN=1;SAF=1;SAP=14.8328;SAR=8;SRF=28;SRP=9.09042;SRR=42;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18672T>C|p.Ile6224Ile|18672/21291|18672/21291|6224/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:79:70,9:70:2657:9:341:-7.26564,0,-215.557 +NC_045512.2 18945 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=147.33;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.703;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2944;RO=78;RPL=1;RPP=5.18177;RPPR=21.8297;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=29;SRP=14.1461;SRR=49;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18681A>G|p.Glu6227Glu|18681/21291|18681/21291|6227/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:78,1:78:2944:1:38:0,-19.9841,-261.354 +NC_045512.2 18970 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=139.813;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.6458;PAIRED=1;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=2363;RO=63;RPL=0;RPP=5.18177;RPPR=5.80219;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=27;SRP=5.80219;SRR=36;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18706A>G|p.Lys6236Glu|18706/21291|18706/21291|6236/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2363:1:27:0,-16.5661,-210.202 +NC_045512.2 18976 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=120.42;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.4976;PAIRED=1;PAIREDR=0.948276;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=2065;RO=58;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.16006;SRR=30;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18712C>T|p.Gln6238*|18712/21291|18712/21291|6238/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2065:1:37:0,-14.0629,-182.414 +NC_045512.2 18978 . A C,G 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,2;CIGAR=1X,1X;DP=56;DPB=56;DPRA=0,0;EPP=5.18177,3.0103;EPPR=118.098;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=59.135;PAIRED=1,1;PAIREDR=0.943396;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=34,76;QR=1899;RO=53;RPL=1,0;RPP=5.18177,7.35324;RPPR=3.37904;RPR=0,2;RUN=1,1;SAF=0,1;SAP=5.18177,3.0103;SAR=1,1;SRF=28;SRP=3.37904;SRR=25;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18714A>C|p.Gln6238His|18714/21291|18714/21291|6238/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:56:53,1,2:53:1899:1,2:34,76:0,-13.2099,-167.755,-9.69501,-161.822,-163.977 +NC_045512.2 19150 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=56;DPB=56;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.5146;PAIRED=1;PAIREDR=0.981481;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=2040;RO=54;RPL=2;RPP=7.35324;RPPR=111.745;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=26;SRP=3.17115;SRR=28;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18886G>T|p.Ala6296Ser|18886/21291|18886/21291|6296/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:56:54,2:54:2040:2:19:0,-15.0527,-182.046 +NC_045512.2 19164 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.9715;PAIRED=1;PAIREDR=0.982143;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2048;RO=56;RPL=1;RPP=5.18177;RPPR=124.613;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18900C>A|p.Asp6300Glu|18900/21291|18900/21291|6300/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2048:1:10:0,-16.1587,-183.566 +NC_045512.2 19166 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.2017;PAIRED=1;PAIREDR=0.982143;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2073;RO=56;RPL=1;RPP=5.18177;RPPR=124.613;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18902A>C|p.Lys6301Thr|18902/21291|18902/21291|6301/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:2073:1:9:0,-16.2587,-185.921 +NC_045512.2 19193 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.17115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.6951;PAIRED=1;PAIREDR=0.981481;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2004;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.17115;SRR=28;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18929G>T|p.Trp6310Leu|18929/21291|18929/21291|6310/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:55:54,1:54:2004:1:8:0,-15.7567,-179.813 +NC_045512.2 19239 . ATTTGA ATTGA 2.5736E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D4M;DP=33;DPB=32.8333;DPRA=0;EPP=5.18177;EPPR=48.8827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.806;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1199;RO=32;RPL=1;RPP=5.18177;RPPR=56.2114;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=35.8538;SRR=27;TYPE=del;ANN=ATTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18978delT|p.Phe6326fs|18978/21291|18978/21291|6326/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1199:1:38:0,-6.13672,-104.416 +NC_045512.2 19267 . A C 2.45626E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.9531;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1094;RO=29;RPL=1;RPP=5.18177;RPPR=49.8093;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=49.8093;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19003A>C|p.Asn6335His|19003/21291|19003/21291|6335/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:30:29,1:29:1094:1:11:0,-7.9309,-97.6685 +NC_045512.2 19342 . G T 0.00214027 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.61514;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=108;RO=3;RPL=0;RPP=5.18177;RPPR=9.52472;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19078G>T|p.Ala6360Ser|19078/21291|19078/21291|6360/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:108:1:8:0,-0.404122,-9.27426 +NC_045512.2 19450 . G T 0.00339158 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.15462;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=114;RO=3;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19186G>T|p.Ala6396Ser|19186/21291|19186/21291|6396/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:114:1:10:0,-0.204124,-9.63236 +NC_045512.2 19457 . G T 0.00339158 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.15462;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=114;RO=3;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19193G>T|p.Cys6398Phe|19193/21291|19193/21291|6398/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:114:1:10:0,-0.204124,-9.63236 +NC_045512.2 19493 . G A 0.0671625 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.16145;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=113;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19229G>A|p.Arg6410Lys|19229/21291|19229/21291|6410/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:3,1:3:113:1:23:-1.09579,0,-9.33542 +NC_045512.2 19495 . C A 0.0169709 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.54285;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=114;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19231C>A|p.His6411Asn|19231/21291|19231/21291|6411/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:3,1:3:114:1:17:-0.495859,0,-9.42823 +NC_045512.2 19685 . T G 0.0843803 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.93125;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=113;RO=3;RPL=0;RPP=5.18177;RPPR=9.52472;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19421T>G|p.Val6474Gly|19421/21291|19421/21291|6474/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:3,1:3:113:1:24:-1.19577,0,-9.33542 +NC_045512.2 19854 . C G 0.00537403 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.69411;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=114;RO=3;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19590C>G|p.Asp6530Glu|19590/21291|19590/21291|6530/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:114:1:12:0,-0.0041264,-9.43236 +NC_045512.2 19984 . T G 0.00214026 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.61514;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=113;RO=3;RPL=0;RPP=5.18177;RPPR=9.52472;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19720T>G|p.Phe6574Val|19720/21291|19720/21291|6574/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:113:1:8:0,-0.404122,-9.73954 +NC_045512.2 20011 . G T 0.0671625 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.16145;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=114;RO=3;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19747G>T|p.Val6583Leu|19747/21291|19747/21291|6583/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:3,1:3:114:1:23:-1.09579,0,-9.42823 +NC_045512.2 20044 . C T 29.8367 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.65031;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=75;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19780C>T|p.Leu6594Phe|19780/21291|19780/21291|6594/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:75:2:76:-6.01069,0,-5.91622 +NC_045512.2 20178 . C T 3.9275 . AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.384946;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=76;RO=2;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19914C>T|p.Val6638Val|19914/21291|19914/21291|6638/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3:2,1:2:76:1:38:-2.89418,0,-6.31172 +NC_045512.2 20284 . A T 0.408985 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.54246;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=38;RO=1;RPL=0;RPP=5.18177;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20020A>T|p.Ile6674Phe|20020/21291|20020/21291|6674/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2:1,1:1:38:1:21:-1.49789,0,-3.19521 +NC_045512.2 20823 . C T 3.52352E-4 . AB=0.117647;ABP=24.5973;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=7.35324;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.41939;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=566;RO=15;RPL=0;RPP=7.35324;RPPR=27.4756;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=14;SRP=27.4756;SRR=1;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20559C>T|p.Asn6853Asn|20559/21291|20559/21291|6853/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:17:15,2:15:566:2:76:-2.0973,0,-46.1642 +NC_045512.2 20889 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=3.28173;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1152;RO=32;RPL=0;RPP=5.18177;RPPR=64.083;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20625A>G|p.Gly6875Gly|20625/21291|20625/21291|6875/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1152:1:11:0,-8.83399,-102.88 +NC_045512.2 20908 . G T 3.85731E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3519;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1143;RO=31;RPL=0;RPP=5.18177;RPPR=70.3259;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20644G>T|p.Val6882Phe|20644/21291|20644/21291|6882/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1143:1:8:0,-8.83296,-102.371 +NC_045512.2 20921 . G T 6.83316E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.1217;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1122;RO=31;RPL=0;RPP=5.18177;RPPR=70.3259;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20657G>T|p.Trp6886Leu|20657/21291|20657/21291|6886/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1122:1:9:0,-8.73296,-100.376 +NC_045512.2 20923 . T C 2.00505E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.405;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1105;RO=30;RPL=0;RPP=7.35324;RPPR=68.1545;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20659T>C|p.Leu6887Leu|20659/21291|20659/21291|6887/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1105:2:72:0,-2.79659,-92.9157 +NC_045512.2 20934 . T C 4.14407E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.8914;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1142;RO=31;RPL=0;RPP=5.18177;RPPR=61.9202;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20670T>C|p.Gly6890Gly|20670/21291|20670/21291|6890/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1142:1:10:0,-8.63296,-102.078 +NC_045512.2 20960 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6612;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1158;RO=31;RPL=1;RPP=5.18177;RPPR=3.08035;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20696A>C|p.Asn6899Thr|20696/21291|20696/21291|6899/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1158:1:11:0,-8.53296,-103.422 +NC_045512.2 20982 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6612;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1141;RO=31;RPL=0;RPP=5.18177;RPPR=3.08035;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20718T>A|p.Asp6906Glu|20718/21291|20718/21291|6906/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1141:1:11:0,-8.53296,-101.888 +NC_045512.2 20996 . G A,C 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=32;DPB=32;DPRA=0,0;EPP=5.18177,5.18177;EPPR=68.1545;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=42.5599;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,11;QR=1134;RO=30;RPL=0,1;RPP=5.18177,5.18177;RPPR=3.0103;RPR=1,0;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=15;SRP=3.0103;SRR=15;TYPE=snp,snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20732G>A|p.Gly6911Asp|20732/21291|20732/21291|6911/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,1,1:30:1134:1,1:11,11:0,-8.34193,-101.258,-8.34193,-100.879,-101.258 +NC_045512.2 21003 . T A 3.86496E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=7.35324;EPPR=38.0434;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.7511;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1113;RO=30;RPL=1;RPP=3.0103;RPPR=7.64277;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20739T>A|p.Cys6913*|20739/21291|20739/21291|6913/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1113:2:75:0,-2.51262,-93.3529 +NC_045512.2 21038 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.6612;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1160;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20774T>A|p.Ile6925Asn|20774/21291|20774/21291|6925/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1160:1:11:0,-8.53296,-103.605 +NC_045512.2 21077 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=5.88603;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.0373;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1309;RO=37;RPL=1;RPP=5.18177;RPPR=39.6906;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=4.47751;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20813C>A|p.Thr6938Lys|20813/21291|20813/21291|6938/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:37,1:37:1309:1:10:0,-10.4391,-117.096 +NC_045512.2 21115 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1198;RO=32;RPL=1;RPP=5.18177;RPPR=3.28173;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.28173;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20851A>G|p.Ile6951Val|20851/21291|20851/21291|6951/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1198:1:11:0,-8.83399,-107.02 +NC_045512.2 21125 . T C 2.5736E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.806;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1180;RO=32;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20861T>C|p.Phe6954Ser|20861/21291|20861/21291|6954/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1180:1:38:0,-6.13672,-102.699 +NC_045512.2 21141 . A C 4.00351E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.4128;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1210;RO=32;RPL=1;RPP=5.18177;RPPR=3.28173;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.28173;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20877A>C|p.Leu6959Leu|20877/21291|20877/21291|6959/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1210:1:31:0,-6.83454,-106.102 +NC_045512.2 21159 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=7.35324;EPPR=24.1968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.2416;PAIRED=1;PAIREDR=0.918919;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1318;RO=37;RPL=0;RPP=7.35324;RPPR=16.2152;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=17;SRP=3.5385;SRR=20;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20895G>A|p.Val6965Val|20895/21291|20895/21291|6965/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:37,2:37:1318:2:21:0,-9.74518,-116.909 +NC_045512.2 21183 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1182;RO=32;RPL=0;RPP=5.18177;RPPR=72.4974;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20919T>G|p.Ser6973Ser|20919/21291|20919/21291|6973/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1182:1:11:0,-8.83399,-105.583 +NC_045512.2 21201 . T A,G 1.27653E-13 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=28;DPB=28;DPRA=0,0;EPP=5.18177,5.18177;EPPR=8.35546;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=31.4587;PAIRED=1,1;PAIREDR=0.923077;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=10,37;QR=941;RO=26;RPL=0,0;RPP=5.18177,5.18177;RPPR=59.4686;RPR=1,1;RUN=1,1;SAF=0,0;SAP=5.18177,5.18177;SAR=1,1;SRF=17;SRP=8.35546;SRR=9;TYPE=snp,snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20937T>A|p.Tyr6979*|20937/21291|20937/21291|6979/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:28:26,1,1:26:941:1,1:10,37:0,-7.3627,-83.861,-4.66487,-81.1347,-81.423 +NC_045512.2 21217 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=3.28173;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.4772;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1163;RO=32;RPL=0;RPP=5.18177;RPPR=72.4974;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.28173;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20953T>A|p.Phe6985Ile|20953/21291|20953/21291|6985/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1163:1:9:0,-9.03399,-104.064 +NC_045512.2 21253 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1200;RO=32;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20989G>T|p.Ala6997Ser|20989/21291|20989/21291|6997/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1200:1:11:0,-8.83399,-107.201 +NC_045512.2 21294 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1189;RO=32;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21030T>A|p.Leu7010Leu|21030/21291|21030/21291|7010/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1189:1:11:0,-8.83399,-106.209 +NC_045512.2 21334 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.0167;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1186;RO=32;RPL=1;RPP=5.18177;RPPR=72.4974;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21070G>T|p.Ala7024Ser|21070/21291|21070/21291|7024/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1186:1:11:0,-8.83399,-105.939 +NC_045512.2 21359 . CAAATC CAATC 2.0492E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D4M;DP=33;DPB=32.6667;DPRA=0;EPP=3.0103;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.4416;PAIRED=1;PAIREDR=0.903226;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=1122;RO=31;RPL=2;RPP=7.35324;RPPR=61.9202;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=del;ANN=CAATC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21098delA|p.Asn7033fs|21098/21291|21098/21291|7033/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:31,2:31:1122:2:55:0,-4.71008,-96.057 +NC_045512.2 21380 . C T 1.42464E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=10.0459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.2418;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=923;RO=25;RPL=1;RPP=5.18177;RPPR=48.9587;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=7.26639;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21116C>T|p.Ser7039Phe|21116/21291|21116/21291|7039/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:923:1:8:0,-7.02678,-82.5861 +NC_045512.2 21394 . G C 2.78623E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=20.4855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.4032;PAIRED=1;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=759;RO=21;RPL=1;RPP=5.18177;RPPR=40.3389;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=15.5221;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21130G>C|p.Asp7044His|21130/21291|21130/21291|7044/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:22:21,1:21:759:1:10:0,-5.62266,-67.6308 +NC_045512.2 21401 . G C 3.58908E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.5192;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=629;RO=17;RPL=1;RPP=5.18177;RPPR=31.7504;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=31.7504;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21137G>C|p.Ser7046Thr|21137/21291|21137/21291|7046/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:629:1:8:0,-4.61854,-56.1404 +NC_045512.2 21441 . T G 3.40547E-10 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.269;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=608;RO=16;RPL=1;RPP=5.18177;RPPR=29.6108;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=29.6108;SRR=15;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21177T>G|p.Ser7059Ser|21177/21291|21177/21291|7059/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:16,1:16:608:1:12:0,-3.91752,-53.8604 +NC_045512.2 21718 . G A 0.0426806 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.84493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=38;RO=1;RPL=1;RPP=5.18177;RPPR=5.18177;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.156G>A|p.Gln52Gln|156/3822|156/3822|52/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2:1,1:1:38:1:11:-0.497935,0,-3.19521 +NC_045512.2 21764 . ATACATGT AT 60.1178 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1M6D1M;DP=2;DPB=0.5;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=6;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=5.99146;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=AT|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.204_209delACATGT|p.His69_Val70del|204/3822|204/3822|68/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:76:-7.21481,-0.60206,0 +NC_045512.2 21961 . T G 0.408985 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.54246;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=38;RO=1;RPL=1;RPP=5.18177;RPPR=5.18177;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.399T>G|p.Phe133Leu|399/3822|399/3822|133/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2:1,1:1:38:1:21:-1.49789,0,-3.19521 +NC_045512.2 21990 . TTTATTAC TTTAC 116.417 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1M3D4M;DP=4;DPB=2.5;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=8.76405;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=0;RO=0;RPL=1;RPP=5.18177;RPPR=0;RPR=3;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=TTTAC|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.432_434delTTA|p.Tyr145del|432/3822|432/3822|144/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:4:0,4:0:0:4:152:-14.0499,-1.20412,0 +NC_045512.2 22050 . C G 0.0316612 . AB=0.166667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.91757;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=178;RO=5;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.488C>G|p.Ala163Gly|488/3822|488/3822|163/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:5,1:5:178:1:30:-1.19339,0,-14.5601 +NC_045512.2 22520 . G T 2.52656E-4 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.752;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=181;RO=5;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.958G>T|p.Val320Phe|958/3822|958/3822|320/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:6:5,1:5:181:1:9:0,-0.906183,-15.743 +NC_045512.2 22754 . G T 0.00339158 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.15462;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=113;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1192G>T|p.Asp398Tyr|1192/3822|1192/3822|398/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:113:1:10:0,-0.204124,-9.53955 +NC_045512.2 22938 . C T 0.00170016 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.84539;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=113;RO=3;RPL=0;RPP=5.18177;RPPR=9.52472;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1376C>T|p.Ser459Phe|1376/3822|1376/3822|459/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4:3,1:3:113:1:7:0,-0.504122,-9.83954 +NC_045512.2 23063 . A T 124.199 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=8.76405;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=0;RO=0;RPL=3;RPP=5.18177;RPPR=0;RPR=1;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:4:0,4:0:0:4:152:-14.0499,-1.20412,0 +NC_045512.2 23271 . C A 468.578 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=16;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=7.89611;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=25.3996;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=561;QR=0;RO=0;RPL=3;RPP=16.582;RPPR=0;RPR=13;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:16:0,16:0:0:16:561:-50.8092,-4.81648,0 +NC_045512.2 23314 . T A 0.0025889 . AB=0.125;ABP=22.5536;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=7.35324;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.42478;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=500;RO=14;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1752T>A|p.Ile584Ile|1752/3822|1752/3822|584/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:16:14,2:14:500:2:73:-2.11482,0,-40.5123 +NC_045512.2 23396 . T G 2.4077E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.708;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=506;RO=14;RPL=1;RPP=5.18177;RPPR=33.4109;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=3.63072;SRR=8;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1834T>G|p.Tyr612Asp|1834/3822|1834/3822|612/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:506:1:29:0,-1.61579,-42.9732 +NC_045512.2 23403 . A G 387.441 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=15;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=3.15506;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.0133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=493;QR=0;RO=0;RPL=15;RPP=35.5824;RPPR=0;RPR=0;RUN=1;SAF=7;SAP=3.15506;SAR=8;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:15:0,15:0:0:15:493:-44.6733,-4.51545,0 +NC_045512.2 23417 . G A 8.39286E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.7619;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=436;RO=12;RPL=1;RPP=5.18177;RPPR=29.068;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=5.9056;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1855G>A|p.Glu619Lys|1855/3822|1855/3822|619/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:436:1:13:0,-2.6134,-38.2785 +NC_045512.2 23420 . G A 2.10822E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.1434;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=415;RO=12;RPL=1;RPP=5.18177;RPPR=29.068;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=5.9056;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1858G>A|p.Val620Ile|1858/3822|1858/3822|620/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:415:1:7:0,-3.21339,-36.9731 +NC_045512.2 23421 . T A 5.29557E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.2224;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=398;RO=12;RPL=1;RPP=5.18177;RPPR=29.068;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=5.9056;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1859T>A|p.Val620Asp|1859/3822|1859/3822|620/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:13:12,1:12:398:1:11:0,-2.81339,-35.0303 +NC_045512.2 23592 . A G 3.06763 . AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58;NS=1;NUMALT=1;ODDS=0.0262314;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=226;RO=6;RPL=1;RPP=3.0103;RPPR=16.0391;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=3;SRP=3.0103;SRR=3;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2030A>G|p.Gln677Arg|2030/3822|2030/3822|677/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:226:2:63:-3.57453,0,-18.266 +NC_045512.2 23604 . C A 238.779 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=8;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=20.3821;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=58.5;MQMR=0;NS=1;NUMALT=1;ODDS=14.3092;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=301;QR=0;RO=0;RPL=4;RPP=3.0103;RPPR=0;RPR=4;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2042C>A|p.Pro681His|2042/3822|2042/3822|681/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:8:0,8:0:0:8:301:-27.4125,-2.40824,0 +NC_045512.2 23709 . C T 239.688 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=8;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=58.5;MQMR=0;NS=1;NUMALT=1;ODDS=14.3092;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=302;QR=0;RO=0;RPL=8;RPP=20.3821;RPPR=0;RPR=0;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2147C>T|p.Thr716Ile|2147/3822|2147/3822|716/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:8:0,8:0:0:8:302:-27.5033,-2.40824,0 +NC_045512.2 23791 . T G 0.0231838 . AB=0.142857;ABP=10.7656;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58;NS=1;NUMALT=1;ODDS=5.23019;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=213;RO=6;RPL=0;RPP=5.18177;RPPR=4.45795;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=4.45795;SRR=4;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2229T>G|p.Cys743Trp|2229/3822|2229/3822|743/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:6,1:6:213:1:34:-1.2917,0,-17.3711 +NC_045512.2 24004 . G T 2.60705E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.3258;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=331;RO=9;RPL=0;RPP=5.18177;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2442G>T|p.Lys814Asn|2442/3822|2442/3822|814/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:10:9,1:9:331:1:11:0,-1.9103,-29.0393 +NC_045512.2 24035 . A C 1.30655E-5 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.7141;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=327;RO=9;RPL=1;RPP=5.18177;RPPR=22.5536;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2473A>C|p.Lys825Gln|2473/3822|2473/3822|825/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:10:9,1:9:327:1:18:0,-1.21033,-27.9754 +NC_045512.2 24076 . T C 3.7344E-4 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.36126;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=268;RO=8;RPL=1;RPP=5.18177;RPPR=20.3821;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2514T>C|p.Gly838Gly|2514/3822|2514/3822|838/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:9:8,1:8:268:1:27:0,-0.00948704,-21.7426 +NC_045512.2 24077 . G T 4.70386E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.7357;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=285;RO=8;RPL=1;RPP=5.18177;RPPR=20.3821;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=4.09604;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2515G>T|p.Asp839Tyr|2515/3822|2515/3822|839/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:9:8,1:8:285:1:8:0,-1.90927,-25.192 +NC_045512.2 24134 . C A 0.0165884 . AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.5657;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=254;RO=7;RPL=0;RPP=5.18177;RPPR=5.80219;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=5.80219;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2572C>A|p.Leu858Ile|2572/3822|2572/3822|858/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:7,1:7:254:1:38:-1.38903,0,-20.7995 +NC_045512.2 24369 . A C 3.33701E-5 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7764;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=264;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2807A>C|p.Asp936Ala|2807/3822|2807/3822|936/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:8:7,1:7:264:1:11:0,-1.30824,-23.0207 +NC_045512.2 24417 . T A 5.12323E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=70.5741;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.8779;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1285;RO=35;RPL=1;RPP=5.18177;RPPR=48.239;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=55.1877;SRR=3;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2855T>A|p.Val952Asp|2855/3822|2855/3822|952/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1285:1:38:0,-7.03981,-112.143 +NC_045512.2 24494 . AATGA CATGT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=3.93042;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.0068;PAIRED=1;PAIREDR=0.983051;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=2126;RO=59;RPL=0;RPP=5.18177;RPPR=131.127;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.93042;SRR=27;TYPE=complex;ANN=CATGT|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2932_2936delAATGAinsCATGT|p.AsnAsp978HisVal|2932/3822|2932/3822|978/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:60:59,1:59:2126:1:19:0,-16.1618,-189.691 +NC_045512.2 24506 . T G 1843.05 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=62;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=3.15039;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=89.1691;PAIRED=0.983871;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2275;QR=0;RO=0;RPL=0;RPP=137.642;RPPR=0;RPR=62;RUN=1;SAF=32;SAP=3.15039;SAR=30;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:62:0,62:0:0:62:2275:-204.988,-18.6639,0 +NC_045512.2 24513 . T A 1.39679E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=84.8189;PAIRED=1;PAIREDR=0.983607;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2188;RO=61;RPL=0;RPP=5.18177;RPPR=135.47;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2951T>A|p.Leu984His|2951/3822|2951/3822|984/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2188:1:10:0,-17.6639,-196.155 +NC_045512.2 24517 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=3.15039;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.2681;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2284;RO=62;RPL=0;RPP=5.18177;RPPR=137.642;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.15039;SRR=30;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2955C>A|p.Asp985Glu|2955/3822|2955/3822|985/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2284:1:14:0,-17.5649,-204.397 +NC_045512.2 24535 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=61;DPB=61;DPRA=0;EPP=5.18177;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.2186;PAIRED=1;PAIREDR=0.983333;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2210;RO=60;RPL=0;RPP=5.18177;RPPR=133.299;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.15506;SRR=29;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2973G>T|p.Val991Val|2973/3822|2973/3822|991/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:61:60,1:60:2210:1:11:0,-17.2628,-198.042 +NC_045512.2 24543 . A C 7.06671E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=64.7922;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9589;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2257;RO=62;RPL=0;RPP=5.18177;RPPR=17.0198;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.0103;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2981A>C|p.Asp994Ala|2981/3822|2981/3822|994/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2257:1:11:0,-17.8649,-202.264 +NC_045512.2 24553 . C A 1.47517E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=90.5697;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.7356;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=2267;RO=62;RPL=0;RPP=5.18177;RPPR=6.51267;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.15039;SRR=30;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2991C>A|p.Ile997Ile|2991/3822|2991/3822|997/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2267:1:25:0,-16.465,-201.762 +NC_045512.2 24575 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=129.096;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9589;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2307;RO=62;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.15039;SRR=30;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3013C>A|p.Gln1005Lys|3013/3822|3013/3822|1005/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2307:1:11:0,-17.8649,-206.763 +NC_045512.2 24654 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.1891;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2287;RO=62;RPL=1;RPP=5.18177;RPPR=137.642;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.0103;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3092A>C|p.Glu1031Ala|3092/3822|3092/3822|1031/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2287:1:10:0,-17.9649,-205.064 +NC_045512.2 24682 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=63;DPB=63;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.196;PAIRED=1;PAIREDR=0.983871;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=2273;RO=62;RPL=1;RPP=5.18177;RPPR=137.642;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.0103;SRR=31;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3120T>G|p.Val1040Val|3120/3822|3120/3822|1040/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:63:62,1:62:2273:1:23:0,-16.665,-202.507 +NC_045512.2 24693 . G C 1.14064E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=26.3669;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.7195;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1476;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=26.3669;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3131G>C|p.Gly1044Ala|3131/3822|3131/3822|1044/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1476:1:22:0,-10.4433,-130.915 +NC_045512.2 24705 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.18177;EPPR=152.325;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=113.855;PAIRED=1;PAIREDR=0.904762;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=3134;RO=84;RPL=0;RPP=5.18177;RPPR=8.07707;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=53;SRP=15.5221;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3143A>C|p.His1048Pro|3143/3822|3143/3822|1048/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:84,1:84:3134:1:21:0,-23.4876,-280.149 +NC_045512.2 24706 . T C 9.10108E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=5.18177;EPPR=146.711;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=112.239;PAIRED=1;PAIREDR=0.905882;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3104;RO=85;RPL=0;RPP=5.18177;RPPR=8.75832;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=53;SRP=14.2764;SRR=32;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3144T>C|p.His1048His|3144/3822|3144/3822|1048/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:86:85,1:85:3104:1:34:0,-22.4897,-276.147 +NC_045512.2 24709 . TAT TAAT,GAT 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1I2M,1X2M;DP=90;DPB=90.3333;DPRA=0,0;EPP=5.18177,5.18177;EPPR=160.936;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=115.976;PAIRED=1,1;PAIREDR=0.909091;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,8;QR=3284;RO=88;RPL=0,1;RPP=5.18177,5.18177;RPPR=12.8806;RPR=1,0;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=56;SRP=17.2236;SRR=32;TYPE=ins,snp;ANN=TAAT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3148dupA|p.Met1050fs|3149/3822|3149/3822|1050/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:88,1,1:88:3284:1,1:38,8:0,-23.2243,-292.09,-26.2215,-291.975,-294.791 +NC_045512.2 24719 . C A,G 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=99;DPB=99;DPRA=0,0;EPP=5.18177,5.18177;EPPR=188.391;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=128.655;PAIRED=0,1;PAIREDR=0.927835;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=34,38;QR=3609;RO=97;RPL=0,0;RPP=5.18177,5.18177;RPPR=27.389;RPR=1,1;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=64;SRP=24.5235;SRR=33;TYPE=snp,snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3157C>A|p.Pro1053Thr|3157/3822|3157/3822|1053/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:97,1,1:97:3609:1,1:34,38:0,-26.4618,-321.548,-26.0635,-318.733,-321.189 +NC_045512.2 24776 . G A 1.4209E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=127;DPB=127;DPRA=0;EPP=7.35324;EPPR=55.5599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=165.263;PAIRED=1;PAIREDR=0.928;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=4604;RO=125;RPL=0;RPP=7.35324;RPPR=116.987;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=68;SRP=5.11229;SRR=57;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3214G>A|p.Glu1072Lys|3214/3822|3214/3822|1072/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:127:125,2:125:4604:2:42:0,-34.2409,-410.473 +NC_045512.2 24821 . G C 1.555E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=131;DPB=131;DPRA=0;EPP=3.0103;EPPR=4.37378;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=162.587;PAIRED=1;PAIREDR=0.914729;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=4697;RO=129;RPL=0;RPP=7.35324;RPPR=283.13;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=69;SRP=4.37378;SRR=60;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3259G>C|p.Ala1087Pro|3259/3822|3259/3822|1087/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:131:129,2:129:4697:2:73:0,-32.5038,-415.882 +NC_045512.2 24867 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=134;DPB=134;DPRA=0;EPP=7.35324;EPPR=216.802;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=166.047;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4922;RO=132;RPL=1;RPP=3.0103;RPPR=3.27351;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=69;SRP=3.60252;SRR=63;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3305G>T|p.Trp1102Leu|3305/3822|3305/3822|1102/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:134:132,2:132:4922:2:76:0,-33.1232,-435.838 +NC_045512.2 24914 . GACA CACT,CACA 4235.99 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=2,131;CIGAR=1X2M1X,1X3M;DP=134;DPB=134;DPRA=0,0;EPP=3.0103,140.277;EPPR=0;GTI=0;LEN=4,1;MEANALT=3,3;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=165.244;PAIRED=1,0.923664;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,4935;QR=0;RO=0;RPL=2,82;RPP=7.35324,21.0617;RPPR=0;RPR=0,49;RUN=1,1;SAF=1,68;SAP=3.0103,3.4247;SAR=1,63;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=CACA|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273|| GT:DP:AD:RO:QR:AO:QA:GL 2/2:134:0,2,131:0:0:2,131:76,4935:-443.905,-437.672,-437.07,-39.4349,-33.0688,0 +NC_045512.2 24958 . T C 4.6413E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=133;DPB=133;DPRA=0;EPP=3.0103;EPPR=3.4247;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=169.043;PAIRED=1;PAIREDR=0.916031;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=4778;RO=131;RPL=2;RPP=7.35324;RPPR=287.473;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=68;SRP=3.4247;SRR=63;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3396T>C|p.Ile1132Ile|3396/3822|3396/3822|1132/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:133:131,2:131:4778:2:56:0,-34.7187,-424.79 +NC_045512.2 25001 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=149;DPB=149;DPRA=0;EPP=7.35324;EPPR=136.327;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9184;NS=1;NUMALT=1;ODDS=199.815;PAIRED=1;PAIREDR=0.979592;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=5406;RO=147;RPL=2;RPP=7.35324;RPPR=10.8246;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=84;SRP=9.52472;SRR=63;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3439T>C|p.Ser1147Pro|3439/3822|3439/3822|1147/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:149:147,2:147:5406:2:22:0,-42.7635,-484.503 +NC_045512.2 25132 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=132;DPB=132;DPRA=0;EPP=7.35324;EPPR=94.4794;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8154;NS=1;NUMALT=1;ODDS=172.699;PAIRED=1;PAIREDR=0.992308;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=4766;RO=130;RPL=1;RPP=3.0103;RPPR=59.2013;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=64;SRP=3.07711;SRR=66;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3570C>T|p.Ala1190Ala|3570/3822|3570/3822|1190/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:132:130,2:130:4766:2:33:0,-36.601,-425.866 +NC_045512.2 25241 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=131;DPB=131;DPRA=0;EPP=3.0103;EPPR=3.1618;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.907;NS=1;NUMALT=1;ODDS=168.266;PAIRED=1;PAIREDR=0.992248;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=4794;RO=129;RPL=2;RPP=7.35324;RPPR=283.13;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=63;SRP=3.1618;SRR=66;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3679A>G|p.Ile1227Val|3679/3822|3679/3822|1227/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:131:129,2:129:4794:2:47:0,-34.9702,-427.048 +NC_045512.2 25304 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=11.6962;EPPR=206.232;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8899;NS=1;NUMALT=1;ODDS=120.159;PAIRED=1;PAIREDR=0.972477;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=4070;RO=109;RPL=0;RPP=11.6962;RPPR=8.76769;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=48;SRP=6.37708;SRR=61;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3742T>C|p.Cys1248Arg|3742/3822|3742/3822|1248/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:113:109,4:109:4070:4:152:0,-19.9665,-352.341 +NC_045512.2 25394 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=116;DPB=116;DPRA=0;EPP=3.0103;EPPR=3.02952;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=140.627;PAIRED=1;PAIREDR=0.929204;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=4096;RO=113;RPL=0;RPP=7.35324;RPPR=248.387;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=3.02952;SRR=57;TYPE=snp;ANN=C|start_lost|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.2T>C|p.Met1?|2/828|2/828|1/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:116:113,2:113:4096:2:75:0,-27.6697,-361.745 +NC_045512.2 25446 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=116;DPB=116;DPRA=0;EPP=7.35324;EPPR=150.518;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=148.153;PAIRED=1;PAIREDR=0.929825;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=4200;RO=114;RPL=1;RPP=3.0103;RPPR=17.9439;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=3.08649;SRR=58;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.54T>A|p.Gly18Gly|54/828|54/828|18/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:116:114,2:114:4200:2:45:0,-30.6446,-373.841 +NC_045512.2 25479 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=116;DPB=116;DPRA=0;EPP=3.0103;EPPR=171.318;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=141.384;PAIRED=1;PAIREDR=0.929825;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4197;RO=114;RPL=0;RPP=7.35324;RPPR=4.9151;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=3.08649;SRR=58;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.87T>C|p.Val29Val|87/828|87/828|29/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:116:114,2:114:4197:2:76:0,-27.7047,-370.636 +NC_045512.2 25515 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=116;DPB=116;DPRA=0;EPP=7.35324;EPPR=131.089;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=141.601;PAIRED=1;PAIREDR=0.929825;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=4213;RO=114;RPL=1;RPP=3.0103;RPPR=20.1535;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=3.08649;SRR=58;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.123C>A|p.Leu41Leu|123/828|123/828|41/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:116:114,2:114:4213:2:75:0,-27.7991,-372.175 +NC_045512.2 25549 . CTTGC CTGC 1.13914E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D3M;DP=112;DPB=111.6;DPRA=0;EPP=3.0103;EPPR=3.72096;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=137.217;PAIRED=1;PAIREDR=0.927273;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=4006;RO=110;RPL=2;RPP=7.35324;RPPR=241.872;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=52;SRP=3.72096;SRR=58;TYPE=del;ANN=CTGC|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.159delT|p.Ala54fs|159/828|159/828|53/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:112:110,2:110:4006:2:70:0,-27.0686,-354.037 +NC_045512.2 25586 . T C 2.95026E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=82;DPB=82;DPRA=0;EPP=7.35324;EPPR=42.2054;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=104.196;PAIRED=1;PAIREDR=0.925;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=2894;RO=80;RPL=2;RPP=7.35324;RPPR=176.728;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=21;SRP=42.2054;SRR=59;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.194T>C|p.Leu65Pro|194/828|194/828|65/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:82:80,2:80:2894:2:40:0,-20.8846,-256.863 +NC_045512.2 25611 . CT AC 2.38977E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=94.755;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=89.391;PAIRED=0;PAIREDR=0.921875;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2357;RO=64;RPL=1;RPP=5.18177;RPPR=125.156;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=81.1833;SRR=56;TYPE=complex;ANN=AC|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.219_220delCTinsAC|p.Ser74Pro|219/828|219/828|73/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2357:1:8:0,-18.767,-211.56 +NC_045512.2 25620 . T G 1.88948E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=5.18177;EPPR=105.258;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=96.4786;PAIRED=0;PAIREDR=0.927536;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2509;RO=69;RPL=1;RPP=5.18177;RPPR=98.2089;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=61.1995;SRR=56;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.228T>G|p.Gly76Gly|228/828|228/828|76/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:70:69,1:69:2509:1:7:0,-20.3721,-225.328 +NC_045512.2 25624 . C T 6.44894E-14 . AB=0.111111;ABP=97.59;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=20.3821;EPPR=87.8334;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.8431;PAIRED=1;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=303;QR=2285;RO=64;RPL=8;RPP=20.3821;RPPR=74.8046;RPR=0;RUN=1;SAF=0;SAP=20.3821;SAR=8;SRF=16;SRP=37.7539;SRR=48;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.232C>T|p.His78Tyr|232/828|232/828|78/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:72:64,8:64:2285:8:303:-5.95516,0,-184.205 +NC_045512.2 25630 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=109.474;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.9928;PAIRED=0;PAIREDR=0.929577;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2672;RO=71;RPL=1;RPP=5.18177;RPPR=88.9211;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=54.4222;SRR=56;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.238G>T|p.Val80Phe|238/828|238/828|80/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2672:1:8:0,-20.8742,-239.891 +NC_045512.2 25635 . C G 1.63338E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=102.378;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=93.4682;PAIRED=1;PAIREDR=0.915493;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=2625;RO=71;RPL=1;RPP=5.18177;RPPR=88.9211;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=49.5287;SRR=55;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.243C>G|p.Cys81Trp|243/828|243/828|81/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:71,1:71:2625:1:32:0,-18.4748,-233.261 +NC_045512.2 25638 . C T 1.67944E-12 . AB=0.125;ABP=90.9549;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=9.04217;EPPR=99.8304;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.6135;PAIRED=0.888889;PAIREDR=0.920635;PAO=0;PQA=0;PQR=0;PRO=0;QA=290;QR=2320;RO=63;RPL=9;RPP=22.5536;RPPR=72.8076;RPR=0;RUN=1;SAF=2;SAP=9.04217;SAR=7;SRF=14;SRP=45.2334;SRR=49;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.246C>T|p.Asn82Asn|246/828|246/828|82/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:72:63,9:63:2320:9:290:-4.73063,0,-187.353 +NC_045512.2 25643 . T G 1.64844E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.18177;EPPR=114.686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=97.3902;PAIRED=0;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2609;RO=70;RPL=1;RPP=5.18177;RPPR=86.8912;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=57.7314;SRR=56;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.251T>G|p.Leu84Arg|251/828|251/828|84/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:71:70,1:70:2609:1:9:0,-20.4731,-234.125 +NC_045512.2 25673 . T A 1.32597E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.9587;PAIRED=1;PAIREDR=0.878049;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1408;RO=41;RPL=1;RPP=5.18177;RPPR=31.0276;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=31.0276;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.281T>A|p.Leu94His|281/828|281/828|94/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1408:1:34:0,-9.24435,-123.615 +NC_045512.2 25687 . G A 9.38537E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.0449;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=299;RO=8;RPL=0;RPP=5.18177;RPPR=20.3821;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=20.3821;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.295G>A|p.Ala99Thr|295/828|295/828|99/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:9:8,1:8:299:1:11:0,-1.60927,-26.1658 +NC_045512.2 25698 . A C 1.9139E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=5.49198;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.2401;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=511;RO=14;RPL=0;RPP=5.18177;RPPR=33.4109;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=5.49198;SRR=5;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.306A>C|p.Glu102Asp|306/828|306/828|102/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:511:1:18:0,-2.71548,-44.5277 +NC_045512.2 25716 . T C 3.18906E-4 . AB=0.111111;ABP=26.6552;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.51913;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=555;RO=16;RPL=0;RPP=7.35324;RPPR=37.7539;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=3.0103;SRR=8;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.324T>C|p.Leu108Leu|324/828|324/828|108/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:18:16,2:16:555:2:75:-1.7018,0,-44.8486 +NC_045512.2 25718 . A T 3.58908E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.5192;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=601;RO=17;RPL=0;RPP=5.18177;RPPR=39.9253;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.13803;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.326A>T|p.Tyr109Phe|326/828|326/828|109/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:601:1:8:0,-4.61854,-53.6125 +NC_045512.2 25740 . G T 3.64818E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=7.35324;EPPR=4.31318;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.595;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=515;RO=15;RPL=0;RPP=7.35324;RPPR=35.5824;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=9;SRP=4.31318;SRR=6;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.348G>T|p.Gln116His|348/828|348/828|116/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:17:15,2:15:515:2:34:0,-1.88762,-43.4368 +NC_045512.2 25795 . T C 5.68903E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.0587;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=614;RO=17;RPL=0;RPP=5.18177;RPPR=3.13803;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.13803;SRR=8;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.403T>C|p.Ser135Pro|403/828|403/828|135/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:614:1:10:0,-4.41854,-54.5886 +NC_045512.2 25855 . G T 7.15995E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.8284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=591;RO=17;RPL=1;RPP=5.18177;RPPR=39.9253;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=3.13803;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.463G>T|p.Asp155Tyr|463/828|463/828|155/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:591:1:11:0,-4.31854,-52.4038 +NC_045512.2 25862 . G T 4.51976E-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.2889;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=614;RO=17;RPL=1;RPP=5.18177;RPPR=39.9253;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=3.13803;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.470G>T|p.Cys157Phe|470/828|470/828|157/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:614:1:9:0,-4.51854,-54.6854 +NC_045512.2 26010 . C T 1.73144 . AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.713666;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=114;RO=3;RPL=0;RPP=5.18177;RPPR=9.52472;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.618C>T|p.Tyr206Tyr|618/828|618/828|206/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:3,1:3:114:1:38:-2.59315,0,-9.42823 +NC_045512.2 26064 . T G 0.00527516 . AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.71269;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=262;RO=7;RPL=0;RPP=5.18177;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.672T>G|p.Gly224Gly|672/828|672/828|224/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:7,1:7:262:1:33:-0.890895,0,-21.5306 +NC_045512.2 26171 . T C 67.9422 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.6443;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=143;QR=152;RO=4;RPL=4;RPP=11.6962;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.779T>C|p.Met260Thr|779/828|779/828|260/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:4,4:4:152:4:143:-10.8114,0,-11.6417 +NC_045512.2 26187 . T C 0.00632413 . AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.53121;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=227;RO=6;RPL=2;RPP=7.35324;RPPR=16.0391;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=3;SRP=3.0103;SRR=3;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.795T>C|p.Asp265Asp|795/828|795/828|265/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:227:2:33:-0.726674,0,-18.3856 +NC_045512.2 26213 . CTTTGTA CTTGTA 3.56629E-8 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D5M;DP=18;DPB=17.8571;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.6177;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=643;RO=17;RPL=0;RPP=5.18177;RPPR=13.3567;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=13.3567;SRR=4;TYPE=del;ANN=CTTGTA|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.824delT|p.Leu275fs|824/828|824/828|275/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:18:17,1:17:643:1:38:0,-1.62127,-54.4104 +NC_045512.2 26271 . A C 1.82703E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=18.9659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.7863;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=857;RO=23;RPL=0;RPP=5.18177;RPPR=24.253;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=5.3706;SRR=9;TYPE=snp;ANN=C|synonymous_variant|LOW|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.27A>C|p.Thr9Thr|27/228|27/228|9/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:857:1:20:0,-5.22476,-75.4497 +NC_045512.2 26308 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.4772;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1196;RO=32;RPL=0;RPP=5.18177;RPPR=42.0968;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=4.09604;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.64G>T|p.Ala22Ser|64/228|64/228|22/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1196:1:9:0,-9.03399,-107.042 +NC_045512.2 26312 . T A 3.86496E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=3.0103;EPPR=3.29983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.7511;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1117;RO=30;RPL=0;RPP=7.35324;RPPR=44.7026;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=4.16842;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.68T>A|p.Phe23Tyr|68/228|68/228|23/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:30,2:30:1117:2:75:0,-2.51262,-93.7166 +NC_045512.2 26450 . G A 9.34239E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.831;PAIRED=1;PAIREDR=0.964286;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=968;RO=28;RPL=1;RPP=5.18177;RPPR=63.8115;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.32051;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.206G>A|p.Arg69Lys|206/228|206/228|69/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:29:28,1:28:968:1:10:0,-7.72987,-86.4104 +NC_045512.2 26451 . A C 2.55853E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.7881;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=907;RO=25;RPL=1;RPP=5.18177;RPPR=57.2971;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=5.18177;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.207A>C|p.Arg69Ser|207/228|207/228|69/75|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:26:25,1:25:907:1:23:0,-5.52687,-79.6421 +NC_045512.2 26493 . G A 2.2835E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=7.63648;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.5493;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=847;RO=23;RPL=1;RPP=5.18177;RPPR=52.9542;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=7.63648;SRR=15;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-30G>A|||||30| GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:23,1:23:847:1:8:0,-6.42472,-75.7496 +NC_045512.2 26602 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=30.668;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.3977;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1374;RO=38;RPL=0;RPP=5.18177;RPPR=85.5263;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=30.668;SRR=8;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.80T>A|p.Leu27Gln|80/669|80/669|27/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1374:1:10:0,-10.7402,-122.937 +NC_045512.2 26612 . A G,T 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=50;DPB=50;DPRA=0,0;EPP=5.18177,5.18177;EPPR=9.52472;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=67.0323;PAIRED=1,1;PAIREDR=0.979167;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=9,11;QR=1730;RO=48;RPL=0,0;RPP=5.18177,5.18177;RPPR=107.241;RPR=1,1;RUN=1,1;SAF=0,0;SAP=5.18177,5.18177;SAR=1,1;SRF=30;SRP=9.52472;SRR=18;TYPE=snp,snp;ANN=G|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.90A>G|p.Thr30Thr|90/669|90/669|30/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:50:48,1,1:48:1730:1,1:9,11:0,-13.9505,-155.05,-13.7505,-154.667,-154.869 +NC_045512.2 26669 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.35316;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=72.8994;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2147;RO=57;RPL=0;RPP=5.18177;RPPR=102.098;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.35316;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.147T>G|p.Ile49Met|147/669|147/669|49/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2147:1:38:0,-13.6625,-189.678 +NC_045512.2 26718 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=7.35324;EPPR=118.251;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.9433;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=2103;RO=57;RPL=2;RPP=7.35324;RPPR=3.0484;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=28;SRP=3.0484;SRR=29;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.196G>T|p.Val66Leu|196/669|196/669|66/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:57,2:57:2103:2:31:0,-14.8158,-186.571 +NC_045512.2 26720 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=7.35324;EPPR=118.251;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.7253;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2099;RO=57;RPL=1;RPP=3.0103;RPPR=3.35316;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=3.0484;SRR=28;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.198G>T|p.Val66Val|198/669|198/669|66/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:57,2:57:2099:2:76:0,-10.546,-181.94 +NC_045512.2 26731 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=7.35324;EPPR=118.251;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.7253;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2103;RO=57;RPL=1;RPP=3.0103;RPPR=3.35316;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=3.0484;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.209T>C|p.Val70Ala|209/669|209/669|70/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:57,2:57:2103:2:76:0,-10.546,-182.293 +NC_045512.2 26766 . A C 2.98362E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.35316;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.5706;PAIRED=1;PAIREDR=0.982456;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2118;RO=57;RPL=1;RPP=5.18177;RPPR=110.022;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=3.0484;SRR=29;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.244A>C|p.Ile82Leu|244/669|244/669|82/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2118:1:9:0,-16.5597,-189.96 +NC_045512.2 26785 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.3735;PAIRED=1;PAIREDR=0.982143;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2064;RO=56;RPL=2;RPP=7.35324;RPPR=124.613;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.263T>C|p.Val88Ala|263/669|263/669|88/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:56,2:56:2064:2:76:0,-10.2449,-178.791 +NC_045512.2 26810 . C A 3.737E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.7096;PAIRED=1;PAIREDR=0.982759;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2118;RO=58;RPL=1;RPP=5.18177;RPPR=128.956;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.0103;SRR=29;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.288C>A|p.Phe96Leu|288/669|288/669|96/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2118:1:10:0,-16.7608,-189.865 +NC_045512.2 26816 . TT GG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=56;DPB=56;DPRA=0;EPP=5.18177;EPPR=3.36563;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.3004;PAIRED=1;PAIREDR=0.981818;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=2023;RO=55;RPL=1;RPP=5.18177;RPPR=122.441;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=3.36563;SRR=29;TYPE=complex;ANN=GG|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.294_295delTTinsGG|p.Ser99Ala|294/669|294/669|98/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:56:55,1:55:2023:1:20:0,-14.8577,-180.323 +NC_045512.2 26827 . T C 1.15573E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=48.8827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.484;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1213;RO=32;RPL=1;RPP=5.18177;RPPR=72.4974;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=48.8827;SRR=29;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.305T>C|p.Leu102Pro|305/669|305/669|102/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:32,1:32:1213:1:22:0,-7.73406,-107.272 +NC_045512.2 26832 . G T 3.85731E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=54.0749;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3519;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1175;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=54.0749;SRR=29;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.310G>T|p.Ala104Ser|310/669|310/669|104/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:32:31,1:31:1175:1:8:0,-8.83296,-105.254 +NC_045512.2 26890 . C T 2.98944E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=138;DPB=138;DPRA=0;EPP=3.0103;EPPR=281.214;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=171.751;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=5127;RO=136;RPL=0;RPP=7.35324;RPPR=105.197;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=106;SRP=95.234;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.368C>T|p.Pro123Leu|368/669|368/669|123/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:138:136,2:136:5127:2:75:0,-34.4218,-454.365 +NC_045512.2 27142 . A C 5.89448E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=156;DPB=156;DPRA=0;EPP=3.0103;EPPR=149.712;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=197.984;PAIRED=1;PAIREDR=0.88961;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=5723;RO=154;RPL=2;RPP=7.35324;RPPR=263.813;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=35;SRP=102.503;SRR=119;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.620A>C|p.Asn207Thr|620/669|620/669|207/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:156:154,2:154:5723:2:68:0,-40.5033,-508.655 +NC_045512.2 27163 . G T 0.0 . AB=0.0928571;ABP=204.585;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=140;DPB=140;DPRA=0;EPP=31.2394;EPPR=253.345;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.3809;PAIRED=0.769231;PAIREDR=0.889764;PAO=0;PQA=0;PQR=0;PRO=0;QA=478;QR=4695;RO=127;RPL=13;RPP=31.2394;RPPR=132.427;RPR=0;RUN=1;SAF=0;SAP=31.2394;SAR=13;SRF=23;SRP=115.192;SRR=104;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.641G>T|p.Ser214Ile|641/669|641/669|214/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:140:127,13:127:4695:13:478:-1.21456,0,-380.49 +NC_045512.2 27214 . G T 8.9205E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=207.129;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=124.616;PAIRED=1;PAIREDR=0.819149;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3326;RO=94;RPL=1;RPP=5.18177;RPPR=65.4748;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=65.4748;SRR=73;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.13G>T|p.Val5Phe|13/186|13/186|5/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3326:1:34:0,-25.1989,-296.153 +NC_045512.2 27215 . T G 4.22129E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=7.35324;EPPR=183.243;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=102.163;PAIRED=1;PAIREDR=0.795181;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=2947;RO=83;RPL=2;RPP=7.35324;RPPR=46.9892;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=21;SRP=46.9892;SRR=62;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.14T>G|p.Val5Gly|14/186|14/186|5/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:85:83,2:83:2947:2:68:0,-19.1296,-258.998 +NC_045512.2 27217 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=64.7766;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.4475;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1345;RO=36;RPL=0;RPP=5.18177;RPPR=6.8707;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.16G>C|p.Asp6His|16/186|16/186|6/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1345:1:11:0,-10.0381,-120.241 +NC_045512.2 27224 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.908;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1296;RO=36;RPL=0;RPP=5.18177;RPPR=11.6962;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=5.18177;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.23A>G|p.Gln8Arg|23/186|23/186|8/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:36,1:36:1296:1:9:0,-10.2381,-116.036 +NC_045512.2 27237 . A C 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.51141;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.5284;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1432;RO=39;RPL=0;RPP=5.18177;RPPR=87.6977;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.51141;SRR=18;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.36A>C|p.Ala12Ala|36/186|36/186|12/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1432:1:11:0,-10.9412,-128.066 +NC_045512.2 27240 . G A 9.13121E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.89;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1487;RO=40;RPL=0;RPP=5.18177;RPPR=89.8692;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.39G>A|p.Glu13Glu|39/186|39/186|13/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1487:1:11:0,-11.2422,-133.016 +NC_045512.2 27279 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.1375;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1497;RO=40;RPL=0;RPP=5.18177;RPPR=89.8692;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.78T>G|p.Ile26Met|78/186|78/186|26/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1497:1:36:0,-8.74395,-131.417 +NC_045512.2 27285 . T G 6.93087E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.2591;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=1541;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.84T>G|p.Asn28Lys|84/186|84/186|28/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1541:1:24:0,-10.2434,-136.572 +NC_045512.2 27289 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.48696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.7127;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1526;RO=41;RPL=0;RPP=5.18177;RPPR=75.5163;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.88G>T|p.Asp30Tyr|88/186|88/186|30/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:41,1:41:1526:1:9:0,-11.7433,-136.724 +NC_045512.2 27366 . G T 8.01929E-10 . AB=0.0952381;ABP=62.7775;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=11.6962;EPPR=77.0689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.4126;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=151;QR=1439;RO=38;RPL=2;RPP=3.0103;RPPR=3.23888;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=19;SRP=3.0103;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.165G>T|p.Glu55Asp|165/186|165/186|55/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:42:38,4:38:1439:4:151:-1.31465,0,-117.154 +NC_045512.2 27386 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.6793;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1497;RO=40;RPL=1;RPP=5.18177;RPPR=81.4005;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.22745;SRR=21;TYPE=snp;ANN=C|stop_lost&splice_region_variant|HIGH|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.185A>C|p.Ter62Serext*?|185/186|185/186|62/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:41:40,1:40:1497:1:38:0,-8.54496,-131.216 +NC_045512.2 27390 . G T 2.79358E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.845;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1480;RO=40;RPL=2;RPP=7.35324;RPPR=89.8692;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4G>T|||||4| GT:DP:AD:RO:QR:AO:QA:GL 0/0:42:40,2:40:1480:2:76:0,-5.42845,-126.271 +NC_045512.2 27447 . T G 2.01176E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=53.2644;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.7412;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1969;RO=56;RPL=1;RPP=5.18177;RPPR=4.40625;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=10.6105;SRR=21;TYPE=snp;ANN=G|stop_gained|HIGH|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.54T>G|p.Tyr18*|54/366|54/366|18/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:57:56,1:56:1969:1:11:0,-16.0587,-176.371 +NC_045512.2 27460 . T G 2.83271E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=5.18177;EPPR=113.69;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=91.903;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2438;RO=66;RPL=1;RPP=5.18177;RPPR=11.433;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=45;SRP=21.9613;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.67T>G|p.Cys23Gly|67/366|67/366|23/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:67:66,1:66:2438:1:9:0,-19.269,-218.747 +NC_045512.2 27468 . A G 1.86862E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=5.18177;EPPR=135.604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0713;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2392;RO=65;RPL=1;RPP=5.18177;RPPR=20.6827;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=45;SRP=23.8898;SRR=20;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.75A>G|p.Arg25Arg|75/366|75/366|25/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:66:65,1:65:2392:1:11:0,-18.768,-214.402 +NC_045512.2 27472 . A T 2.51333E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=142.112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=87.975;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2541;RO=68;RPL=0;RPP=5.18177;RPPR=21.4039;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=24.5973;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.79A>T|p.Thr27Ser|79/366|79/366|27/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2541:1:38:0,-16.9738,-225.113 +NC_045512.2 27478 . G A 6.69002E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=150.67;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.8765;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2517;RO=68;RPL=1;RPP=5.18177;RPPR=24.5973;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=24.5973;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.85G>A|p.Val29Ile|85/366|85/366|29/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2517:1:8:0,-19.9711,-225.944 +NC_045512.2 27484 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=7.35324;EPPR=139.943;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.6589;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2493;RO=67;RPL=0;RPP=7.35324;RPPR=20.1552;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=46;SRP=23.2666;SRR=21;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.91T>C|p.Leu31Leu|91/366|91/366|31/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:67,2:67:2493:2:76:0,-13.5563,-217.372 +NC_045512.2 27542 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=68;DPB=68;DPRA=0;EPP=5.18177;EPPR=34.1563;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=93.5048;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2463;RO=67;RPL=0;RPP=5.18177;RPPR=148.499;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=34.1563;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.149C>A|p.Ala50Asp|149/366|149/366|50/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:68:67,1:67:2463:1:8:0,-19.67,-221.094 +NC_045512.2 27557 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=5.18177;EPPR=3.59403;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.871;NS=1;NUMALT=1;ODDS=128.994;PAIRED=1;PAIREDR=0.978495;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3315;RO=93;RPL=0;RPP=5.18177;RPPR=204.957;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.59403;SRR=44;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.164C>A|p.Ala55Glu|164/366|164/366|55/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:94:93,1:93:3315:1:9:0,-27.3968,-297.596 +NC_045512.2 27558 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=3.37991;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8723;NS=1;NUMALT=1;ODDS=130.831;PAIRED=1;PAIREDR=0.978723;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3337;RO=94;RPL=0;RPP=5.18177;RPPR=207.129;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=49;SRP=3.37991;SRR=45;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.165A>C|p.Ala55Ala|165/366|165/366|55/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3337:1:7:0,-27.8979,-299.773 +NC_045512.2 27621 . G T 4.34839E-12 . AB=0.118812;ABP=130.482;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=101;DPB=101;DPRA=0;EPP=29.068;EPPR=179.29;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8652;NS=1;NUMALT=1;ODDS=27.6373;PAIRED=1;PAIREDR=0.966292;PAO=0;PQA=0;PQR=0;PRO=0;QA=441;QR=3331;RO=89;RPL=6;RPP=3.0103;RPPR=4.20583;RPR=6;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=43;SRP=3.22989;SRR=46;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.228G>T|p.Gln76His|228/366|228/366|76/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:101:89,12:89:3331:12:441:-9.62867,0,-269.523 +NC_045512.2 27647 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=101;DPB=101;DPRA=0;EPP=7.35324;EPPR=200.965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8788;NS=1;NUMALT=1;ODDS=131.429;PAIRED=0.5;PAIREDR=0.979798;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=3609;RO=99;RPL=0;RPP=7.35324;RPPR=3.55865;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=49;SRP=3.03223;SRR=50;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.254A>C|p.Lys85Thr|254/366|254/366|85/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:101:99,2:99:3609:2:34:0,-27.1741,-321.702 +NC_045512.2 27690 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=88.1852;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8776;NS=1;NUMALT=1;ODDS=135.414;PAIRED=1;PAIREDR=0.969388;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3644;RO=98;RPL=1;RPP=5.18177;RPPR=25.7;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=47;SRP=3.36483;SRR=51;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.297A>C|p.Pro99Pro|297/366|297/366|99/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3644:1:11:0,-28.702,-326.984 +NC_045512.2 27691 . A C 8.82986E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=75.7434;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8763;NS=1;NUMALT=1;ODDS=128.285;PAIRED=1;PAIREDR=0.969072;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=3524;RO=97;RPL=1;RPP=5.18177;RPPR=27.389;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=45;SRP=4.10723;SRR=52;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.298A>C|p.Ile100Leu|298/366|298/366|100/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3524:1:36:0,-25.9027,-313.689 +NC_045512.2 27700 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=7.35324;EPPR=48.3426;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8763;NS=1;NUMALT=1;ODDS=131.759;PAIRED=1;PAIREDR=0.969072;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=3566;RO=97;RPL=2;RPP=7.35324;RPPR=48.3426;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=45;SRP=4.10723;SRR=52;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.307A>T|p.Ile103Phe|307/366|307/366|103/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:97,2:97:3566:2:20:0,-27.902,-319.159 +NC_045512.2 27703 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=39.2015;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.875;NS=1;NUMALT=1;ODDS=133.122;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3493;RO=96;RPL=1;RPP=5.18177;RPPR=55.1256;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=44;SRP=4.45795;SRR=52;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.310G>T|p.Val104Phe|310/366|310/366|104/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3493:1:9:0,-28.2999,-313.599 +NC_045512.2 27722 . T G 9.9451E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=5.18177;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.875;NS=1;NUMALT=1;ODDS=132.892;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3469;RO=96;RPL=1;RPP=5.18177;RPPR=211.472;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=44;SRP=4.45795;SRR=52;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.329T>G|p.Ile110Arg|329/366|329/366|110/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:96,1:96:3469:1:10:0,-28.1999,-311.339 +NC_045512.2 27741 . C A 6.2686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=5.18177;EPPR=4.86177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8737;NS=1;NUMALT=1;ODDS=131.976;PAIRED=1;PAIREDR=0.968421;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=3412;RO=95;RPL=1;RPP=5.18177;RPPR=209.3;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=4.86177;SRR=52;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.348C>A|p.Leu116Leu|348/366|348/366|116/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:96:95,1:95:3412:1:8:0,-28.0989,-306.415 +NC_045512.2 27742 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=5.32038;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8723;NS=1;NUMALT=1;ODDS=130.831;PAIRED=1;PAIREDR=0.968085;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=3437;RO=94;RPL=1;RPP=5.18177;RPPR=207.129;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=42;SRP=5.32038;SRR=52;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.349A>C|p.Lys117Gln|349/366|349/366|117/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3437:1:7:0,-27.8979,-308.766 +NC_045512.2 27779 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=5.18177;EPPR=101.382;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7736;NS=1;NUMALT=1;ODDS=73.6364;PAIRED=1;PAIREDR=0.943396;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2002;RO=53;RPL=1;RPP=5.18177;RPPR=118.098;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=101.382;SRR=51;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.24C>T|p.Asp8Asp|24/132|24/132|8/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:53,1:53:2002:1:11:0,-15.1556,-179.297 +NC_045512.2 27837 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=202.786;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8696;NS=1;NUMALT=1;ODDS=120.948;PAIRED=1;PAIREDR=0.967391;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3460;RO=92;RPL=0;RPP=5.18177;RPPR=12.4515;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=12.4515;SRR=36;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.82T>C|p.Phe28Leu|82/132|82/132|28/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3460:1:38:0,-24.1985,-307.73 +NC_045512.2 27848 . A G 1.11806E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=83;DPB=83;DPRA=0;EPP=5.18177;EPPR=172.491;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8537;NS=1;NUMALT=1;ODDS=107.198;PAIRED=1;PAIREDR=0.963415;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3096;RO=82;RPL=0;RPP=5.18177;RPPR=30.1272;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=26.8435;SRR=26;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.93A>G|p.Ser31Ser|93/132|93/132|31/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:83:82,1:82:3096:1:38:0,-21.1882,-274.993 +NC_045512.2 27853 . A T 2.48317E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=87;DPB=87;DPRA=0;EPP=5.18177;EPPR=133.905;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8605;NS=1;NUMALT=1;ODDS=112.696;PAIRED=1;PAIREDR=0.965116;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3137;RO=86;RPL=0;RPP=5.18177;RPPR=43.4098;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=20.0791;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.98A>T|p.Glu33Val|98/132|98/132|33/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:87:86,1:86:3137:1:38:0,-22.3923,-278.718 +NC_045512.2 27860 . A C,G 6.05765E-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=72;DPB=72;DPRA=0,0;EPP=5.18177,5.18177;EPPR=52.644;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=97.183;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,11;QR=2602;RO=70;RPL=0,0;RPP=5.18177,5.18177;RPPR=155.013;RPR=1,1;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=55;SRP=52.644;SRR=15;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.105A>C|p.Gln35His|105/132|105/132|35/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:72:70,1,1:70:2602:1,1:11,11:0,-20.3831,-233.293,-20.3831,-232.909,-233.293 +NC_045512.2 27865 . A G 1.1934E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=78;DPB=78;DPRA=0;EPP=5.18177;EPPR=37.5565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=106.54;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2847;RO=77;RPL=0;RPP=5.18177;RPPR=170.214;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=56;SRP=37.5565;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.110A>G|p.His37Arg|110/132|110/132|37/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:78:77,1:77:2847:1:11:0,-22.3803,-255.331 +NC_045512.2 27867 . A C 1.87444E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=5.18177;EPPR=36.6819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2913;RO=79;RPL=0;RPP=5.18177;RPPR=174.557;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=57;SRP=36.6819;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.112A>C|p.Asn38His|112/132|112/132|38/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:80:79,1:79:2913:1:11:0,-22.9824,-261.266 +NC_045512.2 27945 . C T 9.25199E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=7.35324;EPPR=133.376;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8929;NS=1;NUMALT=1;ODDS=147.603;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=4164;RO=112;RPL=1;RPP=3.0103;RPPR=20.4596;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=3.0103;SRR=56;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.52C>T|p.Gln18*|52/366|52/366|18/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:114:112,2:112:4164:2:35:0,-30.9925,-371.524 +NC_045512.2 27972 . C T 3512.93 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=114;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=241.948;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.8947;MQMR=0;NS=1;NUMALT=1;ODDS=161.256;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4286;QR=0;RO=0;RPL=56;RPP=3.08649;RPPR=0;RPR=58;RUN=1;SAF=57;SAP=3.0103;SAR=57;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:114:0,114:0:0:114:4286:-385.816,-34.3174,0 +NC_045512.2 27989 . A T 2.67001E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=7.35324;EPPR=246.215;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8929;NS=1;NUMALT=1;ODDS=138.646;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4204;RO=112;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=3.0103;SRR=56;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.96A>T|p.Val32Val|96/366|96/366|32/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:114:112,2:112:4204:2:76:0,-27.1026,-371.222 +NC_045512.2 28011 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=16.9077;EPPR=111.25;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8846;NS=1;NUMALT=1;ODDS=58.0795;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=377;QR=3851;RO=104;RPL=6;RPP=3.87889;RPPR=24.391;RPR=4;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=52;SRP=3.0103;SRR=52;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.118C>T|p.His40Tyr|118/366|118/366|40/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:114:104,10:104:3851:10:377:0,-0.0338464,-312.42 +NC_045512.2 28040 . A C 3.40528E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=7.35324;EPPR=3.08785;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8929;NS=1;NUMALT=1;ODDS=148.989;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=4144;RO=112;RPL=2;RPP=7.35324;RPPR=246.215;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=55;SRP=3.08785;SRR=57;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.147A>C|p.Val49Val|147/366|147/366|49/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:114:112,2:112:4144:2:35:0,-30.9926,-369.723 +NC_045512.2 28048 . G T 3466.34 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=114;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.8947;MQMR=0;NS=1;NUMALT=1;ODDS=161.256;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4257;QR=0;RO=0;RPL=114;RPP=250.558;RPPR=0;RPR=0;RUN=1;SAF=57;SAP=3.0103;SAR=57;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:114:0,114:0:0:114:4257:-383.207,-34.3174,0 +NC_045512.2 28076 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=3.0103;EPPR=3.03022;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8899;NS=1;NUMALT=1;ODDS=116.787;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=151;QR=3918;RO=109;RPL=4;RPP=11.6962;RPPR=239.701;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=54;SRP=3.03022;SRR=55;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.183C>T|p.Cys61Cys|183/366|183/366|61/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:113:109,4:109:3918:4:151:0,-20.0585,-338.77 +NC_045512.2 28095 . A T 3.37517E-14 . AB=0.0921053;ABP=222.672;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=152;DPB=152;DPRA=0;EPP=12.937;EPPR=207.506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.913;NS=1;NUMALT=1;ODDS=78.5974;PAIRED=1;PAIREDR=0.913043;PAO=0;PQA=0;PQR=0;PRO=0;QA=518;QR=5126;RO=138;RPL=14;RPP=33.4109;RPPR=10.6262;RPR=0;RUN=1;SAF=3;SAP=12.937;SAR=11;SRF=92;SRP=36.3062;SRR=46;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.202A>T|p.Lys68*|202/366|202/366|68/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:152:138,14:138:5126:14:518:-1.20379,0,-415.611 +NC_045512.2 28111 . A G 4834.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=155;CIGAR=1X;DP=155;DPB=155;DPRA=0;EPP=258.333;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.9226;MQMR=0;NS=1;NUMALT=1;ODDS=218.095;PAIRED=0.922581;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5780;QR=0;RO=0;RPL=58;RPP=24.3187;RPPR=0;RPR=97;RUN=1;SAF=89;SAP=10.4213;SAR=66;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:155:0,155:0:0:155:5780:-520.182,-46.6597,0 +NC_045512.2 28178 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=197;DPB=197;DPRA=0;EPP=3.0103;EPPR=3.55595;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=255.664;PAIRED=1;PAIREDR=0.830769;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=6947;RO=195;RPL=0;RPP=7.35324;RPPR=426.447;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=94;SRP=3.55595;SRR=101;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.285G>A|p.Leu95Leu|285/366|285/366|95/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:197:195,2:195:6947:2:62:0,-53.4142,-619.313 +NC_045512.2 28217 . T C 2.1097E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=199;DPB=199;DPRA=0;EPP=3.0103;EPPR=3.71935;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=255.272;PAIRED=1;PAIREDR=0.826531;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=7127;RO=196;RPL=0;RPP=7.35324;RPPR=428.619;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=94;SRP=3.71935;SRR=102;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.324T>C|p.Phe108Phe|324/366|324/366|108/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:199:196,2:196:7127:2:72:0,-52.9475,-634.631 +NC_045512.2 28250 . TTTCAT TCTGTTCT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1M3I3M1D1M;DP=201;DPB=202;DPRA=0;EPP=9.52472;EPPR=328.631;GTI=0;LEN=8;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=244.459;PAIRED=0.666667;PAIREDR=0.825641;PAO=0;PQA=0;PQR=0;PRO=0;QA=112;QR=7100;RO=195;RPL=2;RPP=3.73412;RPPR=7.92117;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=91;SRP=4.89224;SRR=104;TYPE=complex;ANN=CTGTTCT|frameshift_variant&missense_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.358_361delTTCAinsCTGTTC|p.Phe120fs|358/366|358/366|120/121||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:201:195,3:195:7100:3:112:0,-49.5153,-628.548 +NC_045512.2 28270 . TAAAATG TAAATG 6191.07 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=201;CIGAR=1M1D5M;DP=201;DPB=172.286;DPRA=0;EPP=276.13;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=281.864;PAIRED=0.820896;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7268;QR=0;RO=0;RPL=102;RPP=3.10753;RPPR=0;RPR=99;RUN=1;SAF=95;SAP=4.3175;SAR=106;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=TAAATG|frameshift_variant&start_lost|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1delA|p.Met1fs|1/1260|1/1260|1/419||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 1/1:201:0,201:0:0:201:7268:-654.066,-60.507,0 +NC_045512.2 28280 . GAT CTA 6324.22 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=200;CIGAR=3X;DP=200;DPB=200;DPRA=0;EPP=274.053;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=280.478;PAIRED=0.825;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7413;QR=0;RO=0;RPL=102;RPP=3.18402;RPPR=0;RPR=98;RUN=1;SAF=95;SAP=4.09604;SAR=105;SRF=0;SRP=0;SRR=0;TYPE=mnp;ANN=CTA|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.7_9delGATinsCTA|p.Asp3Leu|7/1260|7/1260|3/419|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:200:0,200:0:0:200:7413:-667.11,-60.206,0 +NC_045512.2 28295 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=201;DPB=201;DPRA=0;EPP=7.35324;EPPR=231.06;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=190.347;PAIRED=1;PAIREDR=0.817708;PAO=0;PQA=0;PQR=0;PRO=0;QA=303;QR=7085;RO=192;RPL=4;RPP=3.0103;RPPR=5.9056;RPR=4;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=91;SRP=4.14128;SRR=101;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.22A>G|p.Asn8Asp|22/1260|22/1260|8/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:201:192,8:192:7085:8:303:0,-32.7165,-609.995 +NC_045512.2 28338 . A C 5.50272E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=198;DPB=198;DPRA=0;EPP=9.52472;EPPR=4.89224;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=256.352;PAIRED=1;PAIREDR=0.815385;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=6976;RO=195;RPL=3;RPP=9.52472;RPPR=409.254;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=89;SRP=6.22853;SRR=106;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.65A>C|p.Asp22Ala|65/1260|65/1260|22/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:198:195,3:195:6976:3:63:0,-53.7265,-621.923 +NC_045512.2 28434 . C T 1.93167E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=148;DPB=148;DPRA=0;EPP=3.0103;EPPR=270.072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9178;NS=1;NUMALT=1;ODDS=185.256;PAIRED=1;PAIREDR=0.828767;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=5500;RO=146;RPL=2;RPP=7.35324;RPPR=34.4818;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=56;SRP=20.2036;SRR=90;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.161C>T|p.Thr54Ile|161/1260|161/1260|54/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:148:146,2:146:5500:2:76:0,-37.3376,-487.783 +NC_045512.2 28477 . A G 1.1482E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=68.6973;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8125;NS=1;NUMALT=1;ODDS=82.4895;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2375;RO=64;RPL=0;RPP=5.18177;RPPR=141.985;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=54;SRP=68.6973;SRR=10;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.204A>G|p.Arg68Arg|204/1260|204/1260|68/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2375:1:38:0,-15.7697,-210.143 +NC_045512.2 28487 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=3.73412;EPPR=3.03059;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8879;NS=1;NUMALT=1;ODDS=129.428;PAIRED=1;PAIREDR=0.962617;PAO=0;PQA=0;PQR=0;PRO=0;QA=84;QR=3794;RO=107;RPL=0;RPP=9.52472;RPPR=235.358;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=54;SRP=3.03059;SRR=53;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.214G>A|p.Val72Ile|214/1260|214/1260|72/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:110:107,3:107:3794:3:84:0,-25.2779,-333.746 +NC_045512.2 28524 . T G 3.43565E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=111;DPB=111;DPRA=0;EPP=7.35324;EPPR=3.03022;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8899;NS=1;NUMALT=1;ODDS=139.64;PAIRED=1;PAIREDR=0.954128;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=3892;RO=109;RPL=0;RPP=7.35324;RPPR=239.701;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=55;SRP=3.03022;SRR=54;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.251T>G|p.Ile84Ser|251/1260|251/1260|84/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:111:109,2:109:3892:2:59:0,-27.812,-344.778 +NC_045512.2 28525 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=107;DPB=107;DPRA=0;EPP=11.6962;EPPR=4.04333;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8835;NS=1;NUMALT=1;ODDS=116.947;PAIRED=0.75;PAIREDR=0.961165;PAO=0;PQA=0;PQR=0;PRO=0;QA=129;QR=3838;RO=103;RPL=0;RPP=11.6962;RPPR=226.672;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=55;SRP=4.04333;SRR=48;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.252T>G|p.Ile84Met|252/1260|252/1260|84/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:107:103,4:103:3838:4:129:0,-20.2817,-333.611 +NC_045512.2 28539 . G T 2.99544E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=3.0103;EPPR=3.19295;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8879;NS=1;NUMALT=1;ODDS=97.0355;PAIRED=1;PAIREDR=0.953271;PAO=0;PQA=0;PQR=0;PRO=0;QA=226;QR=3977;RO=107;RPL=0;RPP=16.0391;RPPR=235.358;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=52;SRP=3.19295;SRR=55;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.266G>T|p.Arg89Ile|266/1260|266/1260|89/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:113:107,6:107:3977:6:226:0,-13.3137,-337.335 +NC_045512.2 28549 . ACGA AA 8.95021E-14 . AB=0.106195;ABP=155.225;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1M2D1M;DP=113;DPB=107;DPRA=0;EPP=5.9056;EPPR=50.5032;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=59.8812;NS=1;NUMALT=1;ODDS=40.125;PAIRED=1;PAIREDR=0.950495;PAO=0;PQA=0;PQR=0;PRO=0;QA=437;QR=3758;RO=101;RPL=2;RPP=14.5915;RPPR=72.8629;RPR=10;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=49;SRP=3.2038;SRR=52;TYPE=del;ANN=AA|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.277_278delCG|p.Arg93fs|277/1260|277/1260|93/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:113:101,12:101:3758:12:437:-5.65166,0,-304.346 +NC_045512.2 28568 . G C 2.33553E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=3.0103;EPPR=210.552;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8919;NS=1;NUMALT=1;ODDS=137.277;PAIRED=1;PAIREDR=0.954955;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4163;RO=111;RPL=0;RPP=7.35324;RPPR=5.3774;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=54;SRP=3.18637;SRR=57;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.295G>C|p.Gly99Arg|295/1260|295/1260|99/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:113:111,2:111:4163:2:76:0,-26.8016,-367.554 +NC_045512.2 28653 . A C 2.33254E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=7.35324;EPPR=3.49937;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8919;NS=1;NUMALT=1;ODDS=138.664;PAIRED=1;PAIREDR=0.954955;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=4096;RO=111;RPL=2;RPP=7.35324;RPPR=244.044;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=53;SRP=3.49937;SRR=58;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.380A>C|p.Lys127Thr|380/1260|380/1260|127/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:113:111,2:111:4096:2:76:0,-26.8016,-361.545 +NC_045512.2 28657 . C T 2.60976E-14 . AB=0.106195;ABP=155.225;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=3.0103;EPPR=3.2038;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8812;NS=1;NUMALT=1;ODDS=41.1836;PAIRED=1;PAIREDR=0.950495;PAO=0;PQA=0;PQR=0;PRO=0;QA=449;QR=3720;RO=101;RPL=12;RPP=29.068;RPPR=222.329;RPR=0;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=49;SRP=3.2038;SRR=52;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.384C>T|p.Asp128Asp|384/1260|384/1260|128/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:113:101,12:101:3720:12:449:-6.74037,0,-300.93 +NC_045512.2 28718 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=92;DPB=92;DPRA=0;EPP=5.18177;EPPR=167.398;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=119.572;PAIRED=1;PAIREDR=0.956044;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3423;RO=91;RPL=1;RPP=5.18177;RPPR=25.942;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=15.6335;SRR=57;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.445C>T|p.Arg149Cys|445/1260|445/1260|149/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:92:91,1:91:3423:1:38:0,-23.8975,-304.435 +NC_045512.2 28719 . G T 1.04572E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=1X;DP=92;DPB=92;DPRA=0;EPP=13.8677;EPPR=158.782;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.1841;PAIRED=1;PAIREDR=0.954023;PAO=0;PQA=0;PQR=0;PRO=0;QA=176;QR=3269;RO=87;RPL=5;RPP=13.8677;RPPR=21.2057;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=34;SRP=12.0207;SRR=53;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.446G>T|p.Arg149Leu|446/1260|446/1260|149/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:92:87,5:87:3269:5:176:0,-11.5129,-278.201 +NC_045512.2 28725 . C T 1.34102E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=92;DPB=92;DPRA=0;EPP=7.35324;EPPR=165.243;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.965;PAIRED=1;PAIREDR=0.955556;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3397;RO=90;RPL=0;RPP=7.35324;RPPR=30.9017;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=32;SRP=19.3205;SRR=58;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.452C>T|p.Pro151Leu|452/1260|452/1260|151/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:92:90,2:90:3397:2:76:0,-20.4799,-298.68 +NC_045512.2 28739 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=9.52472;EPPR=168.931;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=97.2233;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=114;QR=3316;RO=88;RPL=2;RPP=3.73412;RPPR=25.2185;RPR=1;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=32;SRP=17.2236;SRR=56;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.466G>T|p.Ala156Ser|466/1260|466/1260|156/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:88,3:88:3316:3:114:0,-16.7614,-287.976 +NC_045512.2 28746 . T A 1.43166E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=5.18177;EPPR=161.717;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.158;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=3476;RO=92;RPL=0;RPP=5.18177;RPPR=18.9659;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=30;SRP=27.1797;SRR=62;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.473T>A|p.Val158Glu|473/1260|473/1260|158/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:93:92,1:92:3476:1:11:0,-26.8958,-311.898 +NC_045512.2 28750 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=94;DPB=94;DPRA=0;EPP=5.18177;EPPR=156.204;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=122.323;PAIRED=1;PAIREDR=0.956989;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3511;RO=93;RPL=1;RPP=5.18177;RPPR=13.3073;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=28.4375;SRR=63;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.477A>G|p.Leu159Leu|477/1260|477/1260|159/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:94:93,1:93:3511:1:38:0,-24.4995,-312.351 +NC_045512.2 28753 . A C,G 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=97;DPB=97;DPRA=0,0;EPP=5.18177,5.18177;EPPR=145.665;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=131.516;PAIRED=1,1;PAIREDR=0.957895;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=9,11;QR=3522;RO=95;RPL=0,0;RPP=5.18177,5.18177;RPPR=13.0905;RPR=1,1;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=29;SRP=34.3024;SRR=66;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.480A>C|p.Gln160His|480/1260|480/1260|160/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:95,1,1:95:3522:1,1:9,11:0,-28.0989,-316.226,-27.8989,-315.84,-316.045 +NC_045512.2 28782 . G T 9.80949E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.027;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=2225;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=3.32051;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.509G>T|p.Gly170Val|509/1260|509/1260|170/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2225:1:21:0,-17.166,-198.378 +NC_045512.2 28786 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.872;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.0202;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2261;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.872;SRR=29;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.513C>A|p.Phe171Leu|513/1260|513/1260|171/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2261:1:8:0,-18.4659,-202.923 +NC_045512.2 28802 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.0202;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2293;RO=63;RPL=0;RPP=5.18177;RPPR=122.993;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.872;SRR=29;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.529A>G|p.Arg177Gly|529/1260|529/1260|177/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:64:63,1:63:2293:1:8:0,-18.4659,-205.802 +NC_045512.2 28827 . G T 1.2823E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=5.05404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.8922;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2375;RO=68;RPL=0;RPP=5.18177;RPPR=117.971;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.554G>T|p.Arg185Leu|554/1260|554/1260|185/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2375:1:34:0,-17.3722,-210.566 +NC_045512.2 28835 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=76.5849;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=91.4228;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=2353;RO=68;RPL=1;RPP=5.18177;RPPR=18.4661;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=3.13803;SRR=35;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.562T>G|p.Ser188Ala|562/1260|562/1260|188/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2353:1:23:0,-18.4712,-209.695 +NC_045512.2 28847 . A G 1.09692E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=103.153;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=91.653;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=2483;RO=68;RPL=0;RPP=5.18177;RPPR=7.60871;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.574A>G|p.Asn192Asp|574/1260|574/1260|192/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2483:1:22:0,-18.5711,-221.494 +NC_045512.2 28853 . T G 1.20998E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=117.971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.1857;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2434;RO=68;RPL=0;RPP=5.18177;RPPR=5.05404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.580T>G|p.Ser194Ala|580/1260|580/1260|194/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2434:1:11:0,-19.6711,-218.187 +NC_045512.2 28858 . AAA CAT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=117.971;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=92.8042;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=2499;RO=68;RPL=0;RPP=5.18177;RPPR=5.05404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=complex;ANN=CAT|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.585_587delAAAinsCAT|p.ArgAsn195SerIle|585/1260|585/1260|195/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2499:1:17:0,-19.0711,-223.44 +NC_045512.2 28865 . A C 6.99161E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=117.971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.4159;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2453;RO=68;RPL=0;RPP=5.18177;RPPR=5.05404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.592A>C|p.Thr198Pro|592/1260|592/1260|198/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2453:1:10:0,-19.7711,-219.997 +NC_045512.2 28874 . A G 1.20998E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=117.971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.1857;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2478;RO=68;RPL=0;RPP=5.18177;RPPR=5.05404;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.601A>G|p.Ser201Gly|601/1260|601/1260|201/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2478:1:11:0,-19.6711,-222.142 +NC_045512.2 28881 . GGGGAAC AACGAAT,AACGAAC 2012.13 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=2,66;CIGAR=3X3M1X,3X4M;DP=69;DPB=69;DPRA=0,0;EPP=7.35324,113.69;EPPR=0;GTI=0;LEN=7,3;MEANALT=3,3;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=76.4681;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,2417;QR=0;RO=0;RPL=1,29;RPP=3.0103,5.11597;RPPR=0;RPR=1,37;RUN=1,1;SAF=1,33;SAP=3.0103,3.0103;SAR=1,33;SRF=0;SRP=0;SRR=0;TYPE=complex,mnp;ANN=AACGAAC|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608_610delGGGinsAAC|p.ArgGly203LysArg|608/1260|608/1260|203/419|| GT:DP:AD:RO:QR:AO:QA:GL 2/2:69:0,2,66:0:0:2,66:76,2417:-217.45,-211.217,-210.614,-19.868,-13.4951,0 +NC_045512.2 28889 . T A 1.20998E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=117.971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.1857;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2467;RO=68;RPL=1;RPP=5.18177;RPPR=6.20364;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=3.13803;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.616T>A|p.Ser206Thr|616/1260|616/1260|206/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2467:1:11:0,-19.6711,-221.157 +NC_045512.2 28895 . GCTAG GG,GCAAG 8.98077E-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=4,1;CIGAR=1M3D1M,2M1X2M;DP=69;DPB=66.6;DPRA=0,0;EPP=11.6962,5.18177;EPPR=74.8046;GTI=0;LEN=3,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=61.0091;PAIRED=1,1;PAIREDR=0.984375;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=132,19;QR=2325;RO=64;RPL=2,1;RPP=3.0103,5.18177;RPPR=3.0103;RPR=2,0;RUN=1,1;SAF=2,1;SAP=3.0103,5.18177;SAR=2,0;SRF=31;SRP=3.14602;SRR=33;TYPE=del,snp;ANN=GG|disruptive_inframe_deletion|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.623_625delCTA|p.Ala208_Arg209delinsGly|623/1260|623/1260|208/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:64,4,1:64:2325:4,1:132,19:0,-8.48271,-197.312,-17.885,-197.11,-207.478 +NC_045512.2 28900 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=5.18177;EPPR=70.5814;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=94.1857;PAIRED=1;PAIREDR=0.985294;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2438;RO=68;RPL=0;RPP=5.18177;RPPR=4.1599;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=34;SRP=3.0103;SRR=34;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.627A>G|p.Arg209Arg|627/1260|627/1260|209/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:68,1:68:2438:1:11:0,-19.6711,-218.548 +NC_045512.2 28905 . C T 1.92889E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=7.35324;EPPR=47.3796;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.7981;PAIRED=1;PAIREDR=0.985075;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=2460;RO=67;RPL=1;RPP=3.0103;RPPR=8.4876;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=33;SRP=3.04271;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.632C>T|p.Ala211Val|632/1260|632/1260|211/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:69:67,2:67:2460:2:69:0,-14.2188,-215.074 +NC_045512.2 28960 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.0103;EPPR=3.872;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.8478;PAIRED=1;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2241;RO=63;RPL=2;RPP=7.35324;RPPR=139.813;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=3.872;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.687G>T|p.Gln229His|687/1260|687/1260|229/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:63,2:63:2241:2:76:0,-12.3521,-194.711 +NC_045512.2 28963 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=88.7002;PAIRED=1;PAIREDR=0.984375;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2268;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.55317;SRR=34;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.690T>G|p.Leu230Leu|690/1260|690/1260|230/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:64,1:64:2268:1:11:0,-18.467,-203.257 +NC_045512.2 28975 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.0103;EPPR=3.90025;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.7093;PAIRED=1;PAIREDR=0.983607;PAO=0;PQA=0;PQR=0;PRO=0;QA=150;QR=2168;RO=61;RPL=4;RPP=11.6962;RPPR=135.47;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=28;SRP=3.90025;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.702G>T|p.Met234Ile|702/1260|702/1260|234/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:65:61,4:61:2168:4:150:0,-5.70102,-181.493 +NC_045512.2 28977 . C T 1593.62 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=61;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.90025;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.0468;PAIRED=0.983607;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2116;QR=139;RO=4;RPL=61;RPP=135.47;RPPR=11.6962;RPR=0;RUN=1;SAF=28;SAP=3.90025;SAR=33;SRF=2;SRP=3.0103;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:65:4,61:4:139:61:2116:-177.829,-6.71619,0 +NC_045512.2 28984 . A C 3.29981E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=34.5724;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.6758;PAIRED=1;PAIREDR=0.976744;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1575;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=34.5724;SRR=34;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.711A>C|p.Lys237Asn|711/1260|711/1260|237/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:44:43,1:43:1575:1:21:0,-11.1454,-139.927 +NC_045512.2 28988 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=5.18177;EPPR=99.6557;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=101.047;PAIRED=1;PAIREDR=0.808219;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2528;RO=73;RPL=1;RPP=5.18177;RPPR=6.60959;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=39;SRP=3.75395;SRR=34;TYPE=snp;ANN=T|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.715C>T|p.Gln239*|715/1260|715/1260|239/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:74:73,1:73:2528:1:11:0,-21.1762,-226.654 +NC_045512.2 28991 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=5.18177;EPPR=119.143;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=109.287;PAIRED=1;PAIREDR=0.822785;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2896;RO=79;RPL=1;RPP=5.18177;RPPR=3.69747;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=44;SRP=5.23675;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.718C>A|p.Gln240Lys|718/1260|718/1260|240/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:80:79,1:79:2896:1:11:0,-22.9824,-259.741 +NC_045512.2 29030 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=5.18177;EPPR=165.243;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=118.197;PAIRED=1;PAIREDR=0.844444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=3356;RO=90;RPL=1;RPP=5.18177;RPPR=7.73928;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=56;SRP=14.688;SRR=34;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.757G>A|p.Glu253Lys|757/1260|757/1260|253/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:90,1:90:3356:1:38:0,-23.5965,-298.414 +NC_045512.2 29034 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=91;DPB=91;DPRA=0;EPP=5.18177;EPPR=165.243;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=121.414;PAIRED=1;PAIREDR=0.844444;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=3351;RO=90;RPL=1;RPP=5.18177;RPPR=7.73928;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=56;SRP=14.688;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.761C>T|p.Ala254Val|761/1260|761/1260|254/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:91:90,1:90:3351:1:24:0,-24.9938,-299.358 +NC_045512.2 29071 . A G 1.56708E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=61;DPB=61;DPRA=0;EPP=5.18177;EPPR=86.3948;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.2186;PAIRED=0;PAIREDR=0.8;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2219;RO=60;RPL=0;RPP=5.18177;RPPR=133.299;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=54;SRP=86.3948;SRR=6;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.798A>G|p.Lys266Lys|798/1260|798/1260|266/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:61:60,1:60:2219:1:11:0,-17.2628,-198.845 +NC_045512.2 29081 . G T 3.1906E-10 . AB=0.122449;ABP=124.347;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=3.73412;EPPR=5.53527;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.3344;PAIRED=0.833333;PAIREDR=0.802326;PAO=0;PQA=0;PQR=0;PRO=0;QA=445;QR=3120;RO=86;RPL=0;RPP=29.068;RPPR=189.757;RPR=12;RUN=1;SAF=7;SAP=3.73412;SAR=5;SRF=48;SRP=5.53527;SRR=38;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.808G>T|p.Val270Leu|808/1260|808/1260|270/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:98:86,12:86:3120:12:445:-10.8948,0,-251.489 +NC_045512.2 29149 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=106;DPB=106;DPRA=0;EPP=7.35324;EPPR=164.701;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.702;PAIRED=1;PAIREDR=0.798077;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3770;RO=104;RPL=1;RPP=3.0103;RPPR=6.01695;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=54;SRP=3.34437;SRR=50;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.876C>T|p.Ile292Ile|876/1260|876/1260|292/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:106:104,2:104:3770:2:76:0,-24.6944,-332.23 +NC_045512.2 29170 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=106;DPB=106;DPRA=0;EPP=7.35324;EPPR=203.537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=140.888;PAIRED=1;PAIREDR=0.798077;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=3828;RO=104;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=55;SRP=3.76196;SRR=49;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.897A>C|p.Lys299Asn|897/1260|897/1260|299/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:106:104,2:104:3828:2:22:0,-29.8192,-342.577 +NC_045512.2 29219 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=106;DPB=106;DPRA=0;EPP=7.35324;EPPR=179.735;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=127.702;PAIRED=1;PAIREDR=0.798077;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=3866;RO=104;RPL=1;RPP=3.0103;RPPR=8.35546;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=54;SRP=3.34437;SRR=50;TYPE=snp;ANN=T|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.946G>T|p.Gly316*|946/1260|946/1260|316/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:106:104,2:104:3866:2:76:0,-24.6944,-340.865 +NC_045512.2 29240 . G C 1.33501E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=3.21178;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=134.268;PAIRED=0;PAIREDR=0.835052;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=3538;RO=97;RPL=1;RPP=5.18177;RPPR=205.047;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=46;SRP=3.56996;SRR=51;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.967G>C|p.Glu323Gln|967/1260|967/1260|323/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3538:1:10:0,-28.5009,-317.579 +NC_045512.2 29277 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=3.36483;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=135.874;PAIRED=0;PAIREDR=0.846939;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3504;RO=98;RPL=1;RPP=5.18177;RPPR=215.815;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=3.36483;SRR=51;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1004G>T|p.Gly335Val|1004/1260|1004/1260|335/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3504:1:9:0,-28.902,-314.628 +NC_045512.2 29278 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=5.18177;EPPR=3.36483;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=135.874;PAIRED=0;PAIREDR=0.846939;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=3443;RO=98;RPL=1;RPP=5.18177;RPPR=215.815;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=47;SRP=3.36483;SRR=51;TYPE=snp;ANN=A|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1005T>A|p.Gly335Gly|1005/1260|1005/1260|335/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:99:98,1:98:3443:1:9:0,-28.902,-309.144 +NC_045512.2 29279 . G T 2.55252E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=5.18177;EPPR=3.56996;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=133.347;PAIRED=1;PAIREDR=0.835052;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=3338;RO=97;RPL=1;RPP=5.18177;RPPR=213.643;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=46;SRP=3.56996;SRR=51;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1006G>T|p.Ala336Ser|1006/1260|1006/1260|336/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:98:97,1:97:3338:1:14:0,-28.1009,-299.195 +NC_045512.2 29283 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=5.18177;EPPR=4.48875;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=129.679;PAIRED=1;PAIREDR=0.840426;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=3372;RO=94;RPL=1;RPP=5.18177;RPPR=207.129;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=43;SRP=4.48875;SRR=51;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1010T>C|p.Ile337Thr|1010/1260|1010/1260|337/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:95:94,1:94:3372:1:12:0,-27.3979,-302.457 +NC_045512.2 29300 . G A 5.72593E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=94.4788;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=78.6496;PAIRED=1;PAIREDR=0.859649;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=2110;RO=57;RPL=1;RPP=5.18177;RPPR=110.022;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=80.1547;SRR=51;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1027G>A|p.Asp343Asn|1027/1260|1027/1260|343/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2110:1:13:0,-16.1597,-188.845 +NC_045512.2 29304 . C A 1.85633E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=87.1644;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.5871;PAIRED=1;PAIREDR=0.859649;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=2118;RO=57;RPL=1;RPP=5.18177;RPPR=110.022;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=73.4498;SRR=50;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1031C>A|p.Pro344Gln|1031/1260|1031/1260|344/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:58:57,1:57:2118:1:35:0,-13.9611,-187.362 +NC_045512.2 29344 . T G 3.70687E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=120.42;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.7096;PAIRED=1;PAIREDR=0.862069;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2182;RO=58;RPL=1;RPP=5.18177;RPPR=75.4926;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=69.053;SRR=50;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1071T>G|p.Ile357Met|1071/1260|1071/1260|357/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:59:58,1:58:2182:1:10:0,-16.7608,-195.618 +NC_045512.2 29369 . A C,G 1.6002E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=52;DPB=52;DPRA=0,0;EPP=5.18177,5.18177;EPPR=111.584;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=69.5807;PAIRED=1,0;PAIREDR=0.86;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=12,12;QR=1865;RO=50;RPL=1,1;RPP=5.18177,5.18177;RPPR=59.2949;RPR=0,0;RUN=1,1;SAF=0,0;SAP=5.18177,5.18177;SAR=1,1;SRF=7;SRP=59.2949;SRR=43;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1096A>C|p.Thr366Pro|1096/1260|1096/1260|366/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:50,1,1:50:1865:1,1:12,12:0,-14.2725,-166.908,-14.2725,-166.435,-166.908 +NC_045512.2 29401 . T A 7.14562E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.2253;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=478;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=A|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1128T>A|p.Ala376Ala|1128/1260|1128/1260|376/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:478:1:8:0,-3.41442,-42.562 +NC_045512.2 29420 . C A 7.14562E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.2253;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=482;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1147C>A|p.Pro383Thr|1147/1260|1147/1260|383/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:482:1:8:0,-3.41442,-42.9234 +NC_045512.2 29431 . G A 8.9958E-9 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.9951;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=479;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=A|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1158G>A|p.Gln386Gln|1158/1260|1158/1260|386/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:479:1:9:0,-3.31442,-42.5501 +NC_045512.2 29433 . A G 1.42557E-7 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.2321;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=461;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1160A>G|p.Lys387Arg|1160/1260|1160/1260|387/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:461:1:21:0,-2.11447,-39.7192 +NC_045512.2 29537 . C T 1.71248E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=5.30951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.5197;PAIRED=1;PAIREDR=0.911765;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1276;RO=34;RPL=0;RPP=5.18177;RPPR=28.557;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=27;SRP=28.557;SRR=7;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-21C>T|||||21| GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:34,1:34:1276:1:38:0,-6.73878,-111.339 +NC_045512.2 29543 . G T 5.10816E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=16.9698;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.8779;PAIRED=1;PAIREDR=0.914286;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1288;RO=35;RPL=0;RPP=5.18177;RPPR=10.5174;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=27;SRP=25.4075;SRR=8;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-15G>T|||||15| GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:35,1:35:1288:1:38:0,-7.03981,-112.414 +NC_045512.2 29570 . A C 5.40927E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=7.35324;EPPR=4.07475;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.1239;PAIRED=1;PAIREDR=0.921569;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1844;RO=51;RPL=0;RPP=7.35324;RPPR=25.534;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=28;SRP=4.07475;SRR=23;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding|1/1|c.13A>C|p.Asn5His|13/117|13/117|5/38|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:51,2:51:1844:2:48:0,-11.3949,-161.658 +NC_045512.2 29580 . CTTTTCCG CTTTCCG,TTTTTCCG 3.00147E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=2,4;CIGAR=1M1D6M,1X7M;DP=53;DPB=52.75;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.42611;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=35.3706;PAIRED=1,1;PAIREDR=0.914894;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=75,149;QR=1683;RO=47;RPL=0,0;RPP=7.35324,11.6962;RPPR=19.6891;RPR=2,4;RUN=1,1;SAF=1,2;SAP=3.0103,3.0103;SAR=1,2;SRF=25;SRP=3.42611;SRR=22;TYPE=del,snp;ANN=CTTTCCG|frameshift_variant|HIGH|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding|1/1|c.27delT|p.Pro10fs|27/117|27/117|9/38|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:53:47,2,4:47:1683:2,4:75,149:0,-8.00405,-144.628,-1.95251,-133.031,-137.971 +NC_045512.2 29594 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=4.07475;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.1318;PAIRED=1;PAIREDR=0.921569;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1885;RO=51;RPL=0;RPP=5.18177;RPPR=34.0496;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.05288;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding|1/1|c.37A>T|p.Ile13Leu|37/117|37/117|13/38|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:52:51,1:51:1885:1:10:0,-14.6536,-168.911 +NC_045512.2 29607 . T C 2.67497E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=4.57376;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=67.9229;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1843;RO=50;RPL=1;RPP=5.18177;RPPR=42.0968;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=3.18402;SRR=26;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding|1/1|c.50T>C|p.Leu17Pro|50/117|50/117|17/38|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:50,1:50:1843:1:18:0,-13.5526,-164.33 +NC_045512.2 29735 . A C 3.28521E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9889;PAIRED=0;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1446;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4351A>C|||||4351| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1446:1:9:0,-11.1412,-129.528 +NC_045512.2 29740 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.3977;PAIRED=1;PAIREDR=0.921053;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1417;RO=38;RPL=1;RPP=5.18177;RPPR=85.5263;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.23888;SRR=18;TYPE=snp;ANN=C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4356A>C|||||4356| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1417:1:10:0,-10.7402,-126.821 +NC_045512.2 29765 . T G 3.01588E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=55.2191;PAIRED=1;PAIREDR=0.897436;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1371;RO=39;RPL=1;RPP=5.18177;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4381T>G|||||4381| GT:DP:AD:RO:QR:AO:QA:GL 0/0:40:39,1:39:1371:1:8:0,-11.2412,-122.867 +NC_045512.2 29784 . C G 5.71063E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.0884;PAIRED=0;PAIREDR=0.921053;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1380;RO=38;RPL=1;RPP=5.18177;RPPR=85.5263;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.0103;SRR=19;TYPE=snp;ANN=G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4400C>G|||||4400| GT:DP:AD:RO:QR:AO:QA:GL 0/0:39:38,1:38:1380:1:7:0,-11.0402,-123.787 +NC_045512.2 29798 . G A 1.32952E-12 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=38.1882;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.8331;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=756;RO=20;RPL=1;RPP=5.18177;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=38.1882;SRR=19;TYPE=snp;ANN=A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4414G>A|||||4414| GT:DP:AD:RO:QR:AO:QA:GL 0/0:21:20,1:20:756:1:11:0,-5.22163,-67.2701 +NC_045512.2 29857 . C A 1.90202E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.6411;PAIRED=1;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=532;RO=14;RPL=1;RPP=5.18177;RPPR=33.4109;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=33.4109;SRR=14;TYPE=snp;ANN=A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4473C>A|||||4473| GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:532:1:38:0,-0.718181,-44.428
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SampleC_freebayes_ann.vcf Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,364 @@ +##fileformat=VCFv4.2 +##fileDate=20210722 +##source=freeBayes v1.3.2-dirty +##reference=NC_045512.fasta +##contig=<ID=NC_045512.2,length=29903> +##phasing=none +##commandline="freebayes -f NC_045512.fasta -F 0.01 -C 1 --pooled-continuous L23MM_S3_sorted_uniq.bam" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##SnpEffVersion="5.0 (build 2020-08-09 21:23), by Pablo Cingolani" +##SnpEffCmd="SnpEff NC_045512.2 L23MM_S3_freebayes.vcf " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +NC_045512.2 32 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=564;DPB=564;DPRA=0;EPP=3.0103;EPPR=12.7391;GTI=0;LEN=1;MEANALT=1;MQM=39;MQMR=15.4892;NS=1;NUMALT=1;ODDS=729.572;PAIRED=1;PAIREDR=0.362007;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=18462;RO=558;RPL=0;RPP=16.0391;RPPR=1214.69;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=304;SRP=12.7391;SRR=254;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-234C>A|||||234| GT:DP:AD:RO:QR:AO:QA:GL 0/0:564:558,6:558:18462:6:204:0,-155.891,-622.102 +NC_045512.2 64 . CTC TTT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=99;CIGAR=1X1M1X;DP=1151;DPB=1156;DPRA=0;EPP=4.08507;EPPR=7.37801;GTI=0;LEN=3;MEANALT=1;MQM=41.4444;MQMR=15.4496;NS=1;NUMALT=1;ODDS=740.69;PAIRED=1;PAIREDR=0.415399;PAO=15;PQA=262;PQR=0;PRO=0;QA=3503;QR=37047;RO=1052;RPL=6;RPP=169.029;RPPR=1164.09;RPR=93;RUN=1;SAF=53;SAP=4.08507;SAR=46;SRF=566;SRP=16.2208;SRR=486;TYPE=complex;ANN=TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-202_-200delCTCinsTTT|||||202| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1151:1052,99:1052:37047:99:3503:0,-95.224,-953.379 +NC_045512.2 92 . C T 3142.56 . AB=0.43932;ABP=16.1867;AC=1;AF=0.5;AN=2;AO=181;CIGAR=1X;DP=412;DPB=412;DPRA=0;EPP=3.11827;EPPR=3.47092;GTI=0;LEN=1;MEANALT=1;MQM=43.0718;MQMR=51.9048;NS=1;NUMALT=1;ODDS=723.602;PAIRED=0.933702;PAIREDR=0.982684;PAO=0;PQA=0;PQR=0;PRO=0;QA=6095;QR=8033;RO=231;RPL=38;RPP=135.278;RPPR=91.4578;RPR=143;RUN=1;SAF=92;SAP=3.11827;SAR=89;SRF=120;SRP=3.77173;SRR=111;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-174C>T|||||174| GT:DP:AD:RO:QR:AO:QA:GL 0/1:412:231,181:231:8033:181:6095:-336.686,0,-565.664 +NC_045512.2 100 . C T 3907.17 . AB=0.441501;ABP=16.4753;AC=1;AF=0.5;AN=2;AO=200;CIGAR=1X;DP=453;DPB=453;DPRA=0;EPP=3.05373;EPPR=3.14817;GTI=0;LEN=1;MEANALT=2;MQM=45.335;MQMR=52.9603;NS=1;NUMALT=1;ODDS=899.659;PAIRED=0.935;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=6978;QR=8772;RO=252;RPL=49;RPP=115.97;RPPR=69.74;RPR=151;RUN=1;SAF=102;SAP=3.18402;SAR=98;SRF=130;SRP=3.56179;SRR=122;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-166C>T|||||166| GT:DP:AD:RO:QR:AO:QA:GL 0/1:453:252,200:252:8772:200:6978:-410.991,0,-630.697 +NC_045512.2 124 . G A 1.09393E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=585;DPB=585;DPRA=0;EPP=4.09604;EPPR=6.62691;GTI=0;LEN=1;MEANALT=1;MQM=39.5;MQMR=50.1023;NS=1;NUMALT=1;ODDS=735.632;PAIRED=1;PAIREDR=0.968804;PAO=0;PQA=0;PQR=0;PRO=0;QA=266;QR=19810;RO=577;RPL=5;RPP=4.09604;RPPR=24.1793;RPR=3;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=296;SRP=3.85706;SRR=281;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-142G>A|||||142| GT:DP:AD:RO:QR:AO:QA:GL 0/0:585:577,8:577:19810:8:266:0,-157.006,-1656.16 +NC_045512.2 164 . C T 6382.88 . AB=0.480127;ABP=5.16796;AC=1;AF=0.5;AN=2;AO=302;CIGAR=1X;DP=629;DPB=629;DPRA=0;EPP=3.0103;EPPR=3.96948;GTI=0;LEN=1;MEANALT=2;MQM=45.1656;MQMR=52.0337;NS=1;NUMALT=1;ODDS=1469.71;PAIRED=0.960265;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10610;QR=11356;RO=326;RPL=162;RPP=6.49041;RPPR=5.67468;RPR=140;RUN=1;SAF=153;SAP=3.12534;SAR=149;SRF=166;SRP=3.25009;SRR=160;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-102C>T|||||102| GT:DP:AD:RO:QR:AO:QA:GL 0/1:629:326,302:326:11356:302:10610:-646.358,0,-794.471 +NC_045512.2 210 . G T 14518.1 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=536;CIGAR=1X;DP=537;DPB=537;DPRA=0;EPP=3.0265;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=43.8228;MQMR=52;NS=1;NUMALT=1;ODDS=741.615;PAIRED=0.996269;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18923;QR=14;RO=1;RPL=318;RPP=43.5228;RPPR=5.18177;RPR=218;RUN=1;SAF=265;SAP=3.15615;SAR=271;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-56G>T|||||56| GT:DP:AD:RO:QR:AO:QA:GL 1/1:537:1,536:1:14:536:18923:-1459.38,-160.253,0 +NC_045512.2 241 . C T 12516.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=461;CIGAR=1X;DP=461;DPB=461;DPRA=0;EPP=3.12806;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=43.4707;MQMR=0;NS=1;NUMALT=1;ODDS=643.687;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16150;QR=0;RO=0;RPL=224;RPP=3.80635;RPPR=0;RPR=237;RUN=1;SAF=232;SAP=3.05269;SAR=229;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-25C>T|||||25| GT:DP:AD:RO:QR:AO:QA:GL 1/1:461:0,461:0:0:461:16150:-1256.02,-138.775,0 +NC_045512.2 280 . CC TT 3525.62 . AB=0.387879;ABP=57.0602;AC=1;AF=0.5;AN=2;AO=192;CIGAR=2X;DP=495;DPB=497;DPRA=0;EPP=3.0103;EPPR=3.03906;GTI=0;LEN=2;MEANALT=2;MQM=42.0052;MQMR=49.4834;NS=1;NUMALT=1;ODDS=811.803;PAIRED=1;PAIREDR=0.993377;PAO=4;PQA=140;PQR=0;PRO=0;QA=6736;QR=10479;RO=302;RPL=98;RPP=3.19126;RPPR=3.72933;RPR=94;RUN=1;SAF=94;SAP=3.19126;SAR=98;SRF=148;SRP=3.26915;SRR=154;TYPE=mnp;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.15_16delCCinsTT|p.Pro6Ser|15/21291|15/21291|5/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:495:302,192:302:10479:192:6736:-365.116,0,-736.846 +NC_045512.2 335 . CGC TGT 1775.99 . AB=0.217114;ABP=547.262;AC=1;AF=0.5;AN=2;AO=170;CIGAR=1X1M1X;DP=783;DPB=785.333;DPRA=0;EPP=3.21467;EPPR=8.43363;GTI=0;LEN=3;MEANALT=4;MQM=46.1059;MQMR=51.1593;NS=1;NUMALT=1;ODDS=408.938;PAIRED=0.976471;PAIREDR=0.985222;PAO=7;PQA=223;PQR=0;PRO=0;QA=5931;QR=21070;RO=609;RPL=92;RPP=5.51388;RPPR=296.708;RPR=78;RUN=1;SAF=83;SAP=3.21467;SAR=87;SRF=319;SRP=6.009;SRR=290;TYPE=complex;ANN=TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.70_72delCGCinsTGT|p.Arg24Cys|70/21291|70/21291|24/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:783:609,170:609:21070:170:5931:-241.995,0,-1561.83 +NC_045512.2 346 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=914;DPB=914;DPRA=0;EPP=3.0103;EPPR=5.17216;GTI=0;LEN=1;MEANALT=1;MQM=47.6;MQMR=47.8728;NS=1;NUMALT=1;ODDS=1156.65;PAIRED=1;PAIREDR=0.915929;PAO=0;PQA=0;PQR=0;PRO=0;QA=347;QR=31647;RO=904;RPL=6;RPP=3.87889;RPPR=520.167;RPR=4;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=461;SRP=3.78857;SRR=443;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.81C>T|p.Leu27Leu|81/21291|81/21291|27/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:914:904,10:904:31647:10:347:0,-246.309,-2560.77 +NC_045512.2 396 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=1364;DPB=1364;DPRA=0;EPP=3.12459;EPPR=4.1025;GTI=0;LEN=1;MEANALT=2;MQM=42.2632;MQMR=49.3222;NS=1;NUMALT=1;ODDS=1698.24;PAIRED=0.894737;PAIREDR=0.959821;PAO=0;PQA=0;PQR=0;PRO=0;QA=666;QR=46617;RO=1344;RPL=2;RPP=28.7251;RPPR=62.5707;RPR=17;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=677;SRP=3.17187;SRR=667;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.131A>G|p.Gln44Arg|131/21291|131/21291|44/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1364:1344,19:1344:46617:19:666:0,-362.653,-3817.07 +NC_045512.2 613 . G A 29424.0 . AB=0.828234;ABP=1348.68;AC=1;AF=0.5;AN=2;AO=1191;CIGAR=1X;DP=1438;DPB=1438;DPRA=0;EPP=6.07516;EPPR=4.98836;GTI=0;LEN=1;MEANALT=1;MQM=50.6507;MQMR=52.753;NS=1;NUMALT=1;ODDS=354.736;PAIRED=0.991604;PAIREDR=0.991903;PAO=0;PQA=0;PQR=0;PRO=0;QA=41710;QR=8642;RO=247;RPL=553;RPP=16.1832;RPPR=4.07406;RPR=638;RUN=1;SAF=578;SAP=5.24376;SAR=613;SRF=120;SRP=3.44108;SRR=127;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.348G>A|p.Val116Val|348/21291|348/21291|116/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1438:247,1191:247:8642:1191:41710:-3099.14,0,-308.276 +NC_045512.2 682 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=79;CIGAR=1X;DP=1852;DPB=1852;DPRA=0;EPP=3.03779;EPPR=17.0482;GTI=0;LEN=1;MEANALT=3;MQM=38.1519;MQMR=50.3139;NS=1;NUMALT=1;ODDS=1840.13;PAIRED=0.949367;PAIREDR=0.967815;PAO=0;PQA=0;PQR=0;PRO=0;QA=2754;QR=59839;RO=1771;RPL=4;RPP=141.572;RPPR=68.4377;RPR=75;RUN=1;SAF=39;SAP=3.03779;SAR=40;SRF=896;SRP=3.55102;SRR=875;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.417T>C|p.Asp139Asp|417/21291|417/21291|139/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1852:1771,79:1771:59839:79:2754:0,-360.966,-4800.3 +NC_045512.2 823 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1547;DPB=1547;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=41.9545;MQMR=52.4665;NS=1;NUMALT=1;ODDS=1927.38;PAIRED=0.909091;PAIREDR=0.985564;PAO=0;PQA=0;PQR=0;PRO=0;QA=775;QR=52847;RO=1524;RPL=0;RPP=50.7827;RPPR=3.28957;RPR=22;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=753;SRP=3.47195;SRR=771;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.558C>T|p.Val186Val|558/21291|558/21291|186/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1547:1524,22:1524:52847:22:775:0,-410.536,-4495.54 +NC_045512.2 895 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=89;CIGAR=1X;DP=1742;DPB=1742;DPRA=0;EPP=3.0347;EPPR=3.70522;GTI=0;LEN=1;MEANALT=1;MQM=47.8876;MQMR=51.1881;NS=1;NUMALT=1;ODDS=1489.29;PAIRED=0.977528;PAIREDR=0.989716;PAO=0;PQA=0;PQR=0;PRO=0;QA=3176;QR=58126;RO=1653;RPL=47;RPP=3.62026;RPPR=3.11671;RPR=42;RUN=1;SAF=43;SAP=3.22989;SAR=46;SRF=800;SRP=6.70036;SRR=853;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.630A>T|p.Lys210Asn|630/21291|630/21291|210/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1742:1653,89:1653:58126:89:3176:0,-268.331,-4688.37 +NC_045512.2 913 . C T 353.303 . AB=0.150661;ABP=1846.36;AC=1;AF=0.5;AN=2;AO=262;CIGAR=1X;DP=1739;DPB=1739;DPRA=0;EPP=3.04345;EPPR=3.93292;GTI=0;LEN=1;MEANALT=2;MQM=49.5611;MQMR=51.2447;NS=1;NUMALT=1;ODDS=81.351;PAIRED=1;PAIREDR=0.991842;PAO=0;PQA=0;PQR=0;PRO=0;QA=9234;QR=50659;RO=1471;RPL=143;RPP=7.78422;RPPR=8.5032;RPR=119;RUN=1;SAF=129;SAP=3.14291;SAR=133;SRF=719;SRP=4.61787;SRR=752;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.648C>T|p.Ser216Ser|648/21291|648/21291|216/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1739:1471,262:1471:50659:262:9234:-245.319,0,-3801.26 +NC_045512.2 1048 . G T 55959.4 . AB=0.711473;ABP=1265.83;AC=1;AF=0.5;AN=2;AO=2313;CIGAR=1X;DP=3251;DPB=3251;DPRA=0;EPP=5.26439;EPPR=3.46404;GTI=0;LEN=1;MEANALT=1;MQM=49.3562;MQMR=51.451;NS=1;NUMALT=1;ODDS=3880.56;PAIRED=0.996541;PAIREDR=0.984009;PAO=0;PQA=0;PQR=0;PRO=0;QA=81232;QR=33087;RO=938;RPL=1050;RPP=45.6033;RPPR=91.9434;RPR=1263;RUN=1;SAF=1190;SAP=7.22463;SAR=1123;SRF=477;SRP=3.60294;SRR=461;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.783G>T|p.Lys261Asn|783/21291|783/21291|261/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3251:938,2313:938:33087:2313:81232:-5740.35,0,-1833.27 +NC_045512.2 1259 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=194;CIGAR=1X;DP=2654;DPB=2654;DPRA=0;EPP=3.05507;EPPR=3.26551;GTI=0;LEN=1;MEANALT=2;MQM=51.634;MQMR=51.1745;NS=1;NUMALT=1;ODDS=1663.73;PAIRED=1;PAIREDR=0.9939;PAO=0;PQA=0;PQR=0;PRO=0;QA=6829;QR=85866;RO=2459;RPL=120;RPP=26.695;RPPR=136.638;RPR=74;RUN=1;SAF=94;SAP=3.41325;SAR=100;SRF=1211;SRP=4.21922;SRR=1248;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.994C>T|p.Gln332*|994/21291|994/21291|332/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2654:2459,194:2459:85866:194:6829:0,-215.703,-6715.49 +NC_045512.2 1441 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=1222;DPB=1222;DPRA=0;EPP=3.0103;EPPR=3.02655;GTI=0;LEN=1;MEANALT=2;MQM=53.5;MQMR=52.1155;NS=1;NUMALT=1;ODDS=1481.16;PAIRED=1;PAIREDR=0.978387;PAO=0;PQA=0;PQR=0;PRO=0;QA=644;QR=41870;RO=1203;RPL=12;RPP=7.35324;RPPR=9.29367;RPR=6;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=601;SRP=3.01211;SRR=602;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1176C>T|p.Gly392Gly|1176/21291|1176/21291|392/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1222:1203,18:1203:41870:18:644:0,-310.787,-3538.8 +NC_045512.2 1469 . C T 1.64659E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=109;CIGAR=1X;DP=1145;DPB=1145;DPRA=0;EPP=3.03022;EPPR=3.04384;GTI=0;LEN=1;MEANALT=1;MQM=44.6606;MQMR=52.5444;NS=1;NUMALT=1;ODDS=585.618;PAIRED=1;PAIREDR=0.985521;PAO=0;PQA=0;PQR=0;PRO=0;QA=3677;QR=36019;RO=1036;RPL=64;RPP=10.2021;RPPR=3.31213;RPR=45;RUN=1;SAF=54;SAP=3.03022;SAR=55;SRF=510;SRP=3.54688;SRR=526;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1204C>T|p.Arg402Cys|1204/21291|1204/21291|402/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1145:1036,109:1036:36019:109:3677:0,-58.5213,-2826.07 +NC_045512.2 1485 . GAG GG 1184.03 . AB=0.19145;ABP=892.781;AC=1;AF=0.5;AN=2;AO=206;CIGAR=1M1D1M;DP=1076;DPB=1009.33;DPRA=0;EPP=3.38978;EPPR=3.07291;GTI=0;LEN=1;MEANALT=4;MQM=47.3544;MQMR=51.9769;NS=1;NUMALT=1;ODDS=272.632;PAIRED=0.985437;PAIREDR=0.988466;PAO=3;PQA=102;PQR=102;PRO=3;QA=6730;QR=30243;RO=867;RPL=112;RPP=6.42563;RPPR=3.91445;RPR=94;RUN=1;SAF=100;SAP=3.38978;SAR=106;SRF=421;SRP=4.57566;SRR=446;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1221delA|p.Gly408fs|1221/21291|1221/21291|407/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1076:867,206:867:30243:206:6730:-221.186,0,-2270.15 +NC_045512.2 1644 . ACAT CCAA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1X2M1X;DP=3724;DPB=3727;DPRA=0;EPP=3.0608;EPPR=4.80063;GTI=0;LEN=4;MEANALT=7;MQM=30.7209;MQMR=51.8566;NS=1;NUMALT=1;ODDS=4720.41;PAIRED=0.953488;PAIREDR=0.990461;PAO=12;PQA=304;PQR=0;PRO=0;QA=1484;QR=129421;RO=3669;RPL=20;RPP=3.46479;RPPR=579.566;RPR=23;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1875;SRP=6.89338;SRR=1794;TYPE=complex;ANN=CCAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1379_1382delACATinsCCAA|p.AsnIle460ThrAsn|1379/21291|1379/21291|460/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3724:3669,43:3669:129421:43:1484:0,-1028.38,-11045.6 +NC_045512.2 1656 . TTGG ATGT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1X2M1X;DP=3885;DPB=3898;DPRA=0;EPP=3.0459;EPPR=10.286;GTI=0;LEN=4;MEANALT=8;MQM=32.3279;MQMR=51.9625;NS=1;NUMALT=1;ODDS=4763.18;PAIRED=0.934426;PAIREDR=0.988454;PAO=2;PQA=64;PQR=0;PRO=0;QA=2084;QR=133325;RO=3811;RPL=26;RPP=5.89373;RPPR=94.6332;RPR=35;RUN=1;SAF=32;SAP=3.33068;SAR=29;SRF=1958;SRP=9.29224;SRR=1853;TYPE=complex;ANN=ATGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1391_1394delTTGGinsATGT|p.ValGly464AspVal|1391/21291|1391/21291|464/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3885:3811,61:3811:133325:61:2084:0,-1032.69,-11349.3 +NC_045512.2 1700 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=1X;DP=4549;DPB=4549;DPRA=0;EPP=3.53672;EPPR=3.26665;GTI=0;LEN=1;MEANALT=3;MQM=50.2121;MQMR=52.9005;NS=1;NUMALT=1;ODDS=5535.53;PAIRED=0.939394;PAIREDR=0.996653;PAO=0;PQA=0;PQR=0;PRO=0;QA=2243;QR=155182;RO=4481;RPL=36;RPP=4.19474;RPPR=3.01466;RPR=30;RUN=1;SAF=33;SAP=3.0103;SAR=33;SRF=2333;SRP=19.5956;SRR=2148;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1435T>C|p.Ser479Pro|1435/21291|1435/21291|479/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4549:4481,66:4481:155182:66:2243:0,-1178.54,-13249.9 +NC_045512.2 1820 . G A 1.28256E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=225;CIGAR=1X;DP=4790;DPB=4790;DPRA=0;EPP=3.25157;EPPR=5.0218;GTI=0;LEN=1;MEANALT=3;MQM=53.3333;MQMR=52.6884;NS=1;NUMALT=1;ODDS=4172.54;PAIRED=0.982222;PAIREDR=0.992326;PAO=0;PQA=0;PQR=0;PRO=0;QA=7870;QR=158733;RO=4561;RPL=134;RPP=20.855;RPPR=145.462;RPR=91;RUN=1;SAF=110;SAP=3.25157;SAR=115;SRF=2212;SRP=11.9461;SRR=2349;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1555G>A|p.Gly519Ser|1555/21291|1555/21291|519/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4790:4561,225:4561:158733:225:7870:0,-756.291,-13041.7 +NC_045512.2 2095 . G A 1.24765E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1292;DPB=1292;DPRA=0;EPP=3.0103;EPPR=3.50327;GTI=0;LEN=1;MEANALT=2;MQM=50;MQMR=50.7745;NS=1;NUMALT=1;ODDS=1604.84;PAIRED=1;PAIREDR=0.990573;PAO=0;PQA=0;PQR=0;PRO=0;QA=546;QR=43930;RO=1273;RPL=8;RPP=3.0103;RPPR=3.2167;RPR=8;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=636;SRP=3.01201;SRR=637;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1830G>A|p.Ser610Ser|1830/21291|1830/21291|610/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1292:1273,16:1273:43930:16:546:0,-341.229,-3662.66 +NC_045512.2 2155 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1466;DPB=1466;DPRA=0;EPP=3.44459;EPPR=4.10732;GTI=0;LEN=1;MEANALT=3;MQM=42.65;MQMR=52.0596;NS=1;NUMALT=1;ODDS=1811.26;PAIRED=0.9;PAIREDR=0.991684;PAO=0;PQA=0;PQR=0;PRO=0;QA=708;QR=50315;RO=1443;RPL=11;RPP=3.44459;RPPR=55.6328;RPR=9;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=710;SRP=3.80636;SRR=733;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1890G>A|p.Trp630*|1890/21291|1890/21291|630/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1466:1443,20:1443:50315:20:708:0,-386.729,-4291.72 +NC_045512.2 2763 . TGC TC 2885.41 . AB=0.180095;ABP=2628.85;AC=1;AF=0.5;AN=2;AO=532;CIGAR=1M1D1M;DP=2954;DPB=2776.67;DPRA=0;EPP=3.15724;EPPR=4.17803;GTI=0;LEN=1;MEANALT=5;MQM=48.9643;MQMR=52.4178;NS=1;NUMALT=1;ODDS=664.391;PAIRED=0.99812;PAIREDR=0.992946;PAO=0;PQA=0;PQR=0;PRO=0;QA=17759;QR=83546;RO=2410;RPL=244;RPP=10.9125;RPPR=20.6704;RPR=288;RUN=1;SAF=261;SAP=3.41847;SAR=271;SRF=1192;SRP=3.61939;SRR=1218;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2499delG|p.Gln834fs|2499/21291|2499/21291|833/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2954:2410,532:2410:83546:532:17759:-579.218,0,-6324.54 +NC_045512.2 3037 . CTAC TTAT,TTAC 50614.4 . AB=0.158792,0.840721;ABP=2079.08,2073.16;AC=1,1;AF=0.5,0.5;AN=2;AO=326,1726;CIGAR=1X2M1X,1X3M;DP=2053;DPB=2097.75;DPRA=0,0;EPP=3.0103,3.03043;EPPR=0;GTI=0;LEN=4,1;MEANALT=3,3;MQM=46.1135,50.1877;MQMR=0;NS=1;NUMALT=2;ODDS=76.3459;PAIRED=1,0.998841;PAIREDR=0;PAO=96,83;PQA=2101.5,1661.5;PQR=0;PRO=0;QA=11160,56774;QR=0;RO=0;RPL=162,808;RPP=3.03694,18.2333;RPPR=0;RPR=164,918;RUN=1,1;SAF=165,869;SAP=3.11688,3.19147;SAR=161,857;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=TTAC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/2:2053:0,326,1726:0:0:326,1726:11160,56774:-5303.39,-4514.98,-4416.84,-787.998,0,-268.42 +NC_045512.2 3244 . C T 6.49718E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1X;DP=3062;DPB=3062;DPRA=0;EPP=3.0608;EPPR=6.84328;GTI=0;LEN=1;MEANALT=1;MQM=45.3721;MQMR=48.8029;NS=1;NUMALT=1;ODDS=3757.35;PAIRED=1;PAIREDR=0.991388;PAO=0;PQA=0;PQR=0;PRO=0;QA=1492;QR=106008;RO=3019;RPL=16;RPP=9.12072;RPPR=199.751;RPR=27;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1547;SRP=7.05619;SRR=1472;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2979C>T|p.Gly993Gly|2979/21291|2979/21291|993/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3062:3019,43:3019:106008:43:1492:0,-801.627,-8549.01 +NC_045512.2 3267 . C T 66510.3 . AB=0.84347;ABP=3439.83;AC=1;AF=0.5;AN=2;AO=2829;CIGAR=1X;DP=3354;DPB=3354;DPRA=0;EPP=5.00677;EPPR=3.82253;GTI=0;LEN=1;MEANALT=2;MQM=48.4143;MQMR=52.4637;NS=1;NUMALT=1;ODDS=445.319;PAIRED=0.994344;PAIREDR=0.984733;PAO=0;PQA=0;PQR=0;PRO=0;QA=99448;QR=18506;RO=524;RPL=1337;RPP=21.4513;RPPR=8.99428;RPR=1492;RUN=1;SAF=1456;SAP=8.29813;SAR=1373;SRF=272;SRP=4.66791;SRR=252;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3002C>T|p.Thr1001Ile|3002/21291|3002/21291|1001/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3354:524,2829:524:18506:2829:99448:-7040.97,0,-580.514 +NC_045512.2 3290 . C G 2.34573E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=92;CIGAR=1X;DP=3816;DPB=3816;DPRA=0;EPP=3.0103;EPPR=5.63136;GTI=0;LEN=1;MEANALT=3;MQM=39.1957;MQMR=50.4792;NS=1;NUMALT=1;ODDS=4359.88;PAIRED=0.978261;PAIREDR=0.986287;PAO=0;PQA=0;PQR=0;PRO=0;QA=3202;QR=130715;RO=3719;RPL=46;RPP=3.0103;RPPR=63.9266;RPR=46;RUN=1;SAF=46;SAP=3.0103;SAR=46;SRF=1908;SRP=8.50408;SRR=1811;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3025C>G|p.Gln1009Glu|3025/21291|3025/21291|1009/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3816:3719,92:3719:130715:92:3202:0,-927.881,-10728.8 +NC_045512.2 3327 . AGA AA 0.0 . AB=0.133491;ABP=4451.89;AC=1;AF=0.5;AN=2;AO=509;CIGAR=1M1D1M;DP=3813;DPB=3645.33;DPRA=0;EPP=3.21934;EPPR=4.22957;GTI=0;LEN=1;MEANALT=5;MQM=51.2692;MQMR=52.2961;NS=1;NUMALT=1;ODDS=425.428;PAIRED=0.996071;PAIREDR=0.992104;PAO=2;PQA=68;PQR=102;PRO=3;QA=17227;QR=115481;RO=3293;RPL=269;RPP=6.59814;RPPR=7.55305;RPR=240;RUN=1;SAF=256;SAP=3.0487;SAR=253;SRF=1646;SRP=3.01096;SRR=1647;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3063delG|p.Thr1022fs|3063/21291|3063/21291|1021/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3813:3293,509:3293:115481:509:17227:-318.157,0,-8788 +NC_045512.2 3483 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2793;DPB=2793;DPRA=0;EPP=3.07234;EPPR=8.70913;GTI=0;LEN=1;MEANALT=3;MQM=39.1143;MQMR=51.0527;NS=1;NUMALT=1;ODDS=3506.37;PAIRED=0.885714;PAIREDR=0.984381;PAO=0;PQA=0;PQR=0;PRO=0;QA=1145;QR=96319;RO=2753;RPL=7;RPP=30.3709;RPPR=550.326;RPR=28;RUN=1;SAF=16;SAP=3.56868;SAR=19;SRF=1344;SRP=6.34284;SRR=1409;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3218G>T|p.Gly1073Val|3218/21291|3218/21291|1073/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2793:2753,35:2753:96319:35:1145:0,-756.489,-8079.93 +NC_045512.2 3491 . AA TT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=47;CIGAR=2X;DP=2589;DPB=2589;DPRA=0;EPP=3.0565;EPPR=13.3547;GTI=0;LEN=2;MEANALT=3;MQM=40;MQMR=50.6949;NS=1;NUMALT=1;ODDS=3087.91;PAIRED=0.914894;PAIREDR=0.983858;PAO=0;PQA=0;PQR=0;PRO=0;QA=1679;QR=89098;RO=2540;RPL=16;RPP=13.4056;RPPR=539.265;RPR=31;RUN=1;SAF=22;SAP=3.42611;SAR=25;SRF=1223;SRP=10.5643;SRR=1317;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3226_3227delAAinsTT|p.Asn1076Phe|3226/21291|3226/21291|1076/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2589:2540,47:2540:89098:47:1679:0,-657.215,-7396.86 +NC_045512.2 3500 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=49;CIGAR=1X;DP=2368;DPB=2368;DPRA=0;EPP=3.40914;EPPR=11.1091;GTI=0;LEN=1;MEANALT=1;MQM=47.1429;MQMR=50.5442;NS=1;NUMALT=1;ODDS=2753.48;PAIRED=0.918367;PAIREDR=0.983614;PAO=0;PQA=0;PQR=0;PRO=0;QA=1649;QR=80645;RO=2319;RPL=15;RPP=19.0083;RPPR=387.752;RPR=34;RUN=1;SAF=25;SAP=3.05462;SAR=24;SRF=1130;SRP=6.26985;SRR=1189;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3235A>C|p.Thr1079Pro|3235/21291|3235/21291|1079/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2368:2319,49:2319:80645:49:1649:0,-578.836,-6661.83 +NC_045512.2 3522 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=156;CIGAR=1X;DP=1893;DPB=1893;DPRA=0;EPP=3.51141;EPPR=16.793;GTI=0;LEN=1;MEANALT=1;MQM=49.0577;MQMR=51.5181;NS=1;NUMALT=1;ODDS=1071.28;PAIRED=0.961538;PAIREDR=0.98388;PAO=0;PQA=0;PQR=0;PRO=0;QA=5381;QR=60781;RO=1737;RPL=55;RPP=32.4644;RPPR=275.649;RPR=101;RUN=1;SAF=76;SAP=3.23302;SAR=80;SRF=845;SRP=5.77183;SRR=892;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3257A>T|p.Glu1086Val|3257/21291|3257/21291|1086/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1893:1737,156:1737:60781:156:5381:0,-119.28,-4729.35 +NC_045512.2 3668 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1674;DPB=1674;DPRA=0;EPP=3.13803;EPPR=3.76559;GTI=0;LEN=1;MEANALT=2;MQM=42.4118;MQMR=52.933;NS=1;NUMALT=1;ODDS=2143.47;PAIRED=0.882353;PAIREDR=0.9843;PAO=0;PQA=0;PQR=0;PRO=0;QA=572;QR=58169;RO=1656;RPL=11;RPP=6.20364;RPPR=3.19912;RPR=6;RUN=1;SAF=10;SAP=4.1599;SAR=7;SRF=834;SRP=3.19912;SRR=822;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3403T>G|p.Tyr1135Asp|3403/21291|3403/21291|1135/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1674:1656,17:1656:58169:17:572:0,-462.9,-5012.95 +NC_045512.2 3961 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=1X;DP=455;DPB=455;DPRA=0;EPP=3.44459;EPPR=3.0296;GTI=0;LEN=1;MEANALT=1;MQM=55.2;MQMR=53.5956;NS=1;NUMALT=1;ODDS=575.059;PAIRED=1;PAIREDR=0.991111;PAO=0;PQA=0;PQR=0;PRO=0;QA=180;QR=15627;RO=450;RPL=2;RPP=3.44459;RPPR=3.0103;RPR=3;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=227;SRP=3.08751;SRR=223;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3696C>T|p.Ile1232Ile|3696/21291|3696/21291|1232/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:455:450,5:450:15627:5:180:0,-120.462,-1356.23 +NC_045512.2 4038 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=363;DPB=363;DPRA=0;EPP=3.0103;EPPR=3.30835;GTI=0;LEN=1;MEANALT=1;MQM=37.8333;MQMR=54.3165;NS=1;NUMALT=1;ODDS=446.545;PAIRED=1;PAIREDR=0.994398;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=12513;RO=357;RPL=6;RPP=16.0391;RPPR=22.7725;RPR=0;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=176;SRP=3.16236;SRR=181;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3773A>C|p.Asp1258Ala|3773/21291|3773/21291|1258/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:363:357,6:357:12513:6:216:0,-92.3258,-1088.77 +NC_045512.2 4102 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1952;DPB=1952;DPRA=0;EPP=3.0103;EPPR=4.46694;GTI=0;LEN=1;MEANALT=1;MQM=38.85;MQMR=51.4073;NS=1;NUMALT=1;ODDS=2496.52;PAIRED=1;PAIREDR=0.98913;PAO=0;PQA=0;PQR=0;PRO=0;QA=708;QR=67459;RO=1932;RPL=4;RPP=18.6449;RPPR=1095.71;RPR=16;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=983;SRP=4.30959;SRR=949;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3837A>T|p.Leu1279Phe|3837/21291|3837/21291|1279/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1952:1932,20:1932:67459:20:708:0,-538.151,-5712.79 +NC_045512.2 4162 . G T 3.59212E-13 . AB=0.123522;ABP=2813.62;AC=1;AF=0.5;AN=2;AO=282;CIGAR=1X;DP=2283;DPB=2283;DPRA=0;EPP=3.0411;EPPR=5.40749;GTI=0;LEN=1;MEANALT=1;MQM=49.4752;MQMR=50.932;NS=1;NUMALT=1;ODDS=430.424;PAIRED=0.98227;PAIREDR=0.996002;PAO=0;PQA=0;PQR=0;PRO=0;QA=9779;QR=69865;RO=2001;RPL=137;RPP=3.50312;RPPR=113.441;RPR=145;RUN=1;SAF=145;SAP=3.50312;SAR=137;SRF=1019;SRP=4.49593;SRR=982;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3897G>T|p.Val1299Val|3897/21291|3897/21291|1299/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2283:2001,282:2001:69865:282:9779:-137.285,0,-5222.59 +NC_045512.2 4181 . G T 28777.7 . AB=0.575386;ABP=111.706;AC=1;AF=0.5;AN=2;AO=1267;CIGAR=1X;DP=2202;DPB=2202;DPRA=0;EPP=4.08147;EPPR=3.24279;GTI=0;LEN=1;MEANALT=2;MQM=48.9811;MQMR=52.2934;NS=1;NUMALT=1;ODDS=4866.93;PAIRED=0.998421;PAIREDR=0.995717;PAO=0;PQA=0;PQR=0;PRO=0;QA=43524;QR=32368;RO=934;RPL=667;RPP=10.7039;RPPR=3.15909;RPR=600;RUN=1;SAF=646;SAP=4.08147;SAR=621;SRF=479;SRP=4.34945;SRR=455;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3916G>T|p.Ala1306Ser|3916/21291|3916/21291|1306/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2202:934,1267:934:32368:1267:43524:-2898.44,0,-2133.35 +NC_045512.2 4268 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=32;CIGAR=1X;DP=2364;DPB=2364;DPRA=0;EPP=3.0103;EPPR=3.01402;GTI=0;LEN=1;MEANALT=1;MQM=37.5312;MQMR=52.0746;NS=1;NUMALT=1;ODDS=2958.12;PAIRED=0.5625;PAIREDR=0.985849;PAO=0;PQA=0;PQR=0;PRO=0;QA=1148;QR=82280;RO=2332;RPL=31;RPP=64.083;RPPR=3.0103;RPR=1;RUN=1;SAF=15;SAP=3.28173;SAR=17;SRF=1169;SRP=3.04382;SRR=1163;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4003A>G|p.Asn1335Asp|4003/21291|4003/21291|1335/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2364:2332,32:2332:82280:32:1148:0,-633.643,-7000.81 +NC_045512.2 4435 . T C 3.44749E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=25;CIGAR=1X;DP=1857;DPB=1857;DPRA=0;EPP=3.79203;EPPR=7.42322;GTI=0;LEN=1;MEANALT=2;MQM=57.28;MQMR=53.1436;NS=1;NUMALT=1;ODDS=2286.49;PAIRED=1;PAIREDR=0.995085;PAO=0;PQA=0;PQR=0;PRO=0;QA=807;QR=64472;RO=1831;RPL=10;RPP=5.18177;RPPR=3.63767;RPR=15;RUN=1;SAF=13;SAP=3.09716;SAR=12;SRF=931;SRP=4.15;SRR=900;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4170T>C|p.Pro1390Pro|4170/21291|4170/21291|1390/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1857:1831,25:1831:64472:25:807:0,-486.055,-5542.5 +NC_045512.2 4747 . T C 8.73969E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=644;DPB=644;DPRA=0;EPP=3.55317;EPPR=3.59559;GTI=0;LEN=1;MEANALT=2;MQM=41.0625;MQMR=53.3876;NS=1;NUMALT=1;ODDS=745.803;PAIRED=0.625;PAIREDR=0.985646;PAO=0;PQA=0;PQR=0;PRO=0;QA=576;QR=21917;RO=627;RPL=0;RPP=37.7539;RPPR=23.544;RPR=16;RUN=1;SAF=7;SAP=3.55317;SAR=9;SRF=326;SRP=5.17485;SRR=301;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4482T>C|p.Ser1494Ser|4482/21291|4482/21291|1494/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:644:627,16:627:21917:16:576:0,-153.532,-1879.62 +NC_045512.2 4752 . C T 2.15769E-13 . AB=0.138414;ABP=733.223;AC=1;AF=0.5;AN=2;AO=89;CIGAR=1X;DP=643;DPB=643;DPRA=0;EPP=3.22989;EPPR=3.67391;GTI=0;LEN=1;MEANALT=2;MQM=48.8427;MQMR=53.2984;NS=1;NUMALT=1;ODDS=48.6552;PAIRED=0.977528;PAIREDR=0.976492;PAO=0;PQA=0;PQR=0;PRO=0;QA=3118;QR=19372;RO=553;RPL=48;RPP=4.20583;RPPR=10.9619;RPR=41;RUN=1;SAF=45;SAP=3.0347;SAR=44;SRF=279;SRP=3.10847;SRR=274;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4487C>T|p.Thr1496Ile|4487/21291|4487/21291|1496/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:643:553,89:553:19372:89:3118:-66.622,0,-1499.26 +NC_045512.2 4839 . T C 1.23554E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=596;DPB=596;DPRA=0;EPP=3.0103;EPPR=3.02502;GTI=0;LEN=1;MEANALT=1;MQM=56.5;MQMR=53.1797;NS=1;NUMALT=1;ODDS=758.227;PAIRED=1;PAIREDR=0.99322;PAO=0;PQA=0;PQR=0;PRO=0;QA=212;QR=20811;RO=590;RPL=2;RPP=4.45795;RPPR=5.49829;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=298;SRP=3.1428;SRR=292;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4574T>C|p.Ile1525Thr|4574/21291|4574/21291|1525/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:596:590,6:590:20811:6:212:0,-160.023,-1801.04 +NC_045512.2 4850 . A G 8.74157E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=650;DPB=650;DPRA=0;EPP=3.0103;EPPR=3.06442;GTI=0;LEN=1;MEANALT=1;MQM=40.625;MQMR=53.7212;NS=1;NUMALT=1;ODDS=823.193;PAIRED=1;PAIREDR=0.993769;PAO=0;PQA=0;PQR=0;PRO=0;QA=284;QR=22334;RO=642;RPL=0;RPP=20.3821;RPPR=3.0103;RPR=8;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=320;SRP=3.02383;SRR=322;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4585A>G|p.Lys1529Glu|4585/21291|4585/21291|1529/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:650:642,8:642:22334:8:284:0,-174.183,-1944 +NC_045512.2 4955 . GAAGT GAGT,GACGT 2.43493E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=13,48;CIGAR=1M1D3M,2M1X2M;DP=1155;DPB=1152;DPRA=0,0;EPP=3.17734,3.0103;EPPR=4.68418;GTI=0;LEN=1,1;MEANALT=4,4;MQM=43.8462,51.9167;MQMR=50.1815;NS=1;NUMALT=2;ODDS=1052.3;PAIRED=1,1;PAIREDR=0.983501;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=392,1680;QR=38285;RO=1091;RPL=0,32;RPP=31.2394,14.5915;RPPR=594.194;RPR=13,16;RUN=1,1;SAF=7,24;SAP=3.17734,3.0103;SAR=6,24;SRF=549;SRP=3.10783;SRR=542;TYPE=del,snp;ANN=GAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4692delA|p.Val1565fs|4692/21291|4692/21291|1564/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1155:1091,13,48:1091:38285:13,48:392,1680:0,-298.202,-3197.09,-193.338,-3065.95,-3081.74 +NC_045512.2 5118 . TTT AAA 7.71464E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=3X;DP=2311;DPB=2311;DPRA=0;EPP=5.48477;EPPR=3.51746;GTI=0;LEN=3;MEANALT=3;MQM=46.9535;MQMR=53.1435;NS=1;NUMALT=1;ODDS=2722.45;PAIRED=1;PAIREDR=0.996026;PAO=0;PQA=0;PQR=0;PRO=0;QA=1544;QR=79153;RO=2265;RPL=16;RPP=9.12072;RPPR=37.9849;RPR=27;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1141;SRP=3.28737;SRR=1124;TYPE=complex;ANN=AAA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4853_4855delTTTinsAAA|p.PheTyr1618*|4853/21291|4853/21291|1618/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2311:2265,43:2265:79153:43:1544:0,-573.594,-6798.82 +NC_045512.2 5182 . T C 7092.28 . AB=0.252637;ABP=1061.18;AC=1;AF=0.5;AN=2;AO=503;CIGAR=1X;DP=1991;DPB=1991;DPRA=0;EPP=3.53266;EPPR=4.15595;GTI=0;LEN=1;MEANALT=3;MQM=48.9344;MQMR=52.5188;NS=1;NUMALT=1;ODDS=1633.06;PAIRED=0.986083;PAIREDR=0.992598;PAO=0;PQA=0;PQR=0;PRO=0;QA=17356;QR=52385;RO=1486;RPL=246;RPP=3.53266;RPPR=4.50666;RPR=257;RUN=1;SAF=250;SAP=3.04915;SAR=253;SRF=734;SRP=3.48376;SRR=752;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4917T>C|p.Asp1639Asp|4917/21291|4917/21291|1639/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1991:1486,503:1486:52385:503:17356:-827.643,0,-3932.59 +NC_045512.2 5184 . C T 1768.41 . AB=0.166249;ABP=1935.14;AC=1;AF=0.5;AN=2;AO=332;CIGAR=1X;DP=1997;DPB=1997;DPRA=0;EPP=3.03646;EPPR=3.82738;GTI=0;LEN=1;MEANALT=2;MQM=50.6807;MQMR=51.7821;NS=1;NUMALT=1;ODDS=407.191;PAIRED=1;PAIREDR=0.989163;PAO=0;PQA=0;PQR=0;PRO=0;QA=11718;QR=57567;RO=1661;RPL=186;RPP=13.4752;RPPR=3.16849;RPR=146;RUN=1;SAF=167;SAP=3.03646;SAR=165;SRF=823;SRP=3.30445;SRR=838;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4919C>T|p.Pro1640Leu|4919/21291|4919/21291|1640/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1997:1661,332:1661:57567:332:11718:-395.676,0,-4326.74 +NC_045512.2 5239 . C T 8067.02 . AB=0.283776;ABP=721.382;AC=1;AF=0.5;AN=2;AO=502;CIGAR=1X;DP=1769;DPB=1769;DPRA=0;EPP=3.63319;EPPR=4.45394;GTI=0;LEN=1;MEANALT=2;MQM=46.5538;MQMR=52.3399;NS=1;NUMALT=1;ODDS=1857.5;PAIRED=0.998008;PAIREDR=0.993676;PAO=0;PQA=0;PQR=0;PRO=0;QA=17697;QR=44483;RO=1265;RPL=246;RPP=3.44286;RPPR=34.295;RPR=256;RUN=1;SAF=249;SAP=3.07951;SAR=253;SRF=620;SRP=4.08316;SRR=645;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4974C>T|p.Tyr1658Tyr|4974/21291|4974/21291|1658/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1769:1265,502:1265:44483:502:17697:-888.788,0,-3300.25 +NC_045512.2 5283 . AC GT 3.00147E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=2X;DP=1943;DPB=1943;DPRA=0;EPP=3.0103;EPPR=4.93047;GTI=0;LEN=2;MEANALT=5;MQM=27.9167;MQMR=50.6312;NS=1;NUMALT=1;ODDS=2370.54;PAIRED=0.944444;PAIREDR=0.996318;PAO=0;PQA=0;PQR=0;PRO=0;QA=1258;QR=66807;RO=1901;RPL=24;RPP=11.6962;RPPR=22.019;RPR=12;RUN=1;SAF=16;SAP=3.9754;SAR=20;SRF=946;SRP=3.10282;SRR=955;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5018_5019delACinsGT|p.Asn1673Ser|5018/21291|5018/21291|1673/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1943:1901,36:1901:66807:36:1258:0,-517.448,-5588.85 +NC_045512.2 5388 . C A 15425.8 . AB=0.421856;ABP=89.8904;AC=1;AF=0.5;AN=2;AO=691;CIGAR=1X;DP=1638;DPB=1638;DPRA=0;EPP=4.14475;EPPR=3.12289;GTI=0;LEN=1;MEANALT=2;MQM=50.8871;MQMR=52.8868;NS=1;NUMALT=1;ODDS=3551.93;PAIRED=0.994211;PAIREDR=0.996825;PAO=0;PQA=0;PQR=0;PRO=0;QA=24252;QR=33052;RO=945;RPL=343;RPP=3.08886;RPPR=10.476;RPR=348;RUN=1;SAF=347;SAP=3.03858;SAR=344;SRF=484;SRP=4.22586;SRR=461;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5123C>A|p.Ala1708Asp|5123/21291|5123/21291|1708/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1638:945,691:945:33052:691:24252:-1559.56,0,-2377.37 +NC_045512.2 5584 . A G 4302.11 . AB=0.25588;ABP=729.246;AC=1;AF=0.5;AN=2;AO=359;CIGAR=1X;DP=1403;DPB=1403;DPRA=0;EPP=3.30668;EPPR=3.26222;GTI=0;LEN=1;MEANALT=2;MQM=41.5766;MQMR=50.7507;NS=1;NUMALT=1;ODDS=990.597;PAIRED=1;PAIREDR=0.999041;PAO=0;PQA=0;PQR=0;PRO=0;QA=12643;QR=36358;RO=1043;RPL=241;RPP=94.5206;RPPR=6.51006;RPR=118;RUN=1;SAF=176;SAP=3.30668;SAR=183;SRF=520;SRP=3.02904;SRR=523;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5319A>G|p.Thr1773Thr|5319/21291|5319/21291|1773/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1403:1043,359:1043:36358:359:12643:-522.975,0,-2660.57 +NC_045512.2 5765 . GG AC 2.41084E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=2X;DP=638;DPB=639;DPRA=0;EPP=3.20771;EPPR=3.09772;GTI=0;LEN=2;MEANALT=4;MQM=38;MQMR=53.4525;NS=1;NUMALT=1;ODDS=776.345;PAIRED=1;PAIREDR=0.996779;PAO=2;PQA=64;PQR=0;PRO=0;QA=362;QR=21351;RO=621;RPL=1;RPP=19.0002;RPPR=3.04177;RPR=10;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=308;SRP=3.09772;SRR=313;TYPE=complex;ANN=AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5500_5501delGGinsAC|p.Gly1834Thr|5500/21291|5500/21291|1834/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:638:621,11:621:21351:11:362:0,-164.517,-1844.91 +NC_045512.2 5818 . T C 5838.01 . AB=0.4;ABP=59.4686;AC=1;AF=0.5;AN=2;AO=260;CIGAR=1X;DP=650;DPB=650;DPRA=0;EPP=3.04371;EPPR=3.21074;GTI=0;LEN=1;MEANALT=1;MQM=52.7192;MQMR=53.2333;NS=1;NUMALT=1;ODDS=1344.25;PAIRED=1;PAIREDR=0.984615;PAO=0;PQA=0;PQR=0;PRO=0;QA=9096;QR=13642;RO=390;RPL=135;RPP=3.84548;RPPR=7.37552;RPR=125;RUN=1;SAF=130;SAP=3.0103;SAR=130;SRF=197;SRP=3.09939;SRR=193;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5553T>C|p.Ala1851Ala|5553/21291|5553/21291|1851/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:650:390,260:390:13642:260:9096:-596.985,0,-994.554 +NC_045512.2 5909 . TAT TT 0.0 . AB=0.156273;ABP=1401.75;AC=1;AF=0.5;AN=2;AO=213;CIGAR=1M1D1M;DP=1363;DPB=1294.33;DPRA=0;EPP=5.30411;EPPR=6.83731;GTI=0;LEN=1;MEANALT=2;MQM=35.23;MQMR=50.8407;NS=1;NUMALT=1;ODDS=246.516;PAIRED=1;PAIREDR=0.996519;PAO=3.5;PQA=115.5;PQR=115.5;PRO=3.5;QA=7203;QR=39975;RO=1149;RPL=22;RPP=294.181;RPPR=95.3139;RPR=191;RUN=1;SAF=114;SAP=5.30411;SAR=99;SRF=595;SRP=6.18719;SRR=554;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5645delA|p.Tyr1882fs|5645/21291|5645/21291|1882/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1363:1149,213:1149:39975:213:7203:-87.388,0,-2987.82 +NC_045512.2 5944 . C T 3592.72 . AB=0.230724;ABP=1081.24;AC=1;AF=0.5;AN=2;AO=395;CIGAR=1X;DP=1712;DPB=1712;DPRA=0;EPP=3.93936;EPPR=5.52194;GTI=0;LEN=1;MEANALT=2;MQM=38.6253;MQMR=51.3338;NS=1;NUMALT=1;ODDS=827.255;PAIRED=1;PAIREDR=0.996198;PAO=0;PQA=0;PQR=0;PRO=0;QA=13976;QR=46014;RO=1315;RPL=120;RPP=135.085;RPPR=20.529;RPR=275;RUN=1;SAF=205;SAP=4.24721;SAR=190;SRF=665;SRP=3.38184;SRR=650;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5679C>T|p.Asp1893Asp|5679/21291|5679/21291|1893/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1712:1315,395:1315:46014:395:13976:-494.233,0,-3429.74 +NC_045512.2 5986 . CACAG TACAA,TACAG 13031.4 . AB=0.329331,0.288165;ABP=445.51,684.722;AC=1,0;AF=0.5,0;AN=2;AO=576,504;CIGAR=1X3M1X,1X4M;DP=1749;DPB=1765.2;DPRA=0,0;EPP=3.25157,3.02753;EPPR=3.09318;GTI=0;LEN=5,1;MEANALT=8,8;MQM=48.3976,43.7917;MQMR=52.0015;NS=1;NUMALT=2;ODDS=771.741;PAIRED=0.996528,0.996032;PAIREDR=0.996947;PAO=55,26;PQA=1715.5,887.5;PQR=0;PRO=0;QA=20335,15262;QR=22850;RO=655;RPL=279,257;RPP=4.23175,3.44115;RPPR=8.05276;RPR=297,247;RUN=1,1;SAF=287,256;SAP=3.02538,3.28604;SAR=289,248;SRF=333;SRP=3.41144;SRR=322;TYPE=complex,snp;ANN=TACAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721_5725delCACAGinsTACAA|p.Glu1909Lys|5721/21291|5721/21291|1907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1749:655,576,504:655:22850:576,504:20335,15262:-1312.47,0,-1588.23,-332.158,-584.148,-1942.05 +NC_045512.2 6401 . CC GT,CT 41378.4 . AB=0.0133511,0.5751;ABP=6165.94,149.78;AC=0,1;AF=0,0.5;AN=2;AO=40,1723;CIGAR=2X,1M1X;DP=2996;DPB=2997;DPRA=0,0;EPP=3.0103,4.92719;EPPR=4.20567;GTI=0;LEN=2,1;MEANALT=5,5;MQM=50.125,50.3186;MQMR=53.1954;NS=1;NUMALT=2;ODDS=6500.05;PAIRED=1,0.993035;PAIREDR=0.989414;PAO=1.5,0.5;PQA=48,16;PQR=0;PRO=0;QA=1416,60413;QR=42916;RO=1228;RPL=23,837;RPP=4.96463,6.03625;RPPR=51.7376;RPR=17,886;RUN=1,1;SAF=19,845;SAP=3.22745,4.38275;SAR=21,878;SRF=606;SRP=3.46298;SRR=622;TYPE=complex,snp;ANN=CT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6137C>T|p.Pro2046Leu|6137/21291|6137/21291|2046/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:2996:1228,40,1723:1228:42916:40,1723:1416,60413:-4165.56,-4430.39,-7791.85,0,-3268.69,-2854.85 +NC_045512.2 6459 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=47;CIGAR=1X;DP=2778;DPB=2778;DPRA=0;EPP=3.42611;EPPR=9.88729;GTI=0;LEN=1;MEANALT=1;MQM=40.6809;MQMR=52.4357;NS=1;NUMALT=1;ODDS=3365.28;PAIRED=0.595745;PAIREDR=0.992677;PAO=0;PQA=0;PQR=0;PRO=0;QA=1642;QR=96439;RO=2731;RPL=0;RPP=105.07;RPPR=159.052;RPR=47;RUN=1;SAF=22;SAP=3.42611;SAR=25;SRF=1324;SRP=8.48788;SRR=1407;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6194A>G|p.Asn2065Ser|6194/21291|6194/21291|2065/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2778:2731,47:2731:96439:47:1642:0,-709.432,-8216.17 +NC_045512.2 6581 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=3950;DPB=3950;DPRA=0;EPP=3.0103;EPPR=9.87224;GTI=0;LEN=1;MEANALT=2;MQM=53.7143;MQMR=53.3706;NS=1;NUMALT=1;ODDS=4948;PAIRED=1;PAIREDR=0.99051;PAO=0;PQA=0;PQR=0;PRO=0;QA=1448;QR=137583;RO=3899;RPL=24;RPP=4.87156;RPPR=11.4361;RPR=18;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=1980;SRP=5.08264;SRR=1919;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6316A>G|p.Thr2106Ala|6316/21291|6316/21291|2106/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3950:3899,42:3899:137583:42:1448:0,-1057.38,-11906.7 +NC_045512.2 6654 . TTAATAGTGTCCCTTGGGATACTATAGCT TT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=90;CIGAR=1M27D1M;DP=2584;DPB=2502.62;DPRA=0;EPP=3.87889;EPPR=3.33544;GTI=0;LEN=27;MEANALT=41;MQM=49.5111;MQMR=53.8523;NS=1;NUMALT=1;ODDS=2613.21;PAIRED=1;PAIREDR=0.994608;PAO=8;PQA=245;PQR=626;PRO=23;QA=2527;QR=83585;RO=2411;RPL=56;RPP=14.688;RPPR=13.7109;RPR=34;RUN=1;SAF=44;SAP=3.10681;SAR=46;SRF=1215;SRP=3.33544;SRR=1196;TYPE=del;ANN=TT|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6394_6420delAGTGTCCCTTGGGATACTATAGCTAAT|p.Ser2132_Asn2140del|6394/21291|6394/21291|2132/7096||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:2584:2411,90:2411:83585:90:2527:0,-542.491,-7120.65 +NC_045512.2 6728 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=131;CIGAR=1X;DP=4495;DPB=4495;DPRA=0;EPP=3.02688;EPPR=3.0347;GTI=0;LEN=1;MEANALT=3;MQM=52.626;MQMR=52.7916;NS=1;NUMALT=1;ODDS=4749.06;PAIRED=0.984733;PAIREDR=0.984637;PAO=0;PQA=0;PQR=0;PRO=0;QA=4607;QR=153668;RO=4361;RPL=65;RPP=3.02688;RPPR=567.775;RPR=66;RUN=1;SAF=63;SAP=3.4247;SAR=68;SRF=2187;SRP=3.09445;SRR=2174;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6463A>G|p.Asn2155Asp|6463/21291|6463/21291|2155/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4495:4361,131:4361:153668:131:4607:0,-960.457,-12910.3 +NC_045512.2 6772 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=72;CIGAR=1X;DP=5961;DPB=5961;DPRA=0;EPP=3.13094;EPPR=4.2522;GTI=0;LEN=1;MEANALT=3;MQM=47.5833;MQMR=51.9471;NS=1;NUMALT=1;ODDS=7432.86;PAIRED=1;PAIREDR=0.991159;PAO=0;PQA=0;PQR=0;PRO=0;QA=2518;QR=206887;RO=5882;RPL=9;RPP=90.9549;RPPR=574.318;RPR=63;RUN=1;SAF=38;SAP=3.49285;SAR=34;SRF=2959;SRP=3.48875;SRR=2923;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6507G>A|p.Met2169Ile|6507/21291|6507/21291|2169/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5961:5882,72:5882:206887:72:2518:0,-1588.67,-17552.3 +NC_045512.2 6954 . T C 78261.2 . AB=0.74609;ABP=2290.15;AC=1;AF=0.5;AN=2;AO=3244;CIGAR=1X;DP=4348;DPB=4348;DPRA=0;EPP=3.39586;EPPR=3.51658;GTI=0;LEN=1;MEANALT=3;MQM=49.9263;MQMR=53.5255;NS=1;NUMALT=1;ODDS=4109.19;PAIRED=0.99476;PAIREDR=0.993625;PAO=0;PQA=0;PQR=0;PRO=0;QA=112718;QR=38145;RO=1098;RPL=1650;RPP=5.10948;RPPR=11.1108;RPR=1594;RUN=1;SAF=1620;SAP=3.02101;SAR=1624;SRF=546;SRP=3.0815;SRR=552;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6689T>C|p.Ile2230Thr|6689/21291|6689/21291|2230/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4348:1098,3244:1098:38145:3244:112718:-8076.53,0,-2034.93 +NC_045512.2 7124 . C T 36735.9 . AB=0.593619;ABP=203.456;AC=1;AF=0.5;AN=2;AO=1563;CIGAR=1X;DP=2633;DPB=2633;DPRA=0;EPP=3.87861;EPPR=6.09993;GTI=0;LEN=1;MEANALT=2;MQM=48.3762;MQMR=52.6707;NS=1;NUMALT=1;ODDS=5513.12;PAIRED=0.997441;PAIREDR=0.992516;PAO=0;PQA=0;PQR=0;PRO=0;QA=55234;QR=37290;RO=1069;RPL=642;RPP=111.155;RPPR=68.0956;RPR=921;RUN=1;SAF=815;SAP=9.24686;SAR=748;SRF=544;SRP=3.7436;SRR=525;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6859C>T|p.Pro2287Ser|6859/21291|6859/21291|2287/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2633:1069,1563:1069:37290:1563:55234:-3714.31,0,-2430.12 +NC_045512.2 7262 . C A 7.353E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=2907;DPB=2907;DPRA=0;EPP=32.2045;EPPR=8.10485;GTI=0;LEN=1;MEANALT=2;MQM=54.75;MQMR=52.6598;NS=1;NUMALT=1;ODDS=3772.74;PAIRED=1;PAIREDR=0.995813;PAO=0;PQA=0;PQR=0;PRO=0;QA=526;QR=95172;RO=2866;RPL=29;RPP=32.2045;RPPR=29.2225;RPR=7;RUN=1;SAF=36;SAP=81.1833;SAR=0;SRF=1432;SRP=3.01333;SRR=1434;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6997C>A|p.Leu2333Ile|6997/21291|6997/21291|2333/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2907:2866,36:2866:95172:36:526:0,-827.217,-8169.18 +NC_045512.2 7363 . G C 2.6519E-13 . AB=0.121355;ABP=3974.32;AC=1;AF=0.5;AN=2;AO=387;CIGAR=1X;DP=3189;DPB=3189;DPRA=0;EPP=3.46479;EPPR=5.99569;GTI=0;LEN=1;MEANALT=3;MQM=45.4703;MQMR=50.912;NS=1;NUMALT=1;ODDS=883.768;PAIRED=0.994832;PAIREDR=0.995351;PAO=0;PQA=0;PQR=0;PRO=0;QA=13459;QR=98261;RO=2796;RPL=311;RPP=312.88;RPPR=63.0318;RPR=76;RUN=1;SAF=189;SAP=3.46479;SAR=198;SRF=1396;SRP=3.02273;SRR=1400;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7098G>C|p.Trp2366Cys|7098/21291|7098/21291|2366/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3189:2796,387:2796:98261:387:13459:-103.873,0,-7409.47 +NC_045512.2 7429 . A G 17852.7 . AB=0.408913;ABP=150.168;AC=1;AF=0.5;AN=2;AO=835;CIGAR=1X;DP=2042;DPB=2042;DPRA=0;EPP=4.15715;EPPR=4.42428;GTI=0;LEN=1;MEANALT=2;MQM=50.1353;MQMR=52.887;NS=1;NUMALT=1;ODDS=4110.74;PAIRED=0.99521;PAIREDR=0.994186;PAO=0;PQA=0;PQR=0;PRO=0;QA=28871;QR=42302;RO=1204;RPL=398;RPP=6.96576;RPPR=4.2295;RPR=437;RUN=1;SAF=423;SAP=3.32497;SAR=412;SRF=613;SRP=3.88322;SRR=591;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7164A>G|p.Ala2388Ala|7164/21291|7164/21291|2388/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2042:1204,835:1204:42302:835:28871:-1808.82,0,-3057.19 +NC_045512.2 8172 . C T 7.05188E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=841;DPB=841;DPRA=0;EPP=3.13803;EPPR=3.02084;GTI=0;LEN=1;MEANALT=1;MQM=50.0588;MQMR=52.818;NS=1;NUMALT=1;ODDS=984.169;PAIRED=1;PAIREDR=0.970874;PAO=0;PQA=0;PQR=0;PRO=0;QA=577;QR=28651;RO=824;RPL=11;RPP=6.20364;RPPR=7.22675;RPR=6;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=419;SRP=3.52682;SRR=405;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7907C>T|p.Ala2636Val|7907/21291|7907/21291|2636/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:841:824,17:824:28651:17:577:0,-204.864,-2432.99 +NC_045512.2 8364 . A G 8004.45 . AB=0.408027;ABP=68.917;AC=1;AF=0.5;AN=2;AO=366;CIGAR=1X;DP=897;DPB=897;DPRA=0;EPP=3.0103;EPPR=3.27252;GTI=0;LEN=1;MEANALT=2;MQM=50.4071;MQMR=53.6094;NS=1;NUMALT=1;ODDS=1843.09;PAIRED=1;PAIREDR=0.992453;PAO=0;PQA=0;PQR=0;PRO=0;QA=12874;QR=18616;RO=530;RPL=173;RPP=5.38349;RPPR=9.56569;RPR=193;RUN=1;SAF=184;SAP=3.03403;SAR=182;SRF=268;SRP=3.1578;SRR=262;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8099A>G|p.Asn2700Ser|8099/21291|8099/21291|2700/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:897:530,366:530:18616:366:12874:-814.947,0,-1355.26 +NC_045512.2 8557 . A G 7207.18 . AB=0.361084;ABP=176.158;AC=1;AF=0.5;AN=2;AO=373;CIGAR=1X;DP=1033;DPB=1033;DPRA=0;EPP=3.29556;EPPR=4.60271;GTI=0;LEN=1;MEANALT=1;MQM=46.622;MQMR=52.8197;NS=1;NUMALT=1;ODDS=1659.51;PAIRED=0.991957;PAIREDR=0.993939;PAO=0;PQA=0;PQR=0;PRO=0;QA=13232;QR=23292;RO=660;RPL=194;RPP=4.32017;RPPR=3.85257;RPR=179;RUN=1;SAF=178;SAP=4.69275;SAR=195;SRF=321;SRP=4.0763;SRR=339;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8292A>G|p.Lys2764Lys|8292/21291|8292/21291|2764/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1033:660,373:660:23292:373:13232:-746.33,0,-1718.1 +NC_045512.2 8565 . ATAA GTAG 5776.02 . AB=0.3433;ABP=195.603;AC=1;AF=0.5;AN=2;AO=310;CIGAR=1X2M1X;DP=903;DPB=910;DPRA=0;EPP=3.0103;EPPR=5.48989;GTI=0;LEN=4;MEANALT=2;MQM=46.2516;MQMR=53.3649;NS=1;NUMALT=1;ODDS=1329.98;PAIRED=0.987097;PAIREDR=0.996622;PAO=26;PQA=880;PQR=0;PRO=2;QA=11017;QR=20793;RO=592;RPL=153;RPP=3.12238;RPPR=17.1102;RPR=157;RUN=1;SAF=152;SAP=3.26247;SAR=158;SRF=288;SRP=3.94932;SRR=304;TYPE=complex;ANN=GTAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8300_8303delATAAinsGTAG|p.AsnAsn2767SerSer|8300/21291|8300/21291|2767/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:903:592,310:592:20793:310:11017:-604.693,0,-1551.51 +NC_045512.2 8634 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=71;CIGAR=1X;DP=694;DPB=694;DPRA=0;EPP=3.7749;EPPR=6.1523;GTI=0;LEN=1;MEANALT=2;MQM=47.1831;MQMR=51.8006;NS=1;NUMALT=1;ODDS=331.413;PAIRED=0.971831;PAIREDR=0.96463;PAO=0;PQA=0;PQR=0;PRO=0;QA=2483;QR=21417;RO=622;RPL=71;RPP=157.185;RPPR=178.18;RPR=0;RUN=1;SAF=33;SAP=3.7749;SAR=38;SRF=307;SRP=3.23373;SRR=315;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8369T>C|p.Ile2790Thr|8369/21291|8369/21291|2790/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:694:622,71:622:21417:71:2483:0,-7.8921,-1639.83 +NC_045512.2 8716 . TC GA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=2X;DP=265;DPB=265;DPRA=0;EPP=3.44459;EPPR=3.84548;GTI=0;LEN=2;MEANALT=1;MQM=46.6;MQMR=54.0346;NS=1;NUMALT=1;ODDS=322.356;PAIRED=0.8;PAIREDR=0.965385;PAO=0;PQA=0;PQR=0;PRO=0;QA=178;QR=9081;RO=260;RPL=0;RPP=13.8677;RPPR=3.54482;RPR=5;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=131;SRP=3.04371;SRR=129;TYPE=complex;ANN=GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8451_8452delTCinsGA|p.Arg2818Ser|8451/21291|8451/21291|2817/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:265:260,5:260:9081:5:178:0,-65.7297,-782.204 +NC_045512.2 8782 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=295;DPB=295;DPRA=0;EPP=3.0103;EPPR=3.07746;GTI=0;LEN=1;MEANALT=1;MQM=56.5;MQMR=53.7766;NS=1;NUMALT=1;ODDS=368.964;PAIRED=1;PAIREDR=0.979381;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=10001;RO=291;RPL=0;RPP=11.6962;RPPR=3.37594;RPR=4;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=140;SRP=3.91321;SRR=151;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8517C>A|p.Ser2839Arg|8517/21291|8517/21291|2839/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:295:291,4:291:10001:4:140:0,-75.8695,-867.135 +NC_045512.2 8844 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=330;DPB=330;DPRA=0;EPP=3.0103;EPPR=3.03761;GTI=0;LEN=1;MEANALT=1;MQM=44.6667;MQMR=51.5503;NS=1;NUMALT=1;ODDS=343.81;PAIRED=0.666667;PAIREDR=0.943396;PAO=0;PQA=0;PQR=0;PRO=0;QA=432;QR=11050;RO=318;RPL=0;RPP=29.068;RPPR=3.44733;RPR=12;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=151;SRP=4.7584;SRR=167;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8579G>A|p.Arg2860Lys|8579/21291|8579/21291|2860/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:330:318,12:318:11050:12:432:0,-64.5233,-902.184 +NC_045512.2 8873 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=293;DPB=293;DPRA=0;EPP=3.73412;EPPR=3.61891;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=52.3633;NS=1;NUMALT=1;ODDS=376.316;PAIRED=0.333333;PAIREDR=0.955017;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=9921;RO=289;RPL=3;RPP=9.52472;RPPR=3.01781;RPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=139;SRP=3.91946;SRR=150;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8608C>T|p.Pro2870Ser|8608/21291|8608/21291|2870/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:293:289,3:289:9921:3:104:0,-78.3896,-844.462 +NC_045512.2 8986 . C T 19981.1 . AB=0.873913;ABP=1120.24;AC=1;AF=0.5;AN=2;AO=804;CIGAR=1X;DP=920;DPB=920;DPRA=0;EPP=3.53966;EPPR=3.0103;GTI=0;LEN=1;MEANALT=3;MQM=49.1704;MQMR=53.2895;NS=1;NUMALT=1;ODDS=139.322;PAIRED=0.992537;PAIREDR=0.991228;PAO=0;PQA=0;PQR=0;PRO=0;QA=28119;QR=3988;RO=114;RPL=329;RPP=60.5813;RPPR=3.0103;RPR=475;RUN=1;SAF=414;SAP=4.56598;SAR=390;SRF=60;SRP=3.69603;SRR=54;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8721C>T|p.Asp2907Asp|8721/21291|8721/21291|2907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:920:114,804:114:3988:804:28119:-2078.41,0,-73.1119 +NC_045512.2 9026 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=71;CIGAR=1X;DP=1113;DPB=1113;DPRA=0;EPP=3.04088;EPPR=4.01893;GTI=0;LEN=1;MEANALT=1;MQM=41.831;MQMR=49.8301;NS=1;NUMALT=1;ODDS=885.288;PAIRED=1;PAIREDR=0.997121;PAO=0;PQA=0;PQR=0;PRO=0;QA=2421;QR=36529;RO=1042;RPL=33;RPP=3.7749;RPPR=21.4241;RPR=38;RUN=1;SAF=36;SAP=3.04088;SAR=35;SRF=532;SRP=4.01893;SRR=510;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8761A>T|p.Ile2921Phe|8761/21291|8761/21291|2921/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1113:1042,71:1042:36529:71:2421:0,-157.653,-2908.65 +NC_045512.2 9053 . G T 22309.4 . AB=0.843808;ABP=1113.91;AC=1;AF=0.5;AN=2;AO=913;CIGAR=1X;DP=1082;DPB=1082;DPRA=0;EPP=3.06976;EPPR=3.12594;GTI=0;LEN=1;MEANALT=1;MQM=49.3527;MQMR=52.2071;NS=1;NUMALT=1;ODDS=124.118;PAIRED=0.996714;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32053;QR=5942;RO=169;RPL=427;RPP=11.2895;RPPR=17.0028;RPR=486;RUN=1;SAF=458;SAP=3.03171;SAR=455;SRF=84;SRP=3.02315;SRR=85;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8788G>T|p.Val2930Leu|8788/21291|8788/21291|2930/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1082:169,913:169:5942:913:32053:-2362.09,0,-184.534 +NC_045512.2 9241 . A T 1.11862E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=60;CIGAR=1X;DP=1557;DPB=1557;DPRA=0;EPP=4.31318;EPPR=9.9256;GTI=0;LEN=1;MEANALT=2;MQM=47.4833;MQMR=49.9773;NS=1;NUMALT=1;ODDS=1548.51;PAIRED=0.966667;PAIREDR=0.968562;PAO=0;PQA=0;PQR=0;PRO=0;QA=2105;QR=52635;RO=1495;RPL=6;RPP=86.3948;RPPR=275.336;RPR=54;RUN=1;SAF=33;SAP=4.31318;SAR=27;SRF=749;SRP=3.02337;SRR=746;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8976A>T|p.Ser2992Ser|8976/21291|8976/21291|2992/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1557:1495,60:1495:52635:60:2105:0,-298.895,-4239.78 +NC_045512.2 9445 . T C 2.15045E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=91;CIGAR=1X;DP=1927;DPB=1927;DPRA=0;EPP=3.22506;EPPR=3.12857;GTI=0;LEN=1;MEANALT=1;MQM=49.0769;MQMR=50.7925;NS=1;NUMALT=1;ODDS=1726.32;PAIRED=1;PAIREDR=0.961329;PAO=0;PQA=0;PQR=0;PRO=0;QA=3146;QR=64355;RO=1836;RPL=56;RPP=13.5336;RPPR=8.16222;RPR=35;RUN=1;SAF=44;SAP=3.22506;SAR=47;SRF=896;SRP=5.30004;SRR=940;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9180T>C|p.Leu3060Leu|9180/21291|9180/21291|3060/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1927:1836,91:1836:64355:91:3146:0,-321.171,-5169.55 +NC_045512.2 9511 . T C 4.64324E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=220;CIGAR=1X;DP=2576;DPB=2576;DPRA=0;EPP=3.16823;EPPR=19.815;GTI=0;LEN=1;MEANALT=2;MQM=48.6909;MQMR=51.9338;NS=1;NUMALT=1;ODDS=1399.05;PAIRED=0.986364;PAIREDR=0.990658;PAO=0;PQA=0;PQR=0;PRO=0;QA=7616;QR=83328;RO=2355;RPL=124;RPP=10.7486;RPPR=413.229;RPR=96;RUN=1;SAF=108;SAP=3.16823;SAR=112;SRF=1215;SRP=8.19694;SRR=1140;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9246T>C|p.Thr3082Thr|9246/21291|9246/21291|3082/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2576:2355,220:2355:83328:220:7616:0,-150.664,-6510.68 +NC_045512.2 9521 . C T 5.11094E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=56;CIGAR=1X;DP=2683;DPB=2683;DPRA=0;EPP=3.63072;EPPR=12.4812;GTI=0;LEN=1;MEANALT=2;MQM=42.4643;MQMR=51.472;NS=1;NUMALT=1;ODDS=3128.98;PAIRED=0.946429;PAIREDR=0.992762;PAO=0;PQA=0;PQR=0;PRO=0;QA=1974;QR=91769;RO=2625;RPL=11;RPP=47.8357;RPPR=156.677;RPR=45;RUN=1;SAF=29;SAP=3.16541;SAR=27;SRF=1329;SRP=3.91115;SRR=1296;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9256C>T|p.Leu3086Phe|9256/21291|9256/21291|3086/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2683:2625,56:2625:91769:56:1974:0,-659.011,-7674.21 +NC_045512.2 9627 . CTTTTTTAG CTTTTTAG 3.32693E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1M1D7M;DP=2471;DPB=2468.56;DPRA=0;EPP=3.29983;EPPR=8.18457;GTI=0;LEN=1;MEANALT=11;MQM=48.4667;MQMR=52.5949;NS=1;NUMALT=1;ODDS=3061.58;PAIRED=1;PAIREDR=0.987624;PAO=1.5;PQA=40;PQR=40;PRO=1.5;QA=944;QR=85133;RO=2424;RPL=17;RPP=4.16842;RPPR=20.5684;RPR=13;RUN=1;SAF=15;SAP=3.0103;SAR=15;SRF=1234;SRP=4.74461;SRR=1190;TYPE=del;ANN=CTTTTTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9368delT|p.Leu3123fs|9368/21291|9368/21291|3123/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2471:2424,30:2424:85133:30:944:0,-655.432,-7265.75 +NC_045512.2 9734 . T C 10284.7 . AB=0.267343;ABP=1161.96;AC=1;AF=0.5;AN=2;AO=659;CIGAR=1X;DP=2465;DPB=2465;DPRA=0;EPP=3.09268;EPPR=4.65908;GTI=0;LEN=1;MEANALT=2;MQM=49.393;MQMR=51.5042;NS=1;NUMALT=1;ODDS=2368.13;PAIRED=1;PAIREDR=0.993344;PAO=0;PQA=0;PQR=0;PRO=0;QA=22831;QR=63717;RO=1803;RPL=324;RPP=3.40901;RPPR=35.0091;RPR=335;RUN=1;SAF=327;SAP=3.09268;SAR=332;SRF=892;SRP=3.44508;SRR=911;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9469T>C|p.Phe3157Leu|9469/21291|9469/21291|3157/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2465:1803,659:1803:63717:659:22831:-1156.78,0,-4685.13 +NC_045512.2 9865 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=945;DPB=945;DPRA=0;EPP=3.20771;EPPR=4.13556;GTI=0;LEN=1;MEANALT=1;MQM=50.3636;MQMR=51.8437;NS=1;NUMALT=1;ODDS=1188.97;PAIRED=0.909091;PAIREDR=0.981799;PAO=0;PQA=0;PQR=0;PRO=0;QA=377;QR=32898;RO=934;RPL=4;RPP=4.78696;RPPR=16.439;RPR=7;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=483;SRP=5.39101;SRR=451;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9600T>C|p.Pro3200Pro|9600/21291|9600/21291|3200/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:945:934,11:934:32898:11:377:0,-252.906,-2775.77 +NC_045512.2 9891 . C T 7564.06 . AB=0.350235;ABP=210.495;AC=1;AF=0.5;AN=2;AO=373;CIGAR=1X;DP=1065;DPB=1065;DPRA=0;EPP=3.99416;EPPR=4.97437;GTI=0;LEN=1;MEANALT=2;MQM=50.5684;MQMR=52.7902;NS=1;NUMALT=1;ODDS=1741.69;PAIRED=0.994638;PAIREDR=0.984081;PAO=0;PQA=0;PQR=0;PRO=0;QA=13059;QR=24218;RO=691;RPL=182;RPP=3.48185;RPPR=6.43249;RPR=191;RUN=1;SAF=188;SAP=3.06269;SAR=185;SRF=347;SRP=3.03858;SRR=344;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9626C>T|p.Ala3209Val|9626/21291|9626/21291|3209/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1065:691,373:691:24218:373:13059:-785.258,0,-1781.24 +NC_045512.2 10029 . C T 9917.01 . AB=0.509918;ABP=3.74257;AC=1;AF=0.5;AN=2;AO=437;CIGAR=1X;DP=857;DPB=857;DPRA=0;EPP=4.80412;EPPR=3.01548;GTI=0;LEN=1;MEANALT=2;MQM=48.9451;MQMR=53.5131;NS=1;NUMALT=1;ODDS=2283.48;PAIRED=0.990847;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15164;QR=14518;RO=419;RPL=203;RPP=7.78555;RPPR=4.17637;RPR=234;RUN=1;SAF=216;SAP=3.13453;SAR=221;SRF=209;SRP=3.01548;SRR=210;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9764C>T|p.Thr3255Ile|9764/21291|9764/21291|3255/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:857:419,437:419:14518:437:15164:-1000.27,0,-1019.67 +NC_045512.2 10228 . C T 13986.5 . AB=0.280464;ABP=1267.26;AC=1;AF=0.5;AN=2;AO=847;CIGAR=1X;DP=3020;DPB=3020;DPRA=0;EPP=3.01286;EPPR=3.58669;GTI=0;LEN=1;MEANALT=3;MQM=49.3318;MQMR=52.8512;NS=1;NUMALT=1;ODDS=3220.5;PAIRED=0.995277;PAIREDR=0.99447;PAO=0;PQA=0;PQR=0;PRO=0;QA=29649;QR=76244;RO=2170;RPL=439;RPP=5.47404;RPPR=3.07434;RPR=408;RUN=1;SAF=423;SAP=3.01286;SAR=424;SRF=1084;SRP=3.0143;SRR=1086;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9963C>T|p.Leu3321Leu|9963/21291|9963/21291|3321/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3020:2170,847:2170:76244:847:29649:-1537.73,0,-5713.37 +NC_045512.2 10408 . C T 7069.66 . AB=0.250962;ABP=1263.03;AC=1;AF=0.5;AN=2;AO=587;CIGAR=1X;DP=2339;DPB=2339;DPRA=0;EPP=3.30994;EPPR=4.99565;GTI=0;LEN=1;MEANALT=2;MQM=45.0187;MQMR=51.1657;NS=1;NUMALT=1;ODDS=1627.85;PAIRED=0.945486;PAIREDR=0.993714;PAO=0;PQA=0;PQR=0;PRO=0;QA=20801;QR=61151;RO=1750;RPL=466;RPP=443.316;RPPR=97.5326;RPR=121;RUN=1;SAF=290;SAP=3.19156;SAR=297;SRF=870;SRP=3.13438;SRR=880;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10143C>T|p.Tyr3381Tyr|10143/21291|10143/21291|3381/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2339:1750,587:1750:61151:587:20801:-893.549,0,-4490.38 +NC_045512.2 10487 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=60;CIGAR=1X;DP=1268;DPB=1268;DPRA=0;EPP=3.15506;EPPR=4.85102;GTI=0;LEN=1;MEANALT=1;MQM=50.7;MQMR=52.9139;NS=1;NUMALT=1;ODDS=1130.67;PAIRED=1;PAIREDR=0.990066;PAO=0;PQA=0;PQR=0;PRO=0;QA=2080;QR=42478;RO=1208;RPL=27;RPP=4.31318;RPPR=45.6416;RPR=33;RUN=1;SAF=32;SAP=3.58936;SAR=28;SRF=611;SRP=3.36262;SRR=597;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10222T>C|p.Cys3408Arg|10222/21291|10222/21291|3408/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1268:1208,60:1208:42478:60:2080:0,-207.823,-3511.98 +NC_045512.2 11074 . CTTTTTTTTGTATGA CTTTTTTTGTATGA,CTTTTTTTTTGTATGA 4.6288E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=13,12;CIGAR=1M1D13M,1M1I14M;DP=552;DPB=552;DPRA=0,0;EPP=3.17734,3.0103;EPPR=3.07737;GTI=0;LEN=1,1;MEANALT=9,9;MQM=54,48.9167;MQMR=49.0734;NS=1;NUMALT=2;ODDS=598.293;PAIRED=0.923077,0.833333;PAIREDR=0.878378;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=433,386;QR=17910;RO=518;RPL=4,6;RPP=7.18621,3.0103;RPPR=209.61;RPR=9,6;RUN=1,1;SAF=6,6;SAP=3.17734,3.0103;SAR=7,6;SRF=273;SRP=6.29685;SRR=245;TYPE=del,ins;ANN=CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817delT|p.Leu3606fs|10817/21291|10817/21291|3606/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:552:518,13,12:518:17910:13,12:433,386:0,-121.139,-1418.29,-125.159,-1391.45,-1422.6 +NC_045512.2 11151 . T A 9.76452E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=800;DPB=800;DPRA=0;EPP=3.73412;EPPR=3.40712;GTI=0;LEN=1;MEANALT=1;MQM=42.8333;MQMR=53.0863;NS=1;NUMALT=1;ODDS=993.402;PAIRED=0.5;PAIREDR=0.984772;PAO=0;PQA=0;PQR=0;PRO=0;QA=375;QR=27325;RO=788;RPL=2;RPP=14.5915;RPPR=3.55041;RPR=10;RUN=1;SAF=7;SAP=3.73412;SAR=5;SRF=403;SRP=3.90314;SRR=385;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10886T>A|p.Val3629Asp|10886/21291|10886/21291|3629/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:800:788,12:788:27325:12:375:0,-211.506,-2350.92 +NC_045512.2 11201 . A G 19964.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=744;CIGAR=1X;DP=801;DPB=801;DPRA=0;EPP=8.6608;EPPR=3.16541;GTI=0;LEN=1;MEANALT=2;MQM=52.1452;MQMR=55.5179;NS=1;NUMALT=1;ODDS=516.482;PAIRED=0.978495;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=25349;QR=1957;RO=56;RPL=371;RPP=3.02197;RPPR=4.40625;RPR=373;RUN=1;SAF=363;SAP=3.95594;SAR=381;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10936A>G|p.Thr3646Ala|10936/21291|10936/21291|3646/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:801:56,744:56:1957:744:25349:-1998.63,-65.2713,0 +NC_045512.2 11332 . A G 18029.6 . AB=0.54144;ABP=24.967;AC=1;AF=0.5;AN=2;AO=797;CIGAR=1X;DP=1472;DPB=1472;DPRA=0;EPP=11.2521;EPPR=6.73467;GTI=0;LEN=1;MEANALT=2;MQM=48.9849;MQMR=50.908;NS=1;NUMALT=1;ODDS=3264.3;PAIRED=0.991217;PAIREDR=0.991098;PAO=0;PQA=0;PQR=0;PRO=0;QA=27379;QR=23660;RO=674;RPL=287;RPP=138.5;RPPR=1116.92;RPR=510;RUN=1;SAF=397;SAP=3.03482;SAR=400;SRF=351;SRP=5.53617;SRR=323;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11067A>G|p.Val3689Val|11067/21291|11067/21291|3689/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1472:674,797:674:23660:797:27379:-1828.07,0,-1561.87 +NC_045512.2 11418 . T C 1582.81 . AB=0.162816;ABP=2695.99;AC=1;AF=0.5;AN=2;AO=444;CIGAR=1X;DP=2727;DPB=2727;DPRA=0;EPP=3.08855;EPPR=9.28929;GTI=0;LEN=1;MEANALT=3;MQM=49.1554;MQMR=52.3698;NS=1;NUMALT=1;ODDS=364.456;PAIRED=0.984234;PAIREDR=0.990745;PAO=0;PQA=0;PQR=0;PRO=0;QA=15540;QR=78990;RO=2269;RPL=231;RPP=4.59489;RPPR=4.94826;RPR=213;RUN=1;SAF=227;SAP=3.49937;SAR=217;SRF=1153;SRP=4.32046;SRR=1116;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11153T>C|p.Val3718Ala|11153/21291|11153/21291|3718/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2727:2269,444:2269:78990:444:15540:-458.018,0,-6000.58 +NC_045512.2 11514 . C T 1173.47 . AB=0.159434;ABP=2208.29;AC=1;AF=0.5;AN=2;AO=349;CIGAR=1X;DP=2189;DPB=2189;DPRA=0;EPP=3.01652;EPPR=3.03982;GTI=0;LEN=1;MEANALT=2;MQM=49.7536;MQMR=50.8967;NS=1;NUMALT=1;ODDS=270.201;PAIRED=0.988539;PAIREDR=0.990212;PAO=0;PQA=0;PQR=0;PRO=0;QA=12248;QR=64514;RO=1839;RPL=205;RPP=26.1623;RPPR=43.4228;RPR=144;RUN=1;SAF=175;SAP=3.01652;SAR=174;SRF=924;SRP=3.10594;SRR=915;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11249C>T|p.Thr3750Ile|11249/21291|11249/21291|3750/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2189:1839,349:1839:64514:349:12248:-369.053,0,-4782.23 +NC_045512.2 11522 . T G 3.80427E-13 . AB=0.132833;ABP=2656.4;AC=1;AF=0.5;AN=2;AO=301;CIGAR=1X;DP=2266;DPB=2266;DPRA=0;EPP=3.07523;EPPR=3.19725;GTI=0;LEN=1;MEANALT=2;MQM=49.5449;MQMR=51.4249;NS=1;NUMALT=1;ODDS=255.329;PAIRED=0.993355;PAIREDR=0.987264;PAO=0;PQA=0;PQR=0;PRO=0;QA=10440;QR=68620;RO=1963;RPL=176;RPP=21.7744;RPPR=13.4185;RPR=125;RUN=1;SAF=150;SAP=3.01751;SAR=151;SRF=989;SRP=3.2592;SRR=974;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11257T>G|p.Phe3753Val|11257/21291|11257/21291|3753/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2266:1963,301:1963:68620:301:10440:-194.762,0,-5142.94 +NC_045512.2 11593 . TC GA 1.75387E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=31;CIGAR=2X;DP=2530;DPB=2530;DPRA=0;EPP=3.08035;EPPR=4.33407;GTI=0;LEN=2;MEANALT=3;MQM=42.6452;MQMR=52.4405;NS=1;NUMALT=1;ODDS=3169.29;PAIRED=0.83871;PAIREDR=0.990381;PAO=0;PQA=0;PQR=0;PRO=0;QA=1093;QR=87869;RO=2495;RPL=7;RPP=23.254;RPPR=103.029;RPR=24;RUN=1;SAF=14;SAP=3.64073;SAR=17;SRF=1238;SRP=3.32449;SRR=1257;TYPE=complex;ANN=GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11328_11329delTCinsGA|p.Gln3777Lys|11328/21291|11328/21291|3776/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2530:2495,31:2495:87869:31:1093:0,-680.809,-7515.53 +NC_045512.2 11952 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=3760;DPB=3760;DPRA=0;EPP=3.87889;EPPR=17.5825;GTI=0;LEN=1;MEANALT=1;MQM=37.075;MQMR=52.3812;NS=1;NUMALT=1;ODDS=4814.2;PAIRED=1;PAIREDR=0.988441;PAO=0;PQA=0;PQR=0;PRO=0;QA=1331;QR=131082;RO=3720;RPL=2;RPP=73.366;RPPR=302.263;RPR=38;RUN=1;SAF=20;SAP=3.0103;SAR=20;SRF=1889;SRP=4.97396;SRR=1831;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11687A>T|p.Asn3896Ile|11687/21291|11687/21291|3896/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3760:3720,40:3720:131082:40:1331:0,-1040.87,-11225.6 +NC_045512.2 12165 . C T 7.43742E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=48;CIGAR=1X;DP=4731;DPB=4731;DPRA=0;EPP=3.0103;EPPR=5.62303;GTI=0;LEN=1;MEANALT=3;MQM=48.1042;MQMR=52.3067;NS=1;NUMALT=1;ODDS=5980.48;PAIRED=1;PAIREDR=0.995722;PAO=0;PQA=0;PQR=0;PRO=0;QA=1663;QR=163625;RO=4675;RPL=31;RPP=11.8771;RPPR=191.484;RPR=17;RUN=1;SAF=23;SAP=3.19126;SAR=25;SRF=2325;SRP=3.3006;SRR=2350;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11900C>T|p.Ala3967Val|11900/21291|11900/21291|3967/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4731:4675,48:4675:163625:48:1663:0,-1284.97,-13991 +NC_045512.2 12395 . G A 4.42388E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=28;CIGAR=1X;DP=2722;DPB=2722;DPRA=0;EPP=3.0103;EPPR=8.70195;GTI=0;LEN=1;MEANALT=2;MQM=48.5714;MQMR=52.3105;NS=1;NUMALT=1;ODDS=3439.94;PAIRED=1;PAIREDR=0.995542;PAO=0;PQA=0;PQR=0;PRO=0;QA=1004;QR=93798;RO=2692;RPL=10;RPP=7.97367;RPPR=28.5679;RPR=18;RUN=1;SAF=14;SAP=3.0103;SAR=14;SRF=1323;SRP=4.71715;SRR=1369;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12130G>A|p.Ala4044Thr|12130/21291|12130/21291|4044/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2722:2692,28:2692:93798:28:1004:0,-736.807,-8035.4 +NC_045512.2 12421 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=34;CIGAR=1X;DP=2716;DPB=2716;DPRA=0;EPP=3.0103;EPPR=7.0963;GTI=0;LEN=1;MEANALT=3;MQM=52;MQMR=51.0175;NS=1;NUMALT=1;ODDS=3350.88;PAIRED=1;PAIREDR=0.990668;PAO=0;PQA=0;PQR=0;PRO=0;QA=1216;QR=93869;RO=2679;RPL=26;RPP=23.7032;RPPR=139.93;RPR=8;RUN=1;SAF=17;SAP=3.0103;SAR=17;SRF=1326;SRP=3.60119;SRR=1353;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12156A>G|p.Ala4052Ala|12156/21291|12156/21291|4052/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2716:2679,34:2679:93869:34:1216:0,-710.041,-7872.24 +NC_045512.2 12543 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=41;CIGAR=1X;DP=3019;DPB=3019;DPRA=0;EPP=3.06326;EPPR=8.53125;GTI=0;LEN=1;MEANALT=2;MQM=48.9756;MQMR=52.692;NS=1;NUMALT=1;ODDS=3704.8;PAIRED=0.95122;PAIREDR=0.993618;PAO=0;PQA=0;PQR=0;PRO=0;QA=1456;QR=104157;RO=2977;RPL=19;RPP=3.48696;RPPR=63.0916;RPR=22;RUN=1;SAF=22;SAP=3.48696;SAR=19;SRF=1517;SRP=5.38017;SRR=1460;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12278C>T|p.Ser4093Leu|12278/21291|12278/21291|4093/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3019:2977,41:2977:104157:41:1456:0,-788.671,-8910.43 +NC_045512.2 13061 . G A 9.19732E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=53;CIGAR=1X;DP=3822;DPB=3822;DPRA=0;EPP=3.37904;EPPR=9.37237;GTI=0;LEN=1;MEANALT=3;MQM=49.0943;MQMR=50.8974;NS=1;NUMALT=1;ODDS=4686.48;PAIRED=1;PAIREDR=0.975817;PAO=0;PQA=0;PQR=0;PRO=0;QA=1858;QR=132219;RO=3763;RPL=45;RPP=59.0998;RPPR=63.9621;RPR=8;RUN=1;SAF=25;SAP=3.37904;SAR=28;SRF=1861;SRP=3.98034;SRR=1902;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12796G>A|p.Val4266Ile|12796/21291|12796/21291|4266/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3822:3763,53:3763:132219:53:1858:0,-995.615,-11086.3 +NC_045512.2 13105 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=105;CIGAR=1X;DP=3664;DPB=3664;DPRA=0;EPP=3.03098;EPPR=4.13971;GTI=0;LEN=1;MEANALT=3;MQM=48.1048;MQMR=51.373;NS=1;NUMALT=1;ODDS=3921.12;PAIRED=0.961905;PAIREDR=0.978059;PAO=0;PQA=0;PQR=0;PRO=0;QA=3675;QR=124917;RO=3555;RPL=50;RPP=3.52732;RPPR=26.2368;RPR=55;RUN=1;SAF=51;SAP=3.19643;SAR=54;SRF=1812;SRP=5.91842;SRR=1743;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12840C>T|p.Tyr4280Tyr|12840/21291|12840/21291|4280/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3664:3555,105:3555:124917:105:3675:0,-801.229,-10358.9 +NC_045512.2 13162 . TACACACACT TACACACT 0.0 . AB=0.112724;ABP=3863.02;AC=1;AF=0.5;AN=2;AO=334;CIGAR=1M2D7M;DP=2963;DPB=2897.9;DPRA=0;EPP=3.03631;EPPR=3.61938;GTI=0;LEN=2;MEANALT=21;MQM=50.9461;MQMR=53.5356;NS=1;NUMALT=1;ODDS=846.644;PAIRED=0.982036;PAIREDR=0.993844;PAO=3.5;PQA=96;PQR=96;PRO=3.5;QA=10732;QR=90583;RO=2599;RPL=178;RPP=6.15698;RPPR=30.3822;RPR=156;RUN=1;SAF=164;SAP=3.24435;SAR=170;SRF=1308;SRP=3.25176;SRR=1291;TYPE=del;ANN=TACACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12904_12905delAC|p.Thr4302fs|12904/21291|12904/21291|4302/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2963:2599,334:2599:90583:334:10732:-71.6702,0,-7021.49 +NC_045512.2 13514 . G A 4.65288E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=729;DPB=729;DPRA=0;EPP=3.0103;EPPR=3.15953;GTI=0;LEN=1;MEANALT=1;MQM=51.4375;MQMR=52.5203;NS=1;NUMALT=1;ODDS=839.999;PAIRED=1;PAIREDR=0.995792;PAO=0;PQA=0;PQR=0;PRO=0;QA=524;QR=24566;RO=713;RPL=6;RPP=5.18177;RPPR=53.6912;RPR=10;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=362;SRP=3.37881;SRR=351;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13250G>A|p.Gly4417Asp|13250/21291|13250/21291|4417/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:729:713,16:713:24566:16:524:0,-173.44,-2080.17 +NC_045512.2 13617 . G A 12992.0 . AB=0.366918;ABP=288.526;AC=1;AF=0.5;AN=2;AO=681;CIGAR=1X;DP=1856;DPB=1856;DPRA=0;EPP=4.6971;EPPR=11.4063;GTI=0;LEN=1;MEANALT=3;MQM=50.1747;MQMR=49.3816;NS=1;NUMALT=1;ODDS=2991.51;PAIRED=1;PAIREDR=0.986219;PAO=0;PQA=0;PQR=0;PRO=0;QA=22360;QR=40233;RO=1161;RPL=354;RPP=5.33483;RPPR=1474.54;RPR=327;RUN=1;SAF=324;SAP=6.48274;SAR=357;SRF=609;SRP=9.08706;SRR=552;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13353G>A|p.Lys4451Lys|13353/21291|13353/21291|4451/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1856:1161,681:1161:40233:681:22360:-1335.68,0,-2783.93 +NC_045512.2 13625 . ATG AG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1M1D1M;DP=1903;DPB=1889;DPRA=0;EPP=3.0608;EPPR=6.04849;GTI=0;LEN=1;MEANALT=2;MQM=45.0698;MQMR=49.6837;NS=1;NUMALT=1;ODDS=2220.17;PAIRED=1;PAIREDR=0.989779;PAO=0.5;PQA=16;PQR=16;PRO=0.5;QA=1368;QR=65600;RO=1859;RPL=0;RPP=96.3836;RPPR=658.308;RPR=43;RUN=1;SAF=22;SAP=3.0608;SAR=21;SRF=946;SRP=4.28235;SRR=913;TYPE=del;ANN=AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13362delT|p.Asp4454fs|13362/21291|13362/21291|4454/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1903:1859,43:1859:65600:43:1368:0,-462.878,-5360.42 +NC_045512.2 13837 . C T 1.77195E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=88;CIGAR=1X;DP=3272;DPB=3272;DPRA=0;EPP=3.0103;EPPR=10.8209;GTI=0;LEN=1;MEANALT=2;MQM=49.4205;MQMR=52.6368;NS=1;NUMALT=1;ODDS=3549.8;PAIRED=1;PAIREDR=0.994031;PAO=0;PQA=0;PQR=0;PRO=0;QA=3060;QR=110447;RO=3183;RPL=37;RPP=7.84676;RPPR=68.1483;RPR=51;RUN=1;SAF=43;SAP=3.109;SAR=45;SRF=1567;SRP=4.64828;SRR=1616;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13573C>T|p.His4525Tyr|13573/21291|13573/21291|4525/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3272:3183,88:3183:110447:88:3060:0,-725.794,-9296.11 +NC_045512.2 13884 . ATA AA 5.23755E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=38;CIGAR=1M1D1M;DP=3158;DPB=3145.33;DPRA=0;EPP=3.23888;EPPR=12.2236;GTI=0;LEN=1;MEANALT=3;MQM=39.8947;MQMR=52.8608;NS=1;NUMALT=1;ODDS=3980.02;PAIRED=1;PAIREDR=0.994867;PAO=0;PQA=0;PQR=0;PRO=0;QA=1235;QR=110028;RO=3117;RPL=35;RPP=61.5258;RPPR=7.35812;RPR=3;RUN=1;SAF=17;SAP=3.9246;SAR=21;SRF=1529;SRP=5.43535;SRR=1588;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13621delT|p.Tyr4541fs|13621/21291|13621/21291|4541/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3158:3117,38:3117:110028:38:1235:0,-855.492,-9476.37 +NC_045512.2 13948 . G T 2626.9 . AB=0.192751;ABP=1925.83;AC=1;AF=0.5;AN=2;AO=452;CIGAR=1X;DP=2345;DPB=2345;DPRA=0;EPP=6.77675;EPPR=40.6702;GTI=0;LEN=1;MEANALT=2;MQM=48.3606;MQMR=50.5876;NS=1;NUMALT=1;ODDS=604.866;PAIRED=1;PAIREDR=0.993118;PAO=0;PQA=0;PQR=0;PRO=0;QA=15755;QR=66219;RO=1889;RPL=442;RPP=899.579;RPPR=13.3849;RPR=10;RUN=1;SAF=212;SAP=6.77675;SAR=240;SRF=915;SRP=7.01183;SRR=974;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13684G>T|p.Asp4562Tyr|13684/21291|13684/21291|4562/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2345:1889,452:1889:66219:452:15755:-591.959,0,-4884.54 +NC_045512.2 14343 . T C 2.52654E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=243;CIGAR=1X;DP=3163;DPB=3163;DPRA=0;EPP=3.01924;EPPR=13.9019;GTI=0;LEN=1;MEANALT=2;MQM=48.0741;MQMR=53.283;NS=1;NUMALT=1;ODDS=1944.19;PAIRED=0.987654;PAIREDR=0.994176;PAO=0;PQA=0;PQR=0;PRO=0;QA=8382;QR=101644;RO=2919;RPL=136;RPP=10.5256;RPPR=4.51672;RPR=107;RUN=1;SAF=124;SAP=3.2337;SAR=119;SRF=1486;SRP=5.09994;SRR=1433;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14079T>C|p.Cys4693Cys|14079/21291|14079/21291|4693/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3163:2919,243:2919:101644:243:8382:0,-256.43,-8135.24 +NC_045512.2 14408 . C T 85570.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2863;CIGAR=1X;DP=2866;DPB=2866;DPRA=0;EPP=6.02063;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=51.4149;MQMR=52;NS=1;NUMALT=1;ODDS=3935.49;PAIRED=0.991966;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100761;QR=108;RO=3;RPL=1519;RPP=26.2382;RPPR=3.73412;RPR=1344;RUN=1;SAF=1438;SAP=3.13848;SAR=1425;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144C>T|p.Pro4715Leu|14144/21291|14144/21291|4715/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:2866:3,2863:3:108:2863:100761:-8563.93,-852.723,0 +NC_045512.2 14599 . C T 10548.1 . AB=0.325339;ABP=511.234;AC=1;AF=0.5;AN=2;AO=624;CIGAR=1X;DP=1918;DPB=1918;DPRA=0;EPP=4.1378;EPPR=15.144;GTI=0;LEN=1;MEANALT=2;MQM=45.7196;MQMR=51.9281;NS=1;NUMALT=1;ODDS=2428.8;PAIRED=0.983974;PAIREDR=0.992266;PAO=0;PQA=0;PQR=0;PRO=0;QA=22070;QR=44878;RO=1293;RPL=147;RPP=381.974;RPPR=21.5258;RPR=477;RUN=1;SAF=324;SAP=5.01474;SAR=300;SRF=649;SRP=3.05229;SRR=644;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14335C>T|p.Leu4779Leu|14335/21291|14335/21291|4779/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1918:1293,624:1293:44878:624:22070:-1154.93,0,-3270.18 +NC_045512.2 14676 . C T 4.51306E-13 . AB=0.129404;ABP=3423.16;AC=1;AF=0.5;AN=2;AO=371;CIGAR=1X;DP=2867;DPB=2867;DPRA=0;EPP=3.06298;EPPR=4.0168;GTI=0;LEN=1;MEANALT=3;MQM=50.1213;MQMR=52.666;NS=1;NUMALT=1;ODDS=370.612;PAIRED=0.994609;PAIREDR=0.989575;PAO=0;PQA=0;PQR=0;PRO=0;QA=13140;QR=85679;RO=2494;RPL=194;RPP=4.70182;RPPR=46.6975;RPR=177;RUN=1;SAF=190;SAP=3.4844;SAR=181;SRF=1273;SRP=5.36461;SRR=1221;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14412C>T|p.Pro4804Pro|14412/21291|14412/21291|4804/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2867:2494,371:2494:85679:371:13140:-229.956,0,-6526.74 +NC_045512.2 14925 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=1720;DPB=1720;DPRA=0;EPP=3.52123;EPPR=14.8804;GTI=0;LEN=1;MEANALT=2;MQM=52.1912;MQMR=50.3628;NS=1;NUMALT=1;ODDS=1662.43;PAIRED=1;PAIREDR=0.992126;PAO=0;PQA=0;PQR=0;PRO=0;QA=2343;QR=57307;RO=1651;RPL=10;RPP=76.5849;RPPR=99.6033;RPR=58;RUN=1;SAF=36;SAP=3.52123;SAR=32;SRF=819;SRP=3.23258;SRR=832;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14661C>T|p.Val4887Val|14661/21291|14661/21291|4887/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1720:1651,68:1651:57307:68:2343:0,-314.394,-4648.27 +NC_045512.2 14960 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=1845;DPB=1845;DPRA=0;EPP=3.0103;EPPR=4.84214;GTI=0;LEN=1;MEANALT=1;MQM=49.7381;MQMR=51.802;NS=1;NUMALT=1;ODDS=2084.32;PAIRED=1;PAIREDR=0.988353;PAO=0;PQA=0;PQR=0;PRO=0;QA=1500;QR=63751;RO=1803;RPL=16;RPP=8.18047;RPPR=133.372;RPR=26;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=915;SRP=3.88828;SRR=888;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14696A>T|p.Asn4899Ile|14696/21291|14696/21291|4899/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1845:1803,42:1803:63751:42:1500:0,-430.383,-5341.54 +NC_045512.2 15081 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=1823;DPB=1823;DPRA=0;EPP=3.12459;EPPR=3.49285;GTI=0;LEN=1;MEANALT=3;MQM=48.7368;MQMR=52.8733;NS=1;NUMALT=1;ODDS=2311.42;PAIRED=1;PAIREDR=0.986667;PAO=0;PQA=0;PQR=0;PRO=0;QA=628;QR=61997;RO=1800;RPL=12;RPP=5.8675;RPPR=27.3356;RPR=7;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=897;SRP=3.05373;SRR=903;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14817C>A|p.Ala4939Ala|14817/21291|14817/21291|4939/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1823:1800,19:1800:61997:19:628:0,-496.547,-5321.06 +NC_045512.2 15099 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1724;DPB=1724;DPRA=0;EPP=3.0103;EPPR=3.87276;GTI=0;LEN=1;MEANALT=2;MQM=54.1;MQMR=53.9871;NS=1;NUMALT=1;ODDS=2154.41;PAIRED=1;PAIREDR=0.9953;PAO=0;PQA=0;PQR=0;PRO=0;QA=661;QR=57848;RO=1702;RPL=8;RPP=4.74748;RPPR=3.03071;RPR=12;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=831;SRP=5.05164;SRR=871;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14835A>G|p.Arg4945Arg|14835/21291|14835/21291|4945/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1724:1702,20:1702:57848:20:661:0,-459.131,-5019.76 +NC_045512.2 15112 . G A 2.45301E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1742;DPB=1742;DPRA=0;EPP=3.0103;EPPR=7.71074;GTI=0;LEN=1;MEANALT=2;MQM=51.5;MQMR=53.8941;NS=1;NUMALT=1;ODDS=2148.09;PAIRED=1;PAIREDR=0.993601;PAO=0;PQA=0;PQR=0;PRO=0;QA=784;QR=59941;RO=1719;RPL=12;RPP=3.40511;RPPR=4.73965;RPR=10;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=842;SRP=4.55774;SRR=877;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14848G>A|p.Ala4950Thr|14848/21291|14848/21291|4950/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1742:1719,22:1719:59941:22:784:0,-454.638,-5189.54 +NC_045512.2 15279 . C T 15999.3 . AB=0.501107;ABP=3.02472;AC=1;AF=0.5;AN=2;AO=679;CIGAR=1X;DP=1355;DPB=1355;DPRA=0;EPP=3.72986;EPPR=5.54368;GTI=0;LEN=1;MEANALT=3;MQM=50.6848;MQMR=52.4911;NS=1;NUMALT=1;ODDS=3683.98;PAIRED=0.997054;PAIREDR=0.997024;PAO=0;PQA=0;PQR=0;PRO=0;QA=23811;QR=23325;RO=672;RPL=353;RPP=5.34167;RPPR=13.1438;RPR=326;RUN=1;SAF=347;SAP=3.72986;SAR=332;SRF=340;SRP=3.21711;SRR=332;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15015C>T|p.His5005His|15015/21291|15015/21291|5005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1355:672,679:672:23325:679:23811:-1608.52,0,-1621.57 +NC_045512.2 15451 . G A 8929.57 . AB=0.4;ABP=95.515;AC=1;AF=0.5;AN=2;AO=426;CIGAR=1X;DP=1065;DPB=1065;DPRA=0;EPP=3.52004;EPPR=4.50892;GTI=0;LEN=1;MEANALT=1;MQM=48.9977;MQMR=53.4648;NS=1;NUMALT=1;ODDS=2056.11;PAIRED=0.985915;PAIREDR=0.984351;PAO=0;PQA=0;PQR=0;PRO=0;QA=15055;QR=22076;RO=639;RPL=213;RPP=3.0103;RPPR=25.3061;RPR=213;RUN=1;SAF=209;SAP=3.33653;SAR=217;SRF=315;SRP=3.28556;SRR=324;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15187G>A|p.Gly5063Ser|15187/21291|15187/21291|5063/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1065:639,426:639:22076:426:15055:-910.196,0,-1597.03 +NC_045512.2 15610 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1X;DP=2649;DPB=2649;DPRA=0;EPP=3.0459;EPPR=3.03128;GTI=0;LEN=1;MEANALT=2;MQM=49.2623;MQMR=53.041;NS=1;NUMALT=1;ODDS=2973.3;PAIRED=1;PAIREDR=0.993815;PAO=0;PQA=0;PQR=0;PRO=0;QA=2160;QR=90654;RO=2587;RPL=26;RPP=5.89373;RPPR=286.352;RPR=35;RUN=1;SAF=31;SAP=3.0459;SAR=30;SRF=1324;SRP=6.13363;SRR=1263;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15346C>T|p.Gln5116*|15346/21291|15346/21291|5116/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2649:2587,61:2587:90654:61:2160:0,-613.681,-7700.41 +NC_045512.2 15682 . TATT AATA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=62;CIGAR=1X2M1X;DP=3135;DPB=3136;DPRA=0;EPP=3.15039;EPPR=3.32274;GTI=0;LEN=4;MEANALT=6;MQM=44.4677;MQMR=52.7775;NS=1;NUMALT=1;ODDS=3669.8;PAIRED=0.903226;PAIREDR=0.995432;PAO=3;PQA=100;PQR=0;PRO=1;QA=2133;QR=107768;RO=3065;RPL=25;RPP=8.05372;RPPR=14.0802;RPR=37;RUN=1;SAF=31;SAP=3.0103;SAR=31;SRF=1555;SRP=4.44496;SRR=1510;TYPE=complex;ANN=AATA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15418_15421delTATTinsAATA|p.TyrLeu5140AsnMet|15418/21291|15418/21291|5140/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3135:3065,62:3065:107768:62:2133:0,-777.887,-9178.74 +NC_045512.2 15765 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=29;CIGAR=1X;DP=2620;DPB=2620;DPRA=0;EPP=3.08518;EPPR=7.23508;GTI=0;LEN=1;MEANALT=1;MQM=53.8621;MQMR=53.0471;NS=1;NUMALT=1;ODDS=3289.28;PAIRED=1;PAIREDR=0.990351;PAO=0;PQA=0;PQR=0;PRO=0;QA=963;QR=91316;RO=2591;RPL=13;RPP=3.68421;RPPR=13.7118;RPR=16;RUN=1;SAF=14;SAP=3.08518;SAR=15;SRF=1248;SRP=10.574;SRR=1343;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15501A>G|p.Leu5167Leu|15501/21291|15501/21291|5167/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2620:2591,29:2591:91316:29:963:0,-703.357,-7841.25 +NC_045512.2 15924 . C T 6.44918E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=37;CIGAR=1X;DP=3061;DPB=3061;DPRA=0;EPP=3.06899;EPPR=5.95155;GTI=0;LEN=1;MEANALT=1;MQM=41.2703;MQMR=52.1574;NS=1;NUMALT=1;ODDS=3840.84;PAIRED=0.972973;PAIREDR=0.98578;PAO=0;PQA=0;PQR=0;PRO=0;QA=1310;QR=105103;RO=3024;RPL=10;RPP=19.9713;RPPR=26.2761;RPR=27;RUN=1;SAF=18;SAP=3.06899;SAR=19;SRF=1538;SRP=4.95199;SRR=1486;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15660C>T|p.Tyr5220Tyr|15660/21291|15660/21291|5220/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3061:3024,37:3024:105103:37:1310:0,-825.97,-8954.61 +NC_045512.2 16047 . T C 7.54104E-13 . AB=0.115049;ABP=4578.78;AC=1;AF=0.5;AN=2;AO=409;CIGAR=1X;DP=3555;DPB=3555;DPRA=0;EPP=3.27045;EPPR=3.01306;GTI=0;LEN=1;MEANALT=2;MQM=49.6186;MQMR=53.0083;NS=1;NUMALT=1;ODDS=928.295;PAIRED=0.99511;PAIREDR=0.992048;PAO=0;PQA=0;PQR=0;PRO=0;QA=14401;QR=109684;RO=3144;RPL=183;RPP=12.8271;RPPR=10.4806;RPR=226;RUN=1;SAF=206;SAP=3.05808;SAR=203;SRF=1597;SRP=4.73698;SRR=1547;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15783T>C|p.Leu5261Leu|15783/21291|15783/21291|5261/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3555:3144,409:3144:109684:409:14401:-124.324,0,-8453.5 +NC_045512.2 16176 . T C 0.0 . AB=0.113668;ABP=2820.07;AC=1;AF=0.5;AN=2;AO=247;CIGAR=1X;DP=2173;DPB=2173;DPRA=0;EPP=4.49604;EPPR=9.35551;GTI=0;LEN=1;MEANALT=2;MQM=45.5789;MQMR=50.2919;NS=1;NUMALT=1;ODDS=754.39;PAIRED=0.991903;PAIREDR=0.987532;PAO=0;PQA=0;PQR=0;PRO=0;QA=8569;QR=68076;RO=1925;RPL=193;RPP=172.869;RPPR=930.989;RPR=54;RUN=1;SAF=119;SAP=3.7224;SAR=128;SRF=944;SRP=4.55458;SRR=981;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15912T>C|p.Thr5304Thr|15912/21291|15912/21291|5304/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2173:1925,247:1925:68076:247:8569:-17.686,0,-5092.92 +NC_045512.2 16466 . C T 43588.1 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1613;CIGAR=1X;DP=1646;DPB=1646;DPRA=0;EPP=5.98413;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=46.0539;MQMR=52.5455;NS=1;NUMALT=1;ODDS=1904.12;PAIRED=0.989461;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=56743;QR=1140;RO=33;RPL=677;RPP=93.3169;RPPR=22.0271;RPR=936;RUN=1;SAF=821;SAP=4.14248;SAR=792;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16202C>T|p.Pro5401Leu|16202/21291|16202/21291|5401/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:1646:33,1613:33:1140:1613:56743:-4368.86,-393.99,0 +NC_045512.2 16816 . C T 4316.69 . AB=0.255301;ABP=616.196;AC=1;AF=0.5;AN=2;AO=301;CIGAR=1X;DP=1179;DPB=1179;DPRA=0;EPP=3.19065;EPPR=6.96743;GTI=0;LEN=1;MEANALT=1;MQM=47.6346;MQMR=51.0182;NS=1;NUMALT=1;ODDS=993.955;PAIRED=1;PAIREDR=0.989749;PAO=0;PQA=0;PQR=0;PRO=0;QA=10614;QR=30734;RO=878;RPL=107;RPP=57.6145;RPPR=418.756;RPR=194;RUN=1;SAF=154;SAP=3.3638;SAR=147;SRF=427;SRP=4.43486;SRR=451;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16552C>T|p.Gln5518*|16552/21291|16552/21291|5518/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1179:878,301:878:30734:301:10614:-508.866,0,-2253.86 +NC_045512.2 17218 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2615;DPB=2615;DPRA=0;EPP=3.07234;EPPR=4.04173;GTI=0;LEN=1;MEANALT=2;MQM=53.2286;MQMR=53.1377;NS=1;NUMALT=1;ODDS=3202.13;PAIRED=1;PAIREDR=0.993796;PAO=0;PQA=0;PQR=0;PRO=0;QA=1252;QR=91012;RO=2579;RPL=12;RPP=10.5174;RPPR=149.422;RPR=23;RUN=1;SAF=18;SAP=3.07234;SAR=17;SRF=1302;SRP=3.53654;SRR=1277;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16954G>C|p.Asp5652His|16954/21291|16954/21291|5652/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2615:2579,35:2579:91012:35:1252:0,-677.895,-7808.81 +NC_045512.2 17814 . G A 1651.02 . AB=0.17202;ABP=1312.03;AC=1;AF=0.5;AN=2;AO=241;CIGAR=1X;DP=1401;DPB=1401;DPRA=0;EPP=3.09139;EPPR=3.13031;GTI=0;LEN=1;MEANALT=2;MQM=51.8548;MQMR=52.8454;NS=1;NUMALT=1;ODDS=380.16;PAIRED=0.983402;PAIREDR=0.992228;PAO=0;PQA=0;PQR=0;PRO=0;QA=8561;QR=40234;RO=1158;RPL=118;RPP=3.23556;RPPR=37.6939;RPR=123;RUN=1;SAF=120;SAP=3.01931;SAR=121;SRF=590;SRP=3.91789;SRR=568;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17550G>A|p.Leu5850Leu|17550/21291|17550/21291|5850/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1401:1158,241:1158:40234:241:8561:-314.533,0,-3073.09 +NC_045512.2 18564 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=26;CIGAR=1X;DP=2012;DPB=2012;DPRA=0;EPP=3.0103;EPPR=4.27426;GTI=0;LEN=1;MEANALT=1;MQM=38.3077;MQMR=52.5287;NS=1;NUMALT=1;ODDS=2535.91;PAIRED=1;PAIREDR=0.984894;PAO=0;PQA=0;PQR=0;PRO=0;QA=919;QR=69984;RO=1986;RPL=0;RPP=59.4686;RPPR=40.0281;RPR=26;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=971;SRP=5.1271;SRR=1015;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18300A>C|p.Lys6100Asn|18300/21291|18300/21291|6100/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2012:1986,26:1986:69984:26:919:0,-543.43,-5961.14 +NC_045512.2 18585 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=34;CIGAR=1X;DP=1713;DPB=1713;DPRA=0;EPP=12.2071;EPPR=3.19799;GTI=0;LEN=1;MEANALT=3;MQM=54.7647;MQMR=52.0816;NS=1;NUMALT=1;ODDS=2102.51;PAIRED=1;PAIREDR=0.991597;PAO=0;PQA=0;PQR=0;PRO=0;QA=599;QR=49685;RO=1666;RPL=24;RPP=15.5282;RPPR=146.677;RPR=10;RUN=1;SAF=33;SAP=68.4099;SAR=1;SRF=784;SRP=15.5282;SRR=882;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18321A>G|p.Val6107Val|18321/21291|18321/21291|6107/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1713:1666,34:1666:49685:34:599:0,-457.977,-4212.18 +NC_045512.2 18589 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=1666;DPB=1666;DPRA=0;EPP=28.0461;EPPR=3.12058;GTI=0;LEN=1;MEANALT=3;MQM=54.6029;MQMR=51.9078;NS=1;NUMALT=1;ODDS=1835.86;PAIRED=1;PAIREDR=0.992476;PAO=0;PQA=0;PQR=0;PRO=0;QA=1260;QR=50241;RO=1595;RPL=48;RPP=28.0461;RPPR=206.91;RPR=20;RUN=1;SAF=68;SAP=150.67;SAR=0;SRF=729;SRP=28.5629;SRR=866;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18325G>T|p.Val6109Phe|18325/21291|18325/21291|6109/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1666:1595,68:1595:50241:68:1260:0,-389.132,-4187.65 +NC_045512.2 18591 . C A,G 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=22,53;CIGAR=1X,1X;DP=1626;DPB=1626;DPRA=0,0;EPP=17.2236,21.0786;EPPR=5.84906;GTI=0;LEN=1,1;MEANALT=3,3;MQM=52.2273,56;MQMR=51.7076;NS=1;NUMALT=2;ODDS=1862.57;PAIRED=0.909091,1;PAIREDR=0.993544;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=349,899;QR=45627;RO=1549;RPL=16,37;RPP=12.8806,21.0786;RPPR=195.963;RPR=6,16;RUN=1,1;SAF=21,53;SAP=42.4916,118.098;SAR=1,0;SRF=701;SRP=33.303;SRR=848;TYPE=snp,snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18327C>A|p.Val6109Val|18327/21291|18327/21291|6109/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1626:1549,22,53:1549:45627:22,53:349,899:0,-442.675,-3865.33,-402.972,-3808.63,-3816.3 +NC_045512.2 18596 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=1560;DPB=1560;DPRA=0;EPP=37.7539;EPPR=7.02588;GTI=0;LEN=1;MEANALT=3;MQM=54.8611;MQMR=51.6866;NS=1;NUMALT=1;ODDS=1910.29;PAIRED=1;PAIREDR=0.994733;PAO=0;PQA=0;PQR=0;PRO=0;QA=597;QR=47340;RO=1519;RPL=30;RPP=37.7539;RPPR=206.189;RPR=6;RUN=1;SAF=34;SAP=64.7766;SAR=2;SRF=706;SRP=19.3771;SRR=813;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18332G>T|p.Trp6111Leu|18332/21291|18332/21291|6111/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1560:1519,36:1519:47340:36:597:0,-415.548,-3982.11 +NC_045512.2 18607 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=37;CIGAR=1X;DP=2032;DPB=2032;DPRA=0;EPP=45.7942;EPPR=35.685;GTI=0;LEN=1;MEANALT=2;MQM=52.7297;MQMR=50.0191;NS=1;NUMALT=1;ODDS=2562.27;PAIRED=1;PAIREDR=0.993967;PAO=0;PQA=0;PQR=0;PRO=0;QA=596;QR=62548;RO=1989;RPL=33;RPP=52.3673;RPPR=39.5716;RPR=4;RUN=1;SAF=36;SAP=74.9036;SAR=1;SRF=984;SRP=3.49176;SRR=1005;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18343T>G|p.Phe6115Val|18343/21291|18343/21291|6115/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2032:1989,37:1989:62548:37:596:0,-558.569,-5124.76 +NC_045512.2 18634 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1X;DP=2484;DPB=2484;DPRA=0;EPP=68.1545;EPPR=20.1139;GTI=0;LEN=1;MEANALT=2;MQM=55.0333;MQMR=49.1239;NS=1;NUMALT=1;ODDS=3237.29;PAIRED=1;PAIREDR=0.991031;PAO=0;PQA=0;PQR=0;PRO=0;QA=541;QR=83732;RO=2453;RPL=30;RPP=68.1545;RPPR=122.241;RPR=0;RUN=1;SAF=30;SAP=68.1545;SAR=0;SRF=1223;SRP=3.05368;SRR=1230;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18370G>T|p.Val6124Leu|18370/21291|18370/21291|6124/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2484:2453,30:2453:83732:30:541:0,-698.736,-6808.01 +NC_045512.2 18977 . A G 0.0 . AB=0.128648;ABP=4723.57;AC=1;AF=0.5;AN=2;AO=507;CIGAR=1X;DP=3941;DPB=3941;DPRA=0;EPP=3.97397;EPPR=3.34491;GTI=0;LEN=1;MEANALT=2;MQM=47.2308;MQMR=50.4512;NS=1;NUMALT=1;ODDS=685.817;PAIRED=1;PAIREDR=0.993009;PAO=0;PQA=0;PQR=0;PRO=0;QA=17828;QR=120870;RO=3433;RPL=192;RPP=67.8076;RPPR=178.682;RPR=315;RUN=1;SAF=262;SAP=4.24808;SAR=245;SRF=1718;SRP=3.01599;SRR=1715;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18713A>G|p.Gln6238Arg|18713/21291|18713/21291|6238/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3941:3433,507:3433:120870:507:17828:-246.189,0,-8997.03 +NC_045512.2 19132 . G T 1.25365E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=135;CIGAR=1X;DP=5691;DPB=5691;DPRA=0;EPP=3.02638;EPPR=3.2745;GTI=0;LEN=1;MEANALT=1;MQM=46.3778;MQMR=52.194;NS=1;NUMALT=1;ODDS=6443.64;PAIRED=0.97037;PAIREDR=0.991901;PAO=0;PQA=0;PQR=0;PRO=0;QA=4554;QR=195166;RO=5556;RPL=89;RPP=32.7514;RPPR=54.7942;RPR=46;RUN=1;SAF=64;SAP=3.79846;SAR=71;SRF=2759;SRP=3.57466;SRR=2797;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18868G>T|p.Glu6290*|18868/21291|18868/21291|6290/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5691:5556,135:5556:195166:135:4554:0,-1352.52,-16428.1 +NC_045512.2 19137 . A C 2.02509E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=114;CIGAR=1X;DP=5642;DPB=5642;DPRA=0;EPP=3.08649;EPPR=3.18362;GTI=0;LEN=1;MEANALT=3;MQM=44.7807;MQMR=52.2286;NS=1;NUMALT=1;ODDS=6562.91;PAIRED=0.964912;PAIREDR=0.991855;PAO=0;PQA=0;PQR=0;PRO=0;QA=3986;QR=194895;RO=5525;RPL=72;RPP=20.1535;RPPR=6.40959;RPR=42;RUN=1;SAF=56;SAP=3.08649;SAR=58;SRF=2750;SRP=3.25594;SRR=2775;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18873A>C|p.Leu6291Phe|18873/21291|18873/21291|6291/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5642:5525,114:5525:194895:114:3986:0,-1386.34,-16434.9 +NC_045512.2 19165 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=172;CIGAR=1X;DP=5857;DPB=5857;DPRA=0;EPP=3.81829;EPPR=8.06357;GTI=0;LEN=1;MEANALT=2;MQM=50.7733;MQMR=52.3231;NS=1;NUMALT=1;ODDS=6177.91;PAIRED=1;PAIREDR=0.993665;PAO=0;PQA=0;PQR=0;PRO=0;QA=6042;QR=200372;RO=5683;RPL=91;RPP=4.27278;RPPR=7.55003;RPR=81;RUN=1;SAF=83;SAP=3.46479;SAR=89;SRF=2791;SRP=6.9081;SRR=2892;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18901A>G|p.Lys6301Glu|18901/21291|18901/21291|6301/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5857:5683,172:5683:200372:172:6042:0,-1250.18,-16760.4 +NC_045512.2 19220 . C T 83946.5 . AB=0.650573;ABP=1067.61;AC=1;AF=0.5;AN=2;AO=3517;CIGAR=1X;DP=5406;DPB=5406;DPRA=0;EPP=3.08501;EPPR=3.47085;GTI=0;LEN=1;MEANALT=3;MQM=48.9795;MQMR=51.3181;NS=1;NUMALT=1;ODDS=8974.42;PAIRED=0.997157;PAIREDR=0.993107;PAO=0;PQA=0;PQR=0;PRO=0;QA=123592;QR=66525;RO=1886;RPL=1966;RPP=109.346;RPPR=12.3363;RPR=1551;RUN=1;SAF=1746;SAP=3.39619;SAR=1771;SRF=945;SRP=3.02872;SRR=941;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18956C>T|p.Ala6319Val|18956/21291|18956/21291|6319/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:5406:1886,3517:1886:66525:3517:123592:-8523.51,0,-4016.27 +NC_045512.2 19245 . C T 7.03964E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=399;CIGAR=1X;DP=5068;DPB=5068;DPRA=0;EPP=3.27697;EPPR=11.8692;GTI=0;LEN=1;MEANALT=2;MQM=46.4637;MQMR=49.5467;NS=1;NUMALT=1;ODDS=3051.2;PAIRED=1;PAIREDR=0.995073;PAO=0;PQA=0;PQR=0;PRO=0;QA=14080;QR=164853;RO=4668;RPL=190;RPP=4.97497;RPPR=471.922;RPR=209;RUN=1;SAF=204;SAP=3.45113;SAR=195;SRF=2293;SRP=6.13819;SRR=2375;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18981C>T|p.Asp6327Asp|18981/21291|18981/21291|6327/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5068:4668,399:4668:164853:399:14080:0,-398.339,-12557.8 +NC_045512.2 19333 . G T 18125.6 . AB=0.270052;ABP=1875.49;AC=1;AF=0.5;AN=2;AO=1101;CIGAR=1X;DP=4077;DPB=4077;DPRA=0;EPP=4.05363;EPPR=4.17776;GTI=0;LEN=1;MEANALT=1;MQM=51.0427;MQMR=53.038;NS=1;NUMALT=1;ODDS=4173.56;PAIRED=0.998183;PAIREDR=0.996304;PAO=0;PQA=0;PQR=0;PRO=0;QA=38316;QR=104017;RO=2976;RPL=524;RPP=8.55041;RPPR=31.6159;RPR=577;RUN=1;SAF=565;SAP=4.66898;SAR=536;SRF=1491;SRP=3.03657;SRR=1485;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19069G>T|p.Asp6357Tyr|19069/21291|19069/21291|6357/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4077:2976,1101:2976:104017:1101:38316:-2016.57,0,-7824.46 +NC_045512.2 19452 . T A 3.9056E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=3420;DPB=3420;DPRA=0;EPP=3.0103;EPPR=5.3286;GTI=0;LEN=1;MEANALT=2;MQM=47.9048;MQMR=52.6652;NS=1;NUMALT=1;ODDS=4274.34;PAIRED=0.952381;PAIREDR=0.993179;PAO=0;PQA=0;PQR=0;PRO=0;QA=1464;QR=116982;RO=3372;RPL=42;RPP=94.2121;RPPR=206.405;RPR=0;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=1689;SRP=3.03348;SRR=1683;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19188T>A|p.Ala6396Ala|19188/21291|19188/21291|6396/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3420:3372,42:3372:116982:42:1464:0,-909.276,-9987.69 +NC_045512.2 19751 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=917;DPB=917;DPRA=0;EPP=3.0103;EPPR=3.09677;GTI=0;LEN=1;MEANALT=2;MQM=40.5833;MQMR=53.469;NS=1;NUMALT=1;ODDS=1151.16;PAIRED=0.833333;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=424;QR=32022;RO=904;RPL=0;RPP=29.068;RPPR=3.3562;RPR=12;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=445;SRP=3.48111;SRR=459;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19487A>T|p.Glu6496Val|19487/21291|19487/21291|6496/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:917:904,12:904:32022:12:424:0,-244.122,-2771.61 +NC_045512.2 19887 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=33;CIGAR=1X;DP=1166;DPB=1166;DPRA=0;EPP=3.0761;EPPR=3.56419;GTI=0;LEN=1;MEANALT=1;MQM=43.4242;MQMR=51.2604;NS=1;NUMALT=1;ODDS=1295.27;PAIRED=1;PAIREDR=0.993822;PAO=0;PQA=0;PQR=0;PRO=0;QA=1115;QR=39736;RO=1133;RPL=27;RPP=32.0291;RPPR=52.6897;RPR=6;RUN=1;SAF=16;SAP=3.0761;SAR=17;SRF=563;SRP=3.10421;SRR=570;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19623A>G|p.Lys6541Lys|19623/21291|19623/21291|6541/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1166:1133,33:1133:39736:33:1115:0,-267.97,-3332.94 +NC_045512.2 19895 . C T 2.14568E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=1174;DPB=1174;DPRA=0;EPP=3.0103;EPPR=3.689;GTI=0;LEN=1;MEANALT=2;MQM=43.0556;MQMR=51.1619;NS=1;NUMALT=1;ODDS=1425.78;PAIRED=1;PAIREDR=0.995671;PAO=0;PQA=0;PQR=0;PRO=0;QA=648;QR=40523;RO=1155;RPL=10;RPP=3.49285;RPPR=8.69749;RPR=8;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=579;SRP=3.02722;SRR=576;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19631C>T|p.Ala6544Val|19631/21291|19631/21291|6544/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1174:1155,18:1155:40523:18:648:0,-301.243,-3421.08 +NC_045512.2 19983 . CTTTTTTGA CTTTTTGA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=24;CIGAR=1M1D7M;DP=941;DPB=938.667;DPRA=0;EPP=3.0103;EPPR=3.12892;GTI=0;LEN=1;MEANALT=11;MQM=48.125;MQMR=53.5095;NS=1;NUMALT=1;ODDS=1022.39;PAIRED=1;PAIREDR=0.994426;PAO=0.5;PQA=7;PQR=7;PRO=0.5;QA=783;QR=31500;RO=897;RPL=18;RPP=16.0391;RPPR=3.88421;RPR=6;RUN=1;SAF=12;SAP=3.0103;SAR=12;SRF=461;SRP=4.52331;SRR=436;TYPE=del;ANN=CTTTTTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19725delT|p.Phe6575fs|19725/21291|19725/21291|6575/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:941:897,24:897:31500:24:783:0,-208.308,-2690.68 +NC_045512.2 20088 . T C 5.90698E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=976;DPB=976;DPRA=0;EPP=3.0103;EPPR=3.09122;GTI=0;LEN=1;MEANALT=1;MQM=37.6;MQMR=52.7764;NS=1;NUMALT=1;ODDS=1253.65;PAIRED=1;PAIREDR=0.995859;PAO=0;PQA=0;PQR=0;PRO=0;QA=352;QR=33724;RO=966;RPL=10;RPP=24.725;RPPR=10.0597;RPR=0;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=489;SRP=3.334;SRR=477;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19824T>C|p.Gly6608Gly|19824/21291|19824/21291|6608/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:976:966,10:966:33724:10:352:0,-267.733,-2905.83 +NC_045512.2 20633 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=166;CIGAR=1X;DP=2089;DPB=2089;DPRA=0;EPP=4.31842;EPPR=3.71606;GTI=0;LEN=1;MEANALT=1;MQM=48.7711;MQMR=53.5315;NS=1;NUMALT=1;ODDS=1244.15;PAIRED=1;PAIREDR=0.9948;PAO=0;PQA=0;PQR=0;PRO=0;QA=5737;QR=67701;RO=1923;RPL=103;RPP=23.9402;RPPR=24.2045;RPR=63;RUN=1;SAF=81;SAP=3.2196;SAR=85;SRF=961;SRP=3.01143;SRR=962;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20369T>C|p.Val6790Ala|20369/21291|20369/21291|6790/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2089:1923,166:1923:67701:166:5737:0,-153.829,-5451.28 +NC_045512.2 20686 . G A 4.91807E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=1937;DPB=1937;DPRA=0;EPP=3.0103;EPPR=3.06627;GTI=0;LEN=1;MEANALT=1;MQM=47.8333;MQMR=53.9274;NS=1;NUMALT=1;ODDS=2289.62;PAIRED=1;PAIREDR=0.99474;PAO=0;PQA=0;PQR=0;PRO=0;QA=1232;QR=66116;RO=1901;RPL=12;RPP=11.6962;RPPR=11.6562;RPR=24;RUN=1;SAF=18;SAP=3.0103;SAR=18;SRF=941;SRP=3.42266;SRR=960;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20422G>A|p.Ala6808Thr|20422/21291|20422/21291|6808/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1937:1901,36:1901:66116:36:1232:0,-482.402,-5715.89 +NC_045512.2 20897 . C A 4.32142E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=1649;DPB=1649;DPRA=0;EPP=3.22745;EPPR=4.1453;GTI=0;LEN=1;MEANALT=1;MQM=47.125;MQMR=51.7551;NS=1;NUMALT=1;ODDS=1885.05;PAIRED=1;PAIREDR=0.986948;PAO=0;PQA=0;PQR=0;PRO=0;QA=1318;QR=55575;RO=1609;RPL=16;RPP=6.48466;RPPR=13.2253;RPR=24;RUN=1;SAF=23;SAP=4.96463;SAR=17;SRF=814;SRP=3.4975;SRR=795;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20633C>A|p.Pro6878Gln|20633/21291|20633/21291|6878/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1649:1609,40:1609:55575:40:1318:0,-397.579,-4648.18 +NC_045512.2 20912 . T A 1.13313E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1786;DPB=1786;DPRA=0;EPP=3.0103;EPPR=3.60678;GTI=0;LEN=1;MEANALT=2;MQM=32.05;MQMR=51.4484;NS=1;NUMALT=1;ODDS=2291.88;PAIRED=0.7;PAIREDR=0.988082;PAO=0;PQA=0;PQR=0;PRO=0;QA=694;QR=62244;RO=1762;RPL=0;RPP=46.4397;RPPR=4.11945;RPR=20;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=902;SRP=5.18424;SRR=860;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20648T>A|p.Leu6883*|20648/21291|20648/21291|6883/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1786:1762,20:1762:62244:20:694:0,-495.972,-5248.21 +NC_045512.2 21004 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=2194;DPB=2194;DPRA=0;EPP=3.52123;EPPR=3.93042;GTI=0;LEN=1;MEANALT=2;MQM=51.5882;MQMR=52.7298;NS=1;NUMALT=1;ODDS=2307.07;PAIRED=1;PAIREDR=0.989171;PAO=0;PQA=0;PQR=0;PRO=0;QA=2334;QR=73971;RO=2124;RPL=21;RPP=24.5973;RPPR=17.7321;RPR=47;RUN=1;SAF=35;SAP=3.13803;SAR=33;SRF=1065;SRP=3.0471;SRR=1059;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20740G>T|p.Ala6914Ser|20740/21291|20740/21291|6914/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2194:2124,68:2124:73971:68:2334:0,-465.125,-6190.18 +NC_045512.2 21137 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=62;CIGAR=1X;DP=3005;DPB=3005;DPRA=0;EPP=3.15039;EPPR=15.2971;GTI=0;LEN=1;MEANALT=2;MQM=48.9839;MQMR=50.9398;NS=1;NUMALT=1;ODDS=3469.52;PAIRED=1;PAIREDR=0.991159;PAO=0;PQA=0;PQR=0;PRO=0;QA=2198;QR=103359;RO=2941;RPL=10;RPP=64.7922;RPPR=102.457;RPR=52;RUN=1;SAF=32;SAP=3.15039;SAR=30;SRF=1478;SRP=3.17643;SRR=1463;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20873A>G|p.Lys6958Arg|20873/21291|20873/21291|6958/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3005:2941,62:2941:103359:62:2198:0,-720.982,-8572.97 +NC_045512.2 21357 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=76;CIGAR=1X;DP=3104;DPB=3104;DPRA=0;EPP=3.46745;EPPR=3.74513;GTI=0;LEN=1;MEANALT=2;MQM=49.4211;MQMR=50.8596;NS=1;NUMALT=1;ODDS=3454.76;PAIRED=0.973684;PAIREDR=0.954726;PAO=0;PQA=0;PQR=0;PRO=0;QA=2692;QR=107210;RO=3026;RPL=35;RPP=4.03889;RPPR=55.3237;RPR=41;RUN=1;SAF=37;SAP=3.12459;SAR=39;SRF=1503;SRP=3.29734;SRR=1523;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21093T>C|p.Asn7031Asn|21093/21291|21093/21291|7031/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3104:3026,76:3026:107210:76:2692:0,-714.996,-8823.97 +NC_045512.2 21408 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=33;CIGAR=1X;DP=3187;DPB=3187;DPRA=0;EPP=3.0761;EPPR=14.653;GTI=0;LEN=1;MEANALT=2;MQM=42.0303;MQMR=50.2262;NS=1;NUMALT=1;ODDS=4058.01;PAIRED=0.909091;PAIREDR=0.961294;PAO=0;PQA=0;PQR=0;PRO=0;QA=1172;QR=111449;RO=3152;RPL=24;RPP=17.8158;RPPR=4.87314;RPR=9;RUN=1;SAF=15;SAP=3.60252;SAR=18;SRF=1597;SRP=4.22555;SRR=1555;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21144T>A|p.Phe7048Leu|21144/21291|21144/21291|7048/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3187:3152,33:3152:111449:33:1172:0,-876.049,-9303.39 +NC_045512.2 21417 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=101;CIGAR=1X;DP=3209;DPB=3209;DPRA=0;EPP=3.54779;EPPR=9.44926;GTI=0;LEN=1;MEANALT=1;MQM=44.9208;MQMR=49.8475;NS=1;NUMALT=1;ODDS=3401.21;PAIRED=0.960396;PAIREDR=0.95045;PAO=0;PQA=0;PQR=0;PRO=0;QA=3474;QR=109181;RO=3108;RPL=70;RPP=35.7114;RPPR=41.2668;RPR=31;RUN=1;SAF=47;SAP=4.06379;SAR=54;SRF=1571;SRP=3.81796;SRR=1537;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21153A>T|p.Lys7051Asn|21153/21291|21153/21291|7051/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3209:3108,101:3108:109181:101:3474:0,-695.817,-8846.14 +NC_045512.2 21575 . C T 4774.91 . AB=0.206853;ABP=1767.56;AC=1;AF=0.5;AN=2;AO=489;CIGAR=1X;DP=2364;DPB=2364;DPRA=0;EPP=3.01474;EPPR=3.27143;GTI=0;LEN=1;MEANALT=3;MQM=47.4703;MQMR=52.6018;NS=1;NUMALT=1;ODDS=1099.46;PAIRED=1;PAIREDR=0.99519;PAO=0;PQA=0;PQR=0;PRO=0;QA=17184;QR=65447;RO=1871;RPL=279;RPP=24.1522;RPPR=8.22021;RPR=210;RUN=1;SAF=242;SAP=3.12132;SAR=247;SRF=936;SRP=3.01146;SRR=935;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.13C>T|p.Leu5Phe|13/3822|13/3822|5/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2364:1871,489:1871:65447:489:17184:-675.122,0,-4947.91 +NC_045512.2 21618 . C G 35360.1 . AB=0.703596;ABP=743.974;AC=1;AF=0.5;AN=2;AO=1448;CIGAR=1X;DP=2058;DPB=2058;DPRA=0;EPP=3.0103;EPPR=3.01387;GTI=0;LEN=1;MEANALT=2;MQM=50.1657;MQMR=52.7011;NS=1;NUMALT=1;ODDS=2619.29;PAIRED=0.998619;PAIREDR=0.996716;PAO=0;PQA=0;PQR=0;PRO=0;QA=50596;QR=21344;RO=609;RPL=790;RPP=29.14;RPPR=25.2634;RPR=658;RUN=1;SAF=688;SAP=10.7844;SAR=760;SRF=298;SRP=3.61289;SRR=311;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.56C>G|p.Thr19Arg|56/3822|56/3822|19/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2058:609,1448:609:21344:1448:50596:-3624.67,0,-1224.54 +NC_045512.2 21650 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=198;CIGAR=1X;DP=1834;DPB=1834;DPRA=0;EPP=4.58955;EPPR=5.81888;GTI=0;LEN=1;MEANALT=1;MQM=45.2424;MQMR=51.4438;NS=1;NUMALT=1;ODDS=807.489;PAIRED=1;PAIREDR=0.997555;PAO=0;PQA=0;PQR=0;PRO=0;QA=6993;QR=57736;RO=1636;RPL=198;RPP=432.962;RPPR=3.27045;RPR=0;RUN=1;SAF=93;SAP=4.58955;SAR=105;SRF=794;SRP=6.06841;SRR=842;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.88A>C|p.Asn30His|88/3822|88/3822|30/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1834:1636,198:1636:57736:198:6993:0,-5.24931,-4377.3 +NC_045512.2 21656 . TTCACACG TACC 6.46099E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=51;CIGAR=1M4D2M1X;DP=1573;DPB=1546.88;DPRA=0;EPP=5.09662;EPPR=5.44218;GTI=0;LEN=4;MEANALT=13;MQM=45.3333;MQMR=51.4031;NS=1;NUMALT=1;ODDS=1644.42;PAIRED=1;PAIREDR=0.997335;PAO=0;PQA=0;PQR=0;PRO=0;QA=1783;QR=52647;RO=1501;RPL=51;RPP=113.755;RPPR=24.1912;RPR=0;RUN=1;SAF=22;SAP=5.09662;SAR=29;SRF=731;SRP=5.21071;SRR=770;TYPE=complex;ANN=ACC|frameshift_variant&missense_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.95_101delTCACACGinsACC|p.Phe32fs|95/3822|95/3822|32/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1573:1501,51:1501:52647:51:1783:0,-323.476,-4349.96 +NC_045512.2 21764 . ATACATGT AT 20265.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=744;CIGAR=1M6D1M;DP=744;DPB=186.75;DPRA=0;EPP=6.38425;EPPR=0;GTI=0;LEN=6;MEANALT=1;MQM=49.7083;MQMR=0;NS=1;NUMALT=1;ODDS=1036.01;PAIRED=0.995968;PAIREDR=0;PAO=3;PQA=0;PQR=0;PRO=3;QA=24386;QR=0;RO=0;RPL=373;RPP=3.02197;RPPR=0;RPR=371;RUN=1;SAF=378;SAP=3.43058;SAR=366;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=AT|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.204_209delACATGT|p.His69_Val70del|204/3822|204/3822|68/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:744:0,744:0:0:744:24386:-2031.56,-223.966,0 +NC_045512.2 21855 . C T 10363.6 . AB=0.552296;ABP=21.634;AC=1;AF=0.5;AN=2;AO=433;CIGAR=1X;DP=784;DPB=784;DPRA=0;EPP=3.05543;EPPR=3.16496;GTI=0;LEN=1;MEANALT=1;MQM=50.321;MQMR=52.8519;NS=1;NUMALT=1;ODDS=1907.65;PAIRED=0.995381;PAIREDR=0.997151;PAO=0;PQA=0;PQR=0;PRO=0;QA=15293;QR=12291;RO=351;RPL=218;RPP=3.05543;RPPR=4.79821;RPR=215;RUN=1;SAF=222;SAP=3.61711;SAR=211;SRF=176;SRP=3.01649;SRR=175;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.293C>T|p.Ser98Phe|293/3822|293/3822|98/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:784:351,433:351:12291:433:15293:-1046.09,0,-838.198 +NC_045512.2 21974 . G C 6907.42 . AB=0.470907;ABP=8.44339;AC=1;AF=0.5;AN=2;AO=348;CIGAR=1X;DP=739;DPB=739;DPRA=0;EPP=3.40965;EPPR=3.21074;GTI=0;LEN=1;MEANALT=2;MQM=43.75;MQMR=45.7;NS=1;NUMALT=1;ODDS=1590.49;PAIRED=1;PAIREDR=0.94359;PAO=0;PQA=0;PQR=0;PRO=0;QA=12325;QR=13699;RO=390;RPL=257;RPP=174.956;RPPR=8.02139;RPR=91;RUN=1;SAF=169;SAP=3.63429;SAR=179;SRF=196;SRP=3.03257;SRR=194;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.412G>C|p.Asp138His|412/3822|412/3822|138/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:739:390,348:390:13699:348:12325:-716.861,0,-870.869 +NC_045512.2 21979 . ATTTTTGGGTGTTTATTAC ATTTTGGGTGTTTAC,ATTTTTGGGTGTTTAC 10664.2 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=12,482;CIGAR=1M1D10M3D4M,12M3D4M;DP=548;DPB=469.368;DPRA=0,0;EPP=3.73412,3.65904;EPPR=3.0565;GTI=0;LEN=15,3;MEANALT=5,5;MQM=28.9167,42.9523;MQMR=43.6809;NS=1;NUMALT=2;ODDS=308.58;PAIRED=1,0.977178;PAIREDR=0.829787;PAO=0,0.5;PQA=0,12;PQR=12;PRO=0.5;QA=254,13811;QR=1634;RO=47;RPL=2,311;RPP=14.5915,91.3108;RPPR=80.6751;RPR=10,171;RUN=1,1;SAF=7,234;SAP=3.73412,3.89331;SAR=5,248;SRF=24;SRP=3.0565;SRR=23;TYPE=complex,del;ANN=GGGTGTTTAC|frameshift_variant&missense_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.422_431delTGGGTGTTTAinsGGGTGT|p.Leu141fs|422/3822|422/3822|141/1273||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 2/2:548:47,12,482:47:1634:12,482:254,13811:-1068.01,-1064.49,-1177.28,-28.6243,-127.448,0 +NC_045512.2 22028 . GAGTTCAG GG 0.0 . AB=0.118812;ABP=640.37;AC=1;AF=0.5;AN=2;AO=60;CIGAR=1M6D1M;DP=505;DPB=460;DPRA=0;EPP=3.58936;EPPR=11.6375;GTI=0;LEN=6;MEANALT=2;MQM=49.9;MQMR=43.2995;NS=1;NUMALT=1;ODDS=137.724;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=1971;QR=15417;RO=444;RPL=22;RPP=12.2752;RPPR=53.8932;RPR=38;RUN=1;SAF=32;SAP=3.58936;SAR=28;SRF=208;SRP=6.84461;SRR=236;TYPE=del;ANN=GG|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.467_472delAGTTCA|p.Glu156_Arg158delinsGly|467/3822|467/3822|156/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:505:444,60:444:15417:60:1971:-19.2725,0,-1029.82 +NC_045512.2 22070 . T G 2.82671E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=415;DPB=415;DPRA=0;EPP=3.20771;EPPR=3.2038;GTI=0;LEN=1;MEANALT=1;MQM=56.8182;MQMR=53.0619;NS=1;NUMALT=1;ODDS=464.115;PAIRED=0.909091;PAIREDR=0.992574;PAO=0;PQA=0;PQR=0;PRO=0;QA=372;QR=14318;RO=404;RPL=0;RPP=26.8965;RPPR=3.0963;RPR=11;RUN=1;SAF=5;SAP=3.20771;SAR=6;SRF=209;SRP=4.06379;SRR=195;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.508T>G|p.Tyr170Asp|508/3822|508/3822|170/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:415:404,11:404:14318:11:372:0,-91.1698,-1211.65 +NC_045512.2 22218 . GTTTTTCG GTTTTCG 6.08732E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1M1D6M;DP=973;DPB=971.75;DPRA=0;EPP=3.0103;EPPR=3.15721;GTI=0;LEN=1;MEANALT=7;MQM=53.0833;MQMR=53.0095;NS=1;NUMALT=1;ODDS=1193.66;PAIRED=1;PAIREDR=0.988372;PAO=1;PQA=34;PQR=34;PRO=1;QA=406;QR=32735;RO=946;RPL=2;RPP=14.5915;RPPR=39.4525;RPR=10;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=463;SRP=3.92847;SRR=483;TYPE=del;ANN=GTTTTCG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.661delT|p.Ser221fs|661/3822|661/3822|221/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:973:946,12:946:32735:12:406:0,-251.995,-2798.42 +NC_045512.2 22282 . TTTACTTGCT TT 1.8708E-13 . AB=0.146825;ABP=2733.21;AC=1;AF=0.5;AN=2;AO=370;CIGAR=1M8D1M;DP=2520;DPB=2226.5;DPRA=0;EPP=3.03378;EPPR=34.8149;GTI=0;LEN=8;MEANALT=10;MQM=46.7216;MQMR=49.7873;NS=1;NUMALT=1;ODDS=261.116;PAIRED=0.97027;PAIREDR=0.989247;PAO=11.5;PQA=371.5;PQR=443.5;PRO=13.5;QA=11823;QR=75374;RO=2139;RPL=204;RPP=11.4849;RPPR=2756.8;RPR=166;RUN=1;SAF=176;SAP=4.91181;SAR=194;SRF=1146;SRP=26.7747;SRR=993;TYPE=del;ANN=TT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.723_730delACTTGCTT|p.Leu241fs|723/3822|723/3822|241/1273||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/1:2520:2139,370:2139:75374:370:11823:-194.926,0,-5543.52 +NC_045512.2 22315 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=357;CIGAR=1X;DP=4311;DPB=4311;DPRA=0;EPP=3.30835;EPPR=18.922;GTI=0;LEN=1;MEANALT=3;MQM=48.1261;MQMR=49.6176;NS=1;NUMALT=1;ODDS=2556.05;PAIRED=0.985994;PAIREDR=0.992901;PAO=0;PQA=0;PQR=0;PRO=0;QA=12323;QR=138793;RO=3944;RPL=57;RPP=362.179;RPPR=1298.6;RPR=300;RUN=1;SAF=185;SAP=4.03825;SAR=172;SRF=2048;SRP=15.7308;SRR=1896;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.753T>G|p.Pro251Pro|753/3822|753/3822|251/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4311:3944,357:3944:138793:357:12323:0,-302.488,-10551.5 +NC_045512.2 22600 . ATTTGC ATTGC 4.14663E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=275;CIGAR=1M1D4M;DP=5420;DPB=5374.17;DPRA=0;EPP=11.6093;EPPR=8.62691;GTI=0;LEN=1;MEANALT=12;MQM=50.6836;MQMR=52.2494;NS=1;NUMALT=1;ODDS=4743.11;PAIRED=1;PAIREDR=0.995893;PAO=0;PQA=0;PQR=0;PRO=0;QA=8676;QR=179526;RO=5113;RPL=253;RPP=424.363;RPPR=1086.16;RPR=22;RUN=1;SAF=121;SAP=11.6093;SAR=154;SRF=2497;SRP=9.02442;SRR=2616;TYPE=del;ANN=ATTGC|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1041delT|p.Phe347fs|1041/3822|1041/3822|347/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5420:5113,275:5113:179526:275:8676:0,-851.108,-14682.4 +NC_045512.2 22643 . TGT ACA 1.12947E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=3X;DP=3250;DPB=3250;DPRA=0;EPP=3.1419;EPPR=4.04925;GTI=0;LEN=3;MEANALT=3;MQM=42.2879;MQMR=53.4939;NS=1;NUMALT=1;ODDS=3785.89;PAIRED=0.924242;PAIREDR=0.996854;PAO=0;PQA=0;PQR=0;PRO=0;QA=2317;QR=110756;RO=3179;RPL=27;RPP=7.74806;RPPR=167.685;RPR=39;RUN=1;SAF=31;SAP=3.53672;SAR=35;SRF=1582;SRP=3.16399;SRR=1597;TYPE=complex;ANN=ACA|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1081_1083delTGTinsACA|p.Cys361Thr|1081/3822|1081/3822|361/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3250:3179,66:3179:110756:66:2317:0,-800.501,-9497.37 +NC_045512.2 22852 . A G 0.0 . AB=0.143746;ABP=3193.32;AC=1;AF=0.5;AN=2;AO=416;CIGAR=1X;DP=2894;DPB=2894;DPRA=0;EPP=5.09825;EPPR=10.6047;GTI=0;LEN=1;MEANALT=3;MQM=43.2572;MQMR=50.5285;NS=1;NUMALT=1;ODDS=362.403;PAIRED=1;PAIREDR=0.984634;PAO=0;PQA=0;PQR=0;PRO=0;QA=14466;QR=87462;RO=2473;RPL=335;RPP=339.776;RPPR=45.1235;RPR=81;RUN=1;SAF=199;SAP=4.70154;SAR=217;SRF=1207;SRP=6.06687;SRR=1266;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1290A>G|p.Thr430Thr|1290/3822|1290/3822|430/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2894:2473,416:2473:87462:416:14466:-239.51,0,-6540.23 +NC_045512.2 22917 . T G 25609.5 . AB=0.654307;ABP=365.559;AC=1;AF=0.5;AN=2;AO=1147;CIGAR=1X;DP=1753;DPB=1753;DPRA=0;EPP=5.88982;EPPR=3.93066;GTI=0;LEN=1;MEANALT=2;MQM=49.0113;MQMR=53.3858;NS=1;NUMALT=1;ODDS=2887.26;PAIRED=0.975588;PAIREDR=0.993377;PAO=0;PQA=0;PQR=0;PRO=0;QA=37925;QR=20944;RO=604;RPL=580;RPP=3.33025;RPPR=3.71495;RPR=567;RUN=1;SAF=582;SAP=3.55743;SAR=565;SRF=309;SRP=3.71495;SRR=295;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1355T>G|p.Leu452Arg|1355/3822|1355/3822|452/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1753:604,1147:604:20944:1147:37925:-2607.08,0,-1299.49 +NC_045512.2 22995 . C A 26960.9 . AB=0.637002;ABP=281.467;AC=1;AF=0.5;AN=2;AO=1088;CIGAR=1X;DP=1708;DPB=1708;DPRA=0;EPP=3.13803;EPPR=3.79961;GTI=0;LEN=1;MEANALT=2;MQM=50.7574;MQMR=53.2084;NS=1;NUMALT=1;ODDS=3085.5;PAIRED=0.988051;PAIREDR=0.996769;PAO=0;PQA=0;PQR=0;PRO=0;QA=38250;QR=21584;RO=619;RPL=537;RPP=3.40148;RPPR=4.02412;RPR=551;RUN=1;SAF=541;SAP=3.08215;SAR=547;SRF=306;SRP=3.18219;SRR=313;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1433C>A|p.Thr478Lys|1433/3822|1433/3822|478/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1708:619,1088:619:21584:1088:38250:-2733.04,0,-1376.73 +NC_045512.2 23063 . A T 11471.4 . AB=0.363065;ABP=262.299;AC=1;AF=0.5;AN=2;AO=578;CIGAR=1X;DP=1592;DPB=1592;DPRA=0;EPP=3.0103;EPPR=3.55852;GTI=0;LEN=1;MEANALT=1;MQM=48.7907;MQMR=51.641;NS=1;NUMALT=1;ODDS=2641.38;PAIRED=0.989619;PAIREDR=0.97929;PAO=0;PQA=0;PQR=0;PRO=0;QA=20314;QR=35139;RO=1014;RPL=301;RPP=5.17426;RPPR=3.31867;RPR=277;RUN=1;SAF=288;SAP=3.02533;SAR=290;SRF=504;SRP=3.08739;SRR=510;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1592:1014,578:1014:35139:578:20314:-1181.74,0,-2507.13 +NC_045512.2 23271 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=99;CIGAR=1X;DP=3990;DPB=3990;DPRA=0;EPP=3.03223;EPPR=3.54827;GTI=0;LEN=1;MEANALT=2;MQM=47.1616;MQMR=52.3784;NS=1;NUMALT=1;ODDS=4435.23;PAIRED=1;PAIREDR=0.998453;PAO=0;PQA=0;PQR=0;PRO=0;QA=3411;QR=135408;RO=3879;RPL=40;RPP=10.9285;RPPR=125.097;RPR=59;RUN=1;SAF=50;SAP=3.03223;SAR=49;SRF=1984;SRP=7.44449;SRR=1895;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3990:3879,99:3879:135408:99:3411:0,-922.477,-11401.5 +NC_045512.2 23302 . G C 1478.84 . AB=0.154267;ABP=4370.88;AC=1;AF=0.5;AN=2;AO=649;CIGAR=1X;DP=4207;DPB=4207;DPRA=0;EPP=3.97726;EPPR=3.89208;GTI=0;LEN=1;MEANALT=2;MQM=50.0555;MQMR=53.4027;NS=1;NUMALT=1;ODDS=340.516;PAIRED=0.996918;PAIREDR=0.996625;PAO=0;PQA=0;PQR=0;PRO=0;QA=22618;QR=125381;RO=3556;RPL=295;RPP=14.6573;RPPR=18.2546;RPR=354;RUN=1;SAF=323;SAP=3.04041;SAR=326;SRF=1770;SRP=3.16663;SRR=1786;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1740G>C|p.Gln580His|1740/3822|1740/3822|580/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4207:3556,649:3556:125381:649:22618:-637.692,0,-9696.8 +NC_045512.2 23403 . A G 104667.0 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3570;CIGAR=1X;DP=3572;DPB=3572;DPRA=0;EPP=4.29737;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=50.3319;MQMR=54;NS=1;NUMALT=1;ODDS=4927.87;PAIRED=0.995798;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=124700;QR=72;RO=2;RPL=1945;RPP=65.2957;RPPR=7.35324;RPR=1625;RUN=1;SAF=1745;SAP=6.90314;SAR=1825;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:3572:2,3570:2:72:3570:124700:-10477.8,-1068.47,0 +NC_045512.2 23472 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2386;DPB=2386;DPRA=0;EPP=25.4075;EPPR=10.5077;GTI=0;LEN=1;MEANALT=2;MQM=53.7429;MQMR=48.1756;NS=1;NUMALT=1;ODDS=3053.41;PAIRED=1;PAIREDR=0.976556;PAO=0;PQA=0;PQR=0;PRO=0;QA=546;QR=77493;RO=2346;RPL=27;RPP=25.4075;RPPR=1331.44;RPR=8;RUN=1;SAF=35;SAP=79.0118;SAR=0;SRF=1114;SRP=15.8984;SRR=1232;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1910C>A|p.Ser637Tyr|1910/3822|1910/3822|637/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2386:2346,35:2346:77493:35:546:0,-668.526,-6266.09 +NC_045512.2 23492 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1868;DPB=1868;DPRA=0;EPP=42.4916;EPPR=19.2094;GTI=0;LEN=1;MEANALT=3;MQM=49.7273;MQMR=46.6534;NS=1;NUMALT=1;ODDS=2434.25;PAIRED=1;PAIREDR=0.973842;PAO=0;PQA=0;PQR=0;PRO=0;QA=327;QR=61631;RO=1835;RPL=21;RPP=42.4916;RPPR=2188.54;RPR=1;RUN=1;SAF=22;SAP=50.7827;SAR=0;SRF=857;SRP=20.3359;SRR=978;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1930C>A|p.Gln644Lys|1930/3822|1930/3822|644/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1868:1835,22:1835:61631:22:327:0,-529.793,-4862.4 +NC_045512.2 23575 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=456;DPB=456;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=27.8333;MQMR=51.192;NS=1;NUMALT=1;ODDS=580.51;PAIRED=1;PAIREDR=0.991071;PAO=0;PQA=0;PQR=0;PRO=0;QA=208;QR=15391;RO=448;RPL=4;RPP=4.45795;RPPR=5.35627;RPR=2;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=229;SRP=3.495;SRR=219;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2013C>T|p.Cys671Cys|2013/3822|2013/3822|671/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:456:448,6:448:15391:6:208:0,-124.875,-1294.11 +NC_045512.2 23604 . C G 15167.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=536;CIGAR=1X;DP=536;DPB=536;DPRA=0;EPP=3.0265;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=49.2929;MQMR=0;NS=1;NUMALT=1;ODDS=747.659;PAIRED=0.998134;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18474;QR=0;RO=0;RPL=228;RPP=28.9383;RPPR=0;RPR=308;RUN=1;SAF=275;SAP=3.80435;SAR=261;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2042C>G|p.Pro681Arg|2042/3822|2042/3822|681/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:536:0,536:0:0:536:18474:-1523.85,-161.352,0 +NC_045512.2 23746 . A G 1.18854E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=59;CIGAR=1X;DP=618;DPB=618;DPRA=0;EPP=3.93042;EPPR=3.88433;GTI=0;LEN=1;MEANALT=1;MQM=52.9492;MQMR=52.1896;NS=1;NUMALT=1;ODDS=268.144;PAIRED=1;PAIREDR=0.989267;PAO=0;PQA=0;PQR=0;PRO=0;QA=2051;QR=19534;RO=559;RPL=32;RPP=3.93042;RPPR=5.84215;RPR=27;RUN=1;SAF=29;SAP=3.0471;SAR=30;SRF=268;SRP=5.06524;SRR=291;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2184A>G|p.Pro728Pro|2184/3822|2184/3822|728/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:618:559,59:559:19534:59:2051:0,-8.56006,-1510.11 +NC_045512.2 23865 . C T 7.83587E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=325;DPB=325;DPRA=0;EPP=3.0103;EPPR=3.34385;GTI=0;LEN=1;MEANALT=1;MQM=49;MQMR=51.4671;NS=1;NUMALT=1;ODDS=391.092;PAIRED=1;PAIREDR=0.984326;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=11241;RO=319;RPL=0;RPP=16.0391;RPPR=3.56168;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=161;SRP=3.07156;SRR=158;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2303C>T|p.Thr768Ile|2303/3822|2303/3822|768/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:325:319,6:319:11241:6:204:0,-79.3917,-944.349 +NC_045512.2 23887 . CAAAAACACCCAAG CAAAACACCCAAG 4.52052E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1M1D12M;DP=304;DPB=303.714;DPRA=0;EPP=3.0103;EPPR=4.05261;GTI=0;LEN=1;MEANALT=1;MQM=56.75;MQMR=52.8033;NS=1;NUMALT=1;ODDS=380.478;PAIRED=1;PAIREDR=0.963333;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=10487;RO=300;RPL=4;RPP=11.6962;RPPR=3.12611;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=150;SRP=3.0103;SRR=150;TYPE=del;ANN=CAAAACACCCAAG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2330delA|p.Asn777fs|2330/3822|2330/3822|777/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:304:300,4:300:10487:4:144:0,-78.2128,-896.486 +NC_045512.2 23910 . C T 1.37419E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=401;DPB=401;DPRA=0;EPP=3.0103;EPPR=3.14773;GTI=0;LEN=1;MEANALT=1;MQM=55.1667;MQMR=50.9089;NS=1;NUMALT=1;ODDS=489.483;PAIRED=1;PAIREDR=0.959494;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=13744;RO=395;RPL=2;RPP=4.45795;RPPR=11.3718;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=203;SRP=3.67549;SRR=192;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2348C>T|p.Ala783Val|2348/3822|2348/3822|783/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:401:395,6:395:13744:6:216:0,-100.971,-1131.25 +NC_045512.2 23996 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=555;DPB=555;DPRA=0;EPP=3.0103;EPPR=3.58091;GTI=0;LEN=1;MEANALT=2;MQM=54.6667;MQMR=50.4818;NS=1;NUMALT=1;ODDS=702.743;PAIRED=1;PAIREDR=0.972628;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=19193;RO=548;RPL=0;RPP=16.0391;RPPR=7.06794;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=276;SRP=3.0737;SRR=272;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2434C>T|p.Pro812Ser|2434/3822|2434/3822|812/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:555:548,6:548:19193:6:216:0,-147.202,-1587.52 +NC_045512.2 24110 . A C 9.9567E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=569;DPB=569;DPRA=0;EPP=3.9627;EPPR=3.62103;GTI=0;LEN=1;MEANALT=1;MQM=47.2807;MQMR=48.4238;NS=1;NUMALT=1;ODDS=274.15;PAIRED=1;PAIREDR=0.935547;PAO=0;PQA=0;PQR=0;PRO=0;QA=2023;QR=18082;RO=512;RPL=0;RPP=126.784;RPPR=3.02726;RPR=57;RUN=1;SAF=31;SAP=3.9627;SAR=26;SRF=253;SRP=3.16298;SRR=259;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2548A>C|p.Ile850Leu|2548/3822|2548/3822|850/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:569:512,57:512:18082:57:2023:0,-5.64707,-1298.89 +NC_045512.2 24201 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=542;DPB=542;DPRA=0;EPP=3.73412;EPPR=3.21144;GTI=0;LEN=1;MEANALT=2;MQM=50.9167;MQMR=52.3214;NS=1;NUMALT=1;ODDS=625.015;PAIRED=1;PAIREDR=0.964083;PAO=0;PQA=0;PQR=0;PRO=0;QA=428;QR=18455;RO=529;RPL=11;RPP=21.1059;RPPR=31.2887;RPR=1;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=266;SRP=3.04724;SRR=263;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2639G>A|p.Gly880Asp|2639/3822|2639/3822|880/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:542:529,12:529:18455:12:428:0,-126.755,-1553.36 +NC_045512.2 24320 . CAAAAATTG CAAAATTG 2687.09 . AB=0.320298;ABP=153.634;AC=1;AF=0.5;AN=2;AO=172;CIGAR=1M1D7M;DP=537;DPB=519.222;DPRA=0;EPP=3.46479;EPPR=3.88374;GTI=0;LEN=1;MEANALT=3;MQM=49.6395;MQMR=53.9553;NS=1;NUMALT=1;ODDS=618.726;PAIRED=1;PAIREDR=0.997207;PAO=1;PQA=34.5;PQR=34.5;PRO=1;QA=5084;QR=12491;RO=358;RPL=99;RPP=11.5447;RPPR=3.22866;RPR=73;RUN=1;SAF=84;SAP=3.2123;SAR=88;SRF=175;SRP=3.3985;SRR=183;TYPE=del;ANN=CAAAATTG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2763delA|p.Lys921fs|2763/3822|2763/3822|921/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:537:358,172:358:12491:172:5084:-291.188,0,-941.405 +NC_045512.2 24329 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=563;DPB=563;DPRA=0;EPP=3.0103;EPPR=3.04539;GTI=0;LEN=1;MEANALT=1;MQM=54.3333;MQMR=52.1598;NS=1;NUMALT=1;ODDS=713.029;PAIRED=1;PAIREDR=0.994614;PAO=0;PQA=0;PQR=0;PRO=0;QA=211;QR=19533;RO=557;RPL=2;RPP=4.45795;RPPR=8.93994;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=271;SRP=3.88747;SRR=286;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2767A>G|p.Ile923Val|2767/3822|2767/3822|923/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:563:557,6:557:19533:6:211:0,-150.179,-1654.98 +NC_045512.2 24410 . G A 7223.05 . AB=0.387777;ABP=106.822;AC=1;AF=0.5;AN=2;AO=368;CIGAR=1X;DP=949;DPB=949;DPRA=0;EPP=3.86001;EPPR=6.84407;GTI=0;LEN=1;MEANALT=2;MQM=45.2799;MQMR=49.4586;NS=1;NUMALT=1;ODDS=1663.17;PAIRED=0.98913;PAIREDR=0.993103;PAO=0;PQA=0;PQR=0;PRO=0;QA=13128;QR=20569;RO=580;RPL=255;RPP=121.993;RPPR=1202.4;RPR=113;RUN=1;SAF=177;SAP=4.16685;SAR=191;SRF=307;SRP=7.33827;SRR=273;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2848G>A|p.Asp950Asn|2848/3822|2848/3822|950/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:949:580,368:580:20569:368:13128:-752.784,0,-1403.38 +NC_045512.2 24506 . T G 13690.0 . AB=0.316547;ABP=653.14;AC=1;AF=0.5;AN=2;AO=704;CIGAR=1X;DP=2224;DPB=2224;DPRA=0;EPP=3.61486;EPPR=3.76653;GTI=0;LEN=1;MEANALT=2;MQM=51.4545;MQMR=52.4332;NS=1;NUMALT=1;ODDS=3152.23;PAIRED=0.992898;PAIREDR=0.99605;PAO=0;PQA=0;PQR=0;PRO=0;QA=24742;QR=53799;RO=1519;RPL=390;RPP=20.8262;RPPR=19.9947;RPR=314;RUN=1;SAF=361;SAP=4.00967;SAR=343;SRF=776;SRP=4.56707;SRR=743;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2224:1519,704:1519:53799:704:24742:-1445.67,0,-3985.74 +NC_045512.2 24626 . G A 1.2247E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=45;CIGAR=1X;DP=2469;DPB=2469;DPRA=0;EPP=3.05855;EPPR=4.04844;GTI=0;LEN=1;MEANALT=3;MQM=46.8667;MQMR=52.6319;NS=1;NUMALT=1;ODDS=2917.41;PAIRED=1;PAIREDR=0.995451;PAO=0;PQA=0;PQR=0;PRO=0;QA=1578;QR=84277;RO=2418;RPL=27;RPP=6.91895;RPPR=3.52757;RPR=18;RUN=1;SAF=23;SAP=3.05855;SAR=22;SRF=1205;SRP=3.06777;SRR=1213;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3064G>A|p.Ala1022Thr|3064/3822|3064/3822|1022/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2469:2418,45:2418:84277:45:1578:0,-616.766,-7159.4 +NC_045512.2 24794 . G C 4292.7 . AB=0.176533;ABP=3441.96;AC=1;AF=0.5;AN=2;AO=668;CIGAR=1X;DP=3784;DPB=3784;DPRA=0;EPP=3.4784;EPPR=4.48774;GTI=0;LEN=1;MEANALT=3;MQM=49.018;MQMR=52.3277;NS=1;NUMALT=1;ODDS=988.432;PAIRED=1;PAIREDR=0.994534;PAO=0;PQA=0;PQR=0;PRO=0;QA=23418;QR=109332;RO=3110;RPL=267;RPP=61.38;RPPR=173.402;RPR=401;RUN=1;SAF=341;SAP=3.64744;SAR=327;SRF=1584;SRP=5.35912;SRR=1526;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3232G>C|p.Ala1078Pro|3232/3822|3232/3822|1078/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3784:3110,668:3110:109332:668:23418:-815.381,0,-8328.87 +NC_045512.2 24914 . G C 16119.5 . AB=0.236327;ABP=2962;AC=1;AF=0.5;AN=2;AO=1158;CIGAR=1X;DP=4900;DPB=4900;DPRA=0;EPP=3.19782;EPPR=3.53313;GTI=0;LEN=1;MEANALT=2;MQM=50.032;MQMR=52.79;NS=1;NUMALT=1;ODDS=3711.66;PAIRED=0.996546;PAIREDR=0.991974;PAO=0;PQA=0;PQR=0;PRO=0;QA=40628;QR=131352;RO=3738;RPL=527;RPP=23.2924;RPPR=15.0562;RPR=631;RUN=1;SAF=591;SAP=4.09041;SAR=567;SRF=1865;SRP=3.04748;SRR=1873;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4900:3738,1158:3738:131352:1158:40628:-1933.55,0,-9894.85 +NC_045512.2 24952 . A G 9.54689E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=70;CIGAR=1X;DP=4842;DPB=4842;DPRA=0;EPP=3.0103;EPPR=10.9423;GTI=0;LEN=1;MEANALT=2;MQM=51.7714;MQMR=52.1543;NS=1;NUMALT=1;ODDS=5869.66;PAIRED=1;PAIREDR=0.991824;PAO=0;PQA=0;PQR=0;PRO=0;QA=2463;QR=167916;RO=4770;RPL=37;RPP=3.50664;RPPR=21.9554;RPR=33;RUN=1;SAF=36;SAP=3.13438;SAR=34;SRF=2328;SRP=8.92654;SRR=2442;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3390A>G|p.Ile1130Met|3390/3822|3390/3822|1130/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4842:4770,70:4770:167916:70:2463:0,-1244.69,-14195.3 +NC_045512.2 25047 . C T 6.36456E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=333;CIGAR=1X;DP=4648;DPB=4648;DPRA=0;EPP=3.79933;EPPR=13.3153;GTI=0;LEN=1;MEANALT=2;MQM=46.3183;MQMR=51.3063;NS=1;NUMALT=1;ODDS=3139.76;PAIRED=0.993994;PAIREDR=0.986076;PAO=0;PQA=0;PQR=0;PRO=0;QA=11708;QR=149413;RO=4309;RPL=109;RPP=89.2497;RPPR=163.88;RPR=224;RUN=1;SAF=173;SAP=4.11234;SAR=160;SRF=2131;SRP=4.1235;SRR=2178;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3485C>T|p.Pro1162Leu|3485/3822|3485/3822|1162/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4648:4309,333:4309:149413:333:11708:0,-469.855,-11790.8 +NC_045512.2 25243 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=69;CIGAR=1X;DP=3225;DPB=3225;DPRA=0;EPP=3.04177;EPPR=3.63033;GTI=0;LEN=1;MEANALT=2;MQM=52.7681;MQMR=52.0352;NS=1;NUMALT=1;ODDS=3678.35;PAIRED=1;PAIREDR=0.993655;PAO=0;PQA=0;PQR=0;PRO=0;QA=2355;QR=108908;RO=3152;RPL=40;RPP=6.81824;RPPR=95.2951;RPR=29;RUN=1;SAF=34;SAP=3.04177;SAR=35;SRF=1538;SRP=6.9895;SRR=1614;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3681A>G|p.Ile1227Met|3681/3822|3681/3822|1227/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3225:3152,69:3152:108908:69:2355:0,-765.93,-9146.09 +NC_045512.2 25244 . G T 8.47644E-13 . AB=0.135368;ABP=3748.16;AC=1;AF=0.5;AN=2;AO=439;CIGAR=1X;DP=3243;DPB=3243;DPRA=0;EPP=4.12324;EPPR=4.37735;GTI=0;LEN=1;MEANALT=3;MQM=48.303;MQMR=52.5899;NS=1;NUMALT=1;ODDS=418.437;PAIRED=0.995444;PAIREDR=0.99429;PAO=0;PQA=0;PQR=0;PRO=0;QA=15155;QR=97802;RO=2802;RPL=270;RPP=53.4686;RPPR=74.6301;RPR=169;RUN=1;SAF=216;SAP=3.25267;SAR=223;SRF=1369;SRP=6.18459;SRR=1433;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3682G>T|p.Val1228Leu|3682/3822|3682/3822|1228/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3243:2802,439:2802:97802:439:15155:-248.813,0,-7498.01 +NC_045512.2 25277 . A T 2.24204E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=49;CIGAR=1X;DP=2415;DPB=2415;DPRA=0;EPP=100.904;EPPR=7.6624;GTI=0;LEN=1;MEANALT=3;MQM=51.7551;MQMR=50.6511;NS=1;NUMALT=1;ODDS=3038.7;PAIRED=0.979592;PAIREDR=0.9932;PAO=0;PQA=0;PQR=0;PRO=0;QA=748;QR=81205;RO=2353;RPL=1;RPP=100.904;RPPR=938.828;RPR=48;RUN=1;SAF=0;SAP=109.412;SAR=49;SRF=1196;SRP=4.41396;SRR=1157;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3715A>T|p.Ser1239Cys|3715/3822|3715/3822|1239/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2415:2353,49:2353:81205:49:748:0,-656.393,-6775.09 +NC_045512.2 25286 . A T 6.2686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=2593;DPB=2593;DPRA=0;EPP=163.699;EPPR=57.3406;GTI=0;LEN=1;MEANALT=2;MQM=50.9459;MQMR=49.8839;NS=1;NUMALT=1;ODDS=3162.15;PAIRED=0.959459;PAIREDR=0.988391;PAO=0;PQA=0;PQR=0;PRO=0;QA=1109;QR=84675;RO=2498;RPL=0;RPP=163.699;RPPR=507.755;RPR=74;RUN=1;SAF=0;SAP=163.699;SAR=74;SRF=1342;SRP=33.0841;SRR=1156;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3724A>T|p.Ser1242Cys|3724/3822|3724/3822|1242/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2593:2498,74:2498:84675:74:1109:0,-674.605,-6923.8 +NC_045512.2 25296 . A C,T 1.83222E-13 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=141,54;CIGAR=1X,1X;DP=2571;DPB=2571;DPRA=0,0;EPP=119.577,88.0998;EPPR=157.455;GTI=0;LEN=1,1;MEANALT=3,3;MQM=50.9149,51.6111;MQMR=49.8522;NS=1;NUMALT=2;ODDS=2652.62;PAIRED=0.957447,0.981481;PAIREDR=0.988632;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=2213,924;QR=80940;RO=2375;RPL=28,4;RPP=114.279,88.0998;RPPR=367.051;RPR=113,50;RUN=1,1;SAF=1,0;SAP=300.564,120.27;SAR=140,54;SRF=1364;SRP=116.941;SRR=1011;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3734A>C|p.Lys1245Thr|3734/3822|3734/3822|1245/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2571:2375,141,54:2375:80940:141,54:2213,924:0,-560.207,-6463.48,-648.053,-6439.04,-6577.52 +NC_045512.2 25297 . GGGC GGGG 1.29702E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=63;CIGAR=3M1X;DP=2484;DPB=2543.75;DPRA=0;EPP=114.996;EPPR=62.0599;GTI=0;LEN=1;MEANALT=9;MQM=50.7937;MQMR=49.9929;NS=1;NUMALT=1;ODDS=2993.64;PAIRED=0.952381;PAIREDR=0.987137;PAO=66;PQA=2152;PQR=2152;PRO=66;QA=1266;QR=82158;RO=2410;RPL=3;RPP=114.996;RPPR=193.667;RPR=60;RUN=1;SAF=0;SAP=139.813;SAR=63;SRF=1322;SRP=52.3469;SRR=1088;TYPE=snp;ANN=GGGG|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3738C>G|p.Gly1246Gly|3738/3822|3738/3822|1246/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2484:2410,63:2410:82158:63:1266:0,-632.107,-6695.99 +NC_045512.2 25308 . C G,T 1.02822E-13 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=27,37;CIGAR=1X,1X;DP=2591;DPB=2591;DPRA=0,0;EPP=38.4777,74.9036;EPPR=105.533;GTI=0;LEN=1,1;MEANALT=3,3;MQM=47.9259,50.0541;MQMR=50.213;NS=1;NUMALT=2;ODDS=3317.27;PAIRED=0.888889,0.972973;PAIREDR=0.981357;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=392,554;QR=79400;RO=2521;RPL=4,1;RPP=32.0437,74.9036;RPPR=90.6625;RPR=23,36;RUN=1,1;SAF=1,0;SAP=53.2759,83.3548;SAR=26,37;SRF=1425;SRP=96.2441;SRR=1096;TYPE=snp,snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3746C>G|p.Ser1249Cys|3746/3822|3746/3822|1249/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2591:2521,27,37:2521:79400:27,37:392,554:0,-732.46,-6524.72,-721.199,-6495.15,-6510.45 +NC_045512.2 25312 . T G 1.87444E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=29;CIGAR=1X;DP=2594;DPB=2594;DPRA=0;EPP=3.68421;EPPR=76.7412;GTI=0;LEN=1;MEANALT=3;MQM=46.4483;MQMR=50.2856;NS=1;NUMALT=1;ODDS=3381;PAIRED=0.896552;PAIREDR=0.980101;PAO=0;PQA=0;PQR=0;PRO=0;QA=439;QR=80737;RO=2563;RPL=13;RPP=3.68421;RPPR=17.1092;RPR=16;RUN=1;SAF=0;SAP=65.983;SAR=29;SRF=1423;SRP=70.8648;SRR=1140;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3750T>G|p.Cys1250Trp|3750/3822|3750/3822|1250/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2594:2563,29:2563:80737:29:439:0,-743.535,-6638.88 +NC_045512.2 25314 . G T 5.47261E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=98;CIGAR=1X;DP=2511;DPB=2511;DPRA=0;EPP=124.347;EPPR=150.808;GTI=0;LEN=1;MEANALT=2;MQM=49.5816;MQMR=50.4178;NS=1;NUMALT=1;ODDS=2901.26;PAIRED=0.938776;PAIREDR=0.982068;PAO=0;PQA=0;PQR=0;PRO=0;QA=1409;QR=74838;RO=2398;RPL=12;RPP=124.347;RPPR=10.6747;RPR=86;RUN=1;SAF=0;SAP=215.815;SAR=98;SRF=1406;SRP=158.215;SRR=992;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3752G>T|p.Gly1251Val|3752/3822|3752/3822|1251/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2511:2398,98:2398:74838:98:1409:0,-626.065,-6055.73 +NC_045512.2 25316 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=38;CIGAR=1X;DP=2470;DPB=2470;DPRA=0;EPP=17.6392;EPPR=126.463;GTI=0;LEN=1;MEANALT=3;MQM=48.9737;MQMR=50.4211;NS=1;NUMALT=1;ODDS=3112.87;PAIRED=0.973684;PAIREDR=0.979236;PAO=0;PQA=0;PQR=0;PRO=0;QA=605;QR=74347;RO=2408;RPL=10;RPP=21.525;RPPR=4.75613;RPR=28;RUN=1;SAF=1;SAP=77.0689;SAR=37;SRF=1393;SRP=131.859;SRR=1015;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3754T>C|p.Ser1252Pro|3754/3822|3754/3822|1252/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2470:2408,38:2408:74347:38:605:0,-682.516,-6085.67 +NC_045512.2 25323 . GCAAA GAAAT,CAAAA,GAAAA 0.0 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=71,67,284;CIGAR=1M1X2M1X,2X3M,1M1X3M;DP=2463;DPB=2473.6;DPRA=0,0,0;EPP=76.4428,38.3048,208.658;EPPR=686.769;GTI=0;LEN=5,2,1;MEANALT=17,17,17;MQM=48.8873,49.7164,50.9155;MQMR=51.4338;NS=1;NUMALT=3;ODDS=1480.75;PAIRED=0.901408,0.955224,0.985915;PAIREDR=0.977006;PAO=9,10,10;PQA=126,247,247;PQR=247;PRO=10;QA=1663,1100,5254;QR=66729;RO=1957;RPL=11,17,60;RPP=76.4428,38.3048,208.658;RPPR=21.475;RPR=60,50,224;RUN=1,1,1;SAF=0,0,0;SAP=157.185,148.499,619.708;SAR=71,67,284;SRF=1463;SRP=1044.87;SRR=494;TYPE=complex,mnp,snp;ANN=GAAAA|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3762C>A|p.Cys1254*|3762/3822|3762/3822|1254/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2463:1957,71,67,284:1957:66729:71,67,284:1663,1100,5254:0,-464.981,-5396.57,-511.087,-5339.92,-5443.88,-203.076,-5031.91,-5078.01,-5070.55 +NC_045512.2 25331 . G T 1.83222E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=167;CIGAR=1X;DP=2694;DPB=2694;DPRA=0;EPP=135.652;EPPR=242.371;GTI=0;LEN=1;MEANALT=2;MQM=49.7964;MQMR=51.6339;NS=1;NUMALT=1;ODDS=2682.43;PAIRED=0.946108;PAIREDR=0.978884;PAO=0;PQA=0;PQR=0;PRO=0;QA=2950;QR=74828;RO=2510;RPL=33;RPP=135.652;RPPR=260.919;RPR=134;RUN=1;SAF=0;SAP=365.646;SAR=167;SRF=1594;SRP=400.696;SRR=916;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3769G>T|p.Asp1257Tyr|3769/3822|3769/3822|1257/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2694:2510,167:2510:74828:167:2950:0,-546.112,-6035.79 +NC_045512.2 25334 . GAAG CACG,CACC,GACC,CAAG,TAAG,GACG,GAAC 3.16299E-13 . AB=0,0,0,0,0,0,0;ABP=0,0,0,0,0,0,0;AC=0,0,0,0,0,0,0;AF=0,0,0,0,0,0,0;AN=2;AO=70,48,48,67,57,133,35;CIGAR=1X1M1X1M,1X1M2X,2M2X,1X3M,1X3M,2M1X1M,3M1X;DP=2461;DPB=2518;DPRA=0,0,0,0,0,0,0;EPP=57.7314,14.5915,21.1059,42.7126,49.6779,45.4765,35.8306;EPPR=603.572;GTI=0;LEN=4,4,2,1,1,1,1;MEANALT=17,17,17,17,17,17,17;MQM=49.1143,49.9583,46.0833,52.3134,50.9825,51.203,49.3143;MQMR=53.4979;NS=1;NUMALT=7;ODDS=2128.71;PAIRED=0.971429,0.958333,0.979167,1,0.982456,0.977444,0.971429;PAIREDR=0.975873;PAO=0,8.33333,41.5833,0,0,33.25,44.5833;PQA=0,188.333,1318.58,0,0,1130.25,1409.58;PQR=1221.25;PRO=36.25;QA=1249,803,708,1036,910,1875,507;QR=63002;RO=1948;RPL=14,16,14,16,11,41,6;RPP=57.7314,14.5915,21.1059,42.7126,49.6779,45.4765,35.8306;RPPR=494.485;RPR=56,32,34,51,46,92,29;RUN=1,1,1,1,1,1,1;SAF=0,0,0,0,0,0,0;SAP=155.013,107.241,107.241,148.499,126.784,291.816,79.0118;SAR=70,48,48,67,57,133,35;SRF=1469;SRP=1095.55;SRR=479;TYPE=complex,complex,mnp,snp,snp,snp,snp;ANN=TAAG|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3772G>T|p.Glu1258*|3772/3822|3772/3822|1258/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2461:1948,70,48,48,67,57,133,35:1948:63002:70,48,48,67,57,133,35:1249,803,708,1036,910,1875,507:0,-495.815,-5299.62,-529.806,-5264.1,-5340.23,-539.679,-5273.97,-5307.95,-5350.1,-513.622,-5247.91,-5281.9,-5291.77,-5318.33,-521.963,-5256.25,-5290.24,-5300.11,-5274.06,-5329.68,-458.325,-5192.61,-5226.6,-5236.47,-5210.41,-5218.75,-5243.16,-553.097,-5287.38,-5321.37,-5331.24,-5305.19,-5313.53,-5249.89,-5367.44 +NC_045512.2 25350 . CAGT CT 9.354E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=349;CIGAR=1M2D1M;DP=3349;DPB=3175.5;DPRA=0;EPP=3.76316;EPPR=28.3979;GTI=0;LEN=2;MEANALT=7;MQM=49.7765;MQMR=52.6948;NS=1;NUMALT=1;ODDS=1420.92;PAIRED=0.994269;PAIREDR=0.978268;PAO=0;PQA=0;PQR=68;PRO=2;QA=11744;QR=105020;RO=2991;RPL=33;RPP=501.323;RPPR=873.505;RPR=316;RUN=1;SAF=180;SAP=3.76316;SAR=169;SRF=1504;SRP=3.22011;SRR=1487;TYPE=del;ANN=CT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3789_3790delAG|p.Val1264fs|3789/3822|3789/3822|1263/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3349:2991,349:2991:105020:349:11744:0,-32.0583,-8103.91 +NC_045512.2 25439 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=409;CIGAR=1X;DP=4980;DPB=4980;DPRA=0;EPP=3.14303;EPPR=5.75601;GTI=0;LEN=1;MEANALT=3;MQM=42.0244;MQMR=50.0731;NS=1;NUMALT=1;ODDS=3047.76;PAIRED=0.99511;PAIREDR=0.99387;PAO=0;PQA=0;PQR=0;PRO=0;QA=14327;QR=161011;RO=4568;RPL=229;RPP=15.7577;RPPR=40.8133;RPR=180;RUN=1;SAF=205;SAP=3.01561;SAR=204;SRF=2235;SRP=7.57572;SRR=2333;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.47A>C|p.Lys16Thr|47/828|47/828|16/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4980:4568,409:4568:161011:409:14327:0,-430.196,-12414.4 +NC_045512.2 25469 . C T 90198.9 . AB=0.848337;ABP=4756.25;AC=1;AF=0.5;AN=2;AO=3826;CIGAR=1X;DP=4510;DPB=4510;DPRA=0;EPP=5.48258;EPPR=3.21348;GTI=0;LEN=1;MEANALT=1;MQM=48.1853;MQMR=53.5643;NS=1;NUMALT=1;ODDS=439.848;PAIRED=0.997909;PAIREDR=0.99269;PAO=0;PQA=0;PQR=0;PRO=0;QA=133615;QR=23901;RO=684;RPL=2121;RPP=101.229;RPPR=78.3007;RPR=1705;RUN=1;SAF=1915;SAP=3.01938;SAR=1911;SRF=341;SRP=3.023;SRR=343;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.77C>T|p.Ser26Leu|77/828|77/828|26/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4510:684,3826:684:23901:3826:133615:-9563.49,0,-731.026 +NC_045512.2 25696 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=28.5;MQMR=51.6923;NS=1;NUMALT=1;ODDS=66.8874;PAIRED=0;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1831;RO=52;RPL=2;RPP=7.35324;RPPR=11.1951;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=27;SRP=3.17734;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.304G>A|p.Glu102Lys|304/828|304/828|102/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:52,2:52:1831:2:72:0,-12.7448,-153.498 +NC_045512.2 25702 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=50.8525;NS=1;NUMALT=1;ODDS=85.2841;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2073;RO=61;RPL=0;RPP=5.18177;RPPR=15.8611;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.90025;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.310C>A|p.Pro104Thr|310/828|310/828|104/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2073:1:14:0,-17.2639,-174.471 +NC_045512.2 25734 . C A 2.42589E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=68;DPB=68;DPRA=0;EPP=5.18177;EPPR=3.04271;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=50.6716;NS=1;NUMALT=1;ODDS=93.5095;PAIRED=1;PAIREDR=0.940299;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2355;RO=67;RPL=0;RPP=5.18177;RPPR=23.2666;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.30199;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.342C>A|p.Phe114Leu|342/828|342/828|114/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:68:67,1:67:2355:1:14:0,-19.07,-196.772 +NC_045512.2 25750 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=3.0103;EPPR=3.13094;GTI=0;LEN=1;MEANALT=1;MQM=54.5;MQMR=51.2222;NS=1;NUMALT=1;ODDS=86.3627;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=2546;RO=72;RPL=2;RPP=7.35324;RPPR=6.02623;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=38;SRP=3.49285;SRR=34;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.358T>C|p.Phe120Leu|358/828|358/828|120/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:74:72,2:72:2546:2:72:0,-15.458,-208.988 +NC_045512.2 25785 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=3.0103;EPPR=3.11887;GTI=0;LEN=1;MEANALT=1;MQM=41.7;MQMR=51.4625;NS=1;NUMALT=1;ODDS=45.1658;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=356;QR=2776;RO=80;RPL=2;RPP=10.8276;RPPR=4.74748;RPR=8;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=41;SRP=3.11887;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.393G>T|p.Trp131Cys|393/828|393/828|131/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:80,10:80:2776:10:356:0,-0.705101,-211.729 +NC_045512.2 25797 . CAAAAACCCAT CAAAAAACCCAT,CAAAAACCCAC 73.745 . AB=0.1875,0.0208333;ABP=84.4405,194.462;AC=1,0;AF=0.5,0;AN=2;AO=18,2;CIGAR=1M1I10M,10M1X;DP=96;DPB=97.6364;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.12459;GTI=0;LEN=1,1;MEANALT=2,2;MQM=51.2778,55.5;MQMR=49.3684;NS=1;NUMALT=2;ODDS=16.9804;PAIRED=1,1;PAIREDR=0.973684;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=555,72;QR=2648;RO=76;RPL=8,2;RPP=3.49285,7.35324;RPPR=3.46745;RPR=10,0;RUN=1,1;SAF=9,1;SAP=3.0103,3.0103;SAR=9,1;SRF=39;SRP=3.12459;SRR=37;TYPE=ins,snp;ANN=CAAAAAACCCAT|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.410dupA|p.Asn137fs|411/828|411/828|137/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:96:76,18,2:76:2648:18,2:555,72:-20.9576,0,-190.254,-37.9662,-189.807,-233.088 +NC_045512.2 25811 . T A 1.76315E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=3.0103;EPPR=3.21602;GTI=0;LEN=1;MEANALT=1;MQM=54;MQMR=49.9368;NS=1;NUMALT=1;ODDS=118.555;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=3323;RO=95;RPL=2;RPP=7.35324;RPPR=5.77607;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=49;SRP=3.21602;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.419T>A|p.Leu140His|419/828|419/828|140/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:95,2:95:3323:2:68:0,-22.7518,-268.02 +NC_045512.2 25831 . C T 3.18727E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=30.75;MQMR=54.1733;NS=1;NUMALT=1;ODDS=86.1664;PAIRED=1;PAIREDR=0.973333;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=2659;RO=75;RPL=4;RPP=11.6962;RPPR=6.51361;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=38;SRP=3.03925;SRR=37;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.439C>T|p.Leu147Phe|439/828|439/828|147/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:75,4:75:2659:4:144:0,-15.761,-225.561 +NC_045512.2 26042 . CTCAA TTGAG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=44;CIGAR=1X1M1X1M1X;DP=1484;DPB=1485;DPRA=0;EPP=3.0103;EPPR=3.08455;GTI=0;LEN=5;MEANALT=5;MQM=43.3182;MQMR=53.2568;NS=1;NUMALT=1;ODDS=1592.01;PAIRED=1;PAIREDR=0.993719;PAO=6;PQA=136;PQR=32;PRO=1;QA=1544;QR=50198;RO=1433;RPL=22;RPP=3.0103;RPPR=7.93362;RPR=22;RUN=1;SAF=22;SAP=3.0103;SAR=22;SRF=738;SRP=5.81215;SRR=695;TYPE=complex;ANN=TTGAG|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.650_654delCTCAAinsTTGAG|p.ThrGln217IleGlu|650/828|650/828|217/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1484:1433,44:1433:50198:44:1544:0,-326.758,-4246.55 +NC_045512.2 26057 . A C 1.04572E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=15;CIGAR=1X;DP=1482;DPB=1482;DPRA=0;EPP=3.15506;EPPR=3.02364;GTI=0;LEN=1;MEANALT=2;MQM=47.2667;MQMR=52.9747;NS=1;NUMALT=1;ODDS=1903.72;PAIRED=1;PAIREDR=0.995904;PAO=0;PQA=0;PQR=0;PRO=0;QA=421;QR=49584;RO=1465;RPL=11;RPP=10.1038;RPPR=12.7352;RPR=4;RUN=1;SAF=9;SAP=4.31318;SAR=6;SRF=728;SRP=3.13036;SRR=737;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.665A>C|p.Asp222Ala|665/828|665/828|222/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1482:1465,15:1465:49584:15:421:0,-411.753,-4275.18 +NC_045512.2 26069 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1483;DPB=1483;DPRA=0;EPP=3.0103;EPPR=3.1302;GTI=0;LEN=1;MEANALT=1;MQM=42.8125;MQMR=52.7764;NS=1;NUMALT=1;ODDS=1886.92;PAIRED=0.875;PAIREDR=0.99591;PAO=0;PQA=0;PQR=0;PRO=0;QA=576;QR=51331;RO=1467;RPL=16;RPP=37.7539;RPPR=4.08938;RPR=0;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=725;SRP=3.43808;SRR=742;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.677A>G|p.Glu226Gly|677/828|677/828|226/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1483:1467,16:1467:51331:16:576:0,-402.204,-4405.87 +NC_045512.2 26089 . T A 2.41553E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1477;DPB=1477;DPRA=0;EPP=3.13803;EPPR=4.17635;GTI=0;LEN=1;MEANALT=1;MQM=41.7647;MQMR=52.7048;NS=1;NUMALT=1;ODDS=1870.29;PAIRED=1;PAIREDR=0.994521;PAO=0;PQA=0;PQR=0;PRO=0;QA=586;QR=49501;RO=1460;RPL=16;RPP=31.7504;RPPR=8.36462;RPR=1;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=746;SRP=4.53331;SRR=714;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.697T>A|p.Tyr233Asn|697/828|697/828|233/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1477:1460,17:1460:49501:17:586:0,-399.573,-4252.67 +NC_045512.2 26108 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1558;DPB=1558;DPRA=0;EPP=3.0103;EPPR=3.3708;GTI=0;LEN=1;MEANALT=1;MQM=51.8125;MQMR=52.0246;NS=1;NUMALT=1;ODDS=1968.1;PAIRED=1;PAIREDR=0.990272;PAO=0;PQA=0;PQR=0;PRO=0;QA=553;QR=52400;RO=1542;RPL=8;RPP=3.0103;RPPR=11.1442;RPR=8;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=768;SRP=3.061;SRR=774;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.716A>T|p.Glu239Val|716/828|716/828|239/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1558:1542,16:1542:52400:16:553:0,-419.335,-4448.58 +NC_045512.2 26141 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1542;DPB=1542;DPRA=0;EPP=3.13803;EPPR=3.06166;GTI=0;LEN=1;MEANALT=3;MQM=30.8235;MQMR=52.1393;NS=1;NUMALT=1;ODDS=1984.85;PAIRED=0.764706;PAIREDR=0.996058;PAO=0;PQA=0;PQR=0;PRO=0;QA=551;QR=50688;RO=1522;RPL=16;RPP=31.7504;RPPR=7.17062;RPR=1;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=758;SRP=3.06166;SRR=764;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.749A>T|p.Asp250Val|749/828|749/828|250/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1542:1522,17:1522:50688:17:551:0,-430.965,-4315.93 +NC_045512.2 26145 . T C 4.23704E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1538;DPB=1538;DPRA=0;EPP=3.44459;EPPR=3.21656;GTI=0;LEN=1;MEANALT=2;MQM=47.8;MQMR=51.9208;NS=1;NUMALT=1;ODDS=1909.48;PAIRED=1;PAIREDR=0.991425;PAO=0;PQA=0;PQR=0;PRO=0;QA=678;QR=48753;RO=1516;RPL=14;RPP=9.95901;RPPR=34.3849;RPR=6;RUN=1;SAF=9;SAP=3.44459;SAR=11;SRF=758;SRP=3.0103;SRR=758;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.753T>C|p.Gly251Gly|753/828|753/828|251/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1538:1516,20:1516:48753:20:678:0,-407.159,-4121.98 +NC_045512.2 26221 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=32;CIGAR=1X;DP=2217;DPB=2217;DPRA=0;EPP=3.28173;EPPR=3.583;GTI=0;LEN=1;MEANALT=2;MQM=48.5312;MQMR=50.4084;NS=1;NUMALT=1;ODDS=2709.72;PAIRED=1;PAIREDR=0.995879;PAO=0;PQA=0;PQR=0;PRO=0;QA=1101;QR=76749;RO=2184;RPL=15;RPP=3.28173;RPPR=759.033;RPR=17;RUN=1;SAF=16;SAP=3.0103;SAR=16;SRF=1104;SRP=3.583;SRR=1080;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-24G>A|||||24| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2217:2184,32:2184:76749:32:1101:0,-576.661,-6377.21 +NC_045512.2 26533 . C T 6.38867E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=52;CIGAR=1X;DP=2958;DPB=2958;DPRA=0;EPP=9.02361;EPPR=16.2327;GTI=0;LEN=1;MEANALT=2;MQM=32.3077;MQMR=51.4386;NS=1;NUMALT=1;ODDS=3622.99;PAIRED=0.692308;PAIREDR=0.993804;PAO=0;PQA=0;PQR=0;PRO=0;QA=1770;QR=101214;RO=2905;RPL=12;RPP=35.7494;RPPR=3.28015;RPR=40;RUN=1;SAF=18;SAP=13.7006;SAR=34;SRF=1471;SRP=4.03362;SRR=1434;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.11C>T|p.Ser4Phe|11/669|11/669|4/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2958:2905,52:2905:101214:52:1770:0,-785.764,-8554.41 +NC_045512.2 26542 . CTAT ATAG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=131;CIGAR=1X2M1X;DP=2947;DPB=2947;DPRA=0;EPP=3.15949;EPPR=17.7373;GTI=0;LEN=4;MEANALT=5;MQM=38.9771;MQMR=51.3038;NS=1;NUMALT=1;ODDS=2841.52;PAIRED=0.755725;PAIREDR=0.99359;PAO=1;PQA=32;PQR=0;PRO=0;QA=4580;QR=99098;RO=2808;RPL=36;RPP=60.7118;RPPR=16.0793;RPR=95;RUN=1;SAF=65;SAP=3.02688;SAR=66;SRF=1418;SRP=3.61658;SRR=1390;TYPE=complex;ANN=ATAG|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.20_23delCTATinsATAG|p.ThrIle7AsnSer|20/669|20/669|7/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2947:2808,131:2808:99098:131:4580:0,-569.035,-8155.39 +NC_045512.2 26554 . A G 1.18733E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=3289;DPB=3289;DPRA=0;EPP=3.22745;EPPR=16.114;GTI=0;LEN=1;MEANALT=2;MQM=39.325;MQMR=50.3211;NS=1;NUMALT=1;ODDS=4149.91;PAIRED=0.65;PAIREDR=0.9883;PAO=0;PQA=0;PQR=0;PRO=0;QA=1381;QR=113659;RO=3248;RPL=10;RPP=24.725;RPPR=189.393;RPR=30;RUN=1;SAF=21;SAP=3.22745;SAR=19;SRF=1620;SRP=3.05309;SRR=1628;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.32A>G|p.Glu11Gly|32/669|32/669|11/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3289:3248,40:3248:113659:40:1381:0,-898.198,-9489.65 +NC_045512.2 26611 . C G 0.0 . AB=0.134243;ABP=4858.94;AC=1;AF=0.5;AN=2;AO=561;CIGAR=1X;DP=4179;DPB=4179;DPRA=0;EPP=3.19997;EPPR=9.88753;GTI=0;LEN=1;MEANALT=2;MQM=48.8645;MQMR=51.8661;NS=1;NUMALT=1;ODDS=409.84;PAIRED=0.982175;PAIREDR=0.986999;PAO=0;PQA=0;PQR=0;PRO=0;QA=19867;QR=126762;RO=3615;RPL=206;RPP=88.9441;RPPR=79.5669;RPR=355;RUN=1;SAF=285;SAP=3.32383;SAR=276;SRF=1845;SRP=6.38915;SRR=1770;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.89C>G|p.Thr30Arg|89/669|89/669|30/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4179:3615,561:3615:126762:561:19867:-380.436,0,-9637.08 +NC_045512.2 26705 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=193;CIGAR=1X;DP=4508;DPB=4508;DPRA=0;EPP=3.29158;EPPR=3.62734;GTI=0;LEN=1;MEANALT=3;MQM=49.8187;MQMR=52.6518;NS=1;NUMALT=1;ODDS=4146.13;PAIRED=0.994819;PAIREDR=0.992577;PAO=0;PQA=0;PQR=0;PRO=0;QA=6785;QR=152705;RO=4311;RPL=116;RPP=20.1233;RPPR=31.3029;RPR=77;RUN=1;SAF=97;SAP=3.02155;SAR=96;SRF=2179;SRP=4.12298;SRR=2132;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.183T>C|p.Thr61Thr|183/669|183/669|61/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4508:4311,193:4311:152705:193:6785:0,-781.83,-12614.8 +NC_045512.2 26767 . T C 67526.2 . AB=0.695281;ABP=1322.65;AC=1;AF=0.5;AN=2;AO=2770;CIGAR=1X;DP=3984;DPB=3984;DPRA=0;EPP=6.02371;EPPR=4.62278;GTI=0;LEN=1;MEANALT=2;MQM=50.2946;MQMR=53.2954;NS=1;NUMALT=1;ODDS=5439.65;PAIRED=0.998917;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=96278;QR=42353;RO=1212;RPL=1420;RPP=6.85153;RPPR=11.2949;RPR=1350;RUN=1;SAF=1358;SAP=5.29623;SAR=1412;SRF=599;SRP=3.36146;SRR=613;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.245T>C|p.Ile82Thr|245/669|245/669|82/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3984:1212,2770:1212:42353:2770:96278:-6898.83,0,-2508.19 +NC_045512.2 26837 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=44;CIGAR=1X;DP=3100;DPB=3100;DPRA=0;EPP=4.78696;EPPR=3.17023;GTI=0;LEN=1;MEANALT=2;MQM=50.3409;MQMR=51.6887;NS=1;NUMALT=1;ODDS=3775.78;PAIRED=1;PAIREDR=0.997709;PAO=0;PQA=0;PQR=0;PRO=0;QA=1554;QR=105912;RO=3055;RPL=29;RPP=12.6832;RPPR=391.189;RPR=15;RUN=1;SAF=22;SAP=3.0103;SAR=22;SRF=1491;SRP=6.79812;SRR=1564;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.315T>C|p.Arg105Arg|315/669|315/669|105/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3100:3055,44:3055:105912:44:1554:0,-800.061,-8955.04 +NC_045512.2 27059 . C T 3.69338E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=299;CIGAR=1X;DP=5267;DPB=5267;DPRA=0;EPP=3.88906;EPPR=4.10568;GTI=0;LEN=1;MEANALT=3;MQM=45.204;MQMR=51.677;NS=1;NUMALT=1;ODDS=4275.32;PAIRED=0.986622;PAIREDR=0.993341;PAO=0;PQA=0;PQR=0;PRO=0;QA=10578;QR=173846;RO=4956;RPL=185;RPP=39.6203;RPPR=25.3893;RPR=114;RUN=1;SAF=148;SAP=3.07566;SAR=151;SRF=2474;SRP=3.03834;SRR=2482;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.537C>T|p.Tyr179Tyr|537/669|537/669|179/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5267:4956,299:4956:173846:299:10578:0,-761.739,-14058.3 +NC_045512.2 27115 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=184;CIGAR=1X;DP=4546;DPB=4546;DPRA=0;EPP=3.0103;EPPR=8.93164;GTI=0;LEN=1;MEANALT=2;MQM=48.6087;MQMR=51.3668;NS=1;NUMALT=1;ODDS=4300.67;PAIRED=1;PAIREDR=0.990131;PAO=0;PQA=0;PQR=0;PRO=0;QA=6564;QR=151056;RO=4357;RPL=90;RPP=3.19912;RPPR=3.37362;RPR=94;RUN=1;SAF=90;SAP=3.19912;SAR=94;SRF=2144;SRP=5.38312;SRR=2213;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.593G>A|p.Arg198His|593/669|593/669|198/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4546:4357,184:4357:151056:184:6564:0,-827.983,-12351.2 +NC_045512.2 27143 . C T 1.70204E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=272;CIGAR=1X;DP=4401;DPB=4401;DPRA=0;EPP=3.2977;EPPR=6.99475;GTI=0;LEN=1;MEANALT=3;MQM=47.0993;MQMR=50.1321;NS=1;NUMALT=1;ODDS=3329.47;PAIRED=0.992647;PAIREDR=0.987394;PAO=0;PQA=0;PQR=0;PRO=0;QA=9558;QR=143551;RO=4125;RPL=154;RPP=13.3567;RPPR=237.208;RPR=118;RUN=1;SAF=133;SAP=3.2977;SAR=139;SRF=2054;SRP=3.16243;SRR=2071;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.621C>T|p.Asn207Asn|621/669|621/669|207/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4401:4125,272:4125:143551:272:9558:0,-556.834,-11234.5 +NC_045512.2 27285 . T A 8.19702E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=31;CIGAR=1X;DP=2885;DPB=2885;DPRA=0;EPP=3.08035;EPPR=5.2305;GTI=0;LEN=1;MEANALT=2;MQM=45;MQMR=53.3229;NS=1;NUMALT=1;ODDS=3664.07;PAIRED=1;PAIREDR=0.990182;PAO=0;PQA=0;PQR=0;PRO=0;QA=1108;QR=100423;RO=2852;RPL=0;RPP=70.3259;RPPR=3.99706;RPR=31;RUN=1;SAF=16;SAP=3.08035;SAR=15;SRF=1471;SRP=9.17753;SRR=1381;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.84T>A|p.Asn28Lys|84/186|84/186|28/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2885:2852,31:2852:100423:31:1108:0,-783.645,-8676.19 +NC_045512.2 27291 . TTACA TA 1.11018E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1M3D1M;DP=2674;DPB=2637.6;DPRA=0;EPP=3.0459;EPPR=3.01363;GTI=0;LEN=3;MEANALT=4;MQM=52.6721;MQMR=53.3507;NS=1;NUMALT=1;ODDS=3002.68;PAIRED=1;PAIREDR=0.989639;PAO=0.5;PQA=10.5;PQR=10.5;PRO=0.5;QA=2128;QR=92098;RO=2606;RPL=41;RPP=18.709;RPPR=33.0909;RPR=20;RUN=1;SAF=31;SAP=3.0459;SAR=30;SRF=1312;SRP=3.28028;SRR=1294;TYPE=del;ANN=TA|conservative_inframe_deletion|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.91_93delTAC|p.Tyr31del|91/186|91/186|31/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2674:2606,61:2606:92098:61:2128:0,-619.622,-7867.5 +NC_045512.2 27335 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=78;CIGAR=1X;DP=3108;DPB=3108;DPRA=0;EPP=4.01252;EPPR=6.42569;GTI=0;LEN=1;MEANALT=2;MQM=44.7051;MQMR=53.372;NS=1;NUMALT=1;ODDS=3467.05;PAIRED=0.948718;PAIREDR=0.991411;PAO=0;PQA=0;PQR=0;PRO=0;QA=2703;QR=106229;RO=3027;RPL=39;RPP=3.0103;RPPR=10.3282;RPR=39;RUN=1;SAF=41;SAP=3.45573;SAR=37;SRF=1522;SRP=3.21762;SRR=1505;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.134C>T|p.Thr45Ile|134/186|134/186|45/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3108:3027,78:3027:106229:78:2703:0,-722.646,-9061.78 +NC_045512.2 27344 . AA TT 1.55256E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=95;CIGAR=2X;DP=3040;DPB=3040.5;DPRA=0;EPP=3.21602;EPPR=5.24228;GTI=0;LEN=2;MEANALT=3;MQM=45.7684;MQMR=53.5352;NS=1;NUMALT=1;ODDS=3202.24;PAIRED=0.978947;PAIREDR=0.991505;PAO=1;PQA=36;PQR=0;PRO=0;QA=3335;QR=103633;RO=2943;RPL=40;RPP=8.15326;RPPR=3.01104;RPR=55;RUN=1;SAF=47;SAP=3.03316;SAR=48;SRF=1464;SRP=3.17631;SRR=1479;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.143_144delAAinsTT|p.Lys48Ile|143/186|143/186|48/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3040:2943,95:2943:103633:95:3335:0,-652.573,-8806.08 +NC_045512.2 27354 . A G 1.21024E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=3037;DPB=3037;DPRA=0;EPP=4.1599;EPPR=3.54384;GTI=0;LEN=1;MEANALT=2;MQM=44.5;MQMR=53.3401;NS=1;NUMALT=1;ODDS=3477.58;PAIRED=0.970588;PAIREDR=0.990226;PAO=0;PQA=0;PQR=0;PRO=0;QA=2347;QR=103746;RO=2967;RPL=33;RPP=3.13803;RPPR=3.01689;RPR=35;RUN=1;SAF=32;SAP=3.52123;SAR=36;SRF=1482;SRP=3.01689;SRR=1485;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.153A>G|p.Gln51Gln|153/186|153/186|51/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3037:2967,68:2967:103746:68:2347:0,-731.506,-8865.91 +NC_045512.2 27393 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=73;CIGAR=1X;DP=2871;DPB=2871;DPRA=0;EPP=3.04005;EPPR=4.51494;GTI=0;LEN=1;MEANALT=3;MQM=53.1233;MQMR=53.4395;NS=1;NUMALT=1;ODDS=3121.07;PAIRED=1;PAIREDR=0.993916;PAO=0;PQA=0;PQR=0;PRO=0;QA=2586;QR=97778;RO=2794;RPL=38;RPP=3.27802;RPPR=84.5967;RPR=35;RUN=1;SAF=36;SAP=3.04005;SAR=37;SRF=1368;SRP=5.62477;SRR=1426;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1C>T|||||1| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2871:2794,73:2794:97778:73:2586:0,-633.624,-8285.14 +NC_045512.2 27527 . C T 20959.5 . AB=0.321568;ABP=998.011;AC=1;AF=0.5;AN=2;AO=1157;CIGAR=1X;DP=3598;DPB=3598;DPRA=0;EPP=3.16232;EPPR=3.97985;GTI=0;LEN=1;MEANALT=2;MQM=48.0026;MQMR=50.8844;NS=1;NUMALT=1;ODDS=4826.11;PAIRED=0.994814;PAIREDR=0.99672;PAO=0;PQA=0;PQR=0;PRO=0;QA=40472;QR=84380;RO=2439;RPL=514;RPP=34.2423;RPPR=4.81318;RPR=643;RUN=1;SAF=592;SAP=4.3785;SAR=565;SRF=1214;SRP=3.11803;SRR=1225;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.134C>T|p.Pro45Leu|134/366|134/366|45/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3598:2439,1157:2439:84380:1157:40472:-2209.43,0,-6034.2 +NC_045512.2 27566 . G T 5352.15 . AB=0.189077;ABP=3231.63;AC=1;AF=0.5;AN=2;AO=727;CIGAR=1X;DP=3845;DPB=3845;DPRA=0;EPP=3.08497;EPPR=3.59619;GTI=0;LEN=1;MEANALT=2;MQM=46.6768;MQMR=50.3141;NS=1;NUMALT=1;ODDS=1232.38;PAIRED=0.997249;PAIREDR=0.983959;PAO=0;PQA=0;PQR=0;PRO=0;QA=25485;QR=108948;RO=3117;RPL=374;RPP=4.32752;RPPR=10.1169;RPR=353;RUN=1;SAF=373;SAP=4.08857;SAR=354;SRF=1591;SRP=5.95367;SRR=1526;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.173G>T|p.Cys58Phe|173/366|173/366|58/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3845:3117,727:3117:108948:727:25485:-891.399,0,-7962.88 +NC_045512.2 27607 . A T 5075.59 . AB=0.18089;ABP=3640.94;AC=1;AF=0.5;AN=2;AO=744;CIGAR=1X;DP=4113;DPB=4113;DPRA=0;EPP=3.057;EPPR=3.0161;GTI=0;LEN=1;MEANALT=1;MQM=48.8401;MQMR=48.9326;NS=1;NUMALT=1;ODDS=1168.7;PAIRED=0.995968;PAIREDR=0.996438;PAO=0;PQA=0;PQR=0;PRO=0;QA=26185;QR=118988;RO=3369;RPL=355;RPP=6.38425;RPPR=98.548;RPR=389;RUN=1;SAF=375;SAP=3.11537;SAR=369;SRF=1695;SRP=3.29454;SRR=1674;TYPE=snp;ANN=T|stop_gained|HIGH|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.214A>T|p.Lys72*|214/366|214/366|72/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4113:3369,744:3369:118988:744:26185:-910.007,0,-8604.41 +NC_045512.2 27625 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=75;CIGAR=1X;DP=4049;DPB=4049;DPRA=0;EPP=3.03925;EPPR=4.91287;GTI=0;LEN=1;MEANALT=2;MQM=49.64;MQMR=49.5318;NS=1;NUMALT=1;ODDS=4751.09;PAIRED=1;PAIREDR=0.997231;PAO=0;PQA=0;PQR=0;PRO=0;QA=2649;QR=139228;RO=3973;RPL=31;RPP=7.90335;RPPR=56.556;RPR=44;RUN=1;SAF=37;SAP=3.03925;SAR=38;SRF=1999;SRP=3.3519;SRR=1974;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.232C>T|p.Arg78Cys|232/366|232/366|78/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4049:3973,75:3973:139228:75:2649:0,-1000.05,-11370.5 +NC_045512.2 27629 . C A 6085.31 . AB=0.191634;ABP=3399.26;AC=1;AF=0.5;AN=2;AO=788;CIGAR=1X;DP=4112;DPB=4112;DPRA=0;EPP=3.18666;EPPR=6.31437;GTI=0;LEN=1;MEANALT=3;MQM=47.4569;MQMR=50.4522;NS=1;NUMALT=1;ODDS=1401.19;PAIRED=0.997462;PAIREDR=0.996378;PAO=0;PQA=0;PQR=0;PRO=0;QA=27332;QR=115748;RO=3313;RPL=348;RPP=26.3343;RPPR=44.9644;RPR=440;RUN=1;SAF=396;SAP=3.05439;SAR=392;SRF=1671;SRP=3.56152;SRR=1642;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.236C>A|p.Ala79Asp|236/366|236/366|79/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4112:3313,788:3313:115748:788:27332:-982.348,0,-8505.98 +NC_045512.2 27638 . T C 53884.9 . AB=0.555904;ABP=115.422;AC=1;AF=0.5;AN=2;AO=2302;CIGAR=1X;DP=4141;DPB=4141;DPRA=0;EPP=3.31593;EPPR=4.07359;GTI=0;LEN=1;MEANALT=2;MQM=48.9466;MQMR=52.1322;NS=1;NUMALT=1;ODDS=9722.66;PAIRED=0.996959;PAIREDR=0.996736;PAO=0;PQA=0;PQR=0;PRO=0;QA=80818;QR=63827;RO=1838;RPL=1086;RPP=18.952;RPPR=13.4494;RPR=1216;RUN=1;SAF=1166;SAP=3.85927;SAR=1136;SRF=930;SRP=3.58211;SRR=908;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.245T>C|p.Val82Ala|245/366|245/366|82/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4141:1838,2302:1838:63827:2302:80818:-5410.76,0,-4244.12 +NC_045512.2 27652 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=1X;DP=4346;DPB=4346;DPRA=0;EPP=4.70971;EPPR=4.53826;GTI=0;LEN=1;MEANALT=2;MQM=46.5435;MQMR=50.996;NS=1;NUMALT=1;ODDS=5527.41;PAIRED=1;PAIREDR=0.996743;PAO=0;PQA=0;PQR=0;PRO=0;QA=1543;QR=149454;RO=4299;RPL=1;RPP=94.401;RPPR=11.1572;RPR=45;RUN=1;SAF=25;SAP=3.76559;SAR=21;SRF=2162;SRP=3.32599;SRR=2137;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.259T>A|p.Phe87Ile|259/366|259/366|87/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4346:4299,46:4299:149454:46:1543:0,-1185.76,-12544.7 +NC_045512.2 27696 . T C 9.00448E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=5194;DPB=5194;DPRA=0;EPP=3.0484;EPPR=3.68677;GTI=0;LEN=1;MEANALT=2;MQM=47.6491;MQMR=52.3927;NS=1;NUMALT=1;ODDS=6534.38;PAIRED=1;PAIREDR=0.985592;PAO=0;PQA=0;PQR=0;PRO=0;QA=1986;QR=181866;RO=5136;RPL=28;RPP=3.0484;RPPR=15.8108;RPR=29;RUN=1;SAF=28;SAP=3.0484;SAR=29;SRF=2583;SRP=3.39081;SRR=2553;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.303T>C|p.Phe101Phe|303/366|303/366|101/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5194:5136,57:5136:181866:57:1986:0,-1404.69,-15506.5 +NC_045512.2 27752 . C T 65709.1 . AB=0.548083;ABP=103.035;AC=1;AF=0.5;AN=2;AO=2730;CIGAR=1X;DP=4981;DPB=4981;DPRA=0;EPP=7.60459;EPPR=11.013;GTI=0;LEN=1;MEANALT=2;MQM=50.2674;MQMR=52.0516;NS=1;NUMALT=1;ODDS=12106.1;PAIRED=0.989377;PAIREDR=0.993769;PAO=0;PQA=0;PQR=0;PRO=0;QA=96766;QR=78943;RO=2247;RPL=1468;RPP=36.7644;RPPR=20.1047;RPR=1262;RUN=1;SAF=1333;SAP=6.2683;SAR=1397;SRF=1104;SRP=4.48018;SRR=1143;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.359C>T|p.Thr120Ile|359/366|359/366|120/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4981:2247,2730:2247:78943:2730:96766:-6594.66,0,-5279.74 +NC_045512.2 27777 . G A 2.06367E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=4362;DPB=4362;DPRA=0;EPP=3.0103;EPPR=7.8761;GTI=0;LEN=1;MEANALT=2;MQM=46.5676;MQMR=51.2193;NS=1;NUMALT=1;ODDS=5211.88;PAIRED=1;PAIREDR=0.988567;PAO=0;PQA=0;PQR=0;PRO=0;QA=2614;QR=150803;RO=4286;RPL=49;RPP=19.9126;RPPR=772.005;RPR=25;RUN=1;SAF=36;SAP=3.12768;SAR=38;SRF=2091;SRP=8.49015;SRR=2195;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.22G>A|p.Asp8Asn|22/132|22/132|8/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4362:4286,74:4286:150803:74:2614:0,-1105.72,-12659.9 +NC_045512.2 27857 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1159;DPB=1159;DPRA=0;EPP=3.0103;EPPR=3.05796;GTI=0;LEN=1;MEANALT=2;MQM=46.75;MQMR=48.8033;NS=1;NUMALT=1;ODDS=1424.16;PAIRED=1;PAIREDR=0.924495;PAO=0;PQA=0;PQR=0;PRO=0;QA=528;QR=39898;RO=1139;RPL=10;RPP=5.18177;RPPR=3.10372;RPR=6;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=573;SRP=3.10372;SRR=566;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.102G>A|p.Leu34Leu|102/132|102/132|34/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1159:1139,16:1139:39898:16:528:0,-302.123,-3258.71 +NC_045512.2 27864 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=1X;DP=1237;DPB=1237;DPRA=0;EPP=3.53672;EPPR=3.05674;GTI=0;LEN=1;MEANALT=2;MQM=43.9848;MQMR=49.7802;NS=1;NUMALT=1;ODDS=1098.27;PAIRED=0.984848;PAIREDR=0.939264;PAO=0;PQA=0;PQR=0;PRO=0;QA=2278;QR=40992;RO=1169;RPL=1;RPP=137.773;RPPR=9.04547;RPR=65;RUN=1;SAF=34;SAP=3.1419;SAR=32;SRF=587;SRP=3.05674;SRR=582;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.109C>A|p.His37Asn|109/132|109/132|37/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1237:1169,66:1169:40992:66:2278:0,-193.616,-3261.46 +NC_045512.2 27870 . GAAAC TAAAT,TAAAC,GAAAT 28573.3 . AB=0.0133648,0.0196541,0.855346;ABP=2619.44,2552.24,1398.11;AC=0,0,1;AF=0,0,0.5;AN=2;AO=17,25,1088;CIGAR=1X3M1X,1X4M,4M1X;DP=1272;DPB=1277;DPRA=0,0,0;EPP=3.13803,3.09716,3.52123;EPPR=3.26577;GTI=0;LEN=5,1,1;MEANALT=7,7,7;MQM=35.8824,37.32,50.6305;MQMR=52.1103;NS=1;NUMALT=3;ODDS=350.184;PAIRED=0.823529,0.76,0.983456;PAIREDR=0.941176;PAO=12.5,0.5,12;PQA=409,7,402;PQR=0;PRO=0;QA=597,665,38499;QR=4734;RO=136;RPL=1,0,534;RPP=31.7504,57.2971,3.80864;RPPR=3.26577;RPR=16,25,554;RUN=1,1,1;SAF=8,12,550;SAP=3.13803,3.09716,3.2977;SAR=9,13,538;SRF=70;SRP=3.26577;SRR=66;TYPE=complex,snp,snp;ANN=TAAAC|stop_gained|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.115G>T|p.Glu39*|115/132|115/132|39/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/3:1272:136,17,25,1088:136:4734:17,25,1088:597,665,38499:-2896.73,-2902.78,-3263.11,-2887.86,-3218.42,-3245.78,0,-330.591,-315.679,-37.9604 +NC_045512.2 27942 . C T 0.0 . AB=0.128987;ABP=1690.03;AC=1;AF=0.5;AN=2;AO=182;CIGAR=1X;DP=1411;DPB=1411;DPRA=0;EPP=3.05802;EPPR=4.49623;GTI=0;LEN=1;MEANALT=1;MQM=45.6429;MQMR=53.1587;NS=1;NUMALT=1;ODDS=303.191;PAIRED=0.983516;PAIREDR=0.981286;PAO=0;PQA=0;PQR=0;PRO=0;QA=6276;QR=43106;RO=1229;RPL=105;RPP=12.3643;RPPR=3.09688;RPR=77;RUN=1;SAF=89;SAP=3.2012;SAR=93;SRF=616;SRP=3.0262;SRR=613;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.49C>T|p.His17Tyr|49/366|49/366|17/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1411:1229,182:1229:43106:182:6276:-65.6317,0,-3323.38 +NC_045512.2 27972 . C T 7.85929E-14 . AB=0.114679;ABP=1689.83;AC=1;AF=0.5;AN=2;AO=150;CIGAR=1X;DP=1308;DPB=1308;DPRA=0;EPP=3.0103;EPPR=3.37975;GTI=0;LEN=1;MEANALT=3;MQM=46.5933;MQMR=53.855;NS=1;NUMALT=1;ODDS=387.178;PAIRED=1;PAIREDR=0.987847;PAO=0;PQA=0;PQR=0;PRO=0;QA=5274;QR=39803;RO=1152;RPL=87;RPP=11.3488;RPPR=3.28173;RPR=63;RUN=1;SAF=74;SAP=3.06821;SAR=76;SRF=571;SRP=3.1988;SRR=581;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1308:1152,150:1152:39803:150:5274:-29.6341,0,-3107.07 +NC_045512.2 27981 . CCA CTACA 2.43493E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=15;CIGAR=1M2I2M;DP=1259;DPB=1269.33;DPRA=0;EPP=3.15506;EPPR=4.91888;GTI=0;LEN=2;MEANALT=4;MQM=47;MQMR=53.2139;NS=1;NUMALT=1;ODDS=1576.8;PAIRED=0.933333;PAIREDR=0.991929;PAO=0.5;PQA=0;PQR=0;PRO=0.5;QA=476;QR=43082;RO=1239;RPL=2;RPP=20.5268;RPPR=14.5091;RPR=13;RUN=1;SAF=7;SAP=3.15506;SAR=8;SRF=615;SRP=3.15226;SRR=624;TYPE=ins;ANN=CTACA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.88_89insTA|p.Pro30fs|89/366|89/366|30/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1259:1239,15:1239:43082:15:476:0,-335.717,-3717.41 +NC_045512.2 27987 . GTAG GG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1M2D1M;DP=1259;DPB=1250.5;DPRA=0;EPP=3.13803;EPPR=3.35409;GTI=0;LEN=2;MEANALT=3;MQM=48.1176;MQMR=53.3328;NS=1;NUMALT=1;ODDS=1571.36;PAIRED=0.941176;PAIREDR=0.991115;PAO=0;PQA=0;PQR=0;PRO=0;QA=486;QR=43228;RO=1238;RPL=2;RPP=24.5973;RPPR=31.7481;RPR=15;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=609;SRP=3.71191;SRR=629;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.95_96delTA|p.Val32fs|95/366|95/366|32/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1259:1238,17:1238:43228:17:486:0,-336.27,-3738.37 +NC_045512.2 28048 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=133;CIGAR=1X;DP=1234;DPB=1234;DPRA=0;EPP=3.15724;EPPR=3.24894;GTI=0;LEN=1;MEANALT=1;MQM=42.4511;MQMR=52.6803;NS=1;NUMALT=1;ODDS=498.144;PAIRED=1;PAIREDR=0.993642;PAO=0;PQA=0;PQR=0;PRO=0;QA=4623;QR=38646;RO=1101;RPL=56;RPP=10.2104;RPPR=15.3193;RPR=77;RUN=1;SAF=65;SAP=3.15724;SAR=68;SRF=528;SRP=7.00415;SRR=573;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1234:1101,133:1101:38646:133:4623:0,-20.4073,-2999.34 +NC_045512.2 28095 . A T 1.91419E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=95;CIGAR=1X;DP=2258;DPB=2258;DPRA=0;EPP=3.03316;EPPR=31.6832;GTI=0;LEN=1;MEANALT=1;MQM=36.3368;MQMR=50.2603;NS=1;NUMALT=1;ODDS=2252.59;PAIRED=1;PAIREDR=0.992141;PAO=0;PQA=0;PQR=0;PRO=0;QA=3257;QR=76414;RO=2163;RPL=75;RPP=72.1546;RPPR=1509.51;RPR=20;RUN=1;SAF=46;SAP=3.21602;SAR=49;SRF=1157;SRP=25.9006;SRR=1006;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.202A>T|p.Lys68*|202/366|202/366|68/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2258:2163,95:2163:76414:95:3257:0,-455.717,-6188.95 +NC_045512.2 28111 . A G 30254.2 . AB=0.521647;ABP=14.5739;AC=1;AF=0.5;AN=2;AO=1482;CIGAR=1X;DP=2841;DPB=2841;DPRA=0;EPP=22.0524;EPPR=10.6289;GTI=0;LEN=1;MEANALT=2;MQM=47.7821;MQMR=51.2771;NS=1;NUMALT=1;ODDS=6966.29;PAIRED=0.992578;PAIREDR=0.992631;PAO=0;PQA=0;PQR=0;PRO=0;QA=51828;QR=48256;RO=1357;RPL=66;RPP=2673.39;RPPR=281.268;RPR=1416;RUN=1;SAF=796;SAP=20.7396;SAR=686;SRF=701;SRP=6.25071;SRR=656;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2841:1357,1482:1357:48256:1482:51828:-3367.71,0,-3253.93 +NC_045512.2 28242 . GTTTTAGATTTCA GTTTTAA,GTTTTTAGATTTCA 21929.6 . AB=0.252466,0.0809736;ABP=3348.5,9589.76;AC=1,0;AF=0.5,0;AN=2;AO=1587,509;CIGAR=6M6D1M,1M1I12M;DP=6286;DPB=5604.62;DPRA=0,0;EPP=3.40574,3.11695;EPPR=3.2873;GTI=0;LEN=6,1;MEANALT=21,21;MQM=47.1979,46.4597;MQMR=50.1179;NS=1;NUMALT=2;ODDS=5049.48;PAIRED=0.993699,0.994106;PAIREDR=0.99156;PAO=18.6667,39.1667;PQA=641,1351;PQR=1351;PRO=39.1667;QA=52030,16119;QR=145691;RO=4147;RPL=901,310;RPP=66.2594,55.5736;RPPR=51.0838;RPR=686,199;RUN=1,1;SAF=786,251;SAP=3.31816,3.21934;SAR=801,258;SRF=2052;SRP=3.97848;SRR=2095;TYPE=del,ins;ANN=GTTTTTAGATTTCA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.353dupT|p.Leu118fs|354/366|354/366|118/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6286:4147,1587,509:4147:145691:1587,509:52030,16119:-2465.57,0,-10582,-2450.21,-9796.04,-13356.8 +NC_045512.2 28270 . TAAAATG TAAATG 162166.0 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6075;CIGAR=1M1D5M;DP=6091;DPB=5242.14;DPRA=0;EPP=3.02781;EPPR=0;GTI=0;LEN=1;MEANALT=13;MQM=46.504;MQMR=0;NS=1;NUMALT=1;ODDS=8426.34;PAIRED=0.985021;PAIREDR=0;PAO=62.5;PQA=2061.5;PQR=2085.5;PRO=63.5;QA=184797;QR=0;RO=0;RPL=2885;RPP=36.2615;RPPR=0;RPR=3190;RUN=1;SAF=3053;SAP=3.3538;SAR=3022;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=TAAATG|frameshift_variant&start_lost|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1delA|p.Met1fs|1/1260|1/1260|1/419||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 1/1:6091:0,6075:0:0:6075:184797:-16226,-1828.76,0 +NC_045512.2 28280 . GAT CTA 78730.3 . AB=0.542129;ABP=100.346;AC=1;AF=0.5;AN=2;AO=3423;CIGAR=3X;DP=6314;DPB=6358.67;DPRA=0;EPP=4.66031;EPPR=4.82376;GTI=0;LEN=3;MEANALT=9;MQM=47.7812;MQMR=44.7071;NS=1;NUMALT=1;ODDS=13474;PAIRED=0.991528;PAIREDR=0.969739;PAO=134;PQA=4677;PQR=0;PRO=0;QA=120731;QR=100878;RO=2875;RPL=2093;RPP=372.325;RPPR=363.649;RPR=1330;RUN=1;SAF=1701;SAP=3.29006;SAR=1722;SRF=1446;SRP=3.22858;SRR=1429;TYPE=mnp;ANN=CTA|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.7_9delGATinsCTA|p.Asp3Leu|7/1260|7/1260|3/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6314:2875,3423:2875:100878:3423:120731:-7930.42,0,-5908.15 +NC_045512.2 28295 . A G 1.00676E-12 . AB=0.129612;ABP=9012.63;AC=1;AF=0.5;AN=2;AO=980;CIGAR=1X;DP=7561;DPB=7561;DPRA=0;EPP=3.23188;EPPR=3.26911;GTI=0;LEN=1;MEANALT=3;MQM=45.3653;MQMR=46.2847;NS=1;NUMALT=1;ODDS=1467.02;PAIRED=0.945918;PAIREDR=0.96017;PAO=0;PQA=0;PQR=0;PRO=0;QA=34084;QR=230830;RO=6578;RPL=539;RPP=24.2907;RPPR=6.58078;RPR=441;RUN=1;SAF=482;SAP=3.57754;SAR=498;SRF=3262;SRP=3.9729;SRR=3316;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.22A>G|p.Asn8Asp|22/1260|22/1260|8/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:7561:6578,980:6578:230830:980:34084:-382.745,0,-16005.3 +NC_045512.2 28461 . A G 15382.4 . AB=0.361009;ABP=368.81;AC=1;AF=0.5;AN=2;AO=787;CIGAR=1X;DP=2180;DPB=2180;DPRA=0;EPP=4.00636;EPPR=32.7183;GTI=0;LEN=1;MEANALT=2;MQM=48.2071;MQMR=50.8757;NS=1;NUMALT=1;ODDS=3541.92;PAIRED=0.986023;PAIREDR=0.984914;PAO=0;PQA=0;PQR=0;PRO=0;QA=27472;QR=45714;RO=1392;RPL=252;RPP=223.99;RPPR=356.461;RPR=535;RUN=1;SAF=405;SAP=4.4699;SAR=382;SRF=637;SRP=24.7313;SRR=755;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.188A>G|p.Asp63Gly|188/1260|188/1260|63/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2180:1392,787:1392:45714:787:27472:-1606.4,0,-3204.04 +NC_045512.2 28567 . C T 4.22129E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=26;CIGAR=1X;DP=2372;DPB=2372;DPRA=0;EPP=3.0103;EPPR=4.08121;GTI=0;LEN=1;MEANALT=2;MQM=50.0769;MQMR=52.7534;NS=1;NUMALT=1;ODDS=2985.45;PAIRED=1;PAIREDR=0.995307;PAO=0;PQA=0;PQR=0;PRO=0;QA=906;QR=81075;RO=2344;RPL=4;RPP=30.0702;RPPR=35.7528;RPR=22;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=1173;SRP=3.01401;SRR=1171;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.294C>T|p.Asp98Asp|294/1260|294/1260|98/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2372:2344,26:2344:81075:26:906:0,-636.928,-6974.26 +NC_045512.2 28579 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=86;CIGAR=1X;DP=2340;DPB=2340;DPRA=0;EPP=3.1113;EPPR=5.22994;GTI=0;LEN=1;MEANALT=1;MQM=48.9651;MQMR=52.7955;NS=1;NUMALT=1;ODDS=2324.18;PAIRED=1;PAIREDR=0.996894;PAO=0;PQA=0;PQR=0;PRO=0;QA=2951;QR=78442;RO=2254;RPL=40;RPP=3.91929;RPPR=39.2683;RPR=46;RUN=1;SAF=42;SAP=3.1113;SAR=44;SRF=1099;SRP=6.03148;SRR=1155;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.306A>T|p.Lys102Asn|306/1260|306/1260|102/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2340:2254,86:2254:78442:86:2951:0,-458.341,-6586.23 +NC_045512.2 28598 . T C 2.20595E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=27;CIGAR=1X;DP=2328;DPB=2328;DPRA=0;EPP=3.09072;EPPR=3.05658;GTI=0;LEN=1;MEANALT=2;MQM=46.5185;MQMR=52.5028;NS=1;NUMALT=1;ODDS=2914.06;PAIRED=1;PAIREDR=0.996085;PAO=0;PQA=0;PQR=0;PRO=0;QA=942;QR=80683;RO=2299;RPL=16;RPP=5.02092;RPPR=42.7041;RPR=11;RUN=1;SAF=13;SAP=3.09072;SAR=14;SRF=1156;SRP=3.16993;SRR=1143;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.325T>C|p.Tyr109His|325/1260|325/1260|109/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2328:2299,27:2299:80683:27:942:0,-623.497,-6905.87 +NC_045512.2 28881 . GGGG AACC,AACG,TGGG 91355.5 . AB=0.0998312,0.256089,0.638775;ABP=5771.14,2145.96,696.709;AC=0,1,1;AF=0,0.5,0.5;AN=2;AO=414,1062,2649;CIGAR=4X,3X1M,1X3M;DP=4147;DPB=4199.25;DPRA=0,0,0;EPP=3.03128,3.08391,3.30622;EPPR=5.18177;GTI=0;LEN=4,3,1;MEANALT=14,14,14;MQM=48.314,48.1742,48.4179;MQMR=60;NS=1;NUMALT=3;ODDS=3919.48;PAIRED=1,0.997175,1;PAIREDR=1;PAO=10.5,2.5,101;PQA=343,88,3369;PQR=1079;PRO=62;QA=14330,33717,84424;QR=21;RO=1;RPL=203,506,1423;RPP=3.34599,8.12205,34.8233;RPPR=5.18177;RPR=211,556,1226;RUN=1,1,1;SAF=207,534,1330;SAP=3.0103,3.08391,3.10949;SAR=207,528,1319;SRF=0;SRP=5.18177;SRR=1;TYPE=complex,mnp,snp;ANN=TGGG|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608G>T|p.Arg203Met|608/1260|608/1260|203/419|| GT:DP:AD:RO:QR:AO:QA:GL 2/3:4147:1,414,1062,2649:1:21:414,1062,2649:14330,33717,84424:-9304.73,-8260.38,-8137.34,-6643.97,-5600.91,-6325.87,-2659.48,-1616.42,0,-1863.64 +NC_045512.2 28915 . CG TT,CT 52376.7 . AB=0.0279205,0.547018;ABP=8669.27,88.9772;AC=0,1;AF=0,0.5;AN=2;AO=125,2449;CIGAR=2X,1M1X;DP=4477;DPB=4484;DPRA=0,0;EPP=3.16665,3.56447;EPPR=3.56579;GTI=0;LEN=2,1;MEANALT=7,7;MQM=44.744,46.5545;MQMR=49.2706;NS=1;NUMALT=2;ODDS=9522.4;PAIRED=1,0.998367;PAIREDR=0.996829;PAO=8,6;PQA=264,196;PQR=0;PRO=0;QA=4248,82127;QR=65723;RO=1892;RPL=62,1210;RPP=3.02767,3.756;RPPR=8.96004;RPR=63,1239;RUN=1,1;SAF=64,1220;SAP=3.16665,3.08212;SAR=61,1229;SRF=929;SRP=4.33706;SRR=963;TYPE=mnp,snp;ANN=CT|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.643G>T|p.Gly215Cys|643/1260|643/1260|215/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:4477:1892,125,2449:1892:65723:125,2449:4248,82127:-5262.66,-5540.44,-10401,0,-4606.45,-4161 +NC_045512.2 28972 . A G 5.40026E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=108;CIGAR=1X;DP=4047;DPB=4047;DPRA=0;EPP=3.0103;EPPR=5.63492;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=46.8825;NS=1;NUMALT=1;ODDS=4445.98;PAIRED=0.981481;PAIREDR=0.995684;PAO=0;PQA=0;PQR=0;PRO=0;QA=3804;QR=138740;RO=3939;RPL=56;RPP=3.332;RPPR=289.586;RPR=52;RUN=1;SAF=52;SAP=3.332;SAR=56;SRF=1921;SRP=8.19725;SRR=2018;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.699A>G|p.Lys233Lys|699/1260|699/1260|233/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4047:3939,108:3939:138740:108:3804:0,-922.009,-10833.9 +NC_045512.2 28977 . C T 25897.3 . AB=0.383986;ABP=459.997;AC=1;AF=0.5;AN=2;AO=1501;CIGAR=1X;DP=3909;DPB=3909;DPRA=0;EPP=3.91448;EPPR=5.26474;GTI=0;LEN=1;MEANALT=1;MQM=41.2438;MQMR=50.309;NS=1;NUMALT=1;ODDS=5963.07;PAIRED=0.997335;PAIREDR=0.995432;PAO=0;PQA=0;PQR=0;PRO=0;QA=52393;QR=84353;RO=2408;RPL=949;RPP=231.021;RPPR=135.982;RPR=552;RUN=1;SAF=735;SAP=4.40056;SAR=766;SRF=1191;SRP=3.6199;SRR=1217;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3909:2408,1501:2408:84353:1501:52393:-2668.08,0,-5930.49 +NC_045512.2 29000 . G T 2875.6 . AB=0.194681;ABP=3047.47;AC=1;AF=0.5;AN=2;AO=732;CIGAR=1X;DP=3760;DPB=3760;DPRA=0;EPP=3.97144;EPPR=12.9956;GTI=0;LEN=1;MEANALT=1;MQM=36.9194;MQMR=48.4699;NS=1;NUMALT=1;ODDS=662.131;PAIRED=0.998634;PAIREDR=0.988771;PAO=0;PQA=0;PQR=0;PRO=0;QA=25394;QR=104500;RO=3028;RPL=449;RPP=84.755;RPPR=22.7716;RPR=283;RUN=1;SAF=356;SAP=4.1969;SAR=376;SRF=1504;SRP=3.29715;SRR=1524;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.727G>T|p.Gly243Cys|727/1260|727/1260|243/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3760:3028,732:3028:104500:732:25394:-631.313,0,-7432.98 +NC_045512.2 29029 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=3572;DPB=3572;DPRA=0;EPP=3.47981;EPPR=17.1686;GTI=0;LEN=1;MEANALT=2;MQM=38.5541;MQMR=46.4673;NS=1;NUMALT=1;ODDS=4202.1;PAIRED=0.986486;PAIREDR=0.985702;PAO=0;PQA=0;PQR=0;PRO=0;QA=2455;QR=120356;RO=3497;RPL=47;RPP=14.748;RPPR=272.678;RPR=27;RUN=1;SAF=36;SAP=3.12768;SAR=38;SRF=1756;SRP=3.15001;SRR=1741;TYPE=snp;ANN=C|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.756T>C|p.Ala252Ala|756/1260|756/1260|252/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3572:3497,74:3497:120356:74:2455:0,-898.696,-9450.46 +NC_045512.2 29039 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=149;CIGAR=1X;DP=3516;DPB=3516;DPRA=0;EPP=4.77371;EPPR=20.1454;GTI=0;LEN=1;MEANALT=1;MQM=37.7181;MQMR=47.6341;NS=1;NUMALT=1;ODDS=3473.2;PAIRED=0.973154;PAIREDR=0.985744;PAO=0;PQA=0;PQR=0;PRO=0;QA=5164;QR=118588;RO=3367;RPL=86;RPP=10.7198;RPPR=174.061;RPR=63;RUN=1;SAF=76;SAP=3.14146;SAR=73;SRF=1658;SRP=4.68776;SRR=1709;TYPE=snp;ANN=T|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.766A>T|p.Lys256*|766/1260|766/1260|256/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3516:3367,149:3367:118588:149:5164:0,-709.856,-9327.62 +NC_045512.2 29049 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=101;CIGAR=1X;DP=3347;DPB=3347;DPRA=0;EPP=6.64375;EPPR=12.4923;GTI=0;LEN=1;MEANALT=2;MQM=43.099;MQMR=49.1378;NS=1;NUMALT=1;ODDS=3614.81;PAIRED=0.960396;PAIREDR=0.990133;PAO=0;PQA=0;PQR=0;PRO=0;QA=3321;QR=110630;RO=3243;RPL=47;RPP=4.06379;RPPR=70.2965;RPR=54;RUN=1;SAF=48;SAP=3.54779;SAR=53;SRF=1609;SRP=3.42879;SRR=1634;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.776G>A|p.Arg259Gln|776/1260|776/1260|259/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3347:3243,101:3243:110630:101:3321:0,-752.738,-8988.5 +NC_045512.2 29067 . CTAAAGCATACAATGT CT 2.70012E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=187;CIGAR=1M14D1M;DP=2118;DPB=1955.62;DPRA=0;EPP=3.02191;EPPR=5.31131;GTI=0;LEN=14;MEANALT=13;MQM=48.7647;MQMR=53.2214;NS=1;NUMALT=1;ODDS=1275.56;PAIRED=0.97861;PAIREDR=0.993197;PAO=1;PQA=34;PQR=101;PRO=3;QA=5285;QR=66815;RO=1911;RPL=76;RPP=17.2352;RPPR=87.6977;RPR=111;RUN=1;SAF=98;SAP=3.95088;SAR=89;SRF=986;SRP=7.23848;SRR=925;TYPE=del;ANN=CT|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.798_811delAGCATACAATGTAA|p.Lys266fs|798/1260|798/1260|266/419||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:2118:1911,187:1911:66815:187:5285:0,-187.495,-5392.39 +NC_045512.2 29402 . G T 33928.1 . AB=0.380005;ABP=537.172;AC=1;AF=0.5;AN=2;AO=1623;CIGAR=1X;DP=4271;DPB=4271;DPRA=0;EPP=4.13551;EPPR=7.75762;GTI=0;LEN=1;MEANALT=3;MQM=49.4449;MQMR=52.7301;NS=1;NUMALT=1;ODDS=7812.23;PAIRED=0.997535;PAIREDR=0.995079;PAO=0;PQA=0;PQR=0;PRO=0;QA=57174;QR=92750;RO=2642;RPL=779;RPP=8.66309;RPPR=18.6627;RPR=844;RUN=1;SAF=832;SAP=5.25937;SAR=791;SRF=1339;SRP=4.07549;SRR=1303;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1129G>T|p.Asp377Tyr|1129/1260|1129/1260|377/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4271:2642,1623:2642:92750:1623:57174:-3456.1,0,-6754.07 +NC_045512.2 29681 . TTAATCA TTAATCTAATCA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=59;CIGAR=1M5I6M;DP=2108;DPB=2151.14;DPRA=0;EPP=3.34154;EPPR=24.183;GTI=0;LEN=5;MEANALT=6;MQM=52.322;MQMR=51.6699;NS=1;NUMALT=1;ODDS=2266.18;PAIRED=1;PAIREDR=0.995586;PAO=1;PQA=27.5;PQR=27.5;PRO=1;QA=1893;QR=70994;RO=2039;RPL=34;RPP=5.99147;RPPR=724.345;RPR=25;RUN=1;SAF=31;SAP=3.34154;SAR=28;SRF=963;SRP=16.6089;SRR=1076;TYPE=ins;ANN=TTAATCTAATCA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4302_*4303insTAATC|||||4303| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2108:2039,59:2039:70994:59:1893:0,-462.802,-5912.21 +NC_045512.2 29742 . G T 36691.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1276;CIGAR=1X;DP=1276;DPB=1276;DPRA=0;EPP=3.69101;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=49.6567;MQMR=0;NS=1;NUMALT=1;ODDS=1773.52;PAIRED=0.996082;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44133;QR=0;RO=0;RPL=591;RPP=18.0472;RPPR=0;RPR=685;RUN=1;SAF=637;SAP=3.01711;SAR=639;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4358G>T|||||4358| GT:DP:AD:RO:QR:AO:QA:GL 1/1:1276:0,1276:0:0:1276:44133:-3675.72,-384.114,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage_hits.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,731 @@ +Gene_Name AA_alt sample DP AD_alt AF lineage +M I82T SampleC_freebayes_ann 3984 2770 0.695281124497992 AY.1 +N D63G SampleC_freebayes_ann 2180 787 0.361009174311927 AY.1 +N R203M SampleC_freebayes_ann 4147 4125 0.994694960212202 AY.1 +N G215C SampleC_freebayes_ann 4477 2574 0.574938574938575 AY.1 +N D377Y SampleC_freebayes_ann 4271 1623 0.380004682744088 AY.1 +ORF1a A1306S SampleC_freebayes_ann 2202 1267 0.575386012715713 AY.1 +ORF1a P2046L SampleC_freebayes_ann 2996 1763 0.58845126835781 AY.1 +ORF1a P2287S SampleC_freebayes_ann 2633 1563 0.59361944549943 AY.1 +ORF1a V2930L SampleC_freebayes_ann 1082 913 0.843807763401109 AY.1 +ORF1a T3255I SampleC_freebayes_ann 857 437 0.509918319719953 AY.1 +ORF1a T3646A SampleC_freebayes_ann 801 744 0.928838951310862 AY.1 +ORF3a S26L SampleC_freebayes_ann 4510 3826 0.848337028824834 AY.1 +ORF7a V82A SampleC_freebayes_ann 4141 2302 0.555904370924897 AY.1 +ORF7a T120I SampleC_freebayes_ann 4981 2730 0.548082714314395 AY.1 +S T19R SampleC_freebayes_ann 2058 1448 0.703595724003887 AY.1 +S L452R SampleC_freebayes_ann 1753 1147 0.654306902452938 AY.1 +S T478K SampleC_freebayes_ann 1708 1088 0.637002341920375 AY.1 +S D614G SampleA_freebayes_ann 41 41 1 AY.1 +S D614G SampleB_freebayes_ann 15 15 1 AY.1 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 AY.1 +S P681R SampleC_freebayes_ann 536 536 1 AY.1 +S D950N SampleC_freebayes_ann 949 368 0.387776606954689 AY.1 +ORF1b P314L SampleC_freebayes_ann 0 0 0 AY.1 +ORF1b G662S SampleA_freebayes_ann 0 0 0 AY.1 +ORF1b P1000L SampleB_freebayes_ann 0 0 0 AY.1 +ORF1b A1918V SampleC_freebayes_ann 0 0 0 AY.1 +ORF7b T40I SampleA_freebayes_ann 0 0 0 AY.1 +ORF8 D119I SampleB_freebayes_ann 0 0 0 AY.1 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 AY.1 +S E156G SampleA_freebayes_ann 0 0 0 AY.1 +S del157/158 SampleB_freebayes_ann 0 0 0 AY.1 +S W258L SampleC_freebayes_ann 0 0 0 AY.1 +S K417N SampleA_freebayes_ann 0 0 0 AY.1 +ORF1b P314L SampleB_freebayes_ann 0 0 0 AY.1 +ORF1b G662S SampleC_freebayes_ann 0 0 0 AY.1 +ORF1b P1000L SampleA_freebayes_ann 0 0 0 AY.1 +ORF1b A1918V SampleB_freebayes_ann 0 0 0 AY.1 +ORF7b T40I SampleC_freebayes_ann 0 0 0 AY.1 +ORF8 D119I SampleA_freebayes_ann 0 0 0 AY.1 +ORF8 del120/121 SampleB_freebayes_ann 0 0 0 AY.1 +S E156G SampleC_freebayes_ann 0 0 0 AY.1 +S del157/158 SampleA_freebayes_ann 0 0 0 AY.1 +S W258L SampleB_freebayes_ann 0 0 0 AY.1 +S K417N SampleC_freebayes_ann 0 0 0 AY.1 +ORF1b P314L SampleA_freebayes_ann 0 0 0 AY.1 +ORF1b G662S SampleB_freebayes_ann 0 0 0 AY.1 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 AY.1 +ORF1b A1918V SampleA_freebayes_ann 0 0 0 AY.1 +ORF7b T40I SampleB_freebayes_ann 0 0 0 AY.1 +ORF8 D119I SampleC_freebayes_ann 0 0 0 AY.1 +ORF8 del120/121 SampleA_freebayes_ann 0 0 0 AY.1 +S E156G SampleB_freebayes_ann 0 0 0 AY.1 +S del157/158 SampleC_freebayes_ann 0 0 0 AY.1 +S W258L SampleA_freebayes_ann 0 0 0 AY.1 +S K417N SampleB_freebayes_ann 0 0 0 AY.1 +M I82T SampleC_freebayes_ann 3984 2770 0.695281124497992 AY.2 +N D63G SampleC_freebayes_ann 2180 787 0.361009174311927 AY.2 +N R203M SampleC_freebayes_ann 4147 4125 0.994694960212202 AY.2 +N D377Y SampleC_freebayes_ann 4271 1623 0.380004682744088 AY.2 +ORF1a P1640L SampleC_freebayes_ann 1997 332 0.166249374061092 AY.2 +ORF1a A3209V SampleC_freebayes_ann 1065 373 0.350234741784038 AY.2 +ORF1a V3718A SampleC_freebayes_ann 2727 444 0.162816281628163 AY.2 +ORF1a T3750I SampleC_freebayes_ann 2189 349 0.159433531292828 AY.2 +ORF3a S26L SampleC_freebayes_ann 4510 3826 0.848337028824834 AY.2 +ORF7a V82A SampleC_freebayes_ann 4141 2302 0.555904370924897 AY.2 +ORF7a T120I SampleC_freebayes_ann 4981 2730 0.548082714314395 AY.2 +S T19R SampleC_freebayes_ann 2058 1448 0.703595724003887 AY.2 +S L452R SampleC_freebayes_ann 1753 1147 0.654306902452938 AY.2 +S T478K SampleC_freebayes_ann 1708 1088 0.637002341920375 AY.2 +S D614G SampleA_freebayes_ann 41 41 1 AY.2 +S D614G SampleB_freebayes_ann 15 15 1 AY.2 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 AY.2 +S P681R SampleC_freebayes_ann 536 536 1 AY.2 +S D950N SampleC_freebayes_ann 949 368 0.387776606954689 AY.2 +ORF1a A1146T SampleC_freebayes_ann 0 0 0 AY.2 +ORF1b P314L SampleA_freebayes_ann 0 0 0 AY.2 +ORF1b G662S SampleB_freebayes_ann 0 0 0 AY.2 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 AY.2 +ORF1b T1290I SampleA_freebayes_ann 0 0 0 AY.2 +ORF8 D119I SampleB_freebayes_ann 0 0 0 AY.2 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 AY.2 +S V70F SampleA_freebayes_ann 0 0 0 AY.2 +S E156G SampleB_freebayes_ann 0 0 0 AY.2 +S del157/158 SampleC_freebayes_ann 0 0 0 AY.2 +S A222V SampleA_freebayes_ann 0 0 0 AY.2 +S K417N SampleB_freebayes_ann 0 0 0 AY.2 +ORF1a A1146T SampleC_freebayes_ann 0 0 0 AY.2 +ORF1b P314L SampleA_freebayes_ann 0 0 0 AY.2 +ORF1b G662S SampleB_freebayes_ann 0 0 0 AY.2 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 AY.2 +ORF1b T1290I SampleA_freebayes_ann 0 0 0 AY.2 +ORF8 D119I SampleB_freebayes_ann 0 0 0 AY.2 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 AY.2 +S V70F SampleA_freebayes_ann 0 0 0 AY.2 +S E156G SampleB_freebayes_ann 0 0 0 AY.2 +S del157/158 SampleC_freebayes_ann 0 0 0 AY.2 +S A222V SampleA_freebayes_ann 0 0 0 AY.2 +S K417N SampleB_freebayes_ann 0 0 0 AY.2 +ORF1a A1146T SampleC_freebayes_ann 0 0 0 AY.2 +ORF1b P314L SampleA_freebayes_ann 0 0 0 AY.2 +ORF1b G662S SampleB_freebayes_ann 0 0 0 AY.2 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 AY.2 +ORF1b T1290I SampleA_freebayes_ann 0 0 0 AY.2 +ORF8 D119I SampleB_freebayes_ann 0 0 0 AY.2 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 AY.2 +S V70F SampleA_freebayes_ann 0 0 0 AY.2 +S E156G SampleB_freebayes_ann 0 0 0 AY.2 +S del157/158 SampleC_freebayes_ann 0 0 0 AY.2 +S A222V SampleA_freebayes_ann 0 0 0 AY.2 +S K417N SampleB_freebayes_ann 0 0 0 AY.2 +M I82T SampleC_freebayes_ann 3984 2770 0.695281124497992 AY.3.1 +N D63G SampleC_freebayes_ann 2180 787 0.361009174311927 AY.3.1 +N R203M SampleC_freebayes_ann 4147 4125 0.994694960212202 AY.3.1 +N G215C SampleC_freebayes_ann 4477 2574 0.574938574938575 AY.3.1 +N D377Y SampleC_freebayes_ann 4271 1623 0.380004682744088 AY.3.1 +ORF1a A1306S SampleC_freebayes_ann 2202 1267 0.575386012715713 AY.3.1 +ORF1a P2046L SampleC_freebayes_ann 2996 1763 0.58845126835781 AY.3.1 +ORF1a P2287S SampleC_freebayes_ann 2633 1563 0.59361944549943 AY.3.1 +ORF1a V2930L SampleC_freebayes_ann 1082 913 0.843807763401109 AY.3.1 +ORF1a T3255I SampleC_freebayes_ann 857 437 0.509918319719953 AY.3.1 +ORF1a T3646A SampleC_freebayes_ann 801 744 0.928838951310862 AY.3.1 +ORF1b H5944Y SampleB_freebayes_ann 96 1 0.0104166666666667 AY.3.1 +ORF3a S26L SampleC_freebayes_ann 4510 3826 0.848337028824834 AY.3.1 +ORF7a V82A SampleC_freebayes_ann 4141 2302 0.555904370924897 AY.3.1 +ORF7a T120I SampleC_freebayes_ann 4981 2730 0.548082714314395 AY.3.1 +S T19R SampleC_freebayes_ann 2058 1448 0.703595724003887 AY.3.1 +S L452R SampleC_freebayes_ann 1753 1147 0.654306902452938 AY.3.1 +S T478K SampleC_freebayes_ann 1708 1088 0.637002341920375 AY.3.1 +S D614G SampleA_freebayes_ann 41 41 1 AY.3.1 +S D614G SampleB_freebayes_ann 15 15 1 AY.3.1 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 AY.3.1 +S P681R SampleC_freebayes_ann 536 536 1 AY.3.1 +S D950N SampleC_freebayes_ann 949 368 0.387776606954689 AY.3.1 +ORF1a D1127Y SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF1a I3731V SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF1b P314L SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF1b G662S SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF1b P1000L SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF1b A1918V SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF7b T40I SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF8 D119I SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF8 del120/121 SampleA_freebayes_ann 0 0 0 AY.3.1 +S E156G SampleC_freebayes_ann 0 0 0 AY.3.1 +S del157/158 SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF1a D1127Y SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF1a I3731V SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF1b P314L SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF1b G662S SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF1b A1918V SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF7b T40I SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF8 D119I SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF8 del120/121 SampleB_freebayes_ann 0 0 0 AY.3.1 +S E156G SampleA_freebayes_ann 0 0 0 AY.3.1 +S del157/158 SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF1a D1127Y SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF1a I3731V SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF1b P314L SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF1b G662S SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF1b P1000L SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF1b A1918V SampleC_freebayes_ann 0 0 0 AY.3.1 +ORF7b T40I SampleB_freebayes_ann 0 0 0 AY.3.1 +ORF8 D119I SampleA_freebayes_ann 0 0 0 AY.3.1 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 AY.3.1 +S E156G SampleB_freebayes_ann 0 0 0 AY.3.1 +S del157/158 SampleA_freebayes_ann 0 0 0 AY.3.1 +M I82T SampleC_freebayes_ann 3984 2770 0.695281124497992 AY.3 +N D63G SampleC_freebayes_ann 2180 787 0.361009174311927 AY.3 +N R203M SampleC_freebayes_ann 4147 4125 0.994694960212202 AY.3 +N G215C SampleC_freebayes_ann 4477 2574 0.574938574938575 AY.3 +N D377Y SampleC_freebayes_ann 4271 1623 0.380004682744088 AY.3 +ORF1a A1306S SampleC_freebayes_ann 2202 1267 0.575386012715713 AY.3 +ORF1a P2046L SampleC_freebayes_ann 2996 1763 0.58845126835781 AY.3 +ORF1a P2287S SampleC_freebayes_ann 2633 1563 0.59361944549943 AY.3 +ORF1a V2930L SampleC_freebayes_ann 1082 913 0.843807763401109 AY.3 +ORF1a T3255I SampleC_freebayes_ann 857 437 0.509918319719953 AY.3 +ORF1a T3646A SampleC_freebayes_ann 801 744 0.928838951310862 AY.3 +ORF3a S26L SampleC_freebayes_ann 4510 3826 0.848337028824834 AY.3 +ORF7a V82A SampleC_freebayes_ann 4141 2302 0.555904370924897 AY.3 +ORF7a T120I SampleC_freebayes_ann 4981 2730 0.548082714314395 AY.3 +S T19R SampleC_freebayes_ann 2058 1448 0.703595724003887 AY.3 +S L452R SampleC_freebayes_ann 1753 1147 0.654306902452938 AY.3 +S T478K SampleC_freebayes_ann 1708 1088 0.637002341920375 AY.3 +S D614G SampleA_freebayes_ann 41 41 1 AY.3 +S D614G SampleB_freebayes_ann 15 15 1 AY.3 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 AY.3 +S P681R SampleC_freebayes_ann 536 536 1 AY.3 +S D950N SampleC_freebayes_ann 949 368 0.387776606954689 AY.3 +ORF1a I3731V SampleC_freebayes_ann 0 0 0 AY.3 +ORF1b P314L SampleA_freebayes_ann 0 0 0 AY.3 +ORF1b G662S SampleB_freebayes_ann 0 0 0 AY.3 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 AY.3 +ORF1b A1918V SampleA_freebayes_ann 0 0 0 AY.3 +ORF7b T40I SampleB_freebayes_ann 0 0 0 AY.3 +ORF8 D119I SampleC_freebayes_ann 0 0 0 AY.3 +ORF8 del120/121 SampleA_freebayes_ann 0 0 0 AY.3 +S E156G SampleB_freebayes_ann 0 0 0 AY.3 +S del157/158 SampleC_freebayes_ann 0 0 0 AY.3 +ORF1a I3731V SampleA_freebayes_ann 0 0 0 AY.3 +ORF1b P314L SampleB_freebayes_ann 0 0 0 AY.3 +ORF1b G662S SampleC_freebayes_ann 0 0 0 AY.3 +ORF1b P1000L SampleA_freebayes_ann 0 0 0 AY.3 +ORF1b A1918V SampleB_freebayes_ann 0 0 0 AY.3 +ORF7b T40I SampleC_freebayes_ann 0 0 0 AY.3 +ORF8 D119I SampleA_freebayes_ann 0 0 0 AY.3 +ORF8 del120/121 SampleB_freebayes_ann 0 0 0 AY.3 +S E156G SampleC_freebayes_ann 0 0 0 AY.3 +S del157/158 SampleA_freebayes_ann 0 0 0 AY.3 +ORF1a I3731V SampleB_freebayes_ann 0 0 0 AY.3 +ORF1b P314L SampleC_freebayes_ann 0 0 0 AY.3 +ORF1b G662S SampleA_freebayes_ann 0 0 0 AY.3 +ORF1b P1000L SampleB_freebayes_ann 0 0 0 AY.3 +ORF1b A1918V SampleC_freebayes_ann 0 0 0 AY.3 +ORF7b T40I SampleA_freebayes_ann 0 0 0 AY.3 +ORF8 D119I SampleB_freebayes_ann 0 0 0 AY.3 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 AY.3 +S E156G SampleA_freebayes_ann 0 0 0 AY.3 +S del157/158 SampleB_freebayes_ann 0 0 0 AY.3 +N D3L SampleA_freebayes_ann 54 54 1 B.1.1.7 +N D3L SampleB_freebayes_ann 200 200 1 B.1.1.7 +N D3L SampleC_freebayes_ann 6314 3423 0.542128603104213 B.1.1.7 +N RG203KR SampleA_freebayes_ann 14 14 1 B.1.1.7 +N RG203KR SampleB_freebayes_ann 69 68 0.985507246376812 B.1.1.7 +N S235F SampleA_freebayes_ann 14 14 1 B.1.1.7 +N S235F SampleB_freebayes_ann 65 61 0.938461538461539 B.1.1.7 +N S235F SampleC_freebayes_ann 3909 1501 0.383985674085444 B.1.1.7 +ORF1a T1001I SampleA_freebayes_ann 35 35 1 B.1.1.7 +ORF1a T1001I SampleB_freebayes_ann 51 51 1 B.1.1.7 +ORF1a T1001I SampleC_freebayes_ann 3354 2829 0.843470483005367 B.1.1.7 +ORF1a A1708D SampleA_freebayes_ann 44 32 0.727272727272727 B.1.1.7 +ORF1a A1708D SampleB_freebayes_ann 69 69 1 B.1.1.7 +ORF1a A1708D SampleC_freebayes_ann 1638 691 0.421855921855922 B.1.1.7 +ORF1a I2230T SampleC_freebayes_ann 4348 3244 0.746090156393744 B.1.1.7 +ORF8 Q27* SampleA_freebayes_ann 66 66 1 B.1.1.7 +ORF8 Q27* SampleB_freebayes_ann 114 114 1 B.1.1.7 +ORF8 Q27* SampleC_freebayes_ann 1308 150 0.114678899082569 B.1.1.7 +ORF8 R52I SampleA_freebayes_ann 66 66 1 B.1.1.7 +ORF8 R52I SampleB_freebayes_ann 114 114 1 B.1.1.7 +ORF8 R52I SampleC_freebayes_ann 1234 133 0.107779578606159 B.1.1.7 +ORF8 Y73C SampleA_freebayes_ann 59 59 1 B.1.1.7 +ORF8 Y73C SampleB_freebayes_ann 155 155 1 B.1.1.7 +ORF8 Y73C SampleC_freebayes_ann 2841 1482 0.521647307286167 B.1.1.7 +S del69/70 SampleB_freebayes_ann 2 2 1 B.1.1.7 +S del69/70 SampleC_freebayes_ann 744 744 1 B.1.1.7 +S N501Y SampleA_freebayes_ann 6 6 1 B.1.1.7 +S N501Y SampleB_freebayes_ann 4 4 1 B.1.1.7 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 B.1.1.7 +S A570D SampleA_freebayes_ann 42 42 1 B.1.1.7 +S A570D SampleB_freebayes_ann 16 16 1 B.1.1.7 +S A570D SampleC_freebayes_ann 3990 99 0.024812030075188 B.1.1.7 +S D614G SampleA_freebayes_ann 41 41 1 B.1.1.7 +S D614G SampleB_freebayes_ann 15 15 1 B.1.1.7 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 B.1.1.7 +S P681H SampleA_freebayes_ann 36 13 0.361111111111111 B.1.1.7 +S P681H SampleB_freebayes_ann 8 8 1 B.1.1.7 +S T716I SampleA_freebayes_ann 36 13 0.361111111111111 B.1.1.7 +S T716I SampleB_freebayes_ann 8 8 1 B.1.1.7 +S S982A SampleA_freebayes_ann 26 26 1 B.1.1.7 +S S982A SampleB_freebayes_ann 62 62 1 B.1.1.7 +S S982A SampleC_freebayes_ann 2224 704 0.316546762589928 B.1.1.7 +S D1118H SampleA_freebayes_ann 40 40 1 B.1.1.7 +S D1118H SampleB_freebayes_ann 134 133 0.992537313432836 B.1.1.7 +S D1118H SampleC_freebayes_ann 4900 1158 0.236326530612245 B.1.1.7 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 B.1.1.7 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 B.1.1.7 +ORF1b P314L SampleC_freebayes_ann 0 0 0 B.1.1.7 +S del144/145 SampleA_freebayes_ann 0 0 0 B.1.1.7 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 B.1.1.7 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 B.1.1.7 +ORF1b P314L SampleA_freebayes_ann 0 0 0 B.1.1.7 +S del144/145 SampleB_freebayes_ann 0 0 0 B.1.1.7 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 B.1.1.7 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 B.1.1.7 +ORF1b P314L SampleB_freebayes_ann 0 0 0 B.1.1.7 +S del144/145 SampleC_freebayes_ann 0 0 0 B.1.1.7 +N D3L SampleA_freebayes_ann 54 54 1 B.1.1.7+S_E484K +N D3L SampleB_freebayes_ann 200 200 1 B.1.1.7+S_E484K +N D3L SampleC_freebayes_ann 6314 3423 0.542128603104213 B.1.1.7+S_E484K +N RG203KR SampleA_freebayes_ann 14 14 1 B.1.1.7+S_E484K +N RG203KR SampleB_freebayes_ann 69 68 0.985507246376812 B.1.1.7+S_E484K +N S235F SampleA_freebayes_ann 14 14 1 B.1.1.7+S_E484K +N S235F SampleB_freebayes_ann 65 61 0.938461538461539 B.1.1.7+S_E484K +N S235F SampleC_freebayes_ann 3909 1501 0.383985674085444 B.1.1.7+S_E484K +ORF1a T1001I SampleA_freebayes_ann 35 35 1 B.1.1.7+S_E484K +ORF1a T1001I SampleB_freebayes_ann 51 51 1 B.1.1.7+S_E484K +ORF1a T1001I SampleC_freebayes_ann 3354 2829 0.843470483005367 B.1.1.7+S_E484K +ORF1a A1708D SampleA_freebayes_ann 44 32 0.727272727272727 B.1.1.7+S_E484K +ORF1a A1708D SampleB_freebayes_ann 69 69 1 B.1.1.7+S_E484K +ORF1a A1708D SampleC_freebayes_ann 1638 691 0.421855921855922 B.1.1.7+S_E484K +ORF1a I2230T SampleC_freebayes_ann 4348 3244 0.746090156393744 B.1.1.7+S_E484K +ORF8 Q27* SampleA_freebayes_ann 66 66 1 B.1.1.7+S_E484K +ORF8 Q27* SampleB_freebayes_ann 114 114 1 B.1.1.7+S_E484K +ORF8 Q27* SampleC_freebayes_ann 1308 150 0.114678899082569 B.1.1.7+S_E484K +ORF8 R52I SampleA_freebayes_ann 66 66 1 B.1.1.7+S_E484K +ORF8 R52I SampleB_freebayes_ann 114 114 1 B.1.1.7+S_E484K +ORF8 R52I SampleC_freebayes_ann 1234 133 0.107779578606159 B.1.1.7+S_E484K +ORF8 Y73C SampleA_freebayes_ann 59 59 1 B.1.1.7+S_E484K +ORF8 Y73C SampleB_freebayes_ann 155 155 1 B.1.1.7+S_E484K +ORF8 Y73C SampleC_freebayes_ann 2841 1482 0.521647307286167 B.1.1.7+S_E484K +S del69/70 SampleB_freebayes_ann 2 2 1 B.1.1.7+S_E484K +S del69/70 SampleC_freebayes_ann 744 744 1 B.1.1.7+S_E484K +S N501Y SampleA_freebayes_ann 6 6 1 B.1.1.7+S_E484K +S N501Y SampleB_freebayes_ann 4 4 1 B.1.1.7+S_E484K +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 B.1.1.7+S_E484K +S A570D SampleA_freebayes_ann 42 42 1 B.1.1.7+S_E484K +S A570D SampleB_freebayes_ann 16 16 1 B.1.1.7+S_E484K +S A570D SampleC_freebayes_ann 3990 99 0.024812030075188 B.1.1.7+S_E484K +S D614G SampleA_freebayes_ann 41 41 1 B.1.1.7+S_E484K +S D614G SampleB_freebayes_ann 15 15 1 B.1.1.7+S_E484K +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 B.1.1.7+S_E484K +S P681H SampleA_freebayes_ann 36 13 0.361111111111111 B.1.1.7+S_E484K +S P681H SampleB_freebayes_ann 8 8 1 B.1.1.7+S_E484K +S T716I SampleA_freebayes_ann 36 13 0.361111111111111 B.1.1.7+S_E484K +S T716I SampleB_freebayes_ann 8 8 1 B.1.1.7+S_E484K +S S982A SampleA_freebayes_ann 26 26 1 B.1.1.7+S_E484K +S S982A SampleB_freebayes_ann 62 62 1 B.1.1.7+S_E484K +S S982A SampleC_freebayes_ann 2224 704 0.316546762589928 B.1.1.7+S_E484K +S D1118H SampleA_freebayes_ann 40 40 1 B.1.1.7+S_E484K +S D1118H SampleB_freebayes_ann 134 133 0.992537313432836 B.1.1.7+S_E484K +S D1118H SampleC_freebayes_ann 4900 1158 0.236326530612245 B.1.1.7+S_E484K +ORF1a S3675K SampleA_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1b P314L SampleC_freebayes_ann 0 0 0 B.1.1.7+S_E484K +S del144/145 SampleA_freebayes_ann 0 0 0 B.1.1.7+S_E484K +S E484K SampleB_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1a S3675K SampleC_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1b P314L SampleB_freebayes_ann 0 0 0 B.1.1.7+S_E484K +S del144/145 SampleC_freebayes_ann 0 0 0 B.1.1.7+S_E484K +S E484K SampleA_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1a S3675K SampleB_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF1b P314L SampleA_freebayes_ann 0 0 0 B.1.1.7+S_E484K +S del144/145 SampleB_freebayes_ann 0 0 0 B.1.1.7+S_E484K +S E484K SampleC_freebayes_ann 0 0 0 B.1.1.7+S_E484K +ORF3a S171L SampleA_freebayes_ann 11 1 0.0909090909090909 B.1.351.2 +S D80A SampleA_freebayes_ann 31 11 0.354838709677419 B.1.351.2 +S N501Y SampleA_freebayes_ann 6 6 1 B.1.351.2 +S N501Y SampleB_freebayes_ann 4 4 1 B.1.351.2 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 B.1.351.2 +S D614G SampleA_freebayes_ann 41 41 1 B.1.351.2 +S D614G SampleB_freebayes_ann 15 15 1 B.1.351.2 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 B.1.351.2 +S A701V SampleA_freebayes_ann 36 23 0.638888888888889 B.1.351.2 +E P71L SampleA_freebayes_ann 0 0 0 B.1.351.2 +N T205I SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a T265I SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a K1655N SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a N2596S SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a K3353R SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a A3456V SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1b P314L SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF3a Q57H SampleB_freebayes_ann 0 0 0 B.1.351.2 +S L18F SampleC_freebayes_ann 0 0 0 B.1.351.2 +S D215G SampleA_freebayes_ann 0 0 0 B.1.351.2 +S del241/243 SampleB_freebayes_ann 0 0 0 B.1.351.2 +S K417N SampleC_freebayes_ann 0 0 0 B.1.351.2 +S E484K SampleA_freebayes_ann 0 0 0 B.1.351.2 +E P71L SampleB_freebayes_ann 0 0 0 B.1.351.2 +N T205I SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a T265I SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a K1655N SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a N2596S SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a K3353R SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a A3456V SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1b P314L SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF3a Q57H SampleC_freebayes_ann 0 0 0 B.1.351.2 +S L18F SampleA_freebayes_ann 0 0 0 B.1.351.2 +S D215G SampleB_freebayes_ann 0 0 0 B.1.351.2 +S del241/243 SampleC_freebayes_ann 0 0 0 B.1.351.2 +S K417N SampleA_freebayes_ann 0 0 0 B.1.351.2 +S E484K SampleB_freebayes_ann 0 0 0 B.1.351.2 +E P71L SampleC_freebayes_ann 0 0 0 B.1.351.2 +N T205I SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a T265I SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a K1655N SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a N2596S SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a K3353R SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1a A3456V SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 B.1.351.2 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 B.1.351.2 +ORF1b P314L SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF3a Q57H SampleA_freebayes_ann 0 0 0 B.1.351.2 +S L18F SampleB_freebayes_ann 0 0 0 B.1.351.2 +S D215G SampleC_freebayes_ann 0 0 0 B.1.351.2 +S del241/243 SampleA_freebayes_ann 0 0 0 B.1.351.2 +S K417N SampleB_freebayes_ann 0 0 0 B.1.351.2 +S E484K SampleC_freebayes_ann 0 0 0 B.1.351.2 +ORF1a P2046L SampleC_freebayes_ann 2996 1763 0.58845126835781 B.1.351.3 +ORF3a S171L SampleA_freebayes_ann 11 1 0.0909090909090909 B.1.351.3 +S D80A SampleA_freebayes_ann 31 11 0.354838709677419 B.1.351.3 +S N501Y SampleA_freebayes_ann 6 6 1 B.1.351.3 +S N501Y SampleB_freebayes_ann 4 4 1 B.1.351.3 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 B.1.351.3 +S D614G SampleA_freebayes_ann 41 41 1 B.1.351.3 +S D614G SampleB_freebayes_ann 15 15 1 B.1.351.3 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 B.1.351.3 +S A701V SampleA_freebayes_ann 36 23 0.638888888888889 B.1.351.3 +E P71L SampleC_freebayes_ann 0 0 0 B.1.351.3 +N T205I SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1a T265I SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1a K1655N SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1a N2596S SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1a K3353R SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1b P314L SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1b I1074V SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF3a Q57H SampleA_freebayes_ann 0 0 0 B.1.351.3 +S L18F SampleB_freebayes_ann 0 0 0 B.1.351.3 +S D215G SampleC_freebayes_ann 0 0 0 B.1.351.3 +S del241/243 SampleA_freebayes_ann 0 0 0 B.1.351.3 +S K417N SampleB_freebayes_ann 0 0 0 B.1.351.3 +S E484K SampleC_freebayes_ann 0 0 0 B.1.351.3 +E P71L SampleA_freebayes_ann 0 0 0 B.1.351.3 +N T205I SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1a T265I SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1a K1655N SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1a N2596S SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1a K3353R SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1b P314L SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1b I1074V SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF3a Q57H SampleB_freebayes_ann 0 0 0 B.1.351.3 +S L18F SampleC_freebayes_ann 0 0 0 B.1.351.3 +S D215G SampleA_freebayes_ann 0 0 0 B.1.351.3 +S del241/243 SampleB_freebayes_ann 0 0 0 B.1.351.3 +S K417N SampleC_freebayes_ann 0 0 0 B.1.351.3 +S E484K SampleA_freebayes_ann 0 0 0 B.1.351.3 +E P71L SampleB_freebayes_ann 0 0 0 B.1.351.3 +N T205I SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1a T265I SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1a K1655N SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1a N2596S SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1a K3353R SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 B.1.351.3 +ORF1b P314L SampleA_freebayes_ann 0 0 0 B.1.351.3 +ORF1b I1074V SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF3a Q57H SampleC_freebayes_ann 0 0 0 B.1.351.3 +S L18F SampleA_freebayes_ann 0 0 0 B.1.351.3 +S D215G SampleB_freebayes_ann 0 0 0 B.1.351.3 +S del241/243 SampleC_freebayes_ann 0 0 0 B.1.351.3 +S K417N SampleA_freebayes_ann 0 0 0 B.1.351.3 +S E484K SampleB_freebayes_ann 0 0 0 B.1.351.3 +ORF3a S171L SampleA_freebayes_ann 11 1 0.0909090909090909 B.1.351 +S D80A SampleA_freebayes_ann 31 11 0.354838709677419 B.1.351 +S N501Y SampleA_freebayes_ann 6 6 1 B.1.351 +S N501Y SampleB_freebayes_ann 4 4 1 B.1.351 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 B.1.351 +S D614G SampleA_freebayes_ann 41 41 1 B.1.351 +S D614G SampleB_freebayes_ann 15 15 1 B.1.351 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 B.1.351 +S A701V SampleA_freebayes_ann 36 23 0.638888888888889 B.1.351 +E P71L SampleA_freebayes_ann 0 0 0 B.1.351 +N T205I SampleB_freebayes_ann 0 0 0 B.1.351 +ORF1a T265I SampleC_freebayes_ann 0 0 0 B.1.351 +ORF1a K1655N SampleA_freebayes_ann 0 0 0 B.1.351 +ORF1a K3353R SampleB_freebayes_ann 0 0 0 B.1.351 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 B.1.351 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 B.1.351 +ORF1b P314L SampleB_freebayes_ann 0 0 0 B.1.351 +ORF3a Q57H SampleC_freebayes_ann 0 0 0 B.1.351 +S D215G SampleA_freebayes_ann 0 0 0 B.1.351 +S del241/243 SampleB_freebayes_ann 0 0 0 B.1.351 +S K417N SampleC_freebayes_ann 0 0 0 B.1.351 +S E484K SampleA_freebayes_ann 0 0 0 B.1.351 +E P71L SampleB_freebayes_ann 0 0 0 B.1.351 +N T205I SampleC_freebayes_ann 0 0 0 B.1.351 +ORF1a T265I SampleA_freebayes_ann 0 0 0 B.1.351 +ORF1a K1655N SampleB_freebayes_ann 0 0 0 B.1.351 +ORF1a K3353R SampleC_freebayes_ann 0 0 0 B.1.351 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 B.1.351 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 B.1.351 +ORF1b P314L SampleC_freebayes_ann 0 0 0 B.1.351 +ORF3a Q57H SampleA_freebayes_ann 0 0 0 B.1.351 +S D215G SampleB_freebayes_ann 0 0 0 B.1.351 +S del241/243 SampleC_freebayes_ann 0 0 0 B.1.351 +S K417N SampleA_freebayes_ann 0 0 0 B.1.351 +S E484K SampleB_freebayes_ann 0 0 0 B.1.351 +E P71L SampleC_freebayes_ann 0 0 0 B.1.351 +N T205I SampleA_freebayes_ann 0 0 0 B.1.351 +ORF1a T265I SampleB_freebayes_ann 0 0 0 B.1.351 +ORF1a K1655N SampleC_freebayes_ann 0 0 0 B.1.351 +ORF1a K3353R SampleA_freebayes_ann 0 0 0 B.1.351 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 B.1.351 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 B.1.351 +ORF1b P314L SampleA_freebayes_ann 0 0 0 B.1.351 +ORF3a Q57H SampleB_freebayes_ann 0 0 0 B.1.351 +S D215G SampleC_freebayes_ann 0 0 0 B.1.351 +S del241/243 SampleA_freebayes_ann 0 0 0 B.1.351 +S K417N SampleB_freebayes_ann 0 0 0 B.1.351 +S E484K SampleC_freebayes_ann 0 0 0 B.1.351 +M I82T SampleC_freebayes_ann 3984 2770 0.695281124497992 B.1.617.2 +N D63G SampleC_freebayes_ann 2180 787 0.361009174311927 B.1.617.2 +N R203M SampleC_freebayes_ann 4147 4125 0.994694960212202 B.1.617.2 +N D377Y SampleC_freebayes_ann 4271 1623 0.380004682744088 B.1.617.2 +ORF3a S26L SampleC_freebayes_ann 4510 3826 0.848337028824834 B.1.617.2 +ORF7a V82A SampleC_freebayes_ann 4141 2302 0.555904370924897 B.1.617.2 +ORF7a T120I SampleC_freebayes_ann 4981 2730 0.548082714314395 B.1.617.2 +S T19R SampleC_freebayes_ann 2058 1448 0.703595724003887 B.1.617.2 +S L452R SampleC_freebayes_ann 1753 1147 0.654306902452938 B.1.617.2 +S T478K SampleC_freebayes_ann 1708 1088 0.637002341920375 B.1.617.2 +S D614G SampleA_freebayes_ann 41 41 1 B.1.617.2 +S D614G SampleB_freebayes_ann 15 15 1 B.1.617.2 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 B.1.617.2 +S P681R SampleC_freebayes_ann 536 536 1 B.1.617.2 +S D950N SampleC_freebayes_ann 949 368 0.387776606954689 B.1.617.2 +ORF1b P314L SampleC_freebayes_ann 0 0 0 B.1.617.2 +ORF1b G662S SampleA_freebayes_ann 0 0 0 B.1.617.2 +ORF1b P1000L SampleB_freebayes_ann 0 0 0 B.1.617.2 +ORF8 D119I SampleC_freebayes_ann 0 0 0 B.1.617.2 +ORF8 del120/121 SampleA_freebayes_ann 0 0 0 B.1.617.2 +S G142D SampleB_freebayes_ann 0 0 0 B.1.617.2 +S E156G SampleC_freebayes_ann 0 0 0 B.1.617.2 +S del157/158 SampleA_freebayes_ann 0 0 0 B.1.617.2 +ORF1b P314L SampleB_freebayes_ann 0 0 0 B.1.617.2 +ORF1b G662S SampleC_freebayes_ann 0 0 0 B.1.617.2 +ORF1b P1000L SampleA_freebayes_ann 0 0 0 B.1.617.2 +ORF8 D119I SampleB_freebayes_ann 0 0 0 B.1.617.2 +ORF8 del120/121 SampleC_freebayes_ann 0 0 0 B.1.617.2 +S G142D SampleA_freebayes_ann 0 0 0 B.1.617.2 +S E156G SampleB_freebayes_ann 0 0 0 B.1.617.2 +S del157/158 SampleC_freebayes_ann 0 0 0 B.1.617.2 +ORF1b P314L SampleA_freebayes_ann 0 0 0 B.1.617.2 +ORF1b G662S SampleB_freebayes_ann 0 0 0 B.1.617.2 +ORF1b P1000L SampleC_freebayes_ann 0 0 0 B.1.617.2 +ORF8 D119I SampleA_freebayes_ann 0 0 0 B.1.617.2 +ORF8 del120/121 SampleB_freebayes_ann 0 0 0 B.1.617.2 +S G142D SampleC_freebayes_ann 0 0 0 B.1.617.2 +S E156G SampleA_freebayes_ann 0 0 0 B.1.617.2 +S del157/158 SampleB_freebayes_ann 0 0 0 B.1.617.2 +S N501Y SampleA_freebayes_ann 6 6 1 P.1.1 +S N501Y SampleB_freebayes_ann 4 4 1 P.1.1 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 P.1.1 +S D614G SampleA_freebayes_ann 41 41 1 P.1.1 +S D614G SampleB_freebayes_ann 15 15 1 P.1.1 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 P.1.1 +N P80R SampleA_freebayes_ann 0 0 0 P.1.1 +ORF1a S1188L SampleB_freebayes_ann 0 0 0 P.1.1 +ORF1a K1795Q SampleC_freebayes_ann 0 0 0 P.1.1 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 P.1.1 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 P.1.1 +ORF1b P314L SampleC_freebayes_ann 0 0 0 P.1.1 +ORF1b E1264D SampleA_freebayes_ann 0 0 0 P.1.1 +ORF3a S253P SampleB_freebayes_ann 0 0 0 P.1.1 +ORF8 E92K SampleC_freebayes_ann 0 0 0 P.1.1 +S L18F SampleA_freebayes_ann 0 0 0 P.1.1 +S T20N SampleB_freebayes_ann 0 0 0 P.1.1 +S P26S SampleC_freebayes_ann 0 0 0 P.1.1 +S D138Y SampleA_freebayes_ann 0 0 0 P.1.1 +S R190S SampleB_freebayes_ann 0 0 0 P.1.1 +S K417T SampleC_freebayes_ann 0 0 0 P.1.1 +S E484K SampleA_freebayes_ann 0 0 0 P.1.1 +S H655Y SampleB_freebayes_ann 0 0 0 P.1.1 +S T1027I SampleC_freebayes_ann 0 0 0 P.1.1 +S V1176F SampleA_freebayes_ann 0 0 0 P.1.1 +N P80R SampleB_freebayes_ann 0 0 0 P.1.1 +ORF1a S1188L SampleC_freebayes_ann 0 0 0 P.1.1 +ORF1a K1795Q SampleA_freebayes_ann 0 0 0 P.1.1 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 P.1.1 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 P.1.1 +ORF1b P314L SampleA_freebayes_ann 0 0 0 P.1.1 +ORF1b E1264D SampleB_freebayes_ann 0 0 0 P.1.1 +ORF3a S253P SampleC_freebayes_ann 0 0 0 P.1.1 +ORF8 E92K SampleA_freebayes_ann 0 0 0 P.1.1 +S L18F SampleB_freebayes_ann 0 0 0 P.1.1 +S T20N SampleC_freebayes_ann 0 0 0 P.1.1 +S P26S SampleA_freebayes_ann 0 0 0 P.1.1 +S D138Y SampleB_freebayes_ann 0 0 0 P.1.1 +S R190S SampleC_freebayes_ann 0 0 0 P.1.1 +S K417T SampleA_freebayes_ann 0 0 0 P.1.1 +S E484K SampleB_freebayes_ann 0 0 0 P.1.1 +S H655Y SampleC_freebayes_ann 0 0 0 P.1.1 +S T1027I SampleA_freebayes_ann 0 0 0 P.1.1 +S V1176F SampleB_freebayes_ann 0 0 0 P.1.1 +N P80R SampleC_freebayes_ann 0 0 0 P.1.1 +ORF1a S1188L SampleA_freebayes_ann 0 0 0 P.1.1 +ORF1a K1795Q SampleB_freebayes_ann 0 0 0 P.1.1 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 P.1.1 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 P.1.1 +ORF1b P314L SampleB_freebayes_ann 0 0 0 P.1.1 +ORF1b E1264D SampleC_freebayes_ann 0 0 0 P.1.1 +ORF3a S253P SampleA_freebayes_ann 0 0 0 P.1.1 +ORF8 E92K SampleB_freebayes_ann 0 0 0 P.1.1 +S L18F SampleC_freebayes_ann 0 0 0 P.1.1 +S T20N SampleA_freebayes_ann 0 0 0 P.1.1 +S P26S SampleB_freebayes_ann 0 0 0 P.1.1 +S D138Y SampleC_freebayes_ann 0 0 0 P.1.1 +S R190S SampleA_freebayes_ann 0 0 0 P.1.1 +S K417T SampleB_freebayes_ann 0 0 0 P.1.1 +S E484K SampleC_freebayes_ann 0 0 0 P.1.1 +S H655Y SampleA_freebayes_ann 0 0 0 P.1.1 +S T1027I SampleB_freebayes_ann 0 0 0 P.1.1 +S V1176F SampleC_freebayes_ann 0 0 0 P.1.1 +N RG203KR SampleA_freebayes_ann 14 14 1 P.1.2 +N RG203KR SampleB_freebayes_ann 69 68 0.985507246376812 P.1.2 +S N501Y SampleA_freebayes_ann 6 6 1 P.1.2 +S N501Y SampleB_freebayes_ann 4 4 1 P.1.2 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 P.1.2 +S D614G SampleA_freebayes_ann 41 41 1 P.1.2 +S D614G SampleB_freebayes_ann 15 15 1 P.1.2 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 P.1.2 +N P80R SampleA_freebayes_ann 0 0 0 P.1.2 +ORF1a S1188L SampleB_freebayes_ann 0 0 0 P.1.2 +ORF1a K1795Q SampleC_freebayes_ann 0 0 0 P.1.2 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 P.1.2 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 P.1.2 +ORF1b P314L SampleC_freebayes_ann 0 0 0 P.1.2 +ORF1b E1264D SampleA_freebayes_ann 0 0 0 P.1.2 +ORF3a S253P SampleB_freebayes_ann 0 0 0 P.1.2 +ORF8 E92K SampleC_freebayes_ann 0 0 0 P.1.2 +S L18F SampleA_freebayes_ann 0 0 0 P.1.2 +S T20N SampleB_freebayes_ann 0 0 0 P.1.2 +S P26S SampleC_freebayes_ann 0 0 0 P.1.2 +S D138Y SampleA_freebayes_ann 0 0 0 P.1.2 +S R190S SampleB_freebayes_ann 0 0 0 P.1.2 +S K417T SampleC_freebayes_ann 0 0 0 P.1.2 +S E484K SampleA_freebayes_ann 0 0 0 P.1.2 +S H655Y SampleB_freebayes_ann 0 0 0 P.1.2 +S T1027I SampleC_freebayes_ann 0 0 0 P.1.2 +S V1176F SampleA_freebayes_ann 0 0 0 P.1.2 +N P80R SampleB_freebayes_ann 0 0 0 P.1.2 +ORF1a S1188L SampleC_freebayes_ann 0 0 0 P.1.2 +ORF1a K1795Q SampleA_freebayes_ann 0 0 0 P.1.2 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 P.1.2 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 P.1.2 +ORF1b P314L SampleA_freebayes_ann 0 0 0 P.1.2 +ORF1b E1264D SampleB_freebayes_ann 0 0 0 P.1.2 +ORF3a S253P SampleC_freebayes_ann 0 0 0 P.1.2 +ORF8 E92K SampleA_freebayes_ann 0 0 0 P.1.2 +S L18F SampleB_freebayes_ann 0 0 0 P.1.2 +S T20N SampleC_freebayes_ann 0 0 0 P.1.2 +S P26S SampleA_freebayes_ann 0 0 0 P.1.2 +S D138Y SampleB_freebayes_ann 0 0 0 P.1.2 +S R190S SampleC_freebayes_ann 0 0 0 P.1.2 +S K417T SampleA_freebayes_ann 0 0 0 P.1.2 +S E484K SampleB_freebayes_ann 0 0 0 P.1.2 +S H655Y SampleC_freebayes_ann 0 0 0 P.1.2 +S T1027I SampleA_freebayes_ann 0 0 0 P.1.2 +S V1176F SampleB_freebayes_ann 0 0 0 P.1.2 +N P80R SampleC_freebayes_ann 0 0 0 P.1.2 +ORF1a S1188L SampleA_freebayes_ann 0 0 0 P.1.2 +ORF1a K1795Q SampleB_freebayes_ann 0 0 0 P.1.2 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 P.1.2 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 P.1.2 +ORF1b P314L SampleB_freebayes_ann 0 0 0 P.1.2 +ORF1b E1264D SampleC_freebayes_ann 0 0 0 P.1.2 +ORF3a S253P SampleA_freebayes_ann 0 0 0 P.1.2 +ORF8 E92K SampleB_freebayes_ann 0 0 0 P.1.2 +S L18F SampleC_freebayes_ann 0 0 0 P.1.2 +S T20N SampleA_freebayes_ann 0 0 0 P.1.2 +S P26S SampleB_freebayes_ann 0 0 0 P.1.2 +S D138Y SampleC_freebayes_ann 0 0 0 P.1.2 +S R190S SampleA_freebayes_ann 0 0 0 P.1.2 +S K417T SampleB_freebayes_ann 0 0 0 P.1.2 +S E484K SampleC_freebayes_ann 0 0 0 P.1.2 +S H655Y SampleA_freebayes_ann 0 0 0 P.1.2 +S T1027I SampleB_freebayes_ann 0 0 0 P.1.2 +S V1176F SampleC_freebayes_ann 0 0 0 P.1.2 +N RG203KR SampleA_freebayes_ann 14 14 1 P.1 +N RG203KR SampleB_freebayes_ann 69 68 0.985507246376812 P.1 +S N501Y SampleA_freebayes_ann 6 6 1 P.1 +S N501Y SampleB_freebayes_ann 4 4 1 P.1 +S N501Y SampleC_freebayes_ann 1592 578 0.363065326633166 P.1 +S D614G SampleA_freebayes_ann 41 41 1 P.1 +S D614G SampleB_freebayes_ann 15 15 1 P.1 +S D614G SampleC_freebayes_ann 3572 3570 0.999440089585666 P.1 +N P80R SampleA_freebayes_ann 0 0 0 P.1 +ORF1a S1188L SampleB_freebayes_ann 0 0 0 P.1 +ORF1a K1795Q SampleC_freebayes_ann 0 0 0 P.1 +ORF1a S3675K SampleA_freebayes_ann 0 0 0 P.1 +ORF1a del3676/3678 SampleB_freebayes_ann 0 0 0 P.1 +ORF1b P314L SampleC_freebayes_ann 0 0 0 P.1 +ORF1b E1264D SampleA_freebayes_ann 0 0 0 P.1 +ORF3a S253P SampleB_freebayes_ann 0 0 0 P.1 +ORF8 E92K SampleC_freebayes_ann 0 0 0 P.1 +S L18F SampleA_freebayes_ann 0 0 0 P.1 +S T20N SampleB_freebayes_ann 0 0 0 P.1 +S P26S SampleC_freebayes_ann 0 0 0 P.1 +S D138Y SampleA_freebayes_ann 0 0 0 P.1 +S R190S SampleB_freebayes_ann 0 0 0 P.1 +S K417T SampleC_freebayes_ann 0 0 0 P.1 +S E484K SampleA_freebayes_ann 0 0 0 P.1 +S H655Y SampleB_freebayes_ann 0 0 0 P.1 +S T1027I SampleC_freebayes_ann 0 0 0 P.1 +S V1176F SampleA_freebayes_ann 0 0 0 P.1 +N P80R SampleB_freebayes_ann 0 0 0 P.1 +ORF1a S1188L SampleC_freebayes_ann 0 0 0 P.1 +ORF1a K1795Q SampleA_freebayes_ann 0 0 0 P.1 +ORF1a S3675K SampleB_freebayes_ann 0 0 0 P.1 +ORF1a del3676/3678 SampleC_freebayes_ann 0 0 0 P.1 +ORF1b P314L SampleA_freebayes_ann 0 0 0 P.1 +ORF1b E1264D SampleB_freebayes_ann 0 0 0 P.1 +ORF3a S253P SampleC_freebayes_ann 0 0 0 P.1 +ORF8 E92K SampleA_freebayes_ann 0 0 0 P.1 +S L18F SampleB_freebayes_ann 0 0 0 P.1 +S T20N SampleC_freebayes_ann 0 0 0 P.1 +S P26S SampleA_freebayes_ann 0 0 0 P.1 +S D138Y SampleB_freebayes_ann 0 0 0 P.1 +S R190S SampleC_freebayes_ann 0 0 0 P.1 +S K417T SampleA_freebayes_ann 0 0 0 P.1 +S E484K SampleB_freebayes_ann 0 0 0 P.1 +S H655Y SampleC_freebayes_ann 0 0 0 P.1 +S T1027I SampleA_freebayes_ann 0 0 0 P.1 +S V1176F SampleB_freebayes_ann 0 0 0 P.1 +N P80R SampleC_freebayes_ann 0 0 0 P.1 +ORF1a S1188L SampleA_freebayes_ann 0 0 0 P.1 +ORF1a K1795Q SampleB_freebayes_ann 0 0 0 P.1 +ORF1a S3675K SampleC_freebayes_ann 0 0 0 P.1 +ORF1a del3676/3678 SampleA_freebayes_ann 0 0 0 P.1 +ORF1b P314L SampleB_freebayes_ann 0 0 0 P.1 +ORF1b E1264D SampleC_freebayes_ann 0 0 0 P.1 +ORF3a S253P SampleA_freebayes_ann 0 0 0 P.1 +ORF8 E92K SampleB_freebayes_ann 0 0 0 P.1 +S L18F SampleC_freebayes_ann 0 0 0 P.1 +S T20N SampleA_freebayes_ann 0 0 0 P.1 +S P26S SampleB_freebayes_ann 0 0 0 P.1 +S D138Y SampleC_freebayes_ann 0 0 0 P.1 +S R190S SampleA_freebayes_ann 0 0 0 P.1 +S K417T SampleB_freebayes_ann 0 0 0 P.1 +S E484K SampleC_freebayes_ann 0 0 0 P.1 +S H655Y SampleA_freebayes_ann 0 0 0 P.1 +S T1027I SampleB_freebayes_ann 0 0 0 P.1 +S V1176F SampleC_freebayes_ann 0 0 0 P.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage_report.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,40 @@ +lineage sample meanAF meanAF_uniq minAF_uniq_nonzero N lineage N. rules lineage prop. +AY.1 SampleA_freebayes_ann 0.0833333333333333 0 1 31 0.032258064516129 +AY.1 SampleB_freebayes_ann 0.0833333333333333 0 1 31 0.032258064516129 +AY.1 SampleC_freebayes_ann 0.431625679248108 0 6 31 0.193548387096774 +AY.2 SampleA_freebayes_ann 0.0769230769230769 0 1 29 0.0344827586206897 +AY.2 SampleB_freebayes_ann 0.0769230769230769 0 1 29 0.0344827586206897 +AY.2 SampleC_freebayes_ann 0.331178263776345 0.119819132680874 0.159433531292828 4 29 0.137931034482759 +AY.3 SampleA_freebayes_ann 0.0909090909090909 0 1 30 0.0333333333333333 +AY.3 SampleB_freebayes_ann 0.0909090909090909 0 1 30 0.0333333333333333 +AY.3 SampleC_freebayes_ann 0.446013201889711 0 6 30 0.2 +AY.3.1 SampleA_freebayes_ann 0.0833333333333333 0 1 32 0.03125 +AY.3.1 SampleB_freebayes_ann 0.077724358974359 0.00520833333333333 0.0104166666666667 1 32 0.03125 +AY.3.1 SampleC_freebayes_ann 0.431625679248108 0 6 32 0.1875 +B.1.1.7 SampleA_freebayes_ann 0.707868155236576 0 12 21 0.571428571428571 +B.1.1.7 SampleB_freebayes_ann 0.795825304913559 0 16 21 0.761904761904762 +B.1.1.7 SampleC_freebayes_ann 0.367879297939765 0 3 21 0.142857142857143 +B.1.1.7+S_E484K SampleA_freebayes_ann 0.672474747474747 0 12 22 0.545454545454545 +B.1.1.7+S_E484K SampleB_freebayes_ann 0.757928861822438 0 16 22 0.727272727272727 +B.1.1.7+S_E484K SampleC_freebayes_ann 0.348517229627146 0 3 22 0.136363636363636 +B.1.351 SampleA_freebayes_ann 0.171368704970856 0 2 18 0.111111111111111 +B.1.351 SampleB_freebayes_ann 0.133333333333333 0 2 18 0.111111111111111 +B.1.351 SampleC_freebayes_ann 0.0908336944145888 0 1 18 0.0555555555555556 +B.1.351.2 SampleA_freebayes_ann 0.14688746140359 0 2 21 0.0952380952380952 +B.1.351.2 SampleB_freebayes_ann 0.111111111111111 0 2 21 0.0952380952380952 +B.1.351.2 SampleC_freebayes_ann 0.0756947453454907 0 1 21 0.0476190476190476 +B.1.351.3 SampleA_freebayes_ann 0.14688746140359 0 2 22 0.0909090909090909 +B.1.351.3 SampleB_freebayes_ann 0.111111111111111 0 2 22 0.0909090909090909 +B.1.351.3 SampleC_freebayes_ann 0.102681930767192 0 1 22 0.0454545454545455 +B.1.617.2 SampleA_freebayes_ann 0.111111111111111 0 1 21 0.0476190476190476 +B.1.617.2 SampleB_freebayes_ann 0.111111111111111 0 1 21 0.0476190476190476 +B.1.617.2 SampleC_freebayes_ann 0.417401700987995 0 4 21 0.19047619047619 +P.1 SampleA_freebayes_ann 0.136363636363636 0 3 22 0.136363636363636 +P.1 SampleB_freebayes_ann 0.13570487483531 0 3 22 0.136363636363636 +P.1 SampleC_freebayes_ann 0.0648812102961349 0 1 22 0.0454545454545455 +P.1.1 SampleA_freebayes_ann 0.0952380952380952 0 2 21 0.0952380952380952 +P.1.1 SampleB_freebayes_ann 0.0952380952380952 0 2 21 0.0952380952380952 +P.1.1 SampleC_freebayes_ann 0.0648812102961349 0 1 21 0.0476190476190476 +P.1.2 SampleA_freebayes_ann 0.136363636363636 0 3 22 0.136363636363636 +P.1.2 SampleB_freebayes_ann 0.13570487483531 0 3 22 0.136363636363636 +P.1.2 SampleC_freebayes_ann 0.0648812102961349 0 1 22 0.0454545454545455
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pangolin_constellations.loc Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,11 @@ +# this is a tab separated file describing the location of constellations databases used for the +# scorpio part of the pangolin SARS-CoV-2 lineage typing tool +# +# the columns are: +# value description min_scorpio_version date path +# +# min_scorpio_version is the minimum scorpio tool major version that is needed to read the constellations data +# +# for example +v0.1.12 constellations release v0.1.12 0.3.17 2023-06-28T09:48:05 ${__HERE__}/test-constellations +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-constellations/definitions/cAY.4.2.json Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,30 @@ +{ + "label": "Delta (AY.4.2-like)", + "description": "AY.4.2 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "AY.4.2" + ], + "mrca_lineage": "AY.4.2", + "lineage_name": "AY.4.2", + "parent_lineage": "AY.4", + "PHE_label": "V-21OCT-01", + "representative_genome": "" + }, + "tags": [ + "AY.4.2", + "V-21OCT-01" + ], + "sites": [ + "nuc:T17040C", + "spike:A222V", + "spike:Y145H" + ], + "rules": { + "min_alt": 2, + "max_ref": 0 + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-constellations/definitions/cAY.4.json Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,54 @@ +{ + "label": "Delta (AY.4-like)", + "description": "AY.4 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "AY.4" + ], + "mrca_lineage": "AY.4", + "lineage_name": "AY.4", + "parent_lineage": "B.1.617.2", + "incompatible_lineage_calls": [ + "AY.4.2" + ], + "representative_genome": "" + }, + "tags": [ + "AY.4" + ], + "sites": [ + "del:28271:1", + "del:22029:6", + "del:28248:6", + "orf1a:A1306S", + "orf1a:P2046L", + "orf1a:P2287S", + "orf1a:A2529V", + "nuc:C8986T", + "orf1a:V2930L", + "orf1a:T3255I", + "orf1a:T3646A", + "nuc:A11332G", + "orf1b:P314L", + "orf1b:G662S", + "orf1b:P1000L", + "orf1b:A1918V", + "nuc:C27874T", + "n:G215C", + "nuc:G29742T" + ], + "intermediate": [ + "nuc:G210T:0.961862", + "nuc:C241T:0.972018", + "nuc:T17040C:0.468120", + "spike:T95I:0.967111" + ], + "rules": { + "min_alt": 12, + "max_ref": 3, + "orf1a:A2529V": "alt" + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-constellations/definitions/cB.1.351.json Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,46 @@ +{ + "label": "Beta (B.1.351-like)", + "description": "Defining of lineage B.1.351", + "sources": [ + "https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1" + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "B.1.351" + ], + "mrca_lineage": "B.1.351", + "PHE_label": "VOC-20DEC-02", + "WHO_label": "Beta", + "representative_genome": "" + }, + "tags": [ + "B.1.351", + "VOC-20DEC-02", + "VOC202012/02", + "Beta", + "501.V2", + "20H", + "GH" + ], + "sites": [ + "NSP2:T85I", + "ORF1ab:K1655N", + "ORF1ab:K3353R", + "S:D80A", + "S:D215G", + "S:E484K", + "S:N501Y", + "S:A701V", + "ORF3a:Q57H", + "ORF3a:S171L", + "E:P71L", + "N:T205I", + "del:22280:9", + "del:11287:9" + ], + "rules": { + "min_alt": 6, + "max_ref": 3 + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-constellations/definitions/cB.1.617.2.json Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,51 @@ +{ + "label": "Delta (B.1.617.2-like)", + "description": "Defining constellation for lineage B.1.617.2", + "sources": [ + "https://github.com/cov-lineages/pango-designation/issues/49" + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "B.1.617.2", + "AY.1", + "AY.2" + ], + "mrca_lineage": "B.1.617.2", + "lineage_name": "B.1.617.2", + "incompatible_lineage_calls": [ + "AY.1", + "AY.2", + "AY.4", + "AY.4.2" + ], + "PHE_label": "VOC-21APR-02", + "WHO_label": "Delta", + "representative_genome": "" + }, + "tags": [ + "B.1.617.2", + "VOC-21APR-02", + "Delta", + "VUI-21APR-02" + ], + "sites": [ + "S:T19R", + "S:G142D", + "S:L452R", + "S:T478K", + "S:P681R", + "S:D950N", + "ORF3a:S26L", + "M:I82T", + "ORF7a:V82A", + "ORF7a:T120I", + "N:D63G", + "N:R203M", + "N:D377Y" + ], + "rules": { + "min_alt": 5, + "max_ref": 3 + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-constellations/definitions/cP.1.json Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,45 @@ +{ + "label": "Gamma (P.1-like)", + "description": "Defining constellation for lineage P.1", + "sources": [ + "https://virological.org/t/586", + "https://cov-lineages.org/global_report_P.1.html" + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "P.1" + ], + "mrca_lineage": "P.1", + "PHE_label": "VOC-21JAN-02", + "WHO_label": "Gamma", + "representative_genome": "" + }, + "tags": [ + "P.1", + "VOC-21JAN-02", + "VOC202101/02" + ], + "sites": [ + "nuc:T733C", + "nuc:C2749T", + "ORF1ab:S1188L", + "ORF1ab:K1795Q", + "del:11287:9", + "nuc:C12778T", + "nuc:C13860T", + "S:T20N", + "S:P26S", + "S:K417T", + "S:E484K", + "S:N501Y", + "S:T1027I", + "ORF8:E92K", + "nuc:28262+AACA", + "N:P80R" + ], + "rules": { + "min_alt": 8, + "max_ref": 3 + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants_table.txt Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,1829 @@ +CHROM POS ID REF ALT DP AD_ref AD_alt Gene_Name Nt_alt AA_alt AF codon_num sample +NC_045512.2 328 NC_045512.2;328;ACA;ACCA ACA ACCA 36 34 1 ORF1a 64dupC Q22fs 0.0277777777777778 21 SampleA_freebayes_ann +NC_045512.2 355 NC_045512.2;355;C;T C T 42 41 1 ORF1a 90C>T G30G 0.0238095238095238 30 SampleA_freebayes_ann +NC_045512.2 366 NC_045512.2;366;C;T C T 42 28 14 ORF1a 101C>T S34F 0.333333333333333 34 SampleA_freebayes_ann +NC_045512.2 401 NC_045512.2;401;CTTAA;CTAA CTTAA CTAA 37 35 2 ORF1a 138delT D48fs 0.0540540540540541 46 SampleA_freebayes_ann +NC_045512.2 406 NC_045512.2;406;AGA;AA AGA AA 35 34 1 ORF1a 142delG D48fs 0.0285714285714286 47 SampleA_freebayes_ann +NC_045512.2 421 NC_045512.2;421;C;A C A 35 34 1 ORF1a 156C>A G52G 0.0285714285714286 52 SampleA_freebayes_ann +NC_045512.2 442 NC_045512.2;442;C;G C G 64 63 1 ORF1a 177C>G G59G 0.015625 59 SampleA_freebayes_ann +NC_045512.2 445 NC_045512.2;445;T;C T C 64 33 31 ORF1a 180T>C V60V 0.484375 60 SampleA_freebayes_ann +NC_045512.2 460 NC_045512.2;460;A;C A C 64 63 1 ORF1a 195A>C E65D 0.015625 65 SampleA_freebayes_ann +NC_045512.2 505 NC_045512.2;505;T;A T A 64 63 1 ORF1a 240T>A P80P 0.015625 80 SampleA_freebayes_ann +NC_045512.2 541 NC_045512.2;541;CGA;CA CGA CA 64 62 2 ORF1a 277delG E93fs 0.03125 92 SampleA_freebayes_ann +NC_045512.2 560 NC_045512.2;560;C;T C T 64 62 2 ORF1a 295C>T R99C 0.03125 99 SampleA_freebayes_ann +NC_045512.2 577 NC_045512.2;577;T;G T G 64 63 1 ORF1a 312T>G L104L 0.015625 104 SampleA_freebayes_ann +NC_045512.2 578 NC_045512.2;578;G;A G A 64 63 1 ORF1a 313G>A G105S 0.015625 105 SampleA_freebayes_ann +NC_045512.2 583 NC_045512.2;583;CC;TT CC TT 64 30 6 ORF1a 318_319delCCinsTT L107F 0.09375 106 SampleA_freebayes_ann +NC_045512.2 583 NC_045512.2;583;CC;TC CC TC 64 30 28 ORF1a 318_319delCCinsTT L107F 0.4375 106 SampleA_freebayes_ann +NC_045512.2 593 NC_045512.2;593;C;T C T 64 36 28 ORF1a 328C>T H110Y 0.4375 110 SampleA_freebayes_ann +NC_045512.2 643 NC_045512.2;643;C;T C T 39 25 14 ORF1a 378C>T N126N 0.358974358974359 126 SampleA_freebayes_ann +NC_045512.2 657 NC_045512.2;657;C;T C T 50 36 14 ORF1a 392C>T A131V 0.28 131 SampleA_freebayes_ann +NC_045512.2 663 NC_045512.2;663;G;C G C 52 51 1 ORF1a 398G>C G133A 0.0192307692307692 133 SampleA_freebayes_ann +NC_045512.2 666 NC_045512.2;666;A;T A T 52 51 1 ORF1a 401A>T H134L 0.0192307692307692 134 SampleA_freebayes_ann +NC_045512.2 682 NC_045512.2;682;T;C T C 52 34 18 ORF1a 417T>C D139D 0.346153846153846 139 SampleA_freebayes_ann +NC_045512.2 721 NC_045512.2;721;T;G T G 48 46 2 ORF1a 456T>G D152E 0.0416666666666667 152 SampleA_freebayes_ann +NC_045512.2 724 NC_045512.2;724;T;G T G 42 41 1 ORF1a 459T>G P153P 0.0238095238095238 153 SampleA_freebayes_ann +NC_045512.2 725 NC_045512.2;725;T;G T G 38 37 1 ORF1a 460T>G Y154D 0.0263157894736842 154 SampleA_freebayes_ann +NC_045512.2 729 NC_045512.2;729;A;G A G 37 36 1 ORF1a 464A>G E155G 0.027027027027027 155 SampleA_freebayes_ann +NC_045512.2 737 NC_045512.2;737;C;A C A 38 37 1 ORF1a 472C>A Q158K 0.0263157894736842 158 SampleA_freebayes_ann +NC_045512.2 913 NC_045512.2;913;C;T C T 38 12 26 ORF1a 648C>T S216S 0.68421052631579 216 SampleA_freebayes_ann +NC_045512.2 924 NC_045512.2;924;A;T A T 38 37 1 ORF1a 659A>T D220V 0.0263157894736842 220 SampleA_freebayes_ann +NC_045512.2 929 NC_045512.2;929;A;T A T 38 37 1 ORF1a 664A>T I222F 0.0263157894736842 222 SampleA_freebayes_ann +NC_045512.2 932 NC_045512.2;932;G;T G T 38 37 1 ORF1a 667G>T D223Y 0.0263157894736842 223 SampleA_freebayes_ann +NC_045512.2 946 NC_045512.2;946;T;G T G 48 47 1 ORF1a 681T>G G227G 0.0208333333333333 227 SampleA_freebayes_ann +NC_045512.2 949 NC_045512.2;949;A;G A G 53 52 1 ORF1a 684A>G V228V 0.0188679245283019 228 SampleA_freebayes_ann +NC_045512.2 954 NC_045512.2;954;G;T G T 53 52 1 ORF1a 689G>T C230F 0.0188679245283019 230 SampleA_freebayes_ann +NC_045512.2 968 NC_045512.2;968;G;T G T 51 50 1 ORF1a 703G>T E235* 0.0196078431372549 235 SampleA_freebayes_ann +NC_045512.2 973 NC_045512.2;973;T;A T A 51 50 1 ORF1a 708T>A H236Q 0.0196078431372549 236 SampleA_freebayes_ann +NC_045512.2 998 NC_045512.2;998;T;C T C 51 50 1 ORF1a 733T>C S245P 0.0196078431372549 245 SampleA_freebayes_ann +NC_045512.2 1019 NC_045512.2;1019;C;T C T 51 50 1 ORF1a 754C>T Q252* 0.0196078431372549 252 SampleA_freebayes_ann +NC_045512.2 1026 NC_045512.2;1026;C;T C T 49 48 1 ORF1a 761C>T P254L 0.0204081632653061 254 SampleA_freebayes_ann +NC_045512.2 1044 NC_045512.2;1044;C;T C T 65 56 9 ORF1a 779C>T A260V 0.138461538461538 260 SampleA_freebayes_ann +NC_045512.2 1069 NC_045512.2;1069;G;A G A 65 57 8 ORF1a 804G>A G268G 0.123076923076923 268 SampleA_freebayes_ann +NC_045512.2 1076 NC_045512.2;1076;C;T C T 65 56 9 ORF1a 811C>T P271S 0.138461538461538 271 SampleA_freebayes_ann +NC_045512.2 1126 NC_045512.2;1126;G;T G T 65 64 1 ORF1a 861G>T R287S 0.0153846153846154 287 SampleA_freebayes_ann +NC_045512.2 1142 NC_045512.2;1142;C;G C G 65 64 1 ORF1a 877C>G L293V 0.0153846153846154 293 SampleA_freebayes_ann +NC_045512.2 1153 NC_045512.2;1153;T;C T C 65 63 2 ORF1a 888T>C F296F 0.0307692307692308 296 SampleA_freebayes_ann +NC_045512.2 1193 NC_045512.2;1193;A;T A T 65 64 1 ORF1a 928A>T N310Y 0.0153846153846154 310 SampleA_freebayes_ann +NC_045512.2 1205 NC_045512.2;1205;C;T C T 65 56 9 ORF1a 940C>T Q314* 0.138461538461538 314 SampleA_freebayes_ann +NC_045512.2 1213 NC_045512.2;1213;C;T C T 65 56 9 ORF1a 948C>T C316C 0.138461538461538 316 SampleA_freebayes_ann +NC_045512.2 1222 NC_045512.2;1222;T;C T C 65 64 1 ORF1a 957T>C T319T 0.0153846153846154 319 SampleA_freebayes_ann +NC_045512.2 1224 NC_045512.2;1224;T;C T C 65 64 1 ORF1a 959T>C L320P 0.0153846153846154 320 SampleA_freebayes_ann +NC_045512.2 1254 NC_045512.2;1254;C;T C T 41 36 5 ORF1a 989C>T S330L 0.121951219512195 330 SampleA_freebayes_ann +NC_045512.2 1288 NC_045512.2;1288;C;T C T 41 36 5 ORF1a 1023C>T C341C 0.121951219512195 341 SampleA_freebayes_ann +NC_045512.2 1292 NC_045512.2;1292;T;C T C 41 34 7 ORF1a 1027T>C F343L 0.170731707317073 343 SampleA_freebayes_ann +NC_045512.2 1314 NC_045512.2;1314;C;T C T 42 37 5 ORF1a 1049C>T T350I 0.119047619047619 350 SampleA_freebayes_ann +NC_045512.2 1336 NC_045512.2;1336;T;G T G 27 26 1 ORF1a 1071T>G C357W 0.037037037037037 357 SampleA_freebayes_ann +NC_045512.2 1406 NC_045512.2;1406;G;T G T 18 16 2 ORF1a 1141G>T E381* 0.111111111111111 381 SampleA_freebayes_ann +NC_045512.2 1441 NC_045512.2;1441;C;T C T 18 3 15 ORF1a 1176C>T G392G 0.833333333333333 392 SampleA_freebayes_ann +NC_045512.2 1456 NC_045512.2;1456;T;C T C 18 17 1 ORF1a 1191T>C L397L 0.0555555555555556 397 SampleA_freebayes_ann +NC_045512.2 1534 NC_045512.2;1534;G;T G T 18 16 2 ORF1a 1269G>T W423C 0.111111111111111 423 SampleA_freebayes_ann +NC_045512.2 1580 NC_045512.2;1580;GTTGG;GTTTGG GTTGG GTTTGG 14 13 1 ORF1a 1317dupT G440fs 0.0714285714285714 439 SampleA_freebayes_ann +NC_045512.2 1601 NC_045512.2;1601;C;T C T 14 13 1 ORF1a 1336C>T L446F 0.0714285714285714 446 SampleA_freebayes_ann +NC_045512.2 1609 NC_045512.2;1609;C;T C T 14 13 1 ORF1a 1344C>T D448D 0.0714285714285714 448 SampleA_freebayes_ann +NC_045512.2 1684 NC_045512.2;1684;C;T C T 10 8 2 ORF1a 1419C>T I473I 0.2 473 SampleA_freebayes_ann +NC_045512.2 1759 NC_045512.2;1759;A;T A T 10 8 2 ORF1a 1494A>T A498A 0.2 498 SampleA_freebayes_ann +NC_045512.2 1841 NC_045512.2;1841;C;T C T 10 8 2 ORF1a 1576C>T Q526* 0.2 526 SampleA_freebayes_ann +NC_045512.2 1883 NC_045512.2;1883;G;A G A 13 12 1 ORF1a 1618G>A A540T 0.0769230769230769 540 SampleA_freebayes_ann +NC_045512.2 1902 NC_045512.2;1902;C;T C T 13 12 1 ORF1a 1637C>T S546L 0.0769230769230769 546 SampleA_freebayes_ann +NC_045512.2 1943 NC_045512.2;1943;C;T C T 13 12 1 ORF1a 1678C>T R560C 0.0769230769230769 560 SampleA_freebayes_ann +NC_045512.2 2134 NC_045512.2;2134;A;C A C 15 14 1 ORF1a 1869A>C K623N 0.0666666666666667 623 SampleA_freebayes_ann +NC_045512.2 2166 NC_045512.2;2166;A;C A C 15 14 1 ORF1a 1901A>C K634T 0.0666666666666667 634 SampleA_freebayes_ann +NC_045512.2 2659 NC_045512.2;2659;G;T G T 15 9 6 ORF1a 2394G>T K798N 0.4 798 SampleA_freebayes_ann +NC_045512.2 2714 NC_045512.2;2714;G;C G C 15 13 2 ORF1a 2449G>C G817R 0.133333333333333 817 SampleA_freebayes_ann +NC_045512.2 2719 NC_045512.2;2719;TGC;TC TGC TC 15 6 9 ORF1a 2455delG A819fs 0.6 818 SampleA_freebayes_ann +NC_045512.2 2811 NC_045512.2;2811;T;C T C 7 6 1 ORF1a 2546T>C I849T 0.142857142857143 849 SampleA_freebayes_ann +NC_045512.2 2828 NC_045512.2;2828;G;T G T 15 14 1 ORF1a 2563G>T E855* 0.0666666666666667 855 SampleA_freebayes_ann +NC_045512.2 2873 NC_045512.2;2873;G;T G T 19 18 1 ORF1a 2608G>T E870* 0.0526315789473684 870 SampleA_freebayes_ann +NC_045512.2 2891 NC_045512.2;2891;GCA;GCCA GCA GCCA 19 18 1 ORF1a 2627dupC D877fs 0.0526315789473684 876 SampleA_freebayes_ann +NC_045512.2 2942 NC_045512.2;2942;C;T C T 22 20 2 ORF1a 2677C>T L893L 0.0909090909090909 893 SampleA_freebayes_ann +NC_045512.2 3037 NC_045512.2;3037;C;T C T 22 0 22 ORF1a 2772C>T F924F 1 924 SampleA_freebayes_ann +NC_045512.2 3061 NC_045512.2;3061;A;G A G 22 21 1 ORF1a 2796A>G E932E 0.0454545454545455 932 SampleA_freebayes_ann +NC_045512.2 3073 NC_045512.2;3073;TGAAGAAGAAGAGT;TGAAGAAGAGT TGAAGAAGAAGAGT TGAAGAAGAGT 22 20 2 ORF1a 2817_2819delAGA E940del 0.0909090909090909 936 SampleA_freebayes_ann +NC_045512.2 3105 NC_045512.2;3105;A;G A G 22 20 2 ORF1a 2840A>G Y947C 0.0909090909090909 947 SampleA_freebayes_ann +NC_045512.2 3110 NC_045512.2;3110;T;C T C 22 21 1 ORF1a 2845T>C Y949H 0.0454545454545455 949 SampleA_freebayes_ann +NC_045512.2 3113 NC_045512.2;3113;G;T G T 22 20 2 ORF1a 2848G>T G950C 0.0909090909090909 950 SampleA_freebayes_ann +NC_045512.2 3118 NC_045512.2;3118;T;A T A 22 20 2 ORF1a 2853T>A T951T 0.0909090909090909 951 SampleA_freebayes_ann +NC_045512.2 3244 NC_045512.2;3244;C;A C A 35 33 2 ORF1a 2979C>A G993G 0.0571428571428571 993 SampleA_freebayes_ann +NC_045512.2 3267 NC_045512.2;3267;C;T C T 35 0 35 ORF1a 3002C>T T1001I 1 1001 SampleA_freebayes_ann +NC_045512.2 3462 NC_045512.2;3462;A;C A C 26 25 1 ORF1a 3197A>C K1066T 0.0384615384615385 1066 SampleA_freebayes_ann +NC_045512.2 3464 NC_045512.2;3464;C;A C A 28 27 1 ORF1a 3199C>A H1067N 0.0357142857142857 1067 SampleA_freebayes_ann +NC_045512.2 3465 NC_045512.2;3465;A;C A C 28 26 2 ORF1a 3200A>C H1067P 0.0714285714285714 1067 SampleA_freebayes_ann +NC_045512.2 3528 NC_045512.2;3528;A;T A T 32 31 1 ORF1a 3263A>T D1088V 0.03125 1088 SampleA_freebayes_ann +NC_045512.2 3529 NC_045512.2;3529;T;G T G 31 29 2 ORF1a 3264T>G D1088E 0.0645161290322581 1088 SampleA_freebayes_ann +NC_045512.2 3562 NC_045512.2;3562;G;T G T 32 30 2 ORF1a 3297G>T V1099V 0.0625 1099 SampleA_freebayes_ann +NC_045512.2 3647 NC_045512.2;3647;ATTCA;ATCA ATTCA ATCA 32 30 2 ORF1a 3384delT Q1129fs 0.0625 1128 SampleA_freebayes_ann +NC_045512.2 3728 NC_045512.2;3728;G;T G T 32 31 1 ORF1a 3463G>T G1155C 0.03125 1155 SampleA_freebayes_ann +NC_045512.2 4060 NC_045512.2;4060;A;C A C 30 29 1 ORF1a 3795A>C P1265P 0.0333333333333333 1265 SampleA_freebayes_ann +NC_045512.2 4126 NC_045512.2;4126;G;T G T 55 53 2 ORF1a 3861G>T V1287V 0.0363636363636364 1287 SampleA_freebayes_ann +NC_045512.2 4142 NC_045512.2;4142;G;A G A 59 58 1 ORF1a 3877G>A E1293K 0.0169491525423729 1293 SampleA_freebayes_ann +NC_045512.2 4163 NC_045512.2;4163;G;T G T 58 57 1 ORF1a 3898G>T V1300F 0.0172413793103448 1300 SampleA_freebayes_ann +NC_045512.2 4304 NC_045512.2;4304;A;T A T 60 59 1 ORF1a 4039A>T K1347* 0.0166666666666667 1347 SampleA_freebayes_ann +NC_045512.2 4391 NC_045512.2;4391;C;T C T 37 36 1 ORF1a 4126C>T R1376* 0.027027027027027 1376 SampleA_freebayes_ann +NC_045512.2 4397 NC_045512.2;4397;A;G A G 37 36 1 ORF1a 4132A>G M1378V 0.027027027027027 1378 SampleA_freebayes_ann +NC_045512.2 4404 NC_045512.2;4404;C;A C A 37 36 1 ORF1a 4139C>A A1380E 0.027027027027027 1380 SampleA_freebayes_ann +NC_045512.2 4751 NC_045512.2;4751;A;C A C 30 28 2 ORF1a 4486A>C T1496P 0.0666666666666667 1496 SampleA_freebayes_ann +NC_045512.2 4850 NC_045512.2;4850;A;C A C 30 28 2 ORF1a 4585A>C K1529Q 0.0666666666666667 1529 SampleA_freebayes_ann +NC_045512.2 4890 NC_045512.2;4890;C;A C A 30 28 2 ORF1a 4625C>A T1542N 0.0666666666666667 1542 SampleA_freebayes_ann +NC_045512.2 5014 NC_045512.2;5014;T;G T G 19 18 1 ORF1a 4749T>G V1583V 0.0526315789473684 1583 SampleA_freebayes_ann +NC_045512.2 5016 NC_045512.2;5016;T;G T G 17 16 1 ORF1a 4751T>G V1584G 0.0588235294117647 1584 SampleA_freebayes_ann +NC_045512.2 5037 NC_045512.2;5037;G;A G A 14 10 4 ORF1a 4772G>A G1591E 0.285714285714286 1591 SampleA_freebayes_ann +NC_045512.2 5172 NC_045512.2;5172;A;G A G 14 13 1 ORF1a 4907A>G H1636R 0.0714285714285714 1636 SampleA_freebayes_ann +NC_045512.2 5267 NC_045512.2;5267;A;T A T 25 24 1 ORF1a 5002A>T K1668* 0.04 1668 SampleA_freebayes_ann +NC_045512.2 5289 NC_045512.2;5289;A;T A T 29 28 1 ORF1a 5024A>T Y1675F 0.0344827586206897 1675 SampleA_freebayes_ann +NC_045512.2 5360 NC_045512.2;5360;T;C T C 44 42 2 ORF1a 5095T>C Y1699H 0.0454545454545455 1699 SampleA_freebayes_ann +NC_045512.2 5367 NC_045512.2;5367;G;T G T 44 42 2 ORF1a 5102G>T R1701I 0.0454545454545455 1701 SampleA_freebayes_ann +NC_045512.2 5368 NC_045512.2;5368;A;G A G 44 43 1 ORF1a 5103A>G R1701R 0.0227272727272727 1701 SampleA_freebayes_ann +NC_045512.2 5376 NC_045512.2;5376;C;A C A 44 42 2 ORF1a 5111C>A A1704D 0.0454545454545455 1704 SampleA_freebayes_ann +NC_045512.2 5388 NC_045512.2;5388;C;A C A 44 12 32 ORF1a 5123C>A A1708D 0.727272727272727 1708 SampleA_freebayes_ann +NC_045512.2 5489 NC_045512.2;5489;G;T G T 44 42 2 ORF1a 5224G>T D1742Y 0.0454545454545455 1742 SampleA_freebayes_ann +NC_045512.2 5523 NC_045512.2;5523;A;C A C 44 43 1 ORF1a 5258A>C K1753T 0.0227272727272727 1753 SampleA_freebayes_ann +NC_045512.2 5544 NC_045512.2;5544;C;A C A 44 43 1 ORF1a 5279C>A T1760K 0.0227272727272727 1760 SampleA_freebayes_ann +NC_045512.2 5546 NC_045512.2;5546;A;C A C 44 43 1 ORF1a 5281A>C T1761P 0.0227272727272727 1761 SampleA_freebayes_ann +NC_045512.2 5553 NC_045512.2;5553;A;C A C 44 43 1 ORF1a 5288A>C K1763T 0.0227272727272727 1763 SampleA_freebayes_ann +NC_045512.2 5641 NC_045512.2;5641;A;G A G 31 30 1 ORF1a 5376A>G Q1792Q 0.032258064516129 1792 SampleA_freebayes_ann +NC_045512.2 5824 NC_045512.2;5824;T;G T G 23 22 1 ORF1a 5559T>G L1853L 0.0434782608695652 1853 SampleA_freebayes_ann +NC_045512.2 5852 NC_045512.2;5852;ATTAC;ATAC ATTAC ATAC 23 20 2 ORF1a 5589delT T1864fs 0.0869565217391304 1863 SampleA_freebayes_ann +NC_045512.2 5852 NC_045512.2;5852;ATTAC;ACTAC ATTAC ACTAC 23 20 1 ORF1a 5589delT T1864fs 0.0434782608695652 1863 SampleA_freebayes_ann +NC_045512.2 5869 NC_045512.2;5869;C;A C A 18 17 1 ORF1a 5604C>A Y1868* 0.0555555555555556 1868 SampleA_freebayes_ann +NC_045512.2 5952 NC_045512.2;5952;T;G T G 21 20 1 ORF1a 5687T>G L1896W 0.0476190476190476 1896 SampleA_freebayes_ann +NC_045512.2 5986 NC_045512.2;5986;C;T C T 19 0 19 ORF1a 5721C>T F1907F 1 1907 SampleA_freebayes_ann +NC_045512.2 6193 NC_045512.2;6193;A;G A G 30 29 1 ORF1a 5928A>G T1976T 0.0333333333333333 1976 SampleA_freebayes_ann +NC_045512.2 6241 NC_045512.2;6241;G;T G T 30 29 1 ORF1a 5976G>T W1992C 0.0333333333333333 1992 SampleA_freebayes_ann +NC_045512.2 6250 NC_045512.2;6250;C;A C A 48 47 1 ORF1a 5985C>A N1995K 0.0208333333333333 1995 SampleA_freebayes_ann +NC_045512.2 6279 NC_045512.2;6279;C;T C T 42 40 2 ORF1a 6014C>T P2005L 0.0476190476190476 2005 SampleA_freebayes_ann +NC_045512.2 6280 NC_045512.2;6280;A;G A G 42 40 2 ORF1a 6015A>G P2005P 0.0476190476190476 2005 SampleA_freebayes_ann +NC_045512.2 6359 NC_045512.2;6359;G;T G T 42 41 1 ORF1a 6094G>T D2032Y 0.0238095238095238 2032 SampleA_freebayes_ann +NC_045512.2 6433 NC_045512.2;6433;C;T C T 42 40 2 ORF1a 6168C>T T2056T 0.0476190476190476 2056 SampleA_freebayes_ann +NC_045512.2 6439 NC_045512.2;6439;G;T G T 42 41 1 ORF1a 6174G>T Q2058H 0.0238095238095238 2058 SampleA_freebayes_ann +NC_045512.2 6447 NC_045512.2;6447;T;G T G 42 41 1 ORF1a 6182T>G V2061G 0.0238095238095238 2061 SampleA_freebayes_ann +NC_045512.2 6455 NC_045512.2;6455;T;G T G 42 41 1 ORF1a 6190T>G C2064G 0.0238095238095238 2064 SampleA_freebayes_ann +NC_045512.2 6593 NC_045512.2;6593;C;A C A 42 41 1 ORF1a 6328C>A P2110T 0.0238095238095238 2110 SampleA_freebayes_ann +NC_045512.2 6643 NC_045512.2;6643;T;C T C 42 41 1 ORF1a 6378T>C G2126G 0.0238095238095238 2126 SampleA_freebayes_ann +NC_045512.2 6722 NC_045512.2;6722;A;C A C 42 40 1 ORF1a 6457A>C T2153P 0.0238095238095238 2153 SampleA_freebayes_ann +NC_045512.2 6722 NC_045512.2;6722;A;T A T 42 40 1 ORF1a 6457A>C T2153P 0.0238095238095238 2153 SampleA_freebayes_ann +NC_045512.2 6742 NC_045512.2;6742;G;A G A 42 41 1 ORF1a 6477G>A R2159R 0.0238095238095238 2159 SampleA_freebayes_ann +NC_045512.2 6744 NC_045512.2;6744;GTTTA;ATTTT GTTTA ATTTT 42 41 1 ORF1a 6479_6483delGTTTAinsATTTT CL2160YF 0.0238095238095238 2160 SampleA_freebayes_ann +NC_045512.2 6762 NC_045512.2;6762;C;A C A 42 41 1 ORF1a 6497C>A T2166N 0.0238095238095238 2166 SampleA_freebayes_ann +NC_045512.2 6828 NC_045512.2;6828;C;T C T 22 21 1 ORF1a 6563C>T S2188F 0.0454545454545455 2188 SampleA_freebayes_ann +NC_045512.2 6839 NC_045512.2;6839;G;T G T 22 21 1 ORF1a 6574G>T A2192S 0.0454545454545455 2192 SampleA_freebayes_ann +NC_045512.2 7975 NC_045512.2;7975;G;A G A 14 13 1 ORF1a 7710G>A L2570L 0.0714285714285714 2570 SampleA_freebayes_ann +NC_045512.2 8252 NC_045512.2;8252;A;C A C 16 15 1 ORF1a 7987A>C I2663L 0.0625 2663 SampleA_freebayes_ann +NC_045512.2 8254 NC_045512.2;8254;AGA;AA AGA AA 16 15 1 ORF1a 7990delG E2664fs 0.0625 2663 SampleA_freebayes_ann +NC_045512.2 8335 NC_045512.2;8335;T;G T G 16 15 1 ORF1a 8070T>G A2690A 0.0625 2690 SampleA_freebayes_ann +NC_045512.2 8339 NC_045512.2;8339;A;T A T 13 12 1 ORF1a 8074A>T I2692F 0.0769230769230769 2692 SampleA_freebayes_ann +NC_045512.2 8340 NC_045512.2;8340;T;G T G 12 11 1 ORF1a 8075T>G I2692S 0.0833333333333333 2692 SampleA_freebayes_ann +NC_045512.2 8375 NC_045512.2;8375;G;T G T 11 9 2 ORF1a 8110G>T A2704S 0.181818181818182 2704 SampleA_freebayes_ann +NC_045512.2 8480 NC_045512.2;8480;C;T C T 11 9 2 ORF1a 8215C>T P2739S 0.181818181818182 2739 SampleA_freebayes_ann +NC_045512.2 8656 NC_045512.2;8656;T;C T C 6 5 1 ORF1a 8391T>C S2797S 0.166666666666667 2797 SampleA_freebayes_ann +NC_045512.2 8891 NC_045512.2;8891;A;C A C 12 11 1 ORF1a 8626A>C T2876P 0.0833333333333333 2876 SampleA_freebayes_ann +NC_045512.2 8897 NC_045512.2;8897;A;T A T 18 17 1 ORF1a 8632A>T N2878Y 0.0555555555555556 2878 SampleA_freebayes_ann +NC_045512.2 8966 NC_045512.2;8966;A;G A G 22 21 1 ORF1a 8701A>G K2901E 0.0454545454545455 2901 SampleA_freebayes_ann +NC_045512.2 8975 NC_045512.2;8975;G;T G T 36 34 2 ORF1a 8710G>T E2904* 0.0555555555555556 2904 SampleA_freebayes_ann +NC_045512.2 8991 NC_045512.2;8991;C;A C A 36 35 1 ORF1a 8726C>A A2909E 0.0277777777777778 2909 SampleA_freebayes_ann +NC_045512.2 9041 NC_045512.2;9041;T;C T C 36 35 1 ORF1a 8776T>C S2926P 0.0277777777777778 2926 SampleA_freebayes_ann +NC_045512.2 9049 NC_045512.2;9049;G;T G T 36 35 1 ORF1a 8784G>T K2928N 0.0277777777777778 2928 SampleA_freebayes_ann +NC_045512.2 9123 NC_045512.2;9123;G;C G C 36 34 2 ORF1a 8858G>C R2953P 0.0555555555555556 2953 SampleA_freebayes_ann +NC_045512.2 9269 NC_045512.2;9269;G;T G T 12 11 1 ORF1a 9004G>T G3002C 0.0833333333333333 3002 SampleA_freebayes_ann +NC_045512.2 10040 NC_045512.2;10040;T;C T C 10 9 1 ORF1a 9775T>C S3259P 0.1 3259 SampleA_freebayes_ann +NC_045512.2 10168 NC_045512.2;10168;T;G T G 60 59 1 ORF1a 9903T>G C3301W 0.0166666666666667 3301 SampleA_freebayes_ann +NC_045512.2 10169 NC_045512.2;10169;CCAAG;CG CCAAG CG 55 50 2 ORF1a 9905C>T P3302L 0.0363636363636364 3302 SampleA_freebayes_ann +NC_045512.2 10169 NC_045512.2;10169;CCAAG;CTAAG CCAAG CTAAG 55 50 1 ORF1a 9905C>T P3302L 0.0181818181818182 3302 SampleA_freebayes_ann +NC_045512.2 10169 NC_045512.2;10169;CCAAG;CCGAG CCAAG CCGAG 55 50 2 ORF1a 9905C>T P3302L 0.0363636363636364 3302 SampleA_freebayes_ann +NC_045512.2 10282 NC_045512.2;10282;G;T G T 55 54 1 ORF1a 10017G>T R3339S 0.0181818181818182 3339 SampleA_freebayes_ann +NC_045512.2 10300 NC_045512.2;10300;GCAA;TCAC GCAA TCAC 55 54 1 ORF1a 10035_10038delGCAAinsTCAC MQ3345IH 0.0181818181818182 3345 SampleA_freebayes_ann +NC_045512.2 10314 NC_045512.2;10314;T;A T A 55 53 2 ORF1a 10049T>A L3350H 0.0363636363636364 3350 SampleA_freebayes_ann +NC_045512.2 10323 NC_045512.2;10323;A;C A C 55 54 1 ORF1a 10058A>C K3353T 0.0181818181818182 3353 SampleA_freebayes_ann +NC_045512.2 10335 NC_045512.2;10335;C;A C A 55 54 1 ORF1a 10070C>A A3357D 0.0181818181818182 3357 SampleA_freebayes_ann +NC_045512.2 10344 NC_045512.2;10344;A;C A C 55 54 1 ORF1a 10079A>C K3360T 0.0181818181818182 3360 SampleA_freebayes_ann +NC_045512.2 10352 NC_045512.2;10352;A;C A C 55 54 1 ORF1a 10087A>C K3363Q 0.0181818181818182 3363 SampleA_freebayes_ann +NC_045512.2 10355 NC_045512.2;10355;T;C T C 55 54 1 ORF1a 10090T>C Y3364H 0.0181818181818182 3364 SampleA_freebayes_ann +NC_045512.2 10358 NC_045512.2;10358;AA;TC AA TC 55 54 1 ORF1a 10093_10094delAAinsTC K3365S 0.0181818181818182 3365 SampleA_freebayes_ann +NC_045512.2 10364 NC_045512.2;10364;G;T G T 65 64 1 ORF1a 10099G>T V3367F 0.0153846153846154 3367 SampleA_freebayes_ann +NC_045512.2 10377 NC_045512.2;10377;C;A C A 59 58 1 ORF1a 10112C>A P3371Q 0.0169491525423729 3371 SampleA_freebayes_ann +NC_045512.2 10454 NC_045512.2;10454;T;G T G 38 37 1 ORF1a 10189T>G F3397V 0.0263157894736842 3397 SampleA_freebayes_ann +NC_045512.2 10548 NC_045512.2;10548;T;G T G 28 27 1 ORF1a 10283T>G M3428R 0.0357142857142857 3428 SampleA_freebayes_ann +NC_045512.2 10602 NC_045512.2;10602;G;T G T 28 27 1 ORF1a 10337G>T G3446V 0.0357142857142857 3446 SampleA_freebayes_ann +NC_045512.2 10649 NC_045512.2;10649;A;C A C 27 26 1 ORF1a 10384A>C T3462P 0.037037037037037 3462 SampleA_freebayes_ann +NC_045512.2 10672 NC_045512.2;10672;T;G T G 17 16 1 ORF1a 10407T>G A3469A 0.0588235294117647 3469 SampleA_freebayes_ann +NC_045512.2 10725 NC_045512.2;10725;C;A C A 20 19 1 ORF1a 10460C>A T3487N 0.05 3487 SampleA_freebayes_ann +NC_045512.2 10735 NC_045512.2;10735;T;C T C 20 19 1 ORF1a 10470T>C L3490L 0.05 3490 SampleA_freebayes_ann +NC_045512.2 11001 NC_045512.2;11001;C;A C A 23 22 1 ORF1a 10736C>A T3579K 0.0434782608695652 3579 SampleA_freebayes_ann +NC_045512.2 11002 NC_045512.2;11002;A;C A C 25 23 2 ORF1a 10737A>C T3579T 0.08 3579 SampleA_freebayes_ann +NC_045512.2 11030 NC_045512.2;11030;A;T A T 31 30 1 ORF1a 10765A>T T3589S 0.032258064516129 3589 SampleA_freebayes_ann +NC_045512.2 11035 NC_045512.2;11035;A;T A T 31 30 1 ORF1a 10770A>T S3590S 0.032258064516129 3590 SampleA_freebayes_ann +NC_045512.2 11038 NC_045512.2;11038;T;A T A 31 30 1 ORF1a 10773T>A L3591L 0.032258064516129 3591 SampleA_freebayes_ann +NC_045512.2 11047 NC_045512.2;11047;A;C A C 31 30 1 ORF1a 10782A>C L3594F 0.032258064516129 3594 SampleA_freebayes_ann +NC_045512.2 11074 NC_045512.2;11074;CTTTTTTTTGTATGA;CTTTTTTTGTATGA CTTTTTTTTGTATGA CTTTTTTTGTATGA 29 22 1 ORF1a 10817delT L3606fs 0.0344827586206897 3603 SampleA_freebayes_ann +NC_045512.2 11074 NC_045512.2;11074;CTTTTTTTTGTATGA;CTTTTTTTTTTATGA CTTTTTTTTGTATGA CTTTTTTTTTTATGA 29 22 6 ORF1a 10817delT L3606fs 0.206896551724138 3603 SampleA_freebayes_ann +NC_045512.2 11094 NC_045512.2;11094;C;G C G 50 49 1 ORF1a 10829C>G A3610G 0.02 3610 SampleA_freebayes_ann +NC_045512.2 11127 NC_045512.2;11127;T;G T G 53 52 1 ORF1a 10862T>G M3621R 0.0188679245283019 3621 SampleA_freebayes_ann +NC_045512.2 11148 NC_045512.2;11148;T;C T C 53 52 1 ORF1a 10883T>C F3628S 0.0188679245283019 3628 SampleA_freebayes_ann +NC_045512.2 11152 NC_045512.2;11152;CAAACAT;CAACAT CAAACAT CAACAT 53 51 2 ORF1a 10890delA K3630fs 0.0377358490566038 3629 SampleA_freebayes_ann +NC_045512.2 11208 NC_045512.2;11208;C;A C A 53 52 1 ORF1a 10943C>A A3648D 0.0188679245283019 3648 SampleA_freebayes_ann +NC_045512.2 11234 NC_045512.2;11234;G;A G A 53 52 1 ORF1a 10969G>A A3657T 0.0188679245283019 3657 SampleA_freebayes_ann +NC_045512.2 11242 NC_045512.2;11242;G;T G T 53 52 1 ORF1a 10977G>T W3659C 0.0188679245283019 3659 SampleA_freebayes_ann +NC_045512.2 11261 NC_045512.2;11261;T;G T G 53 52 1 ORF1a 10996T>G W3666G 0.0188679245283019 3666 SampleA_freebayes_ann +NC_045512.2 11262 NC_045512.2;11262;G;A G A 53 52 1 ORF1a 10997G>A W3666* 0.0188679245283019 3666 SampleA_freebayes_ann +NC_045512.2 11269 NC_045512.2;11269;TA;GT TA GT 53 52 1 ORF1a 11004_11005delTAinsGT DM3668EL 0.0188679245283019 3668 SampleA_freebayes_ann +NC_045512.2 11271 NC_045512.2;11271;TGGT;CGGG TGGT CGGG 53 52 1 ORF1a 11006_11009delTGGTinsCGGG MV3669TG 0.0188679245283019 3669 SampleA_freebayes_ann +NC_045512.2 11276 NC_045512.2;11276;G;T G T 53 52 1 ORF1a 11011G>T D3671Y 0.0188679245283019 3671 SampleA_freebayes_ann +NC_045512.2 11277 NC_045512.2;11277;ATAC;TTCT ATAC TTCT 53 52 1 ORF1a 11012_11015delATACinsTTCT DT3671VL 0.0188679245283019 3671 SampleA_freebayes_ann +NC_045512.2 11287 NC_045512.2;11287;GTCTGGTTTTAAG;GAAG GTCTGGTTTTAAG GAAG 44 6 30 ORF1a 11031dupT K3678fs 0.681818181818182 3674 SampleA_freebayes_ann +NC_045512.2 11287 NC_045512.2;11287;GTCTGGTTTTAAG;GTCTGGTTTTTAAG GTCTGGTTTTAAG GTCTGGTTTTTAAG 44 6 8 ORF1a 11031dupT K3678fs 0.181818181818182 3674 SampleA_freebayes_ann +NC_045512.2 11308 NC_045512.2;11308;C;A C A 57 56 1 ORF1a 11043C>A D3681E 0.0175438596491228 3681 SampleA_freebayes_ann +NC_045512.2 11324 NC_045512.2;11324;T;C T C 48 47 1 ORF1a 11059T>C S3687P 0.0208333333333333 3687 SampleA_freebayes_ann +NC_045512.2 11369 NC_045512.2;11369;G;T G T 47 46 1 ORF1a 11104G>T D3702Y 0.0212765957446809 3702 SampleA_freebayes_ann +NC_045512.2 11377 NC_045512.2;11377;T;G T G 45 44 1 ORF1a 11112T>G G3704G 0.0222222222222222 3704 SampleA_freebayes_ann +NC_045512.2 11437 NC_045512.2;11437;T;G T G 41 40 1 ORF1a 11172T>G G3724G 0.024390243902439 3724 SampleA_freebayes_ann +NC_045512.2 11515 NC_045512.2;11515;T;G T G 41 40 1 ORF1a 11250T>G T3750T 0.024390243902439 3750 SampleA_freebayes_ann +NC_045512.2 11516 NC_045512.2;11516;G;A G A 41 39 2 ORF1a 11251G>A V3751I 0.0487804878048781 3751 SampleA_freebayes_ann +NC_045512.2 11586 NC_045512.2;11586;A;T A T 62 61 1 ORF1a 11321A>T N3774I 0.0161290322580645 3774 SampleA_freebayes_ann +NC_045512.2 11589 NC_045512.2;11589;C;T C T 62 61 1 ORF1a 11324C>T T3775I 0.0161290322580645 3775 SampleA_freebayes_ann +NC_045512.2 11803 NC_045512.2;11803;T;C T C 42 40 2 ORF1a 11538T>C G3846G 0.0476190476190476 3846 SampleA_freebayes_ann +NC_045512.2 11808 NC_045512.2;11808;GTGGC;TTGGT GTGGC TTGGT 42 41 1 ORF1a 11543_11547delGTGGCinsTTGGT G3848V 0.0238095238095238 3848 SampleA_freebayes_ann +NC_045512.2 11824 NC_045512.2;11824;C;A C A 42 41 1 ORF1a 11559C>A I3853I 0.0238095238095238 3853 SampleA_freebayes_ann +NC_045512.2 11828 NC_045512.2;11828;G;T G T 42 41 1 ORF1a 11563G>T V3855L 0.0238095238095238 3855 SampleA_freebayes_ann +NC_045512.2 11833 NC_045512.2;11833;C;T C T 42 41 1 ORF1a 11568C>T A3856A 0.0238095238095238 3856 SampleA_freebayes_ann +NC_045512.2 11840 NC_045512.2;11840;C;T C T 42 41 1 ORF1a 11575C>T Q3859* 0.0238095238095238 3859 SampleA_freebayes_ann +NC_045512.2 11854 NC_045512.2;11854;A;G A G 26 24 2 ORF1a 11589A>G S3863S 0.0769230769230769 3863 SampleA_freebayes_ann +NC_045512.2 11880 NC_045512.2;11880;TAC;TC TAC TC 41 40 1 ORF1a 11616delA L3872fs 0.024390243902439 3872 SampleA_freebayes_ann +NC_045512.2 11886 NC_045512.2;11886;C;T C T 41 32 9 ORF1a 11621C>T S3874L 0.219512195121951 3874 SampleA_freebayes_ann +NC_045512.2 11896 NC_045512.2;11896;A;G A G 41 40 1 ORF1a 11631A>G Q3877Q 0.024390243902439 3877 SampleA_freebayes_ann +NC_045512.2 11919 NC_045512.2;11919;C;T C T 41 32 9 ORF1a 11654C>T S3885F 0.219512195121951 3885 SampleA_freebayes_ann +NC_045512.2 11928 NC_045512.2;11928;G;A G A 41 40 1 ORF1a 11663G>A W3888* 0.024390243902439 3888 SampleA_freebayes_ann +NC_045512.2 11948 NC_045512.2;11948;C;A C A 32 31 1 ORF1a 11683C>A H3895N 0.03125 3895 SampleA_freebayes_ann +NC_045512.2 11984 NC_045512.2;11984;G;T G T 38 36 2 ORF1a 11719G>T A3907S 0.0526315789473684 3907 SampleA_freebayes_ann +NC_045512.2 12244 NC_045512.2;12244;TGA;TA TGA TA 40 38 2 ORF1a 11980delG D3994fs 0.05 3993 SampleA_freebayes_ann +NC_045512.2 12259 NC_045512.2;12259;A;T A T 24 23 1 ORF1a 11994A>T Q3998H 0.0416666666666667 3998 SampleA_freebayes_ann +NC_045512.2 12410 NC_045512.2;12410;A;T A T 21 19 2 ORF1a 12145A>T I4049F 0.0952380952380952 4049 SampleA_freebayes_ann +NC_045512.2 12419 NC_045512.2;12419;G;T G T 28 27 1 ORF1a 12154G>T A4052S 0.0357142857142857 4052 SampleA_freebayes_ann +NC_045512.2 12491 NC_045512.2;12491;G;T G T 21 20 1 ORF1a 12226G>T D4076Y 0.0476190476190476 4076 SampleA_freebayes_ann +NC_045512.2 12674 NC_045512.2;12674;G;C G C 41 39 2 ORF1a 12409G>C V4137L 0.0487804878048781 4137 SampleA_freebayes_ann +NC_045512.2 12748 NC_045512.2;12748;T;C T C 30 29 1 ORF1a 12483T>C T4161T 0.0333333333333333 4161 SampleA_freebayes_ann +NC_045512.2 12795 NC_045512.2;12795;G;T G T 31 30 1 ORF1a 12530G>T G4177V 0.032258064516129 4177 SampleA_freebayes_ann +NC_045512.2 12862 NC_045512.2;12862;T;C T C 21 20 1 ORF1a 12597T>C S4199S 0.0476190476190476 4199 SampleA_freebayes_ann +NC_045512.2 12864 NC_045512.2;12864;A;T A T 21 19 2 ORF1a 12599A>T D4200V 0.0952380952380952 4200 SampleA_freebayes_ann +NC_045512.2 13010 NC_045512.2;13010;A;C A C 44 43 1 ORF1a 12745A>C T4249P 0.0227272727272727 4249 SampleA_freebayes_ann +NC_045512.2 13012 NC_045512.2;13012;A;C A C 45 44 1 ORF1a 12747A>C T4249T 0.0222222222222222 4249 SampleA_freebayes_ann +NC_045512.2 13015 NC_045512.2;13015;A;C A C 48 47 1 ORF1a 12750A>C V4250V 0.0208333333333333 4250 SampleA_freebayes_ann +NC_045512.2 13022 NC_045512.2;13022;CAAGC;CAAAGC CAAGC CAAAGC 47 46 1 ORF1a 12759dupA A4254fs 0.0212765957446809 4253 SampleA_freebayes_ann +NC_045512.2 13050 NC_045512.2;13050;C;T C T 47 46 1 ORF1a 12785C>T A4262V 0.0212765957446809 4262 SampleA_freebayes_ann +NC_045512.2 13088 NC_045512.2;13088;G;T G T 79 78 1 ORF1a 12823G>T D4275Y 0.0126582278481013 4275 SampleA_freebayes_ann +NC_045512.2 13090 NC_045512.2;13090;T;A T A 79 77 2 ORF1a 12825T>A D4275E 0.0253164556962025 4275 SampleA_freebayes_ann +NC_045512.2 13118 NC_045512.2;13118;G;T G T 71 69 2 ORF1a 12853G>T A4285S 0.028169014084507 4285 SampleA_freebayes_ann +NC_045512.2 13168 NC_045512.2;13168;C;A C A 72 71 1 ORF1a 12903C>A H4301Q 0.0138888888888889 4301 SampleA_freebayes_ann +NC_045512.2 13174 NC_045512.2;13174;T;G T G 72 71 1 ORF1a 12909T>G G4303G 0.0138888888888889 4303 SampleA_freebayes_ann +NC_045512.2 13190 NC_045512.2;13190;A;T A T 72 71 1 ORF1a 12925A>T T4309S 0.0138888888888889 4309 SampleA_freebayes_ann +NC_045512.2 13232 NC_045512.2;13232;G;A G A 72 71 1 ORF1a 12967G>A G4323S 0.0138888888888889 4323 SampleA_freebayes_ann +NC_045512.2 13235 NC_045512.2;13235;G;A G A 72 71 1 ORF1a 12970G>A A4324T 0.0138888888888889 4324 SampleA_freebayes_ann +NC_045512.2 13238 NC_045512.2;13238;T;A T A 72 71 1 ORF1a 12973T>A S4325T 0.0138888888888889 4325 SampleA_freebayes_ann +NC_045512.2 13326 NC_045512.2;13326;CAACT;CAAACT CAACT CAAACT 40 38 1 ORF1a 13063dupA T4355fs 0.025 4354 SampleA_freebayes_ann +NC_045512.2 13384 NC_045512.2;13384;C;G C G 25 24 1 ORF1a 13119C>G C4373W 0.04 4373 SampleA_freebayes_ann +NC_045512.2 13385 NC_045512.2;13385;G;C G C 20 19 1 ORF1a 13120G>C G4374R 0.05 4374 SampleA_freebayes_ann +NC_045512.2 13605 NC_045512.2;13605;C;A C A 41 40 1 ORF1b 13341C>A R4447R 0.024390243902439 55 SampleA_freebayes_ann +NC_045512.2 13690 NC_045512.2;13690;G;T G T 62 61 1 ORF1b 13426G>T E4476* 0.0161290322580645 83 SampleA_freebayes_ann +NC_045512.2 13724 NC_045512.2;13724;C;T C T 62 61 1 ORF1b 13460C>T A4487V 0.0161290322580645 95 SampleA_freebayes_ann +NC_045512.2 13748 NC_045512.2;13748;A;T A T 62 61 1 ORF1b 13484A>T K4495M 0.0161290322580645 103 SampleA_freebayes_ann +NC_045512.2 13796 NC_045512.2;13796;T;C T C 62 61 1 ORF1b 13532T>C L4511P 0.0161290322580645 119 SampleA_freebayes_ann +NC_045512.2 13835 NC_045512.2;13835;G;A G A 62 61 1 ORF1b 13571G>A R4524K 0.0161290322580645 132 SampleA_freebayes_ann +NC_045512.2 13932 NC_045512.2;13932;T;G T G 38 37 1 ORF1b 13668T>G D4556E 0.0263157894736842 164 SampleA_freebayes_ann +NC_045512.2 13971 NC_045512.2;13971;CTTAG;CTAG CTTAG CTAG 38 35 2 ORF1b 13709delT L4570fs 0.0526315789473684 177 SampleA_freebayes_ann +NC_045512.2 13971 NC_045512.2;13971;CTTAG;CTTG CTTAG CTTG 38 35 1 ORF1b 13709delT L4570fs 0.0263157894736842 177 SampleA_freebayes_ann +NC_045512.2 13983 NC_045512.2;13983;T;G T G 18 17 1 ORF1b 13719T>G R4573R 0.0555555555555556 181 SampleA_freebayes_ann +NC_045512.2 14038 NC_045512.2;14038;G;A G A 21 20 1 ORF1b 13774G>A G4592S 0.0476190476190476 199 SampleA_freebayes_ann +NC_045512.2 14176 NC_045512.2;14176;A;G A G 21 19 2 ORF1b 13912A>G T4638A 0.0952380952380952 245 SampleA_freebayes_ann +NC_045512.2 14269 NC_045512.2;14269;G;A G A 37 36 1 ORF1b 14005G>A E4669K 0.027027027027027 276 SampleA_freebayes_ann +NC_045512.2 14290 NC_045512.2;14290;G;T G T 38 37 1 ORF1b 14026G>T D4676Y 0.0263157894736842 283 SampleA_freebayes_ann +NC_045512.2 14327 NC_045512.2;14327;C;T C T 50 48 2 ORF1b 14063C>T P4688L 0.04 296 SampleA_freebayes_ann +NC_045512.2 14407 NC_045512.2;14407;CCTACAAGT;CT CCTACAAGT CT 50 0 14 ORF1b 14144_14150delCTACAAG P4715fs 0.28 322 SampleA_freebayes_ann +NC_045512.2 14407 NC_045512.2;14407;CCTACAAGT;CTTACAAGT CCTACAAGT CTTACAAGT 50 0 36 ORF1b 14144_14150delCTACAAG P4715fs 0.72 322 SampleA_freebayes_ann +NC_045512.2 14435 NC_045512.2;14435;A;T A T 50 48 2 ORF1b 14171A>T K4724I 0.04 332 SampleA_freebayes_ann +NC_045512.2 14442 NC_045512.2;14442;T;C T C 50 48 2 ORF1b 14178T>C F4726F 0.04 334 SampleA_freebayes_ann +NC_045512.2 14450 NC_045512.2;14450;G;T G T 50 49 1 ORF1b 14186G>T G4729V 0.02 337 SampleA_freebayes_ann +NC_045512.2 14531 NC_045512.2;14531;C;A C A 24 23 1 ORF1b 14267C>A S4756Y 0.0416666666666667 364 SampleA_freebayes_ann +NC_045512.2 14549 NC_045512.2;14549;A;C A C 38 37 1 ORF1b 14285A>C E4762A 0.0263157894736842 370 SampleA_freebayes_ann +NC_045512.2 14550 NC_045512.2;14550;A;C A C 39 38 1 ORF1b 14286A>C E4762D 0.0256410256410256 370 SampleA_freebayes_ann +NC_045512.2 14553 NC_045512.2;14553;A;C A C 45 44 1 ORF1b 14289A>C L4763F 0.0222222222222222 371 SampleA_freebayes_ann +NC_045512.2 14594 NC_045512.2;14594;GTA;GA GTA GA 40 39 1 ORF1b 14331delT N4778fs 0.025 385 SampleA_freebayes_ann +NC_045512.2 14598 NC_045512.2;14598;T;G T G 36 35 1 ORF1b 14334T>G N4778K 0.0277777777777778 386 SampleA_freebayes_ann +NC_045512.2 14667 NC_045512.2;14667;T;G T G 45 43 2 ORF1b 14403T>G T4801T 0.0444444444444444 409 SampleA_freebayes_ann +NC_045512.2 14672 NC_045512.2;14672;AACCC;GACCT AACCC GACCT 45 23 2 ORF1b 14408_14412delAACCCinsGACCT K4803R 0.0444444444444444 411 SampleA_freebayes_ann +NC_045512.2 14672 NC_045512.2;14672;AACCC;AACCT AACCC AACCT 45 23 20 ORF1b 14408_14412delAACCCinsGACCT K4803R 0.444444444444444 411 SampleA_freebayes_ann +NC_045512.2 14694 NC_045512.2;14694;C;T C T 45 44 1 ORF1b 14430C>T D4810D 0.0222222222222222 418 SampleA_freebayes_ann +NC_045512.2 14708 NC_045512.2;14708;C;A C A 45 43 2 ORF1b 14444C>A A4815D 0.0444444444444444 423 SampleA_freebayes_ann +NC_045512.2 14794 NC_045512.2;14794;G;A G A 45 43 2 ORF1b 14530G>A D4844N 0.0444444444444444 451 SampleA_freebayes_ann +NC_045512.2 14902 NC_045512.2;14902;ATTAA;ATAA ATTAA ATAA 40 39 1 ORF1b 14640delT N4881fs 0.025 487 SampleA_freebayes_ann +NC_045512.2 14924 NC_045512.2;14924;T;G T G 32 31 1 ORF1b 14660T>G V4887G 0.03125 495 SampleA_freebayes_ann +NC_045512.2 14978 NC_045512.2;14978;G;T G T 31 29 2 ORF1b 14714G>T R4905I 0.0645161290322581 513 SampleA_freebayes_ann +NC_045512.2 14990 NC_045512.2;14990;A;T A T 31 29 2 ORF1b 14726A>T D4909V 0.0645161290322581 517 SampleA_freebayes_ann +NC_045512.2 15096 NC_045512.2;15096;T;A T A 31 30 1 ORF1b 14832T>A N4944K 0.032258064516129 552 SampleA_freebayes_ann +NC_045512.2 15173 NC_045512.2;15173;C;T C T 33 32 1 ORF1b 14909C>T S4970L 0.0303030303030303 578 SampleA_freebayes_ann +NC_045512.2 15174 NC_045512.2;15174;A;C A C 34 32 2 ORF1b 14910A>C S4970S 0.0588235294117647 578 SampleA_freebayes_ann +NC_045512.2 15175 NC_045512.2;15175;A;C A C 35 34 1 ORF1b 14911A>C I4971L 0.0285714285714286 578 SampleA_freebayes_ann +NC_045512.2 15245 NC_045512.2;15245;T;G T G 34 33 1 ORF1b 14981T>G L4994* 0.0294117647058824 602 SampleA_freebayes_ann +NC_045512.2 15269 NC_045512.2;15269;A;C A C 45 44 1 ORF1b 15005A>C E5002A 0.0222222222222222 610 SampleA_freebayes_ann +NC_045512.2 15279 NC_045512.2;15279;C;T C T 46 26 20 ORF1b 15015C>T H5005H 0.434782608695652 613 SampleA_freebayes_ann +NC_045512.2 15334 NC_045512.2;15334;A;G A G 46 44 2 ORF1b 15070A>G I5024V 0.0434782608695652 631 SampleA_freebayes_ann +NC_045512.2 15355 NC_045512.2;15355;G;T G T 46 45 1 ORF1b 15091G>T A5031S 0.0217391304347826 638 SampleA_freebayes_ann +NC_045512.2 15374 NC_045512.2;15374;G;T G T 46 45 1 ORF1b 15110G>T C5037F 0.0217391304347826 645 SampleA_freebayes_ann +NC_045512.2 15401 NC_045512.2;15401;G;T G T 46 45 1 ORF1b 15137G>T R5046I 0.0217391304347826 654 SampleA_freebayes_ann +NC_045512.2 15406 NC_045512.2;15406;G;T G T 46 42 4 ORF1b 15142G>T A5048S 0.0869565217391304 655 SampleA_freebayes_ann +NC_045512.2 15412 NC_045512.2;15412;G;A G A 46 45 1 ORF1b 15148G>A E5050K 0.0217391304347826 657 SampleA_freebayes_ann +NC_045512.2 15414 NC_045512.2;15414;G;T G T 46 45 1 ORF1b 15150G>T E5050D 0.0217391304347826 658 SampleA_freebayes_ann +NC_045512.2 15432 NC_045512.2;15432;T;G T G 46 45 1 ORF1b 15168T>G S5056R 0.0217391304347826 664 SampleA_freebayes_ann +NC_045512.2 15461 NC_045512.2;15461;A;T A T 46 45 1 ORF1b 15197A>T Y5066F 0.0217391304347826 674 SampleA_freebayes_ann +NC_045512.2 15463 NC_045512.2;15463;G;T G T 46 45 1 ORF1b 15199G>T V5067F 0.0217391304347826 674 SampleA_freebayes_ann +NC_045512.2 15539 NC_045512.2;15539;TCAC;TC TCAC TC 56 54 1 ORF1b 15277_15278delAC T5093fs 0.0178571428571429 700 SampleA_freebayes_ann +NC_045512.2 15539 NC_045512.2;15539;TCAC;TCCC TCAC TCCC 56 54 1 ORF1b 15277_15278delAC T5093fs 0.0178571428571429 700 SampleA_freebayes_ann +NC_045512.2 15552 NC_045512.2;15552;TAATG;TATG TAATG TATG 53 51 1 ORF1b 15290delA N5097fs 0.0188679245283019 704 SampleA_freebayes_ann +NC_045512.2 15552 NC_045512.2;15552;TAATG;TAATC TAATG TAATC 53 51 1 ORF1b 15290delA N5097fs 0.0188679245283019 704 SampleA_freebayes_ann +NC_045512.2 15593 NC_045512.2;15593;A;T A T 75 74 1 ORF1b 15329A>T K5110M 0.0133333333333333 718 SampleA_freebayes_ann +NC_045512.2 15597 NC_045512.2;15597;T;G T G 77 76 1 ORF1b 15333T>G Y5111* 0.012987012987013 719 SampleA_freebayes_ann +NC_045512.2 15600 NC_045512.2;15600;C;A C A 77 74 3 ORF1b 15336C>A V5112V 0.038961038961039 720 SampleA_freebayes_ann +NC_045512.2 15645 NC_045512.2;15645;A;G A G 78 77 1 ORF1b 15381A>G R5127R 0.0128205128205128 735 SampleA_freebayes_ann +NC_045512.2 15736 NC_045512.2;15736;T;G T G 78 77 1 ORF1b 15472T>G F5158V 0.0128205128205128 765 SampleA_freebayes_ann +NC_045512.2 15737 NC_045512.2;15737;T;G T G 78 77 1 ORF1b 15473T>G F5158C 0.0128205128205128 766 SampleA_freebayes_ann +NC_045512.2 15741 NC_045512.2;15741;T;A T A 78 76 2 ORF1b 15477T>A N5159K 0.0256410256410256 767 SampleA_freebayes_ann +NC_045512.2 15768 NC_045512.2;15768;G;T G T 77 76 1 ORF1b 15504G>T V5168V 0.012987012987013 776 SampleA_freebayes_ann +NC_045512.2 15770 NC_045512.2;15770;C;T C T 77 76 1 ORF1b 15506C>T A5169V 0.012987012987013 777 SampleA_freebayes_ann +NC_045512.2 15873 NC_045512.2;15873;ATTTTGC;ATTTGC ATTTTGC ATTTGC 57 56 1 ORF1b 15613delT C5205fs 0.0175438596491228 811 SampleA_freebayes_ann +NC_045512.2 15885 NC_045512.2;15885;A;C A C 41 40 1 ORF1b 15621A>C Q5207H 0.024390243902439 815 SampleA_freebayes_ann +NC_045512.2 15976 NC_045512.2;15976;G;T G T 28 27 1 ORF1b 15712G>T D5238Y 0.0357142857142857 845 SampleA_freebayes_ann +NC_045512.2 15995 NC_045512.2;15995;G;T G T 28 27 1 ORF1b 15731G>T G5244V 0.0357142857142857 852 SampleA_freebayes_ann +NC_045512.2 16061 NC_045512.2;16061;A;G A G 28 27 1 ORF1b 15797A>G N5266S 0.0357142857142857 874 SampleA_freebayes_ann +NC_045512.2 16078 NC_045512.2;16078;GTCTTTCA;TTTTTTAC GTCTTTCA TTTTTTAC 28 27 1 ORF1b 15814_15821delGTCTTTCAinsTTTTTTAC VFH5272FFT 0.0357142857142857 879 SampleA_freebayes_ann +NC_045512.2 16158 NC_045512.2;16158;G;T G T 25 24 1 ORF1b 15894G>T M5298I 0.04 906 SampleA_freebayes_ann +NC_045512.2 16176 NC_045512.2;16176;T;C T C 25 13 12 ORF1b 15912T>C T5304T 0.48 912 SampleA_freebayes_ann +NC_045512.2 16217 NC_045512.2;16217;C;A C A 24 23 1 ORF1b 15953C>A T5318K 0.0416666666666667 926 SampleA_freebayes_ann +NC_045512.2 16421 NC_045512.2;16421;A;C A C 24 23 1 ORF1b 16157A>C Q5386P 0.0416666666666667 994 SampleA_freebayes_ann +NC_045512.2 16479 NC_045512.2;16479;T;C T C 31 30 1 ORF1b 16215T>C F5405F 0.032258064516129 1013 SampleA_freebayes_ann +NC_045512.2 16493 NC_045512.2;16493;A;T A T 31 30 1 ORF1b 16229A>T N5410I 0.032258064516129 1018 SampleA_freebayes_ann +NC_045512.2 16508 NC_045512.2;16508;G;T G T 27 26 1 ORF1b 16244G>T G5415V 0.037037037037037 1023 SampleA_freebayes_ann +NC_045512.2 16536 NC_045512.2;16536;C;A C A 38 37 1 ORF1b 16272C>A S5424R 0.0263157894736842 1032 SampleA_freebayes_ann +NC_045512.2 16596 NC_045512.2;16596;C;A C A 39 38 1 ORF1b 16332C>A Y5444* 0.0256410256410256 1052 SampleA_freebayes_ann +NC_045512.2 16603 NC_045512.2;16603;G;T G T 39 38 1 ORF1b 16339G>T A5447S 0.0256410256410256 1054 SampleA_freebayes_ann +NC_045512.2 16630 NC_045512.2;16630;C;A C A 39 37 2 ORF1b 16366C>A L5456I 0.0512820512820513 1063 SampleA_freebayes_ann +NC_045512.2 16663 NC_045512.2;16663;G;T G T 39 37 2 ORF1b 16399G>T E5467* 0.0512820512820513 1074 SampleA_freebayes_ann +NC_045512.2 16700 NC_045512.2;16700;G;T G T 39 38 1 ORF1b 16436G>T R5479L 0.0256410256410256 1087 SampleA_freebayes_ann +NC_045512.2 16710 NC_045512.2;16710;G;T G T 39 38 1 ORF1b 16446G>T L5482L 0.0256410256410256 1090 SampleA_freebayes_ann +NC_045512.2 16718 NC_045512.2;16718;G;T G T 27 26 1 ORF1b 16454G>T R5485I 0.037037037037037 1093 SampleA_freebayes_ann +NC_045512.2 16751 NC_045512.2;16751;C;A C A 31 30 1 ORF1b 16487C>A P5496H 0.032258064516129 1104 SampleA_freebayes_ann +NC_045512.2 16985 NC_045512.2;16985;C;A C A 30 28 2 ORF1b 16721C>A T5574N 0.0666666666666667 1182 SampleA_freebayes_ann +NC_045512.2 17078 NC_045512.2;17078;AGGGAC;AGGGGAC AGGGAC AGGGGAC 42 41 1 ORF1b 16817dupG P5607fs 0.0238095238095238 1213 SampleA_freebayes_ann +NC_045512.2 17103 NC_045512.2;17103;T;A T A 42 41 1 ORF1b 16839T>A S5613R 0.0238095238095238 1221 SampleA_freebayes_ann +NC_045512.2 17146 NC_045512.2;17146;A;T A T 48 47 1 ORF1b 16882A>T I5628L 0.0208333333333333 1235 SampleA_freebayes_ann +NC_045512.2 17150 NC_045512.2;17150;T;G T G 47 46 1 ORF1b 16886T>G V5629G 0.0212765957446809 1237 SampleA_freebayes_ann +NC_045512.2 17183 NC_045512.2;17183;C;A C A 55 54 1 ORF1b 16919C>A A5640E 0.0181818181818182 1248 SampleA_freebayes_ann +NC_045512.2 17298 NC_045512.2;17298;G;A G A 55 53 2 ORF1b 17034G>A Q5678Q 0.0363636363636364 1286 SampleA_freebayes_ann +NC_045512.2 17437 NC_045512.2;17437;G;T G T 50 49 1 ORF1b 17173G>T D5725Y 0.02 1332 SampleA_freebayes_ann +NC_045512.2 17442 NC_045512.2;17442;T;G T G 50 49 1 ORF1b 17178T>G P5726P 0.02 1334 SampleA_freebayes_ann +NC_045512.2 17445 NC_045512.2;17445;T;C T C 49 48 1 ORF1b 17181T>C A5727A 0.0204081632653061 1335 SampleA_freebayes_ann +NC_045512.2 17463 NC_045512.2;17463;C;A C A 46 45 1 ORF1b 17199C>A R5733R 0.0217391304347826 1341 SampleA_freebayes_ann +NC_045512.2 17504 NC_045512.2;17504;A;T A T 48 47 1 ORF1b 17240A>T N5747I 0.0208333333333333 1355 SampleA_freebayes_ann +NC_045512.2 17506 NC_045512.2;17506;T;C T C 48 47 1 ORF1b 17242T>C S5748P 0.0208333333333333 1355 SampleA_freebayes_ann +NC_045512.2 17531 NC_045512.2;17531;T;G T G 48 47 1 ORF1b 17267T>G I5756R 0.0208333333333333 1364 SampleA_freebayes_ann +NC_045512.2 17659 NC_045512.2;17659;T;A T A 48 46 2 ORF1b 17395T>A F5799I 0.0416666666666667 1406 SampleA_freebayes_ann +NC_045512.2 17669 NC_045512.2;17669;G;T G T 48 47 1 ORF1b 17405G>T G5802V 0.0208333333333333 1410 SampleA_freebayes_ann +NC_045512.2 17676 NC_045512.2;17676;C;T C T 55 54 1 ORF1b 17412C>T I5804I 0.0181818181818182 1412 SampleA_freebayes_ann +NC_045512.2 17696 NC_045512.2;17696;C;T C T 36 35 1 ORF1b 17432C>T A5811V 0.0277777777777778 1419 SampleA_freebayes_ann +NC_045512.2 17697 NC_045512.2;17697;A;G A G 36 35 1 ORF1b 17433A>G A5811A 0.0277777777777778 1419 SampleA_freebayes_ann +NC_045512.2 17707 NC_045512.2;17707;CCAC;CC CCAC CC 36 35 1 ORF1b 17446_17447delCA Q5816fs 0.0277777777777778 1422 SampleA_freebayes_ann +NC_045512.2 17723 NC_045512.2;17723;T;C T C 36 35 1 ORF1b 17459T>C V5820A 0.0277777777777778 1428 SampleA_freebayes_ann +NC_045512.2 17727 NC_045512.2;17727;A;C A C 36 34 2 ORF1b 17463A>C R5821S 0.0555555555555556 1429 SampleA_freebayes_ann +NC_045512.2 17760 NC_045512.2;17760;A;G A G 31 30 1 ORF1b 17496A>G K5832K 0.032258064516129 1440 SampleA_freebayes_ann +NC_045512.2 17815 NC_045512.2;17815;G;T G T 23 21 2 ORF1b 17551G>T G5851* 0.0869565217391304 1458 SampleA_freebayes_ann +NC_045512.2 17859 NC_045512.2;17859;T;C T C 23 21 2 ORF1b 17595T>C Y5865Y 0.0869565217391304 1473 SampleA_freebayes_ann +NC_045512.2 17931 NC_045512.2;17931;T;A T A 23 22 1 ORF1b 17667T>A I5889I 0.0434782608695652 1497 SampleA_freebayes_ann +NC_045512.2 17985 NC_045512.2;17985;C;T C T 31 30 1 ORF1b 17721C>T D5907D 0.032258064516129 1515 SampleA_freebayes_ann +NC_045512.2 18061 NC_045512.2;18061;T;G T G 44 43 1 ORF1b 17797T>G F5933V 0.0227272727272727 1540 SampleA_freebayes_ann +NC_045512.2 18086 NC_045512.2;18086;C;A C A 35 33 2 ORF1b 17822C>A T5941N 0.0571428571428571 1549 SampleA_freebayes_ann +NC_045512.2 18088 NC_045512.2;18088;G;A G A 35 34 1 ORF1b 17824G>A G5942R 0.0285714285714286 1549 SampleA_freebayes_ann +NC_045512.2 18092 NC_045512.2;18092;T;C T C 35 33 2 ORF1b 17828T>C L5943S 0.0571428571428571 1551 SampleA_freebayes_ann +NC_045512.2 18105 NC_045512.2;18105;G;T G T 35 33 2 ORF1b 17841G>T Q5947H 0.0571428571428571 1555 SampleA_freebayes_ann +NC_045512.2 18221 NC_045512.2;18221;A;C A C 35 34 1 ORF1b 17957A>C K5986T 0.0285714285714286 1594 SampleA_freebayes_ann +NC_045512.2 18342 NC_045512.2;18342;T;G T G 42 41 1 ORF1b 18078T>G V6026V 0.0238095238095238 1634 SampleA_freebayes_ann +NC_045512.2 18346 NC_045512.2;18346;A;C A C 38 37 1 ORF1b 18082A>C T6028P 0.0263157894736842 1635 SampleA_freebayes_ann +NC_045512.2 18395 NC_045512.2;18395;CTGT;CT CTGT CT 50 48 2 ORF1b 18133_18134delGT V6045fs 0.04 1652 SampleA_freebayes_ann +NC_045512.2 18411 NC_045512.2;18411;T;A T A 50 48 2 ORF1b 18147T>A Y6049* 0.04 1657 SampleA_freebayes_ann +NC_045512.2 18468 NC_045512.2;18468;A;G A G 51 49 2 ORF1b 18204A>G G6068G 0.0392156862745098 1676 SampleA_freebayes_ann +NC_045512.2 18483 NC_045512.2;18483;C;T C T 51 49 2 ORF1b 18219C>T H6073H 0.0392156862745098 1681 SampleA_freebayes_ann +NC_045512.2 18506 NC_045512.2;18506;G;T G T 51 50 1 ORF1b 18242G>T G6081V 0.0196078431372549 1689 SampleA_freebayes_ann +NC_045512.2 18556 NC_045512.2;18556;A;C A C 33 32 1 ORF1b 18292A>C T6098P 0.0303030303030303 1705 SampleA_freebayes_ann +NC_045512.2 18619 NC_045512.2;18619;T;G T G 57 56 1 ORF1b 18355T>G S6119A 0.0175438596491228 1726 SampleA_freebayes_ann +NC_045512.2 18659 NC_045512.2;18659;GTTGTC;GTGTC GTTGTC GTGTC 57 56 1 ORF1b 18397delT C6133fs 0.0175438596491228 1740 SampleA_freebayes_ann +NC_045512.2 18668 NC_045512.2;18668;G;A G A 57 56 1 ORF1b 18404G>A C6135Y 0.0175438596491228 1743 SampleA_freebayes_ann +NC_045512.2 18714 NC_045512.2;18714;C;A C A 67 66 1 ORF1b 18450C>A A6150A 0.0149253731343284 1758 SampleA_freebayes_ann +NC_045512.2 18754 NC_045512.2;18754;C;T C T 67 66 1 ORF1b 18490C>T P6164S 0.0149253731343284 1771 SampleA_freebayes_ann +NC_045512.2 18758 NC_045512.2;18758;TTAT;TT TTAT TT 67 65 2 ORF1b 18496_18497delAT M6166fs 0.0298507462686567 1773 SampleA_freebayes_ann +NC_045512.2 18786 NC_045512.2;18786;TAC;TC TAC TC 67 65 2 ORF1b 18523delA T6175fs 0.0298507462686567 1782 SampleA_freebayes_ann +NC_045512.2 18795 NC_045512.2;18795;C;A C A 67 66 1 ORF1b 18531C>A N6177K 0.0149253731343284 1785 SampleA_freebayes_ann +NC_045512.2 18807 NC_045512.2;18807;C;A C A 67 66 1 ORF1b 18543C>A N6181K 0.0149253731343284 1789 SampleA_freebayes_ann +NC_045512.2 18936 NC_045512.2;18936;T;C T C 55 50 5 ORF1b 18672T>C I6224I 0.0909090909090909 1832 SampleA_freebayes_ann +NC_045512.2 18964 NC_045512.2;18964;T;G T G 49 48 1 ORF1b 18700T>G C6234G 0.0204081632653061 1841 SampleA_freebayes_ann +NC_045512.2 18978 NC_045512.2;18978;A;C A C 39 38 1 ORF1b 18714A>C Q6238H 0.0256410256410256 1846 SampleA_freebayes_ann +NC_045512.2 19036 NC_045512.2;19036;G;T G T 39 38 1 ORF1b 18772G>T G6258C 0.0256410256410256 1865 SampleA_freebayes_ann +NC_045512.2 19103 NC_045512.2;19103;C;T C T 39 37 2 ORF1b 18839C>T P6280L 0.0512820512820513 1888 SampleA_freebayes_ann +NC_045512.2 19208 NC_045512.2;19208;A;C A C 28 27 1 ORF1b 18944A>C D6315A 0.0357142857142857 1923 SampleA_freebayes_ann +NC_045512.2 19220 NC_045512.2;19220;C;G C G 29 28 1 ORF1b 18956C>G A6319G 0.0344827586206897 1927 SampleA_freebayes_ann +NC_045512.2 19227 NC_045512.2;19227;C;T C T 28 27 1 ORF1b 18963C>T S6321S 0.0357142857142857 1929 SampleA_freebayes_ann +NC_045512.2 19284 NC_045512.2;19284;TGGTGGC;TGTGGC TGGTGGC TGTGGC 28 27 1 ORF1b 19022delG G6341fs 0.0357142857142857 1948 SampleA_freebayes_ann +NC_045512.2 19295 NC_045512.2;19295;T;G T G 22 21 1 ORF1b 19031T>G L6344W 0.0454545454545455 1952 SampleA_freebayes_ann +NC_045512.2 19437 NC_045512.2;19437;A;T A T 16 14 2 ORF1b 19173A>T V6391V 0.125 1999 SampleA_freebayes_ann +NC_045512.2 19478 NC_045512.2;19478;G;T G T 16 12 4 ORF1b 19214G>T G6405V 0.25 2013 SampleA_freebayes_ann +NC_045512.2 19550 NC_045512.2;19550;C;G C G 11 10 1 ORF1b 19286C>G A6429G 0.0909090909090909 2037 SampleA_freebayes_ann +NC_045512.2 19621 NC_045512.2;19621;A;T A T 6 5 1 ORF1b 19357A>T S6453C 0.166666666666667 2060 SampleA_freebayes_ann +NC_045512.2 19630 NC_045512.2;19630;A;G A G 6 5 1 ORF1b 19366A>G N6456D 0.166666666666667 2063 SampleA_freebayes_ann +NC_045512.2 20219 NC_045512.2;20219;T;A T A 14 13 1 ORF1b 19955T>A L6652* 0.0714285714285714 2260 SampleA_freebayes_ann +NC_045512.2 20498 NC_045512.2;20498;C;G C G 26 25 1 ORF1b 20234C>G S6745C 0.0384615384615385 2353 SampleA_freebayes_ann +NC_045512.2 20593 NC_045512.2;20593;A;T A T 40 38 2 ORF1b 20329A>T T6777S 0.05 2384 SampleA_freebayes_ann +NC_045512.2 20621 NC_045512.2;20621;A;T A T 40 39 1 ORF1b 20357A>T K6786I 0.025 2394 SampleA_freebayes_ann +NC_045512.2 20696 NC_045512.2;20696;A;C A C 40 39 1 ORF1b 20432A>C N6811T 0.025 2419 SampleA_freebayes_ann +NC_045512.2 20726 NC_045512.2;20726;A;G A G 40 38 2 ORF1b 20462A>G E6821G 0.05 2429 SampleA_freebayes_ann +NC_045512.2 20732 NC_045512.2;20732;G;T G T 40 39 1 ORF1b 20468G>T C6823F 0.025 2431 SampleA_freebayes_ann +NC_045512.2 20745 NC_045512.2;20745;T;G T G 40 39 1 ORF1b 20481T>G N6827K 0.025 2435 SampleA_freebayes_ann +NC_045512.2 20766 NC_045512.2;20766;A;C A C 40 39 1 ORF1b 20502A>C L6834F 0.025 2442 SampleA_freebayes_ann +NC_045512.2 20772 NC_045512.2;20772;A;G A G 26 24 2 ORF1b 20508A>G K6836K 0.0769230769230769 2444 SampleA_freebayes_ann +NC_045512.2 20789 NC_045512.2;20789;T;G T G 36 35 1 ORF1b 20525T>G V6842G 0.0277777777777778 2450 SampleA_freebayes_ann +NC_045512.2 20988 NC_045512.2;20988;T;G T G 35 34 1 ORF1b 20724T>G T6908T 0.0285714285714286 2516 SampleA_freebayes_ann +NC_045512.2 21005 NC_045512.2;21005;C;T C T 35 34 1 ORF1b 20741C>T A6914V 0.0285714285714286 2522 SampleA_freebayes_ann +NC_045512.2 21056 NC_045512.2;21056;A;T A T 35 33 2 ORF1b 20792A>T D6931V 0.0571428571428571 2539 SampleA_freebayes_ann +NC_045512.2 21065 NC_045512.2;21065;CTAAAAATG;CGAAAATG CTAAAAATG CGAAAATG 35 14 1 ORF1b 20802_20803delTAinsG K6935fs 0.0285714285714286 2542 SampleA_freebayes_ann +NC_045512.2 21065 NC_045512.2;21065;CTAAAAATG;CTAAAATG CTAAAAATG CTAAAATG 35 14 20 ORF1b 20802_20803delTAinsG K6935fs 0.571428571428571 2542 SampleA_freebayes_ann +NC_045512.2 21132 NC_045512.2;21132;A;G A G 24 23 1 ORF1b 20868A>G Q6956Q 0.0416666666666667 2564 SampleA_freebayes_ann +NC_045512.2 21168 NC_045512.2;21168;G;A G A 22 21 1 ORF1b 20904G>A K6968K 0.0454545454545455 2576 SampleA_freebayes_ann +NC_045512.2 21304 NC_045512.2;21304;C;T C T 14 12 2 ORF1b 21040C>T R7014C 0.142857142857143 2621 SampleA_freebayes_ann +NC_045512.2 21395 NC_045512.2;21395;A;G A G 15 14 1 ORF1b 21131A>G D7044G 0.0666666666666667 2652 SampleA_freebayes_ann +NC_045512.2 21661 NC_045512.2;21661;A;C A C 20 19 1 S 99A>C T33T 0.05 33 SampleA_freebayes_ann +NC_045512.2 21735 NC_045512.2;21735;T;G T G 36 35 1 S 173T>G F58C 0.0277777777777778 58 SampleA_freebayes_ann +NC_045512.2 21764 NC_045512.2;21764;ATACATGTCTC;AGCTC ATACATGTCTC AGCTC 31 11 1 S 203_209delTACATGTinsG I68_V70delinsS 0.032258064516129 68 SampleA_freebayes_ann +NC_045512.2 21764 NC_045512.2;21764;ATACATGTCTC;ATCTA ATACATGTCTC ATCTA 31 11 1 S 203_209delTACATGTinsG I68_V70delinsS 0.032258064516129 68 SampleA_freebayes_ann +NC_045512.2 21764 NC_045512.2;21764;ATACATGTCTC;ATCTC ATACATGTCTC ATCTC 31 11 18 S 203_209delTACATGTinsG I68_V70delinsS 0.580645161290323 68 SampleA_freebayes_ann +NC_045512.2 21776 NC_045512.2;21776;G;A G A 31 30 1 S 214G>A G72R 0.032258064516129 72 SampleA_freebayes_ann +NC_045512.2 21801 NC_045512.2;21801;A;C A C 31 20 11 S 239A>C D80A 0.354838709677419 80 SampleA_freebayes_ann +NC_045512.2 21904 NC_045512.2;21904;C;A C A 31 30 1 S 342C>A T114T 0.032258064516129 114 SampleA_freebayes_ann +NC_045512.2 21910 NC_045512.2;21910;C;A C A 31 30 1 S 348C>A S116S 0.032258064516129 116 SampleA_freebayes_ann +NC_045512.2 21990 NC_045512.2;21990;TTTATTAC;TTTAC TTTATTAC TTTAC 32 4 28 S 432_434delTTA Y145del 0.875 143 SampleA_freebayes_ann +NC_045512.2 22084 NC_045512.2;22084;T;C T C 35 33 2 S 522T>C P174P 0.0571428571428571 174 SampleA_freebayes_ann +NC_045512.2 22088 NC_045512.2;22088;C;A C A 35 33 2 S 526C>A L176I 0.0571428571428571 176 SampleA_freebayes_ann +NC_045512.2 22096 NC_045512.2;22096;C;A C A 35 34 1 S 534C>A D178E 0.0285714285714286 178 SampleA_freebayes_ann +NC_045512.2 22133 NC_045512.2;22133;G;A G A 35 33 2 S 571G>A E191K 0.0571428571428571 191 SampleA_freebayes_ann +NC_045512.2 22194 NC_045512.2;22194;A;G A G 35 33 2 S 632A>G N211S 0.0571428571428571 211 SampleA_freebayes_ann +NC_045512.2 22248 NC_045512.2;22248;TG;GT TG GT 35 34 1 S 686_687delTGinsGT L229C 0.0285714285714286 229 SampleA_freebayes_ann +NC_045512.2 22267 NC_045512.2;22267;C;A C A 31 30 1 S 705C>A I235I 0.032258064516129 235 SampleA_freebayes_ann +NC_045512.2 22304 NC_045512.2;22304;T;C T C 21 20 1 S 742T>C Y248H 0.0476190476190476 248 SampleA_freebayes_ann +NC_045512.2 22535 NC_045512.2;22535;T;A T A 18 17 1 S 973T>A S325T 0.0555555555555556 325 SampleA_freebayes_ann +NC_045512.2 22801 NC_045512.2;22801;G;T G T 30 29 1 S 1239G>T G413G 0.0333333333333333 413 SampleA_freebayes_ann +NC_045512.2 22893 NC_045512.2;22893;A;G A G 17 16 1 S 1331A>G K444R 0.0588235294117647 444 SampleA_freebayes_ann +NC_045512.2 23063 NC_045512.2;23063;A;T A T 6 0 6 S 1501A>T N501Y 1 501 SampleA_freebayes_ann +NC_045512.2 23125 NC_045512.2;23125;A;C A C 22 20 2 S 1563A>C P521P 0.0909090909090909 521 SampleA_freebayes_ann +NC_045512.2 23137 NC_045512.2;23137;T;C T C 24 23 1 S 1575T>C C525C 0.0416666666666667 525 SampleA_freebayes_ann +NC_045512.2 23205 NC_045512.2;23205;G;C G C 25 24 1 S 1643G>C G548A 0.04 548 SampleA_freebayes_ann +NC_045512.2 23212 NC_045512.2;23212;T;C T C 25 23 2 S 1650T>C G550G 0.08 550 SampleA_freebayes_ann +NC_045512.2 23233 NC_045512.2;23233;A;C A C 42 41 1 S 1671A>C K557N 0.0238095238095238 557 SampleA_freebayes_ann +NC_045512.2 23236 NC_045512.2;23236;GT;CG GT CG 42 41 1 S 1674_1675delGTinsCG KF558NV 0.0238095238095238 558 SampleA_freebayes_ann +NC_045512.2 23249 NC_045512.2;23249;CA;AC CA AC 42 41 1 S 1687_1688delCAinsAC Q563T 0.0238095238095238 563 SampleA_freebayes_ann +NC_045512.2 23252 NC_045512.2;23252;C;A C A 42 41 1 S 1690C>A Q564K 0.0238095238095238 564 SampleA_freebayes_ann +NC_045512.2 23257 NC_045512.2;23257;T;G T G 42 41 1 S 1695T>G F565L 0.0238095238095238 565 SampleA_freebayes_ann +NC_045512.2 23258 NC_045512.2;23258;G;T G T 42 41 1 S 1696G>T G566C 0.0238095238095238 566 SampleA_freebayes_ann +NC_045512.2 23264 NC_045512.2;23264;G;T G T 42 41 1 S 1702G>T D568Y 0.0238095238095238 568 SampleA_freebayes_ann +NC_045512.2 23270 NC_045512.2;23270;GC;TA GC TA 42 0 1 S 1709C>A A570D 0.0238095238095238 570 SampleA_freebayes_ann +NC_045512.2 23270 NC_045512.2;23270;GC;GA GC GA 42 0 41 S 1709C>A A570D 0.976190476190476 570 SampleA_freebayes_ann +NC_045512.2 23295 NC_045512.2;23295;A;C A C 42 41 1 S 1733A>C D578A 0.0238095238095238 578 SampleA_freebayes_ann +NC_045512.2 23310 NC_045512.2;23310;A;G A G 42 41 1 S 1748A>G E583G 0.0238095238095238 583 SampleA_freebayes_ann +NC_045512.2 23329 NC_045512.2;23329;A;C A C 42 41 1 S 1767A>C P589P 0.0238095238095238 589 SampleA_freebayes_ann +NC_045512.2 23356 NC_045512.2;23356;A;C A C 42 41 1 S 1794A>C I598I 0.0238095238095238 598 SampleA_freebayes_ann +NC_045512.2 23374 NC_045512.2;23374;T;C T C 42 40 2 S 1812T>C T604T 0.0476190476190476 604 SampleA_freebayes_ann +NC_045512.2 23386 NC_045512.2;23386;T;G T G 42 41 1 S 1824T>G V608V 0.0238095238095238 608 SampleA_freebayes_ann +NC_045512.2 23403 NC_045512.2;23403;A;G A G 41 0 40 S 1841A>G D614G 0.975609756097561 614 SampleA_freebayes_ann +NC_045512.2 23403 NC_045512.2;23403;A;T A T 41 0 1 S 1841A>G D614G 0.024390243902439 614 SampleA_freebayes_ann +NC_045512.2 23431 NC_045512.2;23431;T;A T A 21 20 1 S 1869T>A A623A 0.0476190476190476 623 SampleA_freebayes_ann +NC_045512.2 23445 NC_045512.2;23445;A;C A C 30 28 2 S 1883A>C Q628P 0.0666666666666667 628 SampleA_freebayes_ann +NC_045512.2 23446 NC_045512.2;23446;A;C A C 32 31 1 S 1884A>C Q628H 0.03125 628 SampleA_freebayes_ann +NC_045512.2 23450 NC_045512.2;23450;A;C A C 36 35 1 S 1888A>C T630P 0.0277777777777778 630 SampleA_freebayes_ann +NC_045512.2 23469 NC_045512.2;23469;A;C A C 37 36 1 S 1907A>C Y636S 0.027027027027027 636 SampleA_freebayes_ann +NC_045512.2 23521 NC_045512.2;23521;T;G T G 27 26 1 S 1959T>G A653A 0.037037037037037 653 SampleA_freebayes_ann +NC_045512.2 23571 NC_045512.2;23571;T;C T C 36 35 1 S 2009T>C I670T 0.0277777777777778 670 SampleA_freebayes_ann +NC_045512.2 23604 NC_045512.2;23604;C;A C A 36 23 13 S 2042C>A P681H 0.361111111111111 681 SampleA_freebayes_ann +NC_045512.2 23606 NC_045512.2;23606;C;A C A 36 34 2 S 2044C>A R682R 0.0555555555555556 682 SampleA_freebayes_ann +NC_045512.2 23656 NC_045512.2;23656;A;C A C 36 35 1 S 2094A>C S698S 0.0277777777777778 698 SampleA_freebayes_ann +NC_045512.2 23664 NC_045512.2;23664;C;T C T 36 13 23 S 2102C>T A701V 0.638888888888889 701 SampleA_freebayes_ann +NC_045512.2 23709 NC_045512.2;23709;C;T C T 36 23 13 S 2147C>T T716I 0.361111111111111 716 SampleA_freebayes_ann +NC_045512.2 23766 NC_045512.2;23766;C;T C T 19 7 12 S 2204C>T S735L 0.631578947368421 735 SampleA_freebayes_ann +NC_045512.2 23820 NC_045512.2;23820;T;C T C 24 23 1 S 2258T>C L753S 0.0416666666666667 753 SampleA_freebayes_ann +NC_045512.2 24394 NC_045512.2;24394;A;C A C 17 16 1 S 2832A>C A944A 0.0588235294117647 944 SampleA_freebayes_ann +NC_045512.2 24506 NC_045512.2;24506;T;G T G 26 0 26 S 2944T>G S982A 1 982 SampleA_freebayes_ann +NC_045512.2 24511 NC_045512.2;24511;T;A T A 26 24 2 S 2949T>A R983R 0.0769230769230769 983 SampleA_freebayes_ann +NC_045512.2 24536 NC_045512.2;24536;CAAAT;AAAAG CAAAT AAAAG 26 25 1 S 2974_2978delCAAATinsAAAAG QI992KS 0.0384615384615385 992 SampleA_freebayes_ann +NC_045512.2 24620 NC_045512.2;24620;G;T G T 26 25 1 S 3058G>T A1020S 0.0384615384615385 1020 SampleA_freebayes_ann +NC_045512.2 24672 NC_045512.2;24672;C;T C T 26 25 1 S 3110C>T S1037L 0.0384615384615385 1037 SampleA_freebayes_ann +NC_045512.2 24700 NC_045512.2;24700;C;G C G 30 29 1 S 3138C>G G1046G 0.0333333333333333 1046 SampleA_freebayes_ann +NC_045512.2 24776 NC_045512.2;24776;G;A G A 45 44 1 S 3214G>A E1072K 0.0222222222222222 1072 SampleA_freebayes_ann +NC_045512.2 24788 NC_045512.2;24788;A;C A C 48 47 1 S 3226A>C T1076P 0.0208333333333333 1076 SampleA_freebayes_ann +NC_045512.2 24795 NC_045512.2;24795;C;A C A 40 39 1 S 3233C>A A1078D 0.025 1078 SampleA_freebayes_ann +NC_045512.2 24849 NC_045512.2;24849;T;C T C 40 39 1 S 3287T>C V1096A 0.025 1096 SampleA_freebayes_ann +NC_045512.2 24870 NC_045512.2;24870;T;G T G 40 39 1 S 3308T>G F1103C 0.025 1103 SampleA_freebayes_ann +NC_045512.2 24902 NC_045512.2;24902;A;C A C 40 39 1 S 3340A>C I1114L 0.025 1114 SampleA_freebayes_ann +NC_045512.2 24914 NC_045512.2;24914;G;C G C 40 0 40 S 3352G>C D1118H 1 1118 SampleA_freebayes_ann +NC_045512.2 24949 NC_045512.2;24949;A;C A C 40 39 1 S 3387A>C V1129V 0.025 1129 SampleA_freebayes_ann +NC_045512.2 25010 NC_045512.2;25010;G;A G A 32 31 1 S 3448G>A E1150K 0.03125 1150 SampleA_freebayes_ann +NC_045512.2 25231 NC_045512.2;25231;C;A C A 29 27 2 S 3669C>A G1223G 0.0689655172413793 1223 SampleA_freebayes_ann +NC_045512.2 25238 NC_045512.2;25238;GCCAT;GCAT GCCAT GCAT 29 27 2 S 3678delC I1227fs 0.0689655172413793 1226 SampleA_freebayes_ann +NC_045512.2 25252 NC_045512.2;25252;G;A G A 29 17 12 S 3690G>A V1230V 0.413793103448276 1230 SampleA_freebayes_ann +NC_045512.2 25606 NC_045512.2;25606;GCAC;GC GCAC GC 3 2 1 ORF3a 216_217delAC S74fs 0.333333333333333 72 SampleA_freebayes_ann +NC_045512.2 25784 NC_045512.2;25784;G;T G T 10 8 2 ORF3a 392G>T W131L 0.2 131 SampleA_freebayes_ann +NC_045512.2 25805 NC_045512.2;25805;C;A C A 10 8 2 ORF3a 413C>A P138Q 0.2 138 SampleA_freebayes_ann +NC_045512.2 25904 NC_045512.2;25904;C;T C T 11 10 1 ORF3a 512C>T S171L 0.0909090909090909 171 SampleA_freebayes_ann +NC_045512.2 25905 NC_045512.2;25905;A;C A C 9 8 1 ORF3a 513A>C S171S 0.111111111111111 171 SampleA_freebayes_ann +NC_045512.2 26010 NC_045512.2;26010;C;T C T 4 1 3 ORF3a 618C>T Y206Y 0.75 206 SampleA_freebayes_ann +NC_045512.2 26172 NC_045512.2;26172;G;T G T 8 7 1 ORF3a 780G>T M260I 0.125 260 SampleA_freebayes_ann +NC_045512.2 26173 NC_045512.2;26173;G;T G T 8 7 1 ORF3a 781G>T E261* 0.125 261 SampleA_freebayes_ann +NC_045512.2 26203 NC_045512.2;26203;A;C A C 30 29 1 ORF3a 811A>C T271P 0.0333333333333333 271 SampleA_freebayes_ann +NC_045512.2 26208 NC_045512.2;26208;C;A C A 32 31 1 ORF3a 816C>A S272R 0.03125 272 SampleA_freebayes_ann +NC_045512.2 26305 NC_045512.2;26305;CTTGC;CTGC CTTGC CTGC 60 59 1 E 63delT A22fs 0.0166666666666667 21 SampleA_freebayes_ann +NC_045512.2 26346 NC_045512.2;26346;T;C T C 58 57 1 E 102T>C L34L 0.0172413793103448 34 SampleA_freebayes_ann +NC_045512.2 26349 NC_045512.2;26349;T;C T C 58 57 1 E 105T>C T35T 0.0172413793103448 35 SampleA_freebayes_ann +NC_045512.2 26416 NC_045512.2;26416;G;T G T 58 36 22 E 172G>T V58F 0.379310344827586 58 SampleA_freebayes_ann +NC_045512.2 26590 NC_045512.2;26590;T;A T A 33 32 1 M 68T>A V23E 0.0303030303030303 23 SampleA_freebayes_ann +NC_045512.2 26695 NC_045512.2;26695;G;A G A 38 36 2 M 173G>A W58* 0.0526315789473684 58 SampleA_freebayes_ann +NC_045512.2 26736 NC_045512.2;26736;AGAA;TGAC AGAA TGAC 38 37 1 M 214_217delAGAAinsTGAC RI72* 0.0263157894736842 72 SampleA_freebayes_ann +NC_045512.2 26758 NC_045512.2;26758;GAA;TAC GAA TAC 38 37 1 M 236_238delGAAinsTAC GI79VL 0.0263157894736842 79 SampleA_freebayes_ann +NC_045512.2 26803 NC_045512.2;26803;G;T G T 37 36 1 M 281G>T S94I 0.027027027027027 94 SampleA_freebayes_ann +NC_045512.2 26830 NC_045512.2;26830;T;C T C 17 16 1 M 308T>C F103S 0.0588235294117647 103 SampleA_freebayes_ann +NC_045512.2 26859 NC_045512.2;26859;A;G A G 22 21 1 M 337A>G N113D 0.0454545454545455 113 SampleA_freebayes_ann +NC_045512.2 26885 NC_045512.2;26885;C;T C T 22 21 1 M 363C>T N121N 0.0454545454545455 121 SampleA_freebayes_ann +NC_045512.2 27032 NC_045512.2;27032;T;C T C 12 11 1 M 510T>C V170V 0.0833333333333333 170 SampleA_freebayes_ann +NC_045512.2 27126 NC_045512.2;27126;G;T G T 12 11 1 M 604G>T G202C 0.0833333333333333 202 SampleA_freebayes_ann +NC_045512.2 27143 NC_045512.2;27143;C;A C A 31 30 1 M 621C>A N207K 0.032258064516129 207 SampleA_freebayes_ann +NC_045512.2 27144 NC_045512.2;27144;A;C A C 32 30 2 M 622A>C T208P 0.0625 208 SampleA_freebayes_ann +NC_045512.2 27161 NC_045512.2;27161;C;A C A 49 48 1 M 639C>A S213R 0.0204081632653061 213 SampleA_freebayes_ann +NC_045512.2 27171 NC_045512.2;27171;A;G A G 49 48 1 M 649A>G I217V 0.0204081632653061 217 SampleA_freebayes_ann +NC_045512.2 27191 NC_045512.2;27191;A;T A T 49 48 1 M 669A>T Ter223Yext*? 0.0204081632653061 223 SampleA_freebayes_ann +NC_045512.2 27206 NC_045512.2;27206;T;C T C 51 50 1 ORF6 5T>C F2S 0.0196078431372549 2 SampleA_freebayes_ann +NC_045512.2 27212 NC_045512.2;27212;T;A T A 50 49 1 ORF6 11T>A L4H 0.02 4 SampleA_freebayes_ann +NC_045512.2 27217 NC_045512.2;27217;G;T G T 46 45 1 ORF6 16G>T D6Y 0.0217391304347826 6 SampleA_freebayes_ann +NC_045512.2 27337 NC_045512.2;27337;G;T G T 80 78 2 ORF6 136G>T E46* 0.025 46 SampleA_freebayes_ann +NC_045512.2 27361 NC_045512.2;27361;G;T G T 80 79 1 ORF6 160G>T E54* 0.0125 54 SampleA_freebayes_ann +NC_045512.2 27423 NC_045512.2;27423;A;T A T 80 79 1 ORF7a 30A>T I10I 0.0125 10 SampleA_freebayes_ann +NC_045512.2 27476 NC_045512.2;27476;C;A C A 39 38 1 ORF7a 83C>A T28K 0.0256410256410256 28 SampleA_freebayes_ann +NC_045512.2 27530 NC_045512.2;27530;T;G T G 29 26 3 ORF7a 137T>G F46C 0.103448275862069 46 SampleA_freebayes_ann +NC_045512.2 27531 NC_045512.2;27531;T;G T G 22 21 1 ORF7a 138T>G F46L 0.0454545454545455 46 SampleA_freebayes_ann +NC_045512.2 27758 NC_045512.2;27758;G;T G T 1 0 1 ORF7b 365G>T Ter122Lext*? 1 1 SampleA_freebayes_ann +NC_045512.2 27841 NC_045512.2;27841;G;T G T 34 33 1 ORF7b 86G>T W29L 0.0294117647058824 29 SampleA_freebayes_ann +NC_045512.2 27880 NC_045512.2;27880;ACG;AG ACG AG 65 52 13 ORF7b 126delC H42fs 0.2 42 SampleA_freebayes_ann +NC_045512.2 27920 NC_045512.2;27920;C;A C A 66 64 2 ORF8 27C>A I9I 0.0303030303030303 9 SampleA_freebayes_ann +NC_045512.2 27944 NC_045512.2;27944;C;T C T 66 53 13 ORF8 51C>T H17H 0.196969696969697 17 SampleA_freebayes_ann +NC_045512.2 27972 NC_045512.2;27972;C;T C T 66 0 66 ORF8 79C>T Q27* 1 27 SampleA_freebayes_ann +NC_045512.2 27998 NC_045512.2;27998;C;A C A 66 64 2 ORF8 105C>A D35E 0.0303030303030303 35 SampleA_freebayes_ann +NC_045512.2 28014 NC_045512.2;28014;T;A T A 66 64 2 ORF8 121T>A F41I 0.0303030303030303 41 SampleA_freebayes_ann +NC_045512.2 28016 NC_045512.2;28016;C;A C A 66 65 1 ORF8 123C>A F41L 0.0151515151515152 41 SampleA_freebayes_ann +NC_045512.2 28043 NC_045512.2;28043;A;T A T 66 64 2 ORF8 150A>T G50G 0.0303030303030303 50 SampleA_freebayes_ann +NC_045512.2 28048 NC_045512.2;28048;G;T G T 66 0 66 ORF8 155G>T R52I 1 52 SampleA_freebayes_ann +NC_045512.2 28077 NC_045512.2;28077;GTGG;TTGA GTGG TTGA 66 65 1 ORF8 184_187delGTGGinsTTGA VD62LN 0.0151515151515152 62 SampleA_freebayes_ann +NC_045512.2 28087 NC_045512.2;28087;C;A C A 58 57 1 ORF8 194C>A A65D 0.0172413793103448 65 SampleA_freebayes_ann +NC_045512.2 28111 NC_045512.2;28111;A;G A G 59 0 59 ORF8 218A>G Y73C 1 73 SampleA_freebayes_ann +NC_045512.2 28121 NC_045512.2;28121;C;A C A 59 58 1 ORF8 228C>A I76I 0.0169491525423729 76 SampleA_freebayes_ann +NC_045512.2 28160 NC_045512.2;28160;T;G T G 52 51 1 ORF8 267T>G N89K 0.0192307692307692 89 SampleA_freebayes_ann +NC_045512.2 28166 NC_045512.2;28166;G;A G A 72 71 1 ORF8 273G>A Q91Q 0.0138888888888889 91 SampleA_freebayes_ann +NC_045512.2 28230 NC_045512.2;28230;G;T G T 54 53 1 ORF8 337G>T D113Y 0.0185185185185185 113 SampleA_freebayes_ann +NC_045512.2 28237 NC_045512.2;28237;G;C G C 54 52 2 ORF8 344G>C R115P 0.037037037037037 115 SampleA_freebayes_ann +NC_045512.2 28280 NC_045512.2;28280;GAT;CTA GAT CTA 54 0 54 N 7_9delGATinsCTA D3L 1 3 SampleA_freebayes_ann +NC_045512.2 28349 NC_045512.2;28349;A;C A C 54 53 1 N 76A>C S26R 0.0185185185185185 26 SampleA_freebayes_ann +NC_045512.2 28372 NC_045512.2;28372;TGGGGCGCGA;TGGGCGCGA TGGGGCGCGA TGGGCGCGA 51 47 1 N 103delG A35fs 0.0196078431372549 33 SampleA_freebayes_ann +NC_045512.2 28372 NC_045512.2;28372;TGGGGCGCGA;TGGGTCGCGA TGGGGCGCGA TGGGTCGCGA 51 47 2 N 103delG A35fs 0.0392156862745098 33 SampleA_freebayes_ann +NC_045512.2 28372 NC_045512.2;28372;TGGGGCGCGA;TGGGGCGCTA TGGGGCGCGA TGGGGCGCTA 51 47 1 N 103delG A35fs 0.0196078431372549 33 SampleA_freebayes_ann +NC_045512.2 28435 NC_045512.2;28435;C;A C A 48 47 1 N 162C>A T54T 0.0208333333333333 54 SampleA_freebayes_ann +NC_045512.2 28461 NC_045512.2;28461;A;C A C 43 42 1 N 188A>C D63A 0.0232558139534884 63 SampleA_freebayes_ann +NC_045512.2 28494 NC_045512.2;28494;T;G T G 37 36 1 N 221T>G I74S 0.027027027027027 74 SampleA_freebayes_ann +NC_045512.2 28501 NC_045512.2;28501;C;A C A 37 36 1 N 228C>A T76T 0.027027027027027 76 SampleA_freebayes_ann +NC_045512.2 28627 NC_045512.2;28627;A;G A G 37 36 1 N 354A>G E118E 0.027027027027027 118 SampleA_freebayes_ann +NC_045512.2 28648 NC_045512.2;28648;T;G T G 37 36 1 N 375T>G A125A 0.027027027027027 125 SampleA_freebayes_ann +NC_045512.2 28719 NC_045512.2;28719;G;A G A 25 24 1 N 446G>A R149H 0.04 149 SampleA_freebayes_ann +NC_045512.2 28739 NC_045512.2;28739;G;T G T 25 19 6 N 466G>T A156S 0.24 156 SampleA_freebayes_ann +NC_045512.2 28767 NC_045512.2;28767;C;A C A 31 30 1 N 494C>A T165K 0.032258064516129 165 SampleA_freebayes_ann +NC_045512.2 28771 NC_045512.2;28771;ATTGC;ATTTGC ATTGC ATTTGC 26 25 1 N 500dupT L167fs 0.0384615384615385 166 SampleA_freebayes_ann +NC_045512.2 28881 NC_045512.2;28881;GGG;AAC GGG AAC 14 0 14 N 608_610delGGGinsAAC RG203KR 1 203 SampleA_freebayes_ann +NC_045512.2 28923 NC_045512.2;28923;C;A C A 14 12 2 N 650C>A A217D 0.142857142857143 217 SampleA_freebayes_ann +NC_045512.2 28942 NC_045512.2;28942;G;T G T 14 13 1 N 669G>T L223L 0.0714285714285714 223 SampleA_freebayes_ann +NC_045512.2 28977 NC_045512.2;28977;C;T C T 14 0 14 N 704C>T S235F 1 235 SampleA_freebayes_ann +NC_045512.2 29438 NC_045512.2;29438;C;T C T 10 9 1 N 1165C>T Q389* 0.1 389 SampleA_freebayes_ann +NC_045512.2 269 NC_045512.2;269;G;C G C 76 75 1 ORF1a 4G>C E2Q 0.0131578947368421 2 SampleB_freebayes_ann +NC_045512.2 276 NC_045512.2;276;T;G T G 75 74 1 ORF1a 11T>G L4R 0.0133333333333333 4 SampleB_freebayes_ann +NC_045512.2 283 NC_045512.2;283;T;G T G 76 75 1 ORF1a 18T>G P6P 0.0131578947368421 6 SampleB_freebayes_ann +NC_045512.2 286 NC_045512.2;286;T;G T G 73 72 1 ORF1a 21T>G G7G 0.0136986301369863 7 SampleB_freebayes_ann +NC_045512.2 306 NC_045512.2;306;T;G T G 74 72 2 ORF1a 41T>G V14G 0.027027027027027 14 SampleB_freebayes_ann +NC_045512.2 307 NC_045512.2;307;C;A C A 74 73 1 ORF1a 42C>A V14V 0.0135135135135135 14 SampleB_freebayes_ann +NC_045512.2 320 NC_045512.2;320;C;T C T 70 69 1 ORF1a 55C>T P19S 0.0142857142857143 19 SampleB_freebayes_ann +NC_045512.2 327 NC_045512.2;327;T;G T G 112 110 2 ORF1a 62T>G L21* 0.0178571428571429 21 SampleB_freebayes_ann +NC_045512.2 332 NC_045512.2;332;G;T G T 96 95 1 ORF1a 67G>T V23F 0.0104166666666667 23 SampleB_freebayes_ann +NC_045512.2 338 NC_045512.2;338;G;T G T 103 100 2 ORF1a 73G>T D25Y 0.0194174757281553 25 SampleB_freebayes_ann +NC_045512.2 343 NC_045512.2;343;G;A G A 110 108 2 ORF1a 78G>A V26V 0.0181818181818182 26 SampleB_freebayes_ann +NC_045512.2 346 NC_045512.2;346;C;T C T 110 83 27 ORF1a 81C>T L27L 0.245454545454545 27 SampleB_freebayes_ann +NC_045512.2 408 NC_045512.2;408;A;T A T 97 96 1 ORF1a 143A>T D48V 0.0103092783505155 48 SampleB_freebayes_ann +NC_045512.2 416 NC_045512.2;416;T;G T G 91 90 1 ORF1a 151T>G C51G 0.010989010989011 51 SampleB_freebayes_ann +NC_045512.2 419 NC_045512.2;419;G;A G A 97 96 1 ORF1a 154G>A G52S 0.0103092783505155 52 SampleB_freebayes_ann +NC_045512.2 421 NC_045512.2;421;C;G C G 98 97 1 ORF1a 156C>G G52G 0.0102040816326531 52 SampleB_freebayes_ann +NC_045512.2 422 NC_045512.2;422;T;G T G 98 97 1 ORF1a 157T>G L53V 0.0102040816326531 53 SampleB_freebayes_ann +NC_045512.2 450 NC_045512.2;450;C;T C T 161 158 2 ORF1a 185C>T P62L 0.0124223602484472 62 SampleB_freebayes_ann +NC_045512.2 452 NC_045512.2;452;C;A C A 162 160 2 ORF1a 187C>A Q63K 0.0123456790123457 63 SampleB_freebayes_ann +NC_045512.2 472 NC_045512.2;472;G;T G T 158 155 3 ORF1a 207G>T V69V 0.0189873417721519 69 SampleB_freebayes_ann +NC_045512.2 474 NC_045512.2;474;T;A T A 164 162 2 ORF1a 209T>A F70Y 0.0121951219512195 70 SampleB_freebayes_ann +NC_045512.2 478 NC_045512.2;478;C;A C A 166 164 2 ORF1a 213C>A I71I 0.0120481927710843 71 SampleB_freebayes_ann +NC_045512.2 501 NC_045512.2;501;C;A C A 166 164 2 ORF1a 236C>A A79E 0.0120481927710843 79 SampleB_freebayes_ann +NC_045512.2 556 NC_045512.2;556;C;T C T 165 163 2 ORF1a 291C>T Y97Y 0.0121212121212121 97 SampleB_freebayes_ann +NC_045512.2 570 NC_045512.2;570;A;G A G 164 161 3 ORF1a 305A>G E102G 0.0182926829268293 102 SampleB_freebayes_ann +NC_045512.2 572 NC_045512.2;572;A;T A T 164 162 2 ORF1a 307A>T T103S 0.0121951219512195 103 SampleB_freebayes_ann +NC_045512.2 576 NC_045512.2;576;T;G T G 162 160 2 ORF1a 311T>G L104R 0.0123456790123457 104 SampleB_freebayes_ann +NC_045512.2 581 NC_045512.2;581;G;T G T 162 160 2 ORF1a 316G>T V106F 0.0123456790123457 106 SampleB_freebayes_ann +NC_045512.2 585 NC_045512.2;585;T;C T C 162 160 2 ORF1a 320T>C L107P 0.0123456790123457 107 SampleB_freebayes_ann +NC_045512.2 601 NC_045512.2;601;C;T C T 160 158 2 ORF1a 336C>T G112G 0.0125 112 SampleB_freebayes_ann +NC_045512.2 604 NC_045512.2;604;A;G A G 160 158 2 ORF1a 339A>G E113E 0.0125 113 SampleB_freebayes_ann +NC_045512.2 627 NC_045512.2;627;T;G T G 118 116 2 ORF1a 362T>G V121G 0.0169491525423729 121 SampleB_freebayes_ann +NC_045512.2 639 NC_045512.2;639;A;C A C 91 90 1 ORF1a 374A>C K125T 0.010989010989011 125 SampleB_freebayes_ann +NC_045512.2 682 NC_045512.2;682;T;C T C 118 59 59 ORF1a 417T>C D139D 0.5 139 SampleB_freebayes_ann +NC_045512.2 723 NC_045512.2;723;C;G C G 96 95 1 ORF1a 458C>G P153R 0.0104166666666667 153 SampleB_freebayes_ann +NC_045512.2 732 NC_045512.2;732;A;C A C 58 57 1 ORF1a 467A>C D156A 0.0172413793103448 156 SampleB_freebayes_ann +NC_045512.2 733 NC_045512.2;733;T;G T G 58 57 1 ORF1a 468T>G D156E 0.0172413793103448 156 SampleB_freebayes_ann +NC_045512.2 743 NC_045512.2;743;A;C A C 62 60 2 ORF1a 478A>C N160H 0.032258064516129 160 SampleB_freebayes_ann +NC_045512.2 754 NC_045512.2;754;T;A T A 62 60 2 ORF1a 489T>A T163T 0.032258064516129 163 SampleB_freebayes_ann +NC_045512.2 757 NC_045512.2;757;A;C A C 62 61 1 ORF1a 492A>C K164N 0.0161290322580645 164 SampleB_freebayes_ann +NC_045512.2 775 NC_045512.2;775;C;T C T 60 59 1 ORF1a 510C>T T170T 0.0166666666666667 170 SampleB_freebayes_ann +NC_045512.2 783 NC_045512.2;783;TC;GT TC GT 61 60 1 ORF1a 518_519delTCinsGT L173R 0.0163934426229508 173 SampleB_freebayes_ann +NC_045512.2 820 NC_045512.2;820;T;G T G 64 63 1 ORF1a 555T>G Y185* 0.015625 185 SampleB_freebayes_ann +NC_045512.2 846 NC_045512.2;846;A;C A C 64 63 1 ORF1a 581A>C D194A 0.015625 194 SampleB_freebayes_ann +NC_045512.2 875 NC_045512.2;875;C;A C A 64 63 1 ORF1a 610C>A L204I 0.015625 204 SampleB_freebayes_ann +NC_045512.2 905 NC_045512.2;905;AC;CA AC CA 64 63 1 ORF1a 640_641delACinsCA T214H 0.015625 214 SampleB_freebayes_ann +NC_045512.2 909 NC_045512.2;909;TGTCCGAA;CGTCTGAA TGTCCGAA CGTCTGAA 63 0 1 ORF1a 644_648delTGTCCinsCGTCT L215S 0.0158730158730159 215 SampleB_freebayes_ann +NC_045512.2 909 NC_045512.2;909;TGTCCGAA;TGTCTGAA TGTCCGAA TGTCTGAA 63 0 61 ORF1a 644_648delTGTCCinsCGTCT L215S 0.968253968253968 215 SampleB_freebayes_ann +NC_045512.2 920 NC_045512.2;920;C;A C A 64 62 1 ORF1a 655C>A L219M 0.015625 219 SampleB_freebayes_ann +NC_045512.2 920 NC_045512.2;920;C;G C G 64 62 1 ORF1a 655C>A L219M 0.015625 219 SampleB_freebayes_ann +NC_045512.2 924 NC_045512.2;924;A;G A G 64 62 2 ORF1a 659A>G D220G 0.03125 220 SampleB_freebayes_ann +NC_045512.2 936 NC_045512.2;936;C;A C A 64 63 1 ORF1a 671C>A T224N 0.015625 224 SampleB_freebayes_ann +NC_045512.2 937 NC_045512.2;937;TAAG;AAAA TAAG AAAA 63 62 1 ORF1a 672_675delTAAGinsAAAA 226 0.0158730158730159 224 SampleB_freebayes_ann +NC_045512.2 943 NC_045512.2;943;G;C G C 63 62 1 ORF1a 678G>C R226S 0.0158730158730159 226 SampleB_freebayes_ann +NC_045512.2 946 NC_045512.2;946;T;G T G 56 55 1 ORF1a 681T>G G227G 0.0178571428571429 227 SampleB_freebayes_ann +NC_045512.2 999 NC_045512.2;999;C;T C T 49 45 4 ORF1a 734C>T S245F 0.0816326530612245 245 SampleB_freebayes_ann +NC_045512.2 1010 NC_045512.2;1010;T;C T C 46 44 2 ORF1a 745T>C Y249H 0.0434782608695652 249 SampleB_freebayes_ann +NC_045512.2 1019 NC_045512.2;1019;C;A C A 42 41 1 ORF1a 754C>A Q252K 0.0238095238095238 252 SampleB_freebayes_ann +NC_045512.2 1040 NC_045512.2;1040;T;G T G 24 23 1 ORF1a 775T>G L259V 0.0416666666666667 259 SampleB_freebayes_ann +NC_045512.2 1060 NC_045512.2;1060;C;T C T 27 25 2 ORF1a 795C>T T265T 0.0740740740740741 265 SampleB_freebayes_ann +NC_045512.2 1069 NC_045512.2;1069;G;C G C 28 26 2 ORF1a 804G>C G268G 0.0714285714285714 268 SampleB_freebayes_ann +NC_045512.2 1083 NC_045512.2;1083;T;G T G 23 22 1 ORF1a 818T>G F273C 0.0434782608695652 273 SampleB_freebayes_ann +NC_045512.2 1085 NC_045512.2;1085;G;T G T 28 27 1 ORF1a 820G>T V274L 0.0357142857142857 274 SampleB_freebayes_ann +NC_045512.2 1092 NC_045512.2;1092;C;A C A 28 27 1 ORF1a 827C>A P276H 0.0357142857142857 276 SampleB_freebayes_ann +NC_045512.2 1116 NC_045512.2;1116;T;G T G 28 27 1 ORF1a 851T>G I284S 0.0357142857142857 284 SampleB_freebayes_ann +NC_045512.2 1209 NC_045512.2;1209;T;A T A 28 27 1 ORF1a 944T>A M315K 0.0357142857142857 315 SampleB_freebayes_ann +NC_045512.2 1218 NC_045512.2;1218;C;A C A 28 27 1 ORF1a 953C>A S318* 0.0357142857142857 318 SampleB_freebayes_ann +NC_045512.2 1232 NC_045512.2;1232;T;G T G 28 27 1 ORF1a 967T>G C323G 0.0357142857142857 323 SampleB_freebayes_ann +NC_045512.2 1310 NC_045512.2;1310;T;G T G 16 15 1 ORF1a 1045T>G L349V 0.0625 349 SampleB_freebayes_ann +NC_045512.2 1441 NC_045512.2;1441;C;T C T 4 0 4 ORF1a 1176C>T G392G 1 392 SampleB_freebayes_ann +NC_045512.2 1952 NC_045512.2;1952;C;T C T 18 17 1 ORF1a 1687C>T Q563* 0.0555555555555556 563 SampleB_freebayes_ann +NC_045512.2 1970 NC_045512.2;1970;A;T A T 27 26 1 ORF1a 1705A>T I569L 0.037037037037037 569 SampleB_freebayes_ann +NC_045512.2 2011 NC_045512.2;2011;T;G T G 27 26 1 ORF1a 1746T>G D582E 0.037037037037037 582 SampleB_freebayes_ann +NC_045512.2 2023 NC_045512.2;2023;C;A C A 28 27 1 ORF1a 1758C>A F586L 0.0357142857142857 586 SampleB_freebayes_ann +NC_045512.2 2024 NC_045512.2;2024;A;G A G 28 26 2 ORF1a 1759A>G T587A 0.0714285714285714 587 SampleB_freebayes_ann +NC_045512.2 2047 NC_045512.2;2047;T;C T C 28 27 1 ORF1a 1782T>C N594N 0.0357142857142857 594 SampleB_freebayes_ann +NC_045512.2 2089 NC_045512.2;2089;G;T G T 28 27 1 ORF1a 1824G>T L608F 0.0357142857142857 608 SampleB_freebayes_ann +NC_045512.2 2124 NC_045512.2;2124;T;A T A 28 27 1 ORF1a 1859T>A V620D 0.0357142857142857 620 SampleB_freebayes_ann +NC_045512.2 2130 NC_045512.2;2130;A;C A C 27 26 1 ORF1a 1865A>C E622A 0.037037037037037 622 SampleB_freebayes_ann +NC_045512.2 2133 NC_045512.2;2133;A;C A C 28 27 1 ORF1a 1868A>C K623T 0.0357142857142857 623 SampleB_freebayes_ann +NC_045512.2 2134 NC_045512.2;2134;A;T A T 28 27 1 ORF1a 1869A>T K623N 0.0357142857142857 623 SampleB_freebayes_ann +NC_045512.2 2136 NC_045512.2;2136;T;C T C 28 26 2 ORF1a 1871T>C L624P 0.0714285714285714 624 SampleB_freebayes_ann +NC_045512.2 2149 NC_045512.2;2149;T;G T G 28 27 1 ORF1a 1884T>G L628L 0.0357142857142857 628 SampleB_freebayes_ann +NC_045512.2 2161 NC_045512.2;2161;A;C A C 28 27 1 ORF1a 1896A>C E632D 0.0357142857142857 632 SampleB_freebayes_ann +NC_045512.2 2176 NC_045512.2;2176;A;T A T 20 19 1 ORF1a 1911A>T E637D 0.05 637 SampleB_freebayes_ann +NC_045512.2 2189 NC_045512.2;2189;C;T C T 16 15 1 ORF1a 1924C>T L642F 0.0625 642 SampleB_freebayes_ann +NC_045512.2 2800 NC_045512.2;2800;T;G T G 4 3 1 ORF1a 2535T>G L845L 0.25 845 SampleB_freebayes_ann +NC_045512.2 2895 NC_045512.2;2895;A;C A C 35 34 1 ORF1a 2630A>C D877A 0.0285714285714286 877 SampleB_freebayes_ann +NC_045512.2 2941 NC_045512.2;2941;A;C A C 51 50 1 ORF1a 2676A>C P892P 0.0196078431372549 892 SampleB_freebayes_ann +NC_045512.2 2955 NC_045512.2;2955;T;G T G 51 50 1 ORF1a 2690T>G L897* 0.0196078431372549 897 SampleB_freebayes_ann +NC_045512.2 2965 NC_045512.2;2965;G;T G T 51 50 1 ORF1a 2700G>T W900C 0.0196078431372549 900 SampleB_freebayes_ann +NC_045512.2 3037 NC_045512.2;3037;C;T C T 52 0 52 ORF1a 2772C>T F924F 1 924 SampleB_freebayes_ann +NC_045512.2 3067 NC_045512.2;3067;T;A T A 52 51 1 ORF1a 2802T>A G934G 0.0192307692307692 934 SampleB_freebayes_ann +NC_045512.2 3076 NC_045512.2;3076;A;C A C 52 51 1 ORF1a 2811A>C E937D 0.0192307692307692 937 SampleB_freebayes_ann +NC_045512.2 3094 NC_045512.2;3094;A;T A T 51 50 1 ORF1a 2829A>T P943P 0.0196078431372549 943 SampleB_freebayes_ann +NC_045512.2 3114 NC_045512.2;3114;G;T G T 51 50 1 ORF1a 2849G>T G950V 0.0196078431372549 950 SampleB_freebayes_ann +NC_045512.2 3216 NC_045512.2;3216;G;T G T 26 20 6 ORF1a 2951G>T S984I 0.230769230769231 984 SampleB_freebayes_ann +NC_045512.2 3222 NC_045512.2;3222;A;C A C 26 25 1 ORF1a 2957A>C Q986P 0.0384615384615385 986 SampleB_freebayes_ann +NC_045512.2 3236 NC_045512.2;3236;C;A C A 48 47 1 ORF1a 2971C>A Q991K 0.0208333333333333 991 SampleB_freebayes_ann +NC_045512.2 3240 NC_045512.2;3240;A;G A G 49 47 2 ORF1a 2975A>G D992G 0.0408163265306122 992 SampleB_freebayes_ann +NC_045512.2 3243 NC_045512.2;3243;G;A G A 49 48 1 ORF1a 2978G>A G993D 0.0204081632653061 993 SampleB_freebayes_ann +NC_045512.2 3252 NC_045512.2;3252;A;G A G 51 49 2 ORF1a 2987A>G D996G 0.0392156862745098 996 SampleB_freebayes_ann +NC_045512.2 3258 NC_045512.2;3258;A;C A C 50 49 1 ORF1a 2993A>C Q998P 0.02 998 SampleB_freebayes_ann +NC_045512.2 3267 NC_045512.2;3267;C;T C T 51 0 51 ORF1a 3002C>T T1001I 1 1001 SampleB_freebayes_ann +NC_045512.2 3285 NC_045512.2;3285;A;G A G 51 50 1 ORF1a 3020A>G E1007G 0.0196078431372549 1007 SampleB_freebayes_ann +NC_045512.2 3291 NC_045512.2;3291;A;C A C 51 50 1 ORF1a 3026A>C Q1009P 0.0196078431372549 1009 SampleB_freebayes_ann +NC_045512.2 3343 NC_045512.2;3343;T;C T C 51 50 1 ORF1a 3078T>C N1026N 0.0196078431372549 1026 SampleB_freebayes_ann +NC_045512.2 3416 NC_045512.2;3416;A;C A C 50 49 1 ORF1a 3151A>C K1051Q 0.02 1051 SampleB_freebayes_ann +NC_045512.2 3425 NC_045512.2;3425;C;A C A 51 50 1 ORF1a 3160C>A P1054T 0.0196078431372549 1054 SampleB_freebayes_ann +NC_045512.2 3426 NC_045512.2;3426;C;A C A 51 50 1 ORF1a 3161C>A P1054Q 0.0196078431372549 1054 SampleB_freebayes_ann +NC_045512.2 3435 NC_045512.2;3435;T;G T G 51 50 1 ORF1a 3170T>G V1057G 0.0196078431372549 1057 SampleB_freebayes_ann +NC_045512.2 3442 NC_045512.2;3442;T;A T A 51 50 1 ORF1a 3177T>A N1059K 0.0196078431372549 1059 SampleB_freebayes_ann +NC_045512.2 3449 NC_045512.2;3449;A;C A C 41 40 1 ORF1a 3184A>C N1062H 0.024390243902439 1062 SampleB_freebayes_ann +NC_045512.2 3454 NC_045512.2;3454;T;G T G 37 35 2 ORF1a 3189T>G V1063V 0.0540540540540541 1063 SampleB_freebayes_ann +NC_045512.2 3459 NC_045512.2;3459;T;G T G 31 30 1 ORF1a 3194T>G L1065R 0.032258064516129 1065 SampleB_freebayes_ann +NC_045512.2 3886 NC_045512.2;3886;TAAAGAGGAAGT;TAAGAGGAAGT TAAAGAGGAAGT TAAGAGGAAGT 8 2 6 ORF1a 3624delA E1209fs 0.75 1207 SampleB_freebayes_ann +NC_045512.2 4064 NC_045512.2;4064;T;C T C 20 19 1 ORF1a 3799T>C S1267P 0.05 1267 SampleB_freebayes_ann +NC_045512.2 4095 NC_045512.2;4095;CTTTC;TTTTT CTTTC TTTTT 17 13 4 ORF1a 3830_3834delCTTTCinsTTTTT T1277I 0.235294117647059 1277 SampleB_freebayes_ann +NC_045512.2 4107 NC_045512.2;4107;A;C A C 18 17 1 ORF1a 3842A>C K1281T 0.0555555555555556 1281 SampleB_freebayes_ann +NC_045512.2 4124 NC_045512.2;4124;G;T G T 24 23 1 ORF1a 3859G>T V1287L 0.0416666666666667 1287 SampleB_freebayes_ann +NC_045512.2 4128 NC_045512.2;4128;G;A G A 29 28 1 ORF1a 3863G>A G1288D 0.0344827586206897 1288 SampleB_freebayes_ann +NC_045512.2 4132 NC_045512.2;4132;T;G T G 29 28 1 ORF1a 3867T>G D1289E 0.0344827586206897 1289 SampleB_freebayes_ann +NC_045512.2 4143 NC_045512.2;4143;A;G A G 32 31 1 ORF1a 3878A>G E1293G 0.03125 1293 SampleB_freebayes_ann +NC_045512.2 4171 NC_045512.2;4171;T;G T G 28 27 1 ORF1a 3906T>G P1302P 0.0357142857142857 1302 SampleB_freebayes_ann +NC_045512.2 4180 NC_045512.2;4180;G;T G T 28 27 1 ORF1a 3915G>T K1305N 0.0357142857142857 1305 SampleB_freebayes_ann +NC_045512.2 4206 NC_045512.2;4206;C;T C T 28 18 10 ORF1a 3941C>T A1314V 0.357142857142857 1314 SampleB_freebayes_ann +NC_045512.2 4226 NC_045512.2;4226;C;T C T 28 26 2 ORF1a 3961C>T P1321S 0.0714285714285714 1321 SampleB_freebayes_ann +NC_045512.2 4341 NC_045512.2;4341;T;G T G 52 51 1 ORF1a 4076T>G I1359S 0.0192307692307692 1359 SampleB_freebayes_ann +NC_045512.2 4393 NC_045512.2;4393;A;C A C 59 58 1 ORF1a 4128A>C R1376R 0.0169491525423729 1376 SampleB_freebayes_ann +NC_045512.2 4395 NC_045512.2;4395;A;C A C 61 60 1 ORF1a 4130A>C E1377A 0.0163934426229508 1377 SampleB_freebayes_ann +NC_045512.2 4403 NC_045512.2;4403;G;C G C 62 61 1 ORF1a 4138G>C A1380P 0.0161290322580645 1380 SampleB_freebayes_ann +NC_045512.2 4404 NC_045512.2;4404;C;A C A 63 62 1 ORF1a 4139C>A A1380E 0.0158730158730159 1380 SampleB_freebayes_ann +NC_045512.2 4420 NC_045512.2;4420;A;G A G 64 62 2 ORF1a 4155A>G T1385T 0.03125 1385 SampleB_freebayes_ann +NC_045512.2 4435 NC_045512.2;4435;T;G T G 50 48 2 ORF1a 4170T>G P1390P 0.04 1390 SampleB_freebayes_ann +NC_045512.2 4442 NC_045512.2;4442;G;A G A 54 52 2 ORF1a 4177G>A V1393M 0.037037037037037 1393 SampleB_freebayes_ann +NC_045512.2 4585 NC_045512.2;4585;T;C T C 54 53 1 ORF1a 4320T>C D1440D 0.0185185185185185 1440 SampleB_freebayes_ann +NC_045512.2 4586 NC_045512.2;4586;C;T C T 54 53 1 ORF1a 4321C>T L1441L 0.0185185185185185 1441 SampleB_freebayes_ann +NC_045512.2 4592 NC_045512.2;4592;G;A G A 53 52 1 ORF1a 4327G>A E1443K 0.0188679245283019 1443 SampleB_freebayes_ann +NC_045512.2 4593 NC_045512.2;4593;A;T A T 53 52 1 ORF1a 4328A>T E1443V 0.0188679245283019 1443 SampleB_freebayes_ann +NC_045512.2 4605 NC_045512.2;4605;C;T C T 34 33 1 ORF1a 4340C>T T1447I 0.0294117647058824 1447 SampleB_freebayes_ann +NC_045512.2 4619 NC_045512.2;4619;T;C T C 31 30 1 ORF1a 4354T>C Y1452H 0.032258064516129 1452 SampleB_freebayes_ann +NC_045512.2 4639 NC_045512.2;4639;T;A T A 33 32 1 ORF1a 4374T>A N1458K 0.0303030303030303 1458 SampleB_freebayes_ann +NC_045512.2 4646 NC_045512.2;4646;G;A G A 33 32 1 ORF1a 4381G>A E1461K 0.0303030303030303 1461 SampleB_freebayes_ann +NC_045512.2 4668 NC_045512.2;4668;C;A C A 36 35 1 ORF1a 4403C>A S1468Y 0.0277777777777778 1468 SampleB_freebayes_ann +NC_045512.2 4688 NC_045512.2;4688;G;T G T 24 23 1 ORF1a 4423G>T V1475F 0.0416666666666667 1475 SampleB_freebayes_ann +NC_045512.2 4693 NC_045512.2;4693;T;A T A 6 5 1 ORF1a 4428T>A S1476S 0.166666666666667 1476 SampleB_freebayes_ann +NC_045512.2 4724 NC_045512.2;4724;A;C A C 12 11 1 ORF1a 4459A>C N1487H 0.0833333333333333 1487 SampleB_freebayes_ann +NC_045512.2 4995 NC_045512.2;4995;T;G T G 14 13 1 ORF1a 4730T>G I1577S 0.0714285714285714 1577 SampleB_freebayes_ann +NC_045512.2 5046 NC_045512.2;5046;T;G T G 16 15 1 ORF1a 4781T>G F1594C 0.0625 1594 SampleB_freebayes_ann +NC_045512.2 5047 NC_045512.2;5047;T;G T G 16 15 1 ORF1a 4782T>G F1594L 0.0625 1594 SampleB_freebayes_ann +NC_045512.2 5060 NC_045512.2;5060;TT;GG TT GG 16 15 1 ORF1a 4795_4796delTTinsGG L1599G 0.0625 1599 SampleB_freebayes_ann +NC_045512.2 5070 NC_045512.2;5070;C;T C T 16 15 1 ORF1a 4805C>T A1602V 0.0625 1602 SampleB_freebayes_ann +NC_045512.2 5184 NC_045512.2;5184;C;A C A 14 13 1 ORF1a 4919C>A P1640H 0.0714285714285714 1640 SampleB_freebayes_ann +NC_045512.2 5192 NC_045512.2;5192;C;T C T 15 13 2 ORF1a 4927C>T L1643L 0.133333333333333 1643 SampleB_freebayes_ann +NC_045512.2 5237 NC_045512.2;5237;T;A T A 13 12 1 ORF1a 4972T>A Y1658N 0.0769230769230769 1658 SampleB_freebayes_ann +NC_045512.2 5260 NC_045512.2;5260;T;C T C 24 23 1 ORF1a 4995T>C T1665T 0.0416666666666667 1665 SampleB_freebayes_ann +NC_045512.2 5330 NC_045512.2;5330;A;G A G 41 40 1 ORF1a 5065A>G K1689E 0.024390243902439 1689 SampleB_freebayes_ann +NC_045512.2 5340 NC_045512.2;5340;C;A C A 44 43 1 ORF1a 5075C>A P1692Q 0.0227272727272727 1692 SampleB_freebayes_ann +NC_045512.2 5341 NC_045512.2;5341;A;T A T 44 43 1 ORF1a 5076A>T P1692P 0.0227272727272727 1692 SampleB_freebayes_ann +NC_045512.2 5354 NC_045512.2;5354;G;A G A 69 68 1 ORF1a 5089G>A D1697N 0.0144927536231884 1697 SampleB_freebayes_ann +NC_045512.2 5368 NC_045512.2;5368;A;G A G 69 68 1 ORF1a 5103A>G R1701R 0.0144927536231884 1701 SampleB_freebayes_ann +NC_045512.2 5388 NC_045512.2;5388;CT;AG CT AG 69 0 1 ORF1a 5123C>A A1708D 0.0144927536231884 1708 SampleB_freebayes_ann +NC_045512.2 5388 NC_045512.2;5388;CT;AT CT AT 69 0 68 ORF1a 5123C>A A1708D 0.985507246376812 1708 SampleB_freebayes_ann +NC_045512.2 5395 NC_045512.2;5395;T;G T G 71 70 1 ORF1a 5130T>G F1710L 0.0140845070422535 1710 SampleB_freebayes_ann +NC_045512.2 5398 NC_045512.2;5398;T;G T G 71 70 1 ORF1a 5133T>G C1711W 0.0140845070422535 1711 SampleB_freebayes_ann +NC_045512.2 5434 NC_045512.2;5434;T;A T A 71 69 1 ORF1a 5169T>A G1723G 0.0140845070422535 1723 SampleB_freebayes_ann +NC_045512.2 5434 NC_045512.2;5434;T;C T C 71 69 1 ORF1a 5169T>A G1723G 0.0140845070422535 1723 SampleB_freebayes_ann +NC_045512.2 5482 NC_045512.2;5482;C;A C A 71 70 1 ORF1a 5217C>A A1739A 0.0140845070422535 1739 SampleB_freebayes_ann +NC_045512.2 5512 NC_045512.2;5512;C;T C T 68 67 1 ORF1a 5247C>T N1749N 0.0147058823529412 1749 SampleB_freebayes_ann +NC_045512.2 5526 NC_045512.2;5526;C;T C T 70 69 1 ORF1a 5261C>T T1754I 0.0142857142857143 1754 SampleB_freebayes_ann +NC_045512.2 5527 NC_045512.2;5527;T;A T A 70 69 1 ORF1a 5262T>A T1754T 0.0142857142857143 1754 SampleB_freebayes_ann +NC_045512.2 5531 NC_045512.2;5531;G;C G C 70 69 1 ORF1a 5266G>C G1756R 0.0142857142857143 1756 SampleB_freebayes_ann +NC_045512.2 5557 NC_045512.2;5557;T;G T G 66 64 2 ORF1a 5292T>G G1764G 0.0303030303030303 1764 SampleB_freebayes_ann +NC_045512.2 5577 NC_045512.2;5577;T;A T A 48 47 1 ORF1a 5312T>A M1771K 0.0208333333333333 1771 SampleB_freebayes_ann +NC_045512.2 5683 NC_045512.2;5683;G;A G A 27 26 1 ORF1a 5418G>A M1806I 0.037037037037037 1806 SampleB_freebayes_ann +NC_045512.2 5696 NC_045512.2;5696;C;A C A 27 26 1 ORF1a 5431C>A P1811T 0.037037037037037 1811 SampleB_freebayes_ann +NC_045512.2 5727 NC_045512.2;5727;T;G T G 27 26 1 ORF1a 5462T>G F1821C 0.037037037037037 1821 SampleB_freebayes_ann +NC_045512.2 5776 NC_045512.2;5776;A;T A T 27 26 1 ORF1a 5511A>T K1837N 0.037037037037037 1837 SampleB_freebayes_ann +NC_045512.2 5789 NC_045512.2;5789;A;C A C 27 26 1 ORF1a 5524A>C K1842Q 0.037037037037037 1842 SampleB_freebayes_ann +NC_045512.2 5830 NC_045512.2;5830;G;A G A 27 26 1 ORF1a 5565G>A K1855K 0.037037037037037 1855 SampleB_freebayes_ann +NC_045512.2 5835 NC_045512.2;5835;C;A C A 27 26 1 ORF1a 5570C>A S1857* 0.037037037037037 1857 SampleB_freebayes_ann +NC_045512.2 5848 NC_045512.2;5848;T;G T G 27 26 1 ORF1a 5583T>G G1861G 0.037037037037037 1861 SampleB_freebayes_ann +NC_045512.2 5850 NC_045512.2;5850;C;A C A 27 26 1 ORF1a 5585C>A P1862H 0.037037037037037 1862 SampleB_freebayes_ann +NC_045512.2 5876 NC_045512.2;5876;AAC;CAG AAC CAG 19 18 1 ORF1a 5611_5613delAACinsCAG N1871Q 0.0526315789473684 1871 SampleB_freebayes_ann +NC_045512.2 5881 NC_045512.2;5881;T;C T C 18 17 1 ORF1a 5616T>C S1872S 0.0555555555555556 1872 SampleB_freebayes_ann +NC_045512.2 5882 NC_045512.2;5882;T;G T G 17 16 1 ORF1a 5617T>G Y1873D 0.0588235294117647 1873 SampleB_freebayes_ann +NC_045512.2 5918 NC_045512.2;5918;G;C G C 15 14 1 ORF1a 5653G>C D1885H 0.0666666666666667 1885 SampleB_freebayes_ann +NC_045512.2 5920 NC_045512.2;5920;T;C T C 15 14 1 ORF1a 5655T>C D1885D 0.0666666666666667 1885 SampleB_freebayes_ann +NC_045512.2 5929 NC_045512.2;5929;T;C T C 15 14 1 ORF1a 5664T>C V1888V 0.0666666666666667 1888 SampleB_freebayes_ann +NC_045512.2 5986 NC_045512.2;5986;CACA;TACC CACA TACC 2 0 1 ORF1a 5721C>T F1907F 0.5 1907 SampleB_freebayes_ann +NC_045512.2 5986 NC_045512.2;5986;CACA;TACA CACA TACA 2 0 1 ORF1a 5721C>T F1907F 0.5 1907 SampleB_freebayes_ann +NC_045512.2 6250 NC_045512.2;6250;C;A C A 22 21 1 ORF1a 5985C>A N1995K 0.0454545454545455 1995 SampleB_freebayes_ann +NC_045512.2 6273 NC_045512.2;6273;ATAAA;CTAAC ATAAA CTAAC 21 20 1 ORF1a 6008_6012delATAAAinsCTAAC YK2003SN 0.0476190476190476 2003 SampleB_freebayes_ann +NC_045512.2 6423 NC_045512.2;6423;A;C A C 21 20 1 ORF1a 6158A>C E2053A 0.0476190476190476 2053 SampleB_freebayes_ann +NC_045512.2 6443 NC_045512.2;6443;G;A G A 22 21 1 ORF1a 6178G>A D2060N 0.0454545454545455 2060 SampleB_freebayes_ann +NC_045512.2 6505 NC_045512.2;6505;A;G A G 15 14 1 ORF1a 6240A>G A2080A 0.0666666666666667 2080 SampleB_freebayes_ann +NC_045512.2 6721 NC_045512.2;6721;A;C A C 9 8 1 ORF1a 6456A>C T2152T 0.111111111111111 2152 SampleB_freebayes_ann +NC_045512.2 7281 NC_045512.2;7281;A;T A T 8 7 1 ORF1a 7016A>T Y2339F 0.125 2339 SampleB_freebayes_ann +NC_045512.2 7313 NC_045512.2;7313;T;C T C 20 19 1 ORF1a 7048T>C F2350L 0.05 2350 SampleB_freebayes_ann +NC_045512.2 7381 NC_045512.2;7381;A;C A C 23 22 1 ORF1a 7116A>C V2372V 0.0434782608695652 2372 SampleB_freebayes_ann +NC_045512.2 7665 NC_045512.2;7665;A;T A T 33 32 1 ORF1a 7400A>T D2467V 0.0303030303030303 2467 SampleB_freebayes_ann +NC_045512.2 7670 NC_045512.2;7670;G;T G T 33 32 1 ORF1a 7405G>T V2469F 0.0303030303030303 2469 SampleB_freebayes_ann +NC_045512.2 7675 NC_045512.2;7675;GAGAG;TAGAT GAGAG TAGAT 29 22 1 ORF1a 7413A>T R2471S 0.0344827586206897 2470 SampleB_freebayes_ann +NC_045512.2 7675 NC_045512.2;7675;GAGAG;GAGTG GAGAG GAGTG 29 22 1 ORF1a 7413A>T R2471S 0.0344827586206897 2470 SampleB_freebayes_ann +NC_045512.2 7675 NC_045512.2;7675;GAGAG;GAGAT GAGAG GAGAT 29 22 5 ORF1a 7413A>T R2471S 0.172413793103448 2470 SampleB_freebayes_ann +NC_045512.2 7695 NC_045512.2;7695;T;C T C 20 19 1 ORF1a 7430T>C F2477S 0.05 2477 SampleB_freebayes_ann +NC_045512.2 7702 NC_045512.2;7702;A;C A C 22 21 1 ORF1a 7437A>C R2479S 0.0454545454545455 2479 SampleB_freebayes_ann +NC_045512.2 7705 NC_045512.2;7705;AAT;GAG AAT GAG 24 23 1 ORF1a 7440_7442delAATinsGAG I2481R 0.0416666666666667 2480 SampleB_freebayes_ann +NC_045512.2 7715 NC_045512.2;7715;A;C A C 25 24 1 ORF1a 7450A>C T2484P 0.04 2484 SampleB_freebayes_ann +NC_045512.2 7718 NC_045512.2;7718;G;A G A 28 27 1 ORF1a 7453G>A D2485N 0.0357142857142857 2485 SampleB_freebayes_ann +NC_045512.2 7742 NC_045512.2;7742;A;G A G 40 39 1 ORF1a 7477A>G S2493G 0.025 2493 SampleB_freebayes_ann +NC_045512.2 7745 NC_045512.2;7745;G;T G T 40 39 1 ORF1a 7480G>T V2494F 0.025 2494 SampleB_freebayes_ann +NC_045512.2 7747 NC_045512.2;7747;T;G T G 40 39 1 ORF1a 7482T>G V2494V 0.025 2494 SampleB_freebayes_ann +NC_045512.2 7761 NC_045512.2;7761;G;T G T 40 39 1 ORF1a 7496G>T G2499V 0.025 2499 SampleB_freebayes_ann +NC_045512.2 7775 NC_045512.2;7775;T;G T G 39 38 1 ORF1a 7510T>G Y2504D 0.0256410256410256 2504 SampleB_freebayes_ann +NC_045512.2 7788 NC_045512.2;7788;C;T C T 40 39 1 ORF1a 7523C>T A2508V 0.025 2508 SampleB_freebayes_ann +NC_045512.2 7807 NC_045512.2;7807;A;T A T 40 39 1 ORF1a 7542A>T E2514D 0.025 2514 SampleB_freebayes_ann +NC_045512.2 7816 NC_045512.2;7816;T;G T G 40 39 1 ORF1a 7551T>G S2517S 0.025 2517 SampleB_freebayes_ann +NC_045512.2 7831 NC_045512.2;7831;T;C T C 40 39 1 ORF1a 7566T>C V2522V 0.025 2522 SampleB_freebayes_ann +NC_045512.2 7846 NC_045512.2;7846;G;A G A 40 39 1 ORF1a 7581G>A L2527L 0.025 2527 SampleB_freebayes_ann +NC_045512.2 7847 NC_045512.2;7847;A;G A G 40 39 1 ORF1a 7582A>G R2528G 0.025 2528 SampleB_freebayes_ann +NC_045512.2 7871 NC_045512.2;7871;T;A T A 39 38 1 ORF1a 7606T>A L2536M 0.0256410256410256 2536 SampleB_freebayes_ann +NC_045512.2 7880 NC_045512.2;7880;A;T A T 39 38 1 ORF1a 7615A>T N2539Y 0.0256410256410256 2539 SampleB_freebayes_ann +NC_045512.2 7881 NC_045512.2;7881;A;C A C 37 36 1 ORF1a 7616A>C N2539T 0.027027027027027 2539 SampleB_freebayes_ann +NC_045512.2 7924 NC_045512.2;7924;T;C T C 36 35 1 ORF1a 7659T>C S2553S 0.0277777777777778 2553 SampleB_freebayes_ann +NC_045512.2 7936 NC_045512.2;7936;G;T G T 26 25 1 ORF1a 7671G>T A2557A 0.0384615384615385 2557 SampleB_freebayes_ann +NC_045512.2 8046 NC_045512.2;8046;A;C A C 37 36 1 ORF1a 7781A>C Y2594S 0.027027027027027 2594 SampleB_freebayes_ann +NC_045512.2 8087 NC_045512.2;8087;A;T A T 37 36 1 ORF1a 7822A>T K2608* 0.027027027027027 2608 SampleB_freebayes_ann +NC_045512.2 8089 NC_045512.2;8089;A;C A C 40 39 1 ORF1a 7824A>C K2608N 0.025 2608 SampleB_freebayes_ann +NC_045512.2 8164 NC_045512.2;8164;T;C T C 40 38 2 ORF1a 7899T>C F2633F 0.05 2633 SampleB_freebayes_ann +NC_045512.2 8196 NC_045512.2;8196;C;T C T 40 39 1 ORF1a 7931C>T S2644L 0.025 2644 SampleB_freebayes_ann +NC_045512.2 8201 NC_045512.2;8201;G;T G T 39 38 1 ORF1a 7936G>T V2646L 0.0256410256410256 2646 SampleB_freebayes_ann +NC_045512.2 8204 NC_045512.2;8204;G;A G A 40 39 1 ORF1a 7939G>A E2647K 0.025 2647 SampleB_freebayes_ann +NC_045512.2 8214 NC_045512.2;8214;A;T A T 40 39 1 ORF1a 7949A>T D2650V 0.025 2650 SampleB_freebayes_ann +NC_045512.2 8242 NC_045512.2;8242;T;C T C 36 34 2 ORF1a 7977T>C H2659H 0.0555555555555556 2659 SampleB_freebayes_ann +NC_045512.2 8253 NC_045512.2;8253;T;A T A 32 31 1 ORF1a 7988T>A I2663K 0.03125 2663 SampleB_freebayes_ann +NC_045512.2 8255 NC_045512.2;8255;G;C G C 30 29 1 ORF1a 7990G>C E2664Q 0.0333333333333333 2664 SampleB_freebayes_ann +NC_045512.2 8304 NC_045512.2;8304;T;C T C 26 25 1 ORF1a 8039T>C V2680A 0.0384615384615385 2680 SampleB_freebayes_ann +NC_045512.2 8325 NC_045512.2;8325;A;G A G 26 25 1 ORF1a 8060A>G D2687G 0.0384615384615385 2687 SampleB_freebayes_ann +NC_045512.2 8398 NC_045512.2;8398;G;T G T 12 11 1 ORF1a 8133G>T L2711F 0.0833333333333333 2711 SampleB_freebayes_ann +NC_045512.2 8535 NC_045512.2;8535;AGA;TGT AGA TGT 12 10 1 ORF1a 8270A>T K2757M 0.0833333333333333 2757 SampleB_freebayes_ann +NC_045512.2 8535 NC_045512.2;8535;AGA;TGA AGA TGA 12 10 1 ORF1a 8270A>T K2757M 0.0833333333333333 2757 SampleB_freebayes_ann +NC_045512.2 8538 NC_045512.2;8538;T;C T C 12 11 1 ORF1a 8273T>C I2758T 0.0833333333333333 2758 SampleB_freebayes_ann +NC_045512.2 8543 NC_045512.2;8543;CT;AC CT AC 12 11 1 ORF1a 8278_8279delCTinsAC L2760T 0.0833333333333333 2760 SampleB_freebayes_ann +NC_045512.2 8551 NC_045512.2;8551;T;G T G 7 6 1 ORF1a 8286T>G G2762G 0.142857142857143 2762 SampleB_freebayes_ann +NC_045512.2 8920 NC_045512.2;8920;A;G A G 19 18 1 ORF1a 8655A>G L2885L 0.0526315789473684 2885 SampleB_freebayes_ann +NC_045512.2 8957 NC_045512.2;8957;A;T A T 29 27 2 ORF1a 8692A>T T2898S 0.0689655172413793 2898 SampleB_freebayes_ann +NC_045512.2 9004 NC_045512.2;9004;TGTTT;GGTTA TGTTT GGTTA 35 31 1 ORF1a 8739T>A C2913* 0.0285714285714286 2913 SampleB_freebayes_ann +NC_045512.2 9004 NC_045512.2;9004;TGTTT;TTTTT TGTTT TTTTT 35 31 1 ORF1a 8739T>A C2913* 0.0285714285714286 2913 SampleB_freebayes_ann +NC_045512.2 9004 NC_045512.2;9004;TGTTT;AGTTT TGTTT AGTTT 35 31 2 ORF1a 8739T>A C2913* 0.0571428571428571 2913 SampleB_freebayes_ann +NC_045512.2 9014 NC_045512.2;9014;G;T G T 35 34 1 ORF1a 8749G>T A2917S 0.0285714285714286 2917 SampleB_freebayes_ann +NC_045512.2 9023 NC_045512.2;9023;AC;TA AC TA 35 34 1 ORF1a 8758_8759delACinsTA T2920* 0.0285714285714286 2920 SampleB_freebayes_ann +NC_045512.2 9051 NC_045512.2;9051;C;A C A 35 34 1 ORF1a 8786C>A P2929Q 0.0285714285714286 2929 SampleB_freebayes_ann +NC_045512.2 9104 NC_045512.2;9104;A;C A C 35 34 1 ORF1a 8839A>C S2947R 0.0285714285714286 2947 SampleB_freebayes_ann +NC_045512.2 9113 NC_045512.2;9113;C;G C G 35 34 1 ORF1a 8848C>G P2950A 0.0285714285714286 2950 SampleB_freebayes_ann +NC_045512.2 9134 NC_045512.2;9134;A;C A C 35 34 1 ORF1a 8869A>C M2957L 0.0285714285714286 2957 SampleB_freebayes_ann +NC_045512.2 9161 NC_045512.2;9161;A;C A C 35 34 1 ORF1a 8896A>C N2966H 0.0285714285714286 2966 SampleB_freebayes_ann +NC_045512.2 9163 NC_045512.2;9163;C;A C A 35 33 2 ORF1a 8898C>A N2966K 0.0571428571428571 2966 SampleB_freebayes_ann +NC_045512.2 9170 NC_045512.2;9170;C;A C A 35 34 1 ORF1a 8905C>A L2969I 0.0285714285714286 2969 SampleB_freebayes_ann +NC_045512.2 9171 NC_045512.2;9171;T;G T G 35 34 1 ORF1a 8906T>G L2969R 0.0285714285714286 2969 SampleB_freebayes_ann +NC_045512.2 9214 NC_045512.2;9214;C;G C G 63 62 1 ORF1a 8949C>G Y2983* 0.0158730158730159 2983 SampleB_freebayes_ann +NC_045512.2 9225 NC_045512.2;9225;G;T G T 75 74 1 ORF1a 8960G>T G2987V 0.0133333333333333 2987 SampleB_freebayes_ann +NC_045512.2 9236 NC_045512.2;9236;A;G A G 74 73 1 ORF1a 8971A>G R2991G 0.0135135135135135 2991 SampleB_freebayes_ann +NC_045512.2 9246 NC_045512.2;9246;C;G C G 75 74 1 ORF1a 8981C>G A2994G 0.0133333333333333 2994 SampleB_freebayes_ann +NC_045512.2 9274 NC_045512.2;9274;A;T A T 70 69 1 ORF1a 9009A>T R3003S 0.0142857142857143 3003 SampleB_freebayes_ann +NC_045512.2 9279 NC_045512.2;9279;T;G T G 73 72 1 ORF1a 9014T>G V3005G 0.0136986301369863 3005 SampleB_freebayes_ann +NC_045512.2 9280 NC_045512.2;9280;A;G A G 76 74 1 ORF1a 9015A>G V3005V 0.0131578947368421 3005 SampleB_freebayes_ann +NC_045512.2 9280 NC_045512.2;9280;A;T A T 76 74 1 ORF1a 9015A>G V3005V 0.0131578947368421 3005 SampleB_freebayes_ann +NC_045512.2 9285 NC_045512.2;9285;A;T A T 98 97 1 ORF1a 9020A>T N3007I 0.0102040816326531 3007 SampleB_freebayes_ann +NC_045512.2 9287 NC_045512.2;9287;A;G A G 98 97 1 ORF1a 9022A>G N3008D 0.0102040816326531 3008 SampleB_freebayes_ann +NC_045512.2 9303 NC_045512.2;9303;CTTTAC;CTTAC CTTTAC CTTAC 102 100 2 ORF1a 9041delT L3014fs 0.0196078431372549 3013 SampleB_freebayes_ann +NC_045512.2 9331 NC_045512.2;9331;T;G T G 99 98 1 ORF1a 9066T>G D3022E 0.0101010101010101 3022 SampleB_freebayes_ann +NC_045512.2 9332 NC_045512.2;9332;G;T G T 99 98 1 ORF1a 9067G>T A3023S 0.0101010101010101 3023 SampleB_freebayes_ann +NC_045512.2 9340 NC_045512.2;9340;T;C T C 104 77 27 ORF1a 9075T>C N3025N 0.259615384615385 3025 SampleB_freebayes_ann +NC_045512.2 9341 NC_045512.2;9341;T;G T G 99 98 1 ORF1a 9076T>G L3026V 0.0101010101010101 3026 SampleB_freebayes_ann +NC_045512.2 9355 NC_045512.2;9355;G;A G A 104 102 2 ORF1a 9090G>A M3030I 0.0192307692307692 3030 SampleB_freebayes_ann +NC_045512.2 9380 NC_045512.2;9380;G;C G C 104 102 2 ORF1a 9115G>C G3039R 0.0192307692307692 3039 SampleB_freebayes_ann +NC_045512.2 9391 NC_045512.2;9391;C;T C T 104 93 11 ORF1a 9126C>T D3042D 0.105769230769231 3042 SampleB_freebayes_ann +NC_045512.2 9474 NC_045512.2;9474;CTTTTGGTGA;CTTTGGTGA CTTTTGGTGA CTTTGGTGA 100 97 2 ORF1a 9213delT F3071fs 0.02 3070 SampleB_freebayes_ann +NC_045512.2 9514 NC_045512.2;9514;A;T A T 99 98 1 ORF1a 9249A>T L3083F 0.0101010101010101 3083 SampleB_freebayes_ann +NC_045512.2 9519 NC_045512.2;9519;T;G T G 97 96 1 ORF1a 9254T>G F3085C 0.0103092783505155 3085 SampleB_freebayes_ann +NC_045512.2 9527 NC_045512.2;9527;T;C T C 89 88 1 ORF1a 9262T>C S3088P 0.0112359550561798 3088 SampleB_freebayes_ann +NC_045512.2 9536 NC_045512.2;9536;G;A G A 89 88 1 ORF1a 9271G>A V3091I 0.0112359550561798 3091 SampleB_freebayes_ann +NC_045512.2 9539 NC_045512.2;9539;C;T C T 91 89 2 ORF1a 9274C>T L3092F 0.021978021978022 3092 SampleB_freebayes_ann +NC_045512.2 9543 NC_045512.2;9543;G;T G T 95 94 1 ORF1a 9278G>T C3093F 0.0105263157894737 3093 SampleB_freebayes_ann +NC_045512.2 9584 NC_045512.2;9584;G;T G T 112 110 2 ORF1a 9319G>T V3107F 0.0178571428571429 3107 SampleB_freebayes_ann +NC_045512.2 9592 NC_045512.2;9592;C;T C T 89 88 1 ORF1a 9327C>T Y3109Y 0.0112359550561798 3109 SampleB_freebayes_ann +NC_045512.2 9596 NC_045512.2;9596;T;G T G 90 89 1 ORF1a 9331T>G Y3111D 0.0111111111111111 3111 SampleB_freebayes_ann +NC_045512.2 9605 NC_045512.2;9605;T;G T G 86 85 1 ORF1a 9340T>G F3114V 0.0116279069767442 3114 SampleB_freebayes_ann +NC_045512.2 9623 NC_045512.2;9623;GTTTC;TTTTA GTTTC TTTTA 90 89 1 ORF1a 9358_9362delGTTTCinsTTTTA VS3120FY 0.0111111111111111 3120 SampleB_freebayes_ann +NC_045512.2 9636 NC_045512.2;9636;C;T C T 90 88 2 ORF1a 9371C>T A3124V 0.0222222222222222 3124 SampleB_freebayes_ann +NC_045512.2 9685 NC_045512.2;9685;A;T A T 90 89 1 ORF1a 9420A>T I3140I 0.0111111111111111 3140 SampleB_freebayes_ann +NC_045512.2 9695 NC_045512.2;9695;TAT;TT TAT TT 90 88 2 ORF1a 9431delA Y3144fs 0.0222222222222222 3144 SampleB_freebayes_ann +NC_045512.2 9702 NC_045512.2;9702;T;G T G 90 89 1 ORF1a 9437T>G I3146S 0.0111111111111111 3146 SampleB_freebayes_ann +NC_045512.2 9705 NC_045512.2;9705;G;A G A 90 88 2 ORF1a 9440G>A C3147Y 0.0222222222222222 3147 SampleB_freebayes_ann +NC_045512.2 9725 NC_045512.2;9725;T;A T A 89 87 2 ORF1a 9460T>A Y3154N 0.0224719101123596 3154 SampleB_freebayes_ann +NC_045512.2 9746 NC_045512.2;9746;C;T C T 89 88 1 ORF1a 9481C>T L3161L 0.0112359550561798 3161 SampleB_freebayes_ann +NC_045512.2 9753 NC_045512.2;9753;G;A G A 88 87 1 ORF1a 9488G>A R3163K 0.0113636363636364 3163 SampleB_freebayes_ann +NC_045512.2 9760 NC_045512.2;9760;A;G A G 90 88 2 ORF1a 9495A>G V3165V 0.0222222222222222 3165 SampleB_freebayes_ann +NC_045512.2 9762 NC_045512.2;9762;T;C T C 90 89 1 ORF1a 9497T>C V3166A 0.0111111111111111 3166 SampleB_freebayes_ann +NC_045512.2 9773 NC_045512.2;9773;G;T G T 87 86 1 ORF1a 9508G>T V3170F 0.0114942528735632 3170 SampleB_freebayes_ann +NC_045512.2 9779 NC_045512.2;9779;T;G T G 70 69 1 ORF1a 9514T>G F3172V 0.0142857142857143 3172 SampleB_freebayes_ann +NC_045512.2 9781 NC_045512.2;9781;T;C T C 67 66 1 ORF1a 9516T>C F3172F 0.0149253731343284 3172 SampleB_freebayes_ann +NC_045512.2 9785 NC_045512.2;9785;A;G A G 70 68 1 ORF1a 9520A>G T3174A 0.0142857142857143 3174 SampleB_freebayes_ann +NC_045512.2 9785 NC_045512.2;9785;A;T A T 70 68 1 ORF1a 9520A>G T3174A 0.0142857142857143 3174 SampleB_freebayes_ann +NC_045512.2 9789 NC_045512.2;9789;T;C T C 71 70 1 ORF1a 9524T>C F3175S 0.0140845070422535 3175 SampleB_freebayes_ann +NC_045512.2 9807 NC_045512.2;9807;G;A G A 76 74 1 ORF1a 9542G>A C3181Y 0.0131578947368421 3181 SampleB_freebayes_ann +NC_045512.2 9807 NC_045512.2;9807;G;T G T 76 74 1 ORF1a 9542G>A C3181Y 0.0131578947368421 3181 SampleB_freebayes_ann +NC_045512.2 9820 NC_045512.2;9820;A;G A G 76 75 1 ORF1a 9555A>G L3185L 0.0131578947368421 3185 SampleB_freebayes_ann +NC_045512.2 9843 NC_045512.2;9843;T;G T G 69 68 1 ORF1a 9578T>G L3193W 0.0144927536231884 3193 SampleB_freebayes_ann +NC_045512.2 9856 NC_045512.2;9856;G;A G A 60 59 1 ORF1a 9591G>A V3197V 0.0166666666666667 3197 SampleB_freebayes_ann +NC_045512.2 9872 NC_045512.2;9872;C;A C A 49 48 1 ORF1a 9607C>A Q3203K 0.0204081632653061 3203 SampleB_freebayes_ann +NC_045512.2 9879 NC_045512.2;9879;A;G A G 55 54 1 ORF1a 9614A>G N3205S 0.0181818181818182 3205 SampleB_freebayes_ann +NC_045512.2 9960 NC_045512.2;9960;G;A G A 57 55 2 ORF1a 9695G>A C3232Y 0.0350877192982456 3232 SampleB_freebayes_ann +NC_045512.2 9981 NC_045512.2;9981;A;C A C 57 56 1 ORF1a 9716A>C N3239T 0.0175438596491228 3239 SampleB_freebayes_ann +NC_045512.2 10027 NC_045512.2;10027;A;C A C 57 56 1 ORF1a 9762A>C Q3254H 0.0175438596491228 3254 SampleB_freebayes_ann +NC_045512.2 10040 NC_045512.2;10040;T;C T C 56 54 2 ORF1a 9775T>C S3259P 0.0357142857142857 3259 SampleB_freebayes_ann +NC_045512.2 10041 NC_045512.2;10041;C;A C A 53 52 1 ORF1a 9776C>A S3259* 0.0188679245283019 3259 SampleB_freebayes_ann +NC_045512.2 10048 NC_045512.2;10048;T;C T C 54 27 27 ORF1a 9783T>C V3261V 0.5 3261 SampleB_freebayes_ann +NC_045512.2 10050 NC_045512.2;10050;TG;AA TG AA 54 53 1 ORF1a 9785_9786delTGinsAA L3262* 0.0185185185185185 3262 SampleB_freebayes_ann +NC_045512.2 10053 NC_045512.2;10053;A;C A C 54 53 1 ORF1a 9788A>C Q3263P 0.0185185185185185 3263 SampleB_freebayes_ann +NC_045512.2 10067 NC_045512.2;10067;A;G A G 55 53 2 ORF1a 9802A>G K3268E 0.0363636363636364 3268 SampleB_freebayes_ann +NC_045512.2 10076 NC_045512.2;10076;T;A T A 53 52 1 ORF1a 9811T>A F3271I 0.0188679245283019 3271 SampleB_freebayes_ann +NC_045512.2 10082 NC_045512.2;10082;T;A T A 77 76 1 ORF1a 9817T>A S3273T 0.012987012987013 3273 SampleB_freebayes_ann +NC_045512.2 10084 NC_045512.2;10084;T;G T G 77 76 1 ORF1a 9819T>G S3273S 0.012987012987013 3273 SampleB_freebayes_ann +NC_045512.2 10099 NC_045512.2;10099;T;C T C 62 61 1 ORF1a 9834T>C G3278G 0.0161290322580645 3278 SampleB_freebayes_ann +NC_045512.2 10144 NC_045512.2;10144;T;C T C 58 57 1 ORF1a 9879T>C L3293L 0.0172413793103448 3293 SampleB_freebayes_ann +NC_045512.2 10157 NC_045512.2;10157;G;T G T 63 62 1 ORF1a 9892G>T V3298L 0.0158730158730159 3298 SampleB_freebayes_ann +NC_045512.2 10176 NC_045512.2;10176;A;G A G 51 50 1 ORF1a 9911A>G H3304R 0.0196078431372549 3304 SampleB_freebayes_ann +NC_045512.2 10208 NC_045512.2;10208;C;A C A 51 50 1 ORF1a 9943C>A P3315T 0.0196078431372549 3315 SampleB_freebayes_ann +NC_045512.2 10212 NC_045512.2;10212;A;T A T 52 51 1 ORF1a 9947A>T N3316I 0.0192307692307692 3316 SampleB_freebayes_ann +NC_045512.2 10215 NC_045512.2;10215;A;G A G 51 50 1 ORF1a 9950A>G Y3317C 0.0196078431372549 3317 SampleB_freebayes_ann +NC_045512.2 10233 NC_045512.2;10233;G;A G A 52 51 1 ORF1a 9968G>A R3323H 0.0192307692307692 3323 SampleB_freebayes_ann +NC_045512.2 10244 NC_045512.2;10244;C;T C T 52 51 1 ORF1a 9979C>T H3327Y 0.0192307692307692 3327 SampleB_freebayes_ann +NC_045512.2 10278 NC_045512.2;10278;TCA;ACC TCA ACC 52 51 1 ORF1a 10013_10015delTCAinsACC L3338H 0.0192307692307692 3338 SampleB_freebayes_ann +NC_045512.2 10291 NC_045512.2;10291;A;C A C 52 51 1 ORF1a 10026A>C G3342G 0.0192307692307692 3342 SampleB_freebayes_ann +NC_045512.2 10298 NC_045512.2;10298;A;C A C 52 51 1 ORF1a 10033A>C M3345L 0.0192307692307692 3345 SampleB_freebayes_ann +NC_045512.2 10300 NC_045512.2;10300;G;A G A 52 50 2 ORF1a 10035G>A M3345I 0.0384615384615385 3345 SampleB_freebayes_ann +NC_045512.2 10331 NC_045512.2;10331;A;C A C 47 46 1 ORF1a 10066A>C T3356P 0.0212765957446809 3356 SampleB_freebayes_ann +NC_045512.2 10339 NC_045512.2;10339;T;A T A 50 49 1 ORF1a 10074T>A N3358K 0.02 3358 SampleB_freebayes_ann +NC_045512.2 10364 NC_045512.2;10364;G;T G T 51 50 1 ORF1a 10099G>T V3367F 0.0196078431372549 3367 SampleB_freebayes_ann +NC_045512.2 10485 NC_045512.2;10485;C;T C T 6 5 1 ORF1a 10220C>T S3407L 0.166666666666667 3407 SampleB_freebayes_ann +NC_045512.2 10618 NC_045512.2;10618;G;A G A 6 4 2 ORF1a 10353G>A R3451R 0.333333333333333 3451 SampleB_freebayes_ann +NC_045512.2 10693 NC_045512.2;10693;A;G A G 26 25 1 ORF1a 10428A>G I3476M 0.0384615384615385 3476 SampleB_freebayes_ann +NC_045512.2 10821 NC_045512.2;10821;A;G A G 46 44 2 ORF1a 10556A>G Q3519R 0.0434782608695652 3519 SampleB_freebayes_ann +NC_045512.2 10846 NC_045512.2;10846;GT;TG GT TG 48 47 1 ORF1a 10581_10582delGTinsTG MC3527IG 0.0208333333333333 3527 SampleB_freebayes_ann +NC_045512.2 10942 NC_045512.2;10942;T;G T G 48 47 1 ORF1a 10677T>G V3559V 0.0208333333333333 3559 SampleB_freebayes_ann +NC_045512.2 10947 NC_045512.2;10947;G;T G T 48 47 1 ORF1a 10682G>T R3561I 0.0208333333333333 3561 SampleB_freebayes_ann +NC_045512.2 10963 NC_045512.2;10963;T;G T G 46 44 2 ORF1a 10698T>G V3566V 0.0434782608695652 3566 SampleB_freebayes_ann +NC_045512.2 10969 NC_045512.2;10969;C;T C T 29 28 1 ORF1a 10704C>T F3568F 0.0344827586206897 3568 SampleB_freebayes_ann +NC_045512.2 11069 NC_045512.2;11069;T;A T A 49 48 1 ORF1a 10804T>A L3602M 0.0204081632653061 3602 SampleB_freebayes_ann +NC_045512.2 11074 NC_045512.2;11074;CTTTTTTTTGTATGA;CTTTTTTTTTGTATGA CTTTTTTTTGTATGA CTTTTTTTTTGTATGA 39 37 1 ORF1a 10817dupT L3606fs 0.0256410256410256 3603 SampleB_freebayes_ann +NC_045512.2 11094 NC_045512.2;11094;C;T C T 63 62 1 ORF1a 10829C>T A3610V 0.0158730158730159 3610 SampleB_freebayes_ann +NC_045512.2 11111 NC_045512.2;11111;A;T A T 64 62 2 ORF1a 10846A>T M3616L 0.03125 3616 SampleB_freebayes_ann +NC_045512.2 11113 NC_045512.2;11113;G;T G T 64 63 1 ORF1a 10848G>T M3616I 0.015625 3616 SampleB_freebayes_ann +NC_045512.2 11120 NC_045512.2;11120;A;T A T 65 64 1 ORF1a 10855A>T I3619F 0.0153846153846154 3619 SampleB_freebayes_ann +NC_045512.2 11122 NC_045512.2;11122;T;G T G 65 64 1 ORF1a 10857T>G I3619M 0.0153846153846154 3619 SampleB_freebayes_ann +NC_045512.2 11130 NC_045512.2;11130;C;T C T 64 63 1 ORF1a 10865C>T S3622F 0.015625 3622 SampleB_freebayes_ann +NC_045512.2 11133 NC_045512.2;11133;C;T C T 65 64 1 ORF1a 10868C>T A3623V 0.0153846153846154 3623 SampleB_freebayes_ann +NC_045512.2 11144 NC_045512.2;11144;A;C A C 65 64 1 ORF1a 10879A>C M3627L 0.0153846153846154 3627 SampleB_freebayes_ann +NC_045512.2 11192 NC_045512.2;11192;T;G T G 65 64 1 ORF1a 10927T>G S3643A 0.0153846153846154 3643 SampleB_freebayes_ann +NC_045512.2 11213 NC_045512.2;11213;T;G T G 65 64 1 ORF1a 10948T>G F3650V 0.0153846153846154 3650 SampleB_freebayes_ann +NC_045512.2 11240 NC_045512.2;11240;T;C T C 65 63 2 ORF1a 10975T>C W3659R 0.0307692307692308 3659 SampleB_freebayes_ann +NC_045512.2 11243 NC_045512.2;11243;G;T G T 64 58 6 ORF1a 10978G>T V3660L 0.09375 3660 SampleB_freebayes_ann +NC_045512.2 11246 NC_045512.2;11246;A;G A G 65 64 1 ORF1a 10981A>G M3661V 0.0153846153846154 3661 SampleB_freebayes_ann +NC_045512.2 11248 NC_045512.2;11248;G;T G T 65 64 1 ORF1a 10983G>T M3661I 0.0153846153846154 3661 SampleB_freebayes_ann +NC_045512.2 11255 NC_045512.2;11255;A;T A T 64 63 1 ORF1a 10990A>T M3664L 0.015625 3664 SampleB_freebayes_ann +NC_045512.2 11270 NC_045512.2;11270;A;C A C 65 64 1 ORF1a 11005A>C M3669L 0.0153846153846154 3669 SampleB_freebayes_ann +NC_045512.2 11287 NC_045512.2;11287;GTCTGGTTTTA;GA GTCTGGTTTTA GA 57 0 57 ORF1a 11023_11031delTCTGGTTTT S3675_F3677del 1 3674 SampleB_freebayes_ann +NC_045512.2 11326 NC_045512.2;11326;A;C A C 66 65 1 ORF1a 11061A>C S3687S 0.0151515151515152 3687 SampleB_freebayes_ann +NC_045512.2 11332 NC_045512.2;11332;A;T A T 72 71 1 ORF1a 11067A>T V3689V 0.0138888888888889 3689 SampleB_freebayes_ann +NC_045512.2 11382 NC_045512.2;11382;G;A G A 71 70 1 ORF1a 11117G>A R3706K 0.0140845070422535 3706 SampleB_freebayes_ann +NC_045512.2 11384 NC_045512.2;11384;A;G A G 70 69 1 ORF1a 11119A>G R3707G 0.0142857142857143 3707 SampleB_freebayes_ann +NC_045512.2 11392 NC_045512.2;11392;G;T G T 71 69 2 ORF1a 11127G>T W3709C 0.028169014084507 3709 SampleB_freebayes_ann +NC_045512.2 11395 NC_045512.2;11395;A;T A T 72 71 1 ORF1a 11130A>T T3710T 0.0138888888888889 3710 SampleB_freebayes_ann +NC_045512.2 11409 NC_045512.2;11409;T;C T C 78 77 1 ORF1a 11144T>C L3715S 0.0128205128205128 3715 SampleB_freebayes_ann +NC_045512.2 11415 NC_045512.2;11415;T;G T G 78 77 1 ORF1a 11150T>G L3717R 0.0128205128205128 3717 SampleB_freebayes_ann +NC_045512.2 11417 NC_045512.2;11417;G;T G T 78 77 1 ORF1a 11152G>T V3718F 0.0128205128205128 3718 SampleB_freebayes_ann +NC_045512.2 11421 NC_045512.2;11421;A;T A T 79 78 1 ORF1a 11156A>T Y3719F 0.0126582278481013 3719 SampleB_freebayes_ann +NC_045512.2 11435 NC_045512.2;11435;G;C G C 78 76 1 ORF1a 11170G>C G3724R 0.0128205128205128 3724 SampleB_freebayes_ann +NC_045512.2 11435 NC_045512.2;11435;G;T G T 78 76 1 ORF1a 11170G>C G3724R 0.0128205128205128 3724 SampleB_freebayes_ann +NC_045512.2 11449 NC_045512.2;11449;T;G T G 76 75 1 ORF1a 11184T>G D3728E 0.0131578947368421 3728 SampleB_freebayes_ann +NC_045512.2 11480 NC_045512.2;11480;T;C T C 79 78 1 ORF1a 11215T>C S3739P 0.0126582278481013 3739 SampleB_freebayes_ann +NC_045512.2 11508 NC_045512.2;11508;T;A T A 79 78 1 ORF1a 11243T>A V3748D 0.0126582278481013 3748 SampleB_freebayes_ann +NC_045512.2 11522 NC_045512.2;11522;T;G T G 79 19 60 ORF1a 11257T>G F3753V 0.759493670886076 3753 SampleB_freebayes_ann +NC_045512.2 11529 NC_045512.2;11529;C;T C T 79 77 2 ORF1a 11264C>T A3755V 0.0253164556962025 3755 SampleB_freebayes_ann +NC_045512.2 11533 NC_045512.2;11533;A;C A C 79 78 1 ORF1a 11268A>C R3756S 0.0126582278481013 3756 SampleB_freebayes_ann +NC_045512.2 11536 NC_045512.2;11536;T;G T G 79 78 1 ORF1a 11271T>G G3757G 0.0126582278481013 3757 SampleB_freebayes_ann +NC_045512.2 11549 NC_045512.2;11549;T;A T A 79 78 1 ORF1a 11284T>A C3762S 0.0126582278481013 3762 SampleB_freebayes_ann +NC_045512.2 11559 NC_045512.2;11559;A;T A T 97 96 1 ORF1a 11294A>T Y3765F 0.0103092783505155 3765 SampleB_freebayes_ann +NC_045512.2 11562 NC_045512.2;11562;G;T G T 98 95 3 ORF1a 11297G>T C3766F 0.0306122448979592 3766 SampleB_freebayes_ann +NC_045512.2 11565 NC_045512.2;11565;C;A C A 98 96 1 ORF1a 11300C>A P3767H 0.0102040816326531 3767 SampleB_freebayes_ann +NC_045512.2 11565 NC_045512.2;11565;C;T C T 98 96 1 ORF1a 11300C>A P3767H 0.0102040816326531 3767 SampleB_freebayes_ann +NC_045512.2 11567 NC_045512.2;11567;A;C A C 99 95 1 ORF1a 11302A>C I3768L 0.0101010101010101 3768 SampleB_freebayes_ann +NC_045512.2 11567 NC_045512.2;11567;A;G A G 99 95 2 ORF1a 11302A>C I3768L 0.0202020202020202 3768 SampleB_freebayes_ann +NC_045512.2 11567 NC_045512.2;11567;A;T A T 99 95 1 ORF1a 11302A>C I3768L 0.0101010101010101 3768 SampleB_freebayes_ann +NC_045512.2 11578 NC_045512.2;11578;A;T A T 96 95 1 ORF1a 11313A>T I3771I 0.0104166666666667 3771 SampleB_freebayes_ann +NC_045512.2 11583 NC_045512.2;11583;G;T G T 98 96 2 ORF1a 11318G>T G3773V 0.0204081632653061 3773 SampleB_freebayes_ann +NC_045512.2 11584 NC_045512.2;11584;T;C T C 98 96 2 ORF1a 11319T>C G3773G 0.0204081632653061 3773 SampleB_freebayes_ann +NC_045512.2 11595 NC_045512.2;11595;A;T A T 96 95 1 ORF1a 11330A>T Q3777L 0.0104166666666667 3777 SampleB_freebayes_ann +NC_045512.2 11598 NC_045512.2;11598;G;T G T 96 95 1 ORF1a 11333G>T C3778F 0.0104166666666667 3778 SampleB_freebayes_ann +NC_045512.2 11601 NC_045512.2;11601;T;C T C 95 94 1 ORF1a 11336T>C I3779T 0.0105263157894737 3779 SampleB_freebayes_ann +NC_045512.2 11613 NC_045512.2;11613;A;G A G 77 76 1 ORF1a 11348A>G Y3783C 0.012987012987013 3783 SampleB_freebayes_ann +NC_045512.2 11618 NC_045512.2;11618;T;C T C 73 72 1 ORF1a 11353T>C F3785L 0.0136986301369863 3785 SampleB_freebayes_ann +NC_045512.2 11636 NC_045512.2;11636;A;T A T 72 71 1 ORF1a 11371A>T T3791S 0.0138888888888889 3791 SampleB_freebayes_ann +NC_045512.2 11650 NC_045512.2;11650;C;T C T 83 82 1 ORF1a 11385C>T G3795G 0.0120481927710843 3795 SampleB_freebayes_ann +NC_045512.2 11651 NC_045512.2;11651;C;T C T 83 82 1 ORF1a 11386C>T L3796F 0.0120481927710843 3796 SampleB_freebayes_ann +NC_045512.2 11652 NC_045512.2;11652;T;G T G 84 83 1 ORF1a 11387T>G L3796R 0.0119047619047619 3796 SampleB_freebayes_ann +NC_045512.2 11705 NC_045512.2;11705;T;G T G 48 47 1 ORF1a 11440T>G L3814V 0.0208333333333333 3814 SampleB_freebayes_ann +NC_045512.2 11743 NC_045512.2;11743;G;T G T 49 47 2 ORF1a 11478G>T Q3826H 0.0408163265306122 3826 SampleB_freebayes_ann +NC_045512.2 11782 NC_045512.2;11782;A;G A G 49 43 6 ORF1a 11517A>G K3839K 0.122448979591837 3839 SampleB_freebayes_ann +NC_045512.2 11783 NC_045512.2;11783;C;A C A 49 48 1 ORF1a 11518C>A L3840I 0.0204081632653061 3840 SampleB_freebayes_ann +NC_045512.2 11791 NC_045512.2;11791;T;C T C 49 48 1 ORF1a 11526T>C I3842I 0.0204081632653061 3842 SampleB_freebayes_ann +NC_045512.2 11806 NC_045512.2;11806;TGGT;GGGA TGGT GGGA 45 44 1 ORF1a 11541_11544delTGGTinsGGGA 3849 0.0222222222222222 3847 SampleB_freebayes_ann +NC_045512.2 11812 NC_045512.2;11812;C;G C G 49 47 2 ORF1a 11547C>G G3849G 0.0408163265306122 3849 SampleB_freebayes_ann +NC_045512.2 11828 NC_045512.2;11828;G;A G A 49 46 3 ORF1a 11563G>A V3855I 0.0612244897959184 3855 SampleB_freebayes_ann +NC_045512.2 11847 NC_045512.2;11847;A;C A C 46 45 1 ORF1a 11582A>C K3861T 0.0217391304347826 3861 SampleB_freebayes_ann +NC_045512.2 11874 NC_045512.2;11874;T;G T G 102 100 2 ORF1a 11609T>G V3870G 0.0196078431372549 3870 SampleB_freebayes_ann +NC_045512.2 11960 NC_045512.2;11960;C;A C A 169 166 2 ORF1a 11695C>A L3899I 0.0118343195266272 3899 SampleB_freebayes_ann +NC_045512.2 11966 NC_045512.2;11966;G;A G A 177 174 2 ORF1a 11701G>A A3901T 0.0112994350282486 3901 SampleB_freebayes_ann +NC_045512.2 11997 NC_045512.2;11997;T;C T C 181 179 2 ORF1a 11732T>C M3911T 0.0110497237569061 3911 SampleB_freebayes_ann +NC_045512.2 12002 NC_045512.2;12002;T;G T G 174 172 2 ORF1a 11737T>G S3913A 0.0114942528735632 3913 SampleB_freebayes_ann +NC_045512.2 12003 NC_045512.2;12003;C;T C T 178 176 2 ORF1a 11738C>T S3913L 0.0112359550561798 3913 SampleB_freebayes_ann +NC_045512.2 12060 NC_045512.2;12060;A;G A G 181 179 2 ORF1a 11795A>G E3932G 0.0110497237569061 3932 SampleB_freebayes_ann +NC_045512.2 12064 NC_045512.2;12064;A;G A G 181 179 2 ORF1a 11799A>G E3933E 0.0110497237569061 3933 SampleB_freebayes_ann +NC_045512.2 12086 NC_045512.2;12086;T;A T A 181 179 2 ORF1a 11821T>A L3941I 0.0110497237569061 3941 SampleB_freebayes_ann +NC_045512.2 12186 NC_045512.2;12186;A;C A C 190 188 2 ORF1a 11921A>C E3974A 0.0105263157894737 3974 SampleB_freebayes_ann +NC_045512.2 12205 NC_045512.2;12205;G;T G T 241 227 14 ORF1a 11940G>T L3980F 0.0580912863070539 3980 SampleB_freebayes_ann +NC_045512.2 12332 NC_045512.2;12332;G;A G A 174 172 2 ORF1a 12067G>A A4023T 0.0114942528735632 4023 SampleB_freebayes_ann +NC_045512.2 12370 NC_045512.2;12370;T;C T C 172 169 2 ORF1a 12105T>C T4035T 0.0116279069767442 4035 SampleB_freebayes_ann +NC_045512.2 12393 NC_045512.2;12393;A;T A T 174 172 2 ORF1a 12128A>T D4043V 0.0114942528735632 4043 SampleB_freebayes_ann +NC_045512.2 12408 NC_045512.2;12408;T;A T A 167 164 3 ORF1a 12143T>A I4048N 0.0179640718562874 4048 SampleB_freebayes_ann +NC_045512.2 12459 NC_045512.2;12459;C;T C T 167 140 27 ORF1a 12194C>T T4065I 0.161676646706587 4065 SampleB_freebayes_ann +NC_045512.2 12485 NC_045512.2;12485;A;G A G 152 150 2 ORF1a 12220A>G I4074V 0.0131578947368421 4074 SampleB_freebayes_ann +NC_045512.2 12545 NC_045512.2;12545;G;A G A 142 140 2 ORF1a 12280G>A A4094T 0.0140845070422535 4094 SampleB_freebayes_ann +NC_045512.2 12548 NC_045512.2;12548;T;G T G 140 138 2 ORF1a 12283T>G L4095V 0.0142857142857143 4095 SampleB_freebayes_ann +NC_045512.2 12583 NC_045512.2;12583;TAAAATTG;TAAATTG TAAAATTG TAAATTG 143 141 2 ORF1a 12322delA I4108fs 0.013986013986014 4106 SampleB_freebayes_ann +NC_045512.2 12617 NC_045512.2;12617;A;T A T 143 141 2 ORF1a 12352A>T N4118Y 0.013986013986014 4118 SampleB_freebayes_ann +NC_045512.2 12757 NC_045512.2;12757;T;C T C 165 163 2 ORF1a 12492T>C T4164T 0.0121212121212121 4164 SampleB_freebayes_ann +NC_045512.2 12798 NC_045512.2;12798;G;T G T 218 197 21 ORF1a 12533G>T G4178V 0.0963302752293578 4178 SampleB_freebayes_ann +NC_045512.2 12883 NC_045512.2;12883;T;C T C 186 182 4 ORF1a 12618T>C Y4206Y 0.021505376344086 4206 SampleB_freebayes_ann +NC_045512.2 12892 NC_045512.2;12892;G;A G A 186 184 2 ORF1a 12627G>A L4209L 0.010752688172043 4209 SampleB_freebayes_ann +NC_045512.2 12903 NC_045512.2;12903;G;T G T 186 155 31 ORF1a 12638G>T C4213F 0.166666666666667 4213 SampleB_freebayes_ann +NC_045512.2 12935 NC_045512.2;12935;A;G A G 186 184 2 ORF1a 12670A>G K4224E 0.010752688172043 4224 SampleB_freebayes_ann +NC_045512.2 13117 NC_045512.2;13117;A;G A G 210 184 26 ORF1a 12852A>G L4284L 0.123809523809524 4284 SampleB_freebayes_ann +NC_045512.2 13142 NC_045512.2;13142;A;G A G 210 207 3 ORF1a 12877A>G N4293D 0.0142857142857143 4293 SampleB_freebayes_ann +NC_045512.2 13156 NC_045512.2;13156;G;T G T 211 165 45 ORF1a 12891G>T M4297I 0.213270142180095 4297 SampleB_freebayes_ann +NC_045512.2 13378 NC_045512.2;13378;C;A C A 174 172 2 ORF1a 13113C>A T4371T 0.0114942528735632 4371 SampleB_freebayes_ann +NC_045512.2 13395 NC_045512.2;13395;A;T A T 144 141 2 ORF1a 13130A>T K4377I 0.0138888888888889 4377 SampleB_freebayes_ann +NC_045512.2 13416 NC_045512.2;13416;A;C A C 141 139 2 ORF1a 13151A>C D4384A 0.0141843971631206 4384 SampleB_freebayes_ann +NC_045512.2 13453 NC_045512.2;13453;A;T A T 142 140 2 ORF1b 13188A>T A4396A 0.0140845070422535 4 SampleB_freebayes_ann +NC_045512.2 13474 NC_045512.2;13474;T;C T C 143 141 2 ORF1b 13210T>C C4404R 0.013986013986014 11 SampleB_freebayes_ann +NC_045512.2 13501 NC_045512.2;13501;C;T C T 143 141 2 ORF1b 13237C>T P4413S 0.013986013986014 20 SampleB_freebayes_ann +NC_045512.2 13524 NC_045512.2;13524;T;C T C 143 141 2 ORF1b 13260T>C T4420T 0.013986013986014 28 SampleB_freebayes_ann +NC_045512.2 13535 NC_045512.2;13535;A;G A G 143 141 2 ORF1b 13271A>G Y4424C 0.013986013986014 32 SampleB_freebayes_ann +NC_045512.2 13547 NC_045512.2;13547;A;G A G 143 141 2 ORF1b 13283A>G D4428G 0.013986013986014 36 SampleB_freebayes_ann +NC_045512.2 13569 NC_045512.2;13569;T;C T C 143 141 2 ORF1b 13305T>C A4435A 0.013986013986014 43 SampleB_freebayes_ann +NC_045512.2 13584 NC_045512.2;13584;C;T C T 143 141 2 ORF1b 13320C>T F4440F 0.013986013986014 48 SampleB_freebayes_ann +NC_045512.2 13595 NC_045512.2;13595;A;C A C 142 140 2 ORF1b 13331A>C N4444T 0.0140845070422535 52 SampleB_freebayes_ann +NC_045512.2 13687 NC_045512.2;13687;G;A G A 199 197 2 ORF1b 13423G>A E4475K 0.0100502512562814 82 SampleB_freebayes_ann +NC_045512.2 13844 NC_045512.2;13844;A;C A C 164 162 2 ORF1b 13580A>C D4527A 0.0121951219512195 135 SampleB_freebayes_ann +NC_045512.2 13847 NC_045512.2;13847;A;C A C 163 161 2 ORF1b 13583A>C E4528A 0.0122699386503067 136 SampleB_freebayes_ann +NC_045512.2 13893 NC_045512.2;13893;TTGT;TT TTGT TT 153 150 2 ORF1b 13632_13633delTG C4544fs 0.0130718954248366 151 SampleB_freebayes_ann +NC_045512.2 13899 NC_045512.2;13899;T;G T G 152 150 2 ORF1b 13635T>G D4545E 0.0131578947368421 153 SampleB_freebayes_ann +NC_045512.2 13900 NC_045512.2;13900;G;A G A 146 144 2 ORF1b 13636G>A D4546N 0.0136986301369863 153 SampleB_freebayes_ann +NC_045512.2 13909 NC_045512.2;13909;T;C T C 103 101 2 ORF1b 13645T>C F4549L 0.0194174757281553 156 SampleB_freebayes_ann +NC_045512.2 13995 NC_045512.2;13995;T;G T G 89 88 1 ORF1b 13731T>G A4577A 0.0112359550561798 185 SampleB_freebayes_ann +NC_045512.2 14045 NC_045512.2;14045;T;G T G 141 137 4 ORF1b 13781T>G V4594G 0.0283687943262411 202 SampleB_freebayes_ann +NC_045512.2 14088 NC_045512.2;14088;G;A G A 147 145 2 ORF1b 13824G>A W4608* 0.0136054421768707 216 SampleB_freebayes_ann +NC_045512.2 14204 NC_045512.2;14204;C;A C A 147 145 2 ORF1b 13940C>A S4647* 0.0136054421768707 255 SampleB_freebayes_ann +NC_045512.2 14251 NC_045512.2;14251;T;A T A 121 119 2 ORF1b 13987T>A L4663I 0.0165289256198347 270 SampleB_freebayes_ann +NC_045512.2 14332 NC_045512.2;14332;T;C T C 107 105 2 ORF1b 14068T>C C4690R 0.0186915887850467 297 SampleB_freebayes_ann +NC_045512.2 14380 NC_045512.2;14380;A;C A C 108 106 2 ORF1b 14116A>C N4706H 0.0185185185185185 313 SampleB_freebayes_ann +NC_045512.2 14408 NC_045512.2;14408;C;T C T 108 0 108 ORF1b 14144C>T P4715L 1 323 SampleB_freebayes_ann +NC_045512.2 14442 NC_045512.2;14442;T;C T C 108 102 6 ORF1b 14178T>C F4726F 0.0555555555555556 334 SampleB_freebayes_ann +NC_045512.2 14505 NC_045512.2;14505;T;A T A 104 102 2 ORF1b 14241T>A H4747Q 0.0192307692307692 355 SampleB_freebayes_ann +NC_045512.2 14509 NC_045512.2;14509;C;T C T 78 77 1 ORF1b 14245C>T Q4749* 0.0128205128205128 356 SampleB_freebayes_ann +NC_045512.2 14521 NC_045512.2;14521;T;G T G 69 68 1 ORF1b 14257T>G L4753V 0.0144927536231884 360 SampleB_freebayes_ann +NC_045512.2 14547 NC_045512.2;14547;G;A G A 89 88 1 ORF1b 14283G>A K4761K 0.0112359550561798 369 SampleB_freebayes_ann +NC_045512.2 14549 NC_045512.2;14549;A;G A G 96 95 1 ORF1b 14285A>G E4762G 0.0104166666666667 370 SampleB_freebayes_ann +NC_045512.2 14593 NC_045512.2;14593;G;C G C 99 98 1 ORF1b 14329G>C G4777R 0.0101010101010101 384 SampleB_freebayes_ann +NC_045512.2 14612 NC_045512.2;14612;A;C A C 81 80 1 ORF1b 14348A>C K4783T 0.0123456790123457 391 SampleB_freebayes_ann +NC_045512.2 14623 NC_045512.2;14623;T;A T A 92 91 1 ORF1b 14359T>A C4787S 0.0108695652173913 394 SampleB_freebayes_ann +NC_045512.2 14626 NC_045512.2;14626;T;C T C 94 93 1 ORF1b 14362T>C F4788L 0.0106382978723404 395 SampleB_freebayes_ann +NC_045512.2 14631 NC_045512.2;14631;A;G A G 134 131 2 ORF1b 14367A>G S4789S 0.0149253731343284 397 SampleB_freebayes_ann +NC_045512.2 14637 NC_045512.2;14637;T;C T C 135 133 2 ORF1b 14373T>C A4791A 0.0148148148148148 399 SampleB_freebayes_ann +NC_045512.2 14660 NC_045512.2;14660;T;A T A 136 133 2 ORF1b 14396T>A F4799Y 0.0147058823529412 407 SampleB_freebayes_ann +NC_045512.2 14676 NC_045512.2;14676;C;T C T 136 0 136 ORF1b 14412C>T P4804P 1 412 SampleB_freebayes_ann +NC_045512.2 14711 NC_045512.2;14711;T;C T C 136 134 2 ORF1b 14447T>C V4816A 0.0147058823529412 424 SampleB_freebayes_ann +NC_045512.2 14750 NC_045512.2;14750;TAAAACACT;TAAACACT TAAAACACT TAAACACT 136 132 2 ORF1b 14490delA K4830fs 0.0147058823529412 437 SampleB_freebayes_ann +NC_045512.2 14750 NC_045512.2;14750;TAAAACACT;TAAAGCACT TAAAACACT TAAAGCACT 136 132 2 ORF1b 14490delA K4830fs 0.0147058823529412 437 SampleB_freebayes_ann +NC_045512.2 14816 NC_045512.2;14816;A;G A G 136 134 2 ORF1b 14552A>G N4851S 0.0147058823529412 459 SampleB_freebayes_ann +NC_045512.2 14846 NC_045512.2;14846;T;C T C 120 117 3 ORF1b 14582T>C L4861P 0.025 469 SampleB_freebayes_ann +NC_045512.2 14849 NC_045512.2;14849;T;G T G 97 96 1 ORF1b 14585T>G L4862R 0.0103092783505155 470 SampleB_freebayes_ann +NC_045512.2 14885 NC_045512.2;14885;G;T G T 98 85 13 ORF1b 14621G>T C4874F 0.13265306122449 482 SampleB_freebayes_ann +NC_045512.2 14937 NC_045512.2;14937;C;A C A 61 60 1 ORF1b 14673C>A D4891E 0.0163934426229508 499 SampleB_freebayes_ann +NC_045512.2 14950 NC_045512.2;14950;T;G T G 89 88 1 ORF1b 14686T>G F4896V 0.0112359550561798 503 SampleB_freebayes_ann +NC_045512.2 14980 NC_045512.2;14980;C;T C T 93 92 1 ORF1b 14716C>T L4906F 0.010752688172043 513 SampleB_freebayes_ann +NC_045512.2 14984 NC_045512.2;14984;A;T A T 93 92 1 ORF1b 14720A>T Y4907F 0.010752688172043 515 SampleB_freebayes_ann +NC_045512.2 14992 NC_045512.2;14992;T;G T G 89 88 1 ORF1b 14728T>G S4910A 0.0112359550561798 517 SampleB_freebayes_ann +NC_045512.2 14998 NC_045512.2;14998;A;G A G 93 92 1 ORF1b 14734A>G S4912G 0.010752688172043 519 SampleB_freebayes_ann +NC_045512.2 15024 NC_045512.2;15024;CGCAT;AGCAG CGCAT AGCAG 93 92 1 ORF1b 14760_14764delCGCATinsAGCAG FAY4920LAD 0.010752688172043 528 SampleB_freebayes_ann +NC_045512.2 15036 NC_045512.2;15036;A;G A G 93 90 2 ORF1b 14772A>T K4924N 0.021505376344086 532 SampleB_freebayes_ann +NC_045512.2 15036 NC_045512.2;15036;A;T A T 93 90 1 ORF1b 14772A>T K4924N 0.010752688172043 532 SampleB_freebayes_ann +NC_045512.2 15063 NC_045512.2;15063;A;G A G 93 91 2 ORF1b 14799A>G Q4933Q 0.021505376344086 541 SampleB_freebayes_ann +NC_045512.2 15073 NC_045512.2;15073;A;G A G 93 91 2 ORF1b 14809A>G K4937E 0.021505376344086 544 SampleB_freebayes_ann +NC_045512.2 15104 NC_045512.2;15104;G;T G T 93 92 1 ORF1b 14840G>T R4947L 0.010752688172043 555 SampleB_freebayes_ann +NC_045512.2 15107 NC_045512.2;15107;C;A C A 93 92 1 ORF1b 14843C>A T4948N 0.010752688172043 556 SampleB_freebayes_ann +NC_045512.2 15118 NC_045512.2;15118;G;T G T 93 92 1 ORF1b 14854G>T V4952F 0.010752688172043 559 SampleB_freebayes_ann +NC_045512.2 15130 NC_045512.2;15130;A;C A C 92 91 1 ORF1b 14866A>C S4956R 0.0108695652173913 563 SampleB_freebayes_ann +NC_045512.2 15138 NC_045512.2;15138;G;T G T 90 89 1 ORF1b 14874G>T M4958I 0.0111111111111111 566 SampleB_freebayes_ann +NC_045512.2 15163 NC_045512.2;15163;T;A T A 90 89 1 ORF1b 14899T>A L4967I 0.0111111111111111 574 SampleB_freebayes_ann +NC_045512.2 15164 NC_045512.2;15164;T;G T G 90 89 1 ORF1b 14900T>G L4967* 0.0111111111111111 575 SampleB_freebayes_ann +NC_045512.2 15246 NC_045512.2;15246;A;T A T 98 97 1 ORF1b 14982A>T L4994F 0.0102040816326531 602 SampleB_freebayes_ann +NC_045512.2 15247 NC_045512.2;15247;A;C A C 75 74 1 ORF1b 14983A>C K4995Q 0.0133333333333333 602 SampleB_freebayes_ann +NC_045512.2 15257 NC_045512.2;15257;A;T A T 83 82 1 ORF1b 14993A>T Y4998F 0.0120481927710843 606 SampleB_freebayes_ann +NC_045512.2 15259 NC_045512.2;15259;A;G A G 93 90 2 ORF1b 14995A>G S4999G 0.021505376344086 606 SampleB_freebayes_ann +NC_045512.2 15259 NC_045512.2;15259;A;T A T 93 90 1 ORF1b 14995A>G S4999G 0.010752688172043 606 SampleB_freebayes_ann +NC_045512.2 15270 NC_045512.2;15270;A;C A C 127 124 3 ORF1b 15006A>C E5002D 0.0236220472440945 610 SampleB_freebayes_ann +NC_045512.2 15279 NC_045512.2;15279;C;T C T 129 0 128 ORF1b 15015C>T H5005H 0.992248062015504 613 SampleB_freebayes_ann +NC_045512.2 15285 NC_045512.2;15285;G;T G T 130 128 2 ORF1b 15021G>T M5007I 0.0153846153846154 615 SampleB_freebayes_ann +NC_045512.2 15341 NC_045512.2;15341;C;T C T 131 129 2 ORF1b 15077C>T A5026V 0.0152671755725191 634 SampleB_freebayes_ann +NC_045512.2 15364 NC_045512.2;15364;C;T C T 131 129 2 ORF1b 15100C>T H5034Y 0.0152671755725191 641 SampleB_freebayes_ann +NC_045512.2 15422 NC_045512.2;15422;A;C A C 129 127 2 ORF1b 15158A>C Q5053P 0.0155038759689922 661 SampleB_freebayes_ann +NC_045512.2 15442 NC_045512.2;15442;A;G A G 128 126 2 ORF1b 15178A>G M5060V 0.015625 667 SampleB_freebayes_ann +NC_045512.2 15488 NC_045512.2;15488;G;T G T 114 102 12 ORF1b 15224G>T G5075V 0.105263157894737 683 SampleB_freebayes_ann +NC_045512.2 15577 NC_045512.2;15577;A;C A C 71 70 1 ORF1b 15313A>C N5105H 0.0140845070422535 712 SampleB_freebayes_ann +NC_045512.2 15610 NC_045512.2;15610;C;A C A 96 95 1 ORF1b 15346C>A Q5116K 0.0104166666666667 723 SampleB_freebayes_ann +NC_045512.2 15613 NC_045512.2;15613;C;T C T 95 94 1 ORF1b 15349C>T H5117Y 0.0105263157894737 724 SampleB_freebayes_ann +NC_045512.2 15626 NC_045512.2;15626;A;G A G 94 93 1 ORF1b 15362A>G E5121G 0.0106382978723404 729 SampleB_freebayes_ann +NC_045512.2 15631 NC_045512.2;15631;C;T C T 96 95 1 ORF1b 15367C>T L5123F 0.0104166666666667 730 SampleB_freebayes_ann +NC_045512.2 15634 NC_045512.2;15634;T;C T C 96 94 2 ORF1b 15370T>C Y5124H 0.0208333333333333 731 SampleB_freebayes_ann +NC_045512.2 15642 NC_045512.2;15642;T;G T G 94 93 1 ORF1b 15378T>G N5126K 0.0106382978723404 734 SampleB_freebayes_ann +NC_045512.2 15644 NC_045512.2;15644;G;C G C 96 95 1 ORF1b 15380G>C R5127T 0.0104166666666667 735 SampleB_freebayes_ann +NC_045512.2 15726 NC_045512.2;15726;T;C T C 93 92 1 ORF1b 15462T>C A5154A 0.010752688172043 762 SampleB_freebayes_ann +NC_045512.2 15756 NC_045512.2;15756;T;C T C 95 94 1 ORF1b 15492T>C S5164S 0.0105263157894737 772 SampleB_freebayes_ann +NC_045512.2 15761 NC_045512.2;15761;G;T G T 96 95 1 ORF1b 15497G>T G5166V 0.0104166666666667 774 SampleB_freebayes_ann +NC_045512.2 15767 NC_045512.2;15767;TG;GT TG GT 96 95 1 ORF1b 15503_15504delTGinsGT V5168G 0.0104166666666667 776 SampleB_freebayes_ann +NC_045512.2 15771 NC_045512.2;15771;T;C T C 95 94 1 ORF1b 15507T>C A5169A 0.0105263157894737 777 SampleB_freebayes_ann +NC_045512.2 15780 NC_045512.2;15780;G;A G A 63 62 1 ORF1b 15516G>A K5172K 0.0158730158730159 780 SampleB_freebayes_ann +NC_045512.2 15790 NC_045512.2;15790;T;C T C 58 57 1 ORF1b 15526T>C S5176P 0.0172413793103448 783 SampleB_freebayes_ann +NC_045512.2 15797 NC_045512.2;15797;T;C T C 54 53 1 ORF1b 15533T>C L5178P 0.0185185185185185 786 SampleB_freebayes_ann +NC_045512.2 15823 NC_045512.2;15823;T;C T C 47 46 1 ORF1b 15559T>C S5187P 0.0212765957446809 794 SampleB_freebayes_ann +NC_045512.2 15891 NC_045512.2;15891;A;C A C 93 92 1 ORF1b 15627A>C T5209T 0.010752688172043 817 SampleB_freebayes_ann +NC_045512.2 15918 NC_045512.2;15918;T;C T C 156 154 2 ORF1b 15654T>C Y5218Y 0.0128205128205128 826 SampleB_freebayes_ann +NC_045512.2 15934 NC_045512.2;15934;C;G C G 159 157 2 ORF1b 15670C>G P5224A 0.0125786163522013 831 SampleB_freebayes_ann +NC_045512.2 15965 NC_045512.2;15965;G;T G T 155 153 2 ORF1b 15701G>T C5234F 0.0129032258064516 842 SampleB_freebayes_ann +NC_045512.2 15983 NC_045512.2;15983;T;A T A 161 158 2 ORF1b 15719T>A V5240E 0.0124223602484472 848 SampleB_freebayes_ann +NC_045512.2 16109 NC_045512.2;16109;A;C A C 157 155 2 ORF1b 15845A>C K5282T 0.0127388535031847 890 SampleB_freebayes_ann +NC_045512.2 16112 NC_045512.2;16112;T;C T C 157 155 2 ORF1b 15848T>C L5283P 0.0127388535031847 891 SampleB_freebayes_ann +NC_045512.2 16119 NC_045512.2;16119;T;A T A 172 170 2 ORF1b 15855T>A D5285E 0.0116279069767442 893 SampleB_freebayes_ann +NC_045512.2 16124 NC_045512.2;16124;T;G T G 170 165 5 ORF1b 15860T>G L5287* 0.0294117647058824 895 SampleB_freebayes_ann +NC_045512.2 16176 NC_045512.2;16176;T;C T C 115 0 115 ORF1b 15912T>C T5304T 1 912 SampleB_freebayes_ann +NC_045512.2 16218 NC_045512.2;16218;A;C A C 82 79 1 ORF1b 15954A>C T5318T 0.0121951219512195 926 SampleB_freebayes_ann +NC_045512.2 16218 NC_045512.2;16218;A;G A G 82 79 2 ORF1b 15954A>C T5318T 0.024390243902439 926 SampleB_freebayes_ann +NC_045512.2 16233 NC_045512.2;16233;AC;CA AC CA 83 82 1 ORF1b 15969_15970delACinsCA LQ5323FK 0.0120481927710843 931 SampleB_freebayes_ann +NC_045512.2 16246 NC_045512.2;16246;G;T G T 85 84 1 ORF1b 15982G>T A5328S 0.0117647058823529 935 SampleB_freebayes_ann +NC_045512.2 16247 NC_045512.2;16247;C;G C G 85 84 1 ORF1b 15983C>G A5328G 0.0117647058823529 936 SampleB_freebayes_ann +NC_045512.2 16255 NC_045512.2;16255;C;T C T 84 82 2 ORF1b 15991C>T L5331F 0.0238095238095238 938 SampleB_freebayes_ann +NC_045512.2 16259 NC_045512.2;16259;G;A G A 85 83 2 ORF1b 15995G>A C5332Y 0.0235294117647059 940 SampleB_freebayes_ann +NC_045512.2 16260 NC_045512.2;16260;C;A C A 85 84 1 ORF1b 15996C>A C5332* 0.0117647058823529 940 SampleB_freebayes_ann +NC_045512.2 16270 NC_045512.2;16270;A;G A G 86 85 1 ORF1b 16006A>G T5336A 0.0116279069767442 943 SampleB_freebayes_ann +NC_045512.2 16293 NC_045512.2;16293;C;T C T 86 84 2 ORF1b 16029C>T C5343C 0.0232558139534884 951 SampleB_freebayes_ann +NC_045512.2 16302 NC_045512.2;16302;A;C A C 86 85 1 ORF1b 16038A>C R5346S 0.0116279069767442 954 SampleB_freebayes_ann +NC_045512.2 16306 NC_045512.2;16306;T;A T A 86 85 1 ORF1b 16042T>A F5348I 0.0116279069767442 955 SampleB_freebayes_ann +NC_045512.2 16315 NC_045512.2;16315;T;C T C 86 84 2 ORF1b 16051T>C C5351R 0.0232558139534884 958 SampleB_freebayes_ann +NC_045512.2 16348 NC_045512.2;16348;T;C T C 86 84 2 ORF1b 16084T>C S5362P 0.0232558139534884 969 SampleB_freebayes_ann +NC_045512.2 16355 NC_045512.2;16355;A;G A G 86 85 1 ORF1b 16091A>G K5364R 0.0116279069767442 972 SampleB_freebayes_ann +NC_045512.2 16373 NC_045512.2;16373;A;C A C 83 82 1 ORF1b 16109A>C N5370T 0.0120481927710843 978 SampleB_freebayes_ann +NC_045512.2 16376 NC_045512.2;16376;C;A C A 85 84 1 ORF1b 16112C>A P5371Q 0.0117647058823529 979 SampleB_freebayes_ann +NC_045512.2 16384 NC_045512.2;16384;T;G T G 85 84 1 ORF1b 16120T>G C5374G 0.0117647058823529 981 SampleB_freebayes_ann +NC_045512.2 16409 NC_045512.2;16409;C;A C A 84 82 2 ORF1b 16145C>A T5382K 0.0238095238095238 990 SampleB_freebayes_ann +NC_045512.2 16415 NC_045512.2;16415;T;G T G 82 79 3 ORF1b 16151T>G V5384G 0.0365853658536585 992 SampleB_freebayes_ann +NC_045512.2 16420 NC_045512.2;16420;C;T C T 71 70 1 ORF1b 16156C>T Q5386* 0.0140845070422535 993 SampleB_freebayes_ann +NC_045512.2 16437 NC_045512.2;16437;T;G T G 64 63 1 ORF1b 16173T>G G5391G 0.015625 999 SampleB_freebayes_ann +NC_045512.2 16485 NC_045512.2;16485;G;A G A 63 62 1 ORF1b 16221G>A L5407L 0.0158730158730159 1015 SampleB_freebayes_ann +NC_045512.2 16495 NC_045512.2;16495;G;C G C 52 51 1 ORF1b 16231G>C G5411R 0.0192307692307692 1018 SampleB_freebayes_ann +NC_045512.2 16536 NC_045512.2;16536;C;T C T 30 28 2 ORF1b 16272C>T S5424S 0.0666666666666667 1032 SampleB_freebayes_ann +NC_045512.2 16553 NC_045512.2;16553;T;G T G 32 31 1 ORF1b 16289T>G F5430C 0.03125 1038 SampleB_freebayes_ann +NC_045512.2 16565 NC_045512.2;16565;C;T C T 32 30 2 ORF1b 16301C>T A5434V 0.0625 1042 SampleB_freebayes_ann +NC_045512.2 16610 NC_045512.2;16610;C;A C A 32 31 1 ORF1b 16346C>A T5449N 0.03125 1057 SampleB_freebayes_ann +NC_045512.2 16693 NC_045512.2;16693;A;C A C 32 31 1 ORF1b 16429A>C T5477P 0.03125 1084 SampleB_freebayes_ann +NC_045512.2 16706 NC_045512.2;16706;T;G T G 32 31 1 ORF1b 16442T>G V5481G 0.03125 1089 SampleB_freebayes_ann +NC_045512.2 16708 NC_045512.2;16708;C;A C A 32 31 1 ORF1b 16444C>A L5482M 0.03125 1089 SampleB_freebayes_ann +NC_045512.2 16735 NC_045512.2;16735;T;A T A 22 21 1 ORF1b 16471T>A W5491R 0.0454545454545455 1098 SampleB_freebayes_ann +NC_045512.2 16908 NC_045512.2;16908;T;G T G 15 14 1 ORF1b 16644T>G Y5548* 0.0666666666666667 1156 SampleB_freebayes_ann +NC_045512.2 17027 NC_045512.2;17027;G;T G T 16 15 1 ORF1b 16763G>T S5588I 0.0625 1196 SampleB_freebayes_ann +NC_045512.2 17030 NC_045512.2;17030;A;C A C 16 15 1 ORF1b 16766A>C N5589T 0.0625 1197 SampleB_freebayes_ann +NC_045512.2 17067 NC_045512.2;17067;T;A T A 64 61 3 ORF1b 16803T>A Y5601* 0.046875 1209 SampleB_freebayes_ann +NC_045512.2 17072 NC_045512.2;17072;CAC;CC CAC CC 71 70 1 ORF1b 16809delA L5604fs 0.0140845070422535 1211 SampleB_freebayes_ann +NC_045512.2 17080 NC_045512.2;17080;G;T G T 79 78 1 ORF1b 16816G>T G5606* 0.0126582278481013 1213 SampleB_freebayes_ann +NC_045512.2 17089 NC_045512.2;17089;G;T G T 82 81 1 ORF1b 16825G>T G5609C 0.0121951219512195 1216 SampleB_freebayes_ann +NC_045512.2 17096 NC_045512.2;17096;G;T G T 85 84 1 ORF1b 16832G>T G5611V 0.0117647058823529 1219 SampleB_freebayes_ann +NC_045512.2 17113 NC_045512.2;17113;A;G A G 90 89 1 ORF1b 16849A>G I5617V 0.0111111111111111 1224 SampleB_freebayes_ann +NC_045512.2 17134 NC_045512.2;17134;C;T C T 94 93 1 ORF1b 16870C>T P5624S 0.0106382978723404 1231 SampleB_freebayes_ann +NC_045512.2 17171 NC_045512.2;17171;C;T C T 161 159 2 ORF1b 16907C>T A5636V 0.0124223602484472 1244 SampleB_freebayes_ann +NC_045512.2 17180 NC_045512.2;17180;A;T A T 160 158 2 ORF1b 16916A>T D5639V 0.0125 1247 SampleB_freebayes_ann +NC_045512.2 17185 NC_045512.2;17185;C;T C T 161 158 2 ORF1b 16921C>T L5641L 0.0124223602484472 1248 SampleB_freebayes_ann +NC_045512.2 17195 NC_045512.2;17195;A;T A T 161 159 2 ORF1b 16931A>T K5644M 0.0124223602484472 1252 SampleB_freebayes_ann +NC_045512.2 17208 NC_045512.2;17208;T;G T G 157 153 4 ORF1b 16944T>G Y5648* 0.0254777070063694 1256 SampleB_freebayes_ann +NC_045512.2 17211 NC_045512.2;17211;G;T G T 162 160 2 ORF1b 16947G>T L5649F 0.0123456790123457 1257 SampleB_freebayes_ann +NC_045512.2 17278 NC_045512.2;17278;G;T G T 162 144 18 ORF1b 17014G>T V5672L 0.111111111111111 1279 SampleB_freebayes_ann +NC_045512.2 17331 NC_045512.2;17331;G;T G T 160 158 2 ORF1b 17067G>T E5689D 0.0125 1297 SampleB_freebayes_ann +NC_045512.2 17363 NC_045512.2;17363;T;A T A 156 153 3 ORF1b 17099T>A I5700N 0.0192307692307692 1308 SampleB_freebayes_ann +NC_045512.2 17365 NC_045512.2;17365;T;C T C 158 156 2 ORF1b 17101T>C S5701P 0.0126582278481013 1308 SampleB_freebayes_ann +NC_045512.2 17484 NC_045512.2;17484;A;T A T 147 145 2 ORF1b 17220A>T T5740T 0.0136054421768707 1348 SampleB_freebayes_ann +NC_045512.2 17500 NC_045512.2;17500;T;C T C 147 145 2 ORF1b 17236T>C F5746L 0.0136054421768707 1353 SampleB_freebayes_ann +NC_045512.2 17523 NC_045512.2;17523;G;T G T 147 145 2 ORF1b 17259G>T M5753I 0.0136054421768707 1361 SampleB_freebayes_ann +NC_045512.2 17661 NC_045512.2;17661;T;A T A 146 144 2 ORF1b 17397T>A F5799L 0.0136986301369863 1407 SampleB_freebayes_ann +NC_045512.2 17679 NC_045512.2;17679;G;C G C 182 180 2 ORF1b 17415G>C T5805T 0.010989010989011 1413 SampleB_freebayes_ann +NC_045512.2 17681 NC_045512.2;17681;A;G A G 171 169 2 ORF1b 17417A>G H5806R 0.0116959064327485 1414 SampleB_freebayes_ann +NC_045512.2 17807 NC_045512.2;17807;A;G A G 121 119 2 ORF1b 17543A>G K5848R 0.0165289256198347 1456 SampleB_freebayes_ann +NC_045512.2 17809 NC_045512.2;17809;A;T A T 118 116 2 ORF1b 17545A>T I5849F 0.0169491525423729 1456 SampleB_freebayes_ann +NC_045512.2 17813 NC_045512.2;17813;T;G T G 122 120 2 ORF1b 17549T>G L5850W 0.0163934426229508 1458 SampleB_freebayes_ann +NC_045512.2 17842 NC_045512.2;17842;TCAC;TC TCAC TC 122 119 2 ORF1b 17581_17582delCA Q5861fs 0.0163934426229508 1467 SampleB_freebayes_ann +NC_045512.2 17964 NC_045512.2;17964;G;T G T 119 109 10 ORF1b 17700G>T M5900I 0.0840336134453782 1508 SampleB_freebayes_ann +NC_045512.2 18045 NC_045512.2;18045;A;C A C 110 108 2 ORF1b 17781A>C E5927D 0.0181818181818182 1535 SampleB_freebayes_ann +NC_045512.2 18052 NC_045512.2;18052;A;C A C 134 132 2 ORF1b 17788A>C T5930P 0.0149253731343284 1537 SampleB_freebayes_ann +NC_045512.2 18054 NC_045512.2;18054;A;T A T 134 132 2 ORF1b 17790A>T T5930T 0.0149253731343284 1538 SampleB_freebayes_ann +NC_045512.2 18066 NC_045512.2;18066;A;T A T 100 98 2 ORF1b 17802A>T K5934N 0.02 1542 SampleB_freebayes_ann +NC_045512.2 18094 NC_045512.2;18094;C;T C T 96 95 1 ORF1b 17830C>T H5944Y 0.0104166666666667 1551 SampleB_freebayes_ann +NC_045512.2 18104 NC_045512.2;18104;A;T A T 98 97 1 ORF1b 17840A>T Q5947L 0.0102040816326531 1555 SampleB_freebayes_ann +NC_045512.2 18140 NC_045512.2;18140;A;G A G 101 99 2 ORF1b 17876A>G K5959R 0.0198019801980198 1567 SampleB_freebayes_ann +NC_045512.2 18211 NC_045512.2;18211;A;C A C 97 96 1 ORF1b 17947A>C M5983L 0.0103092783505155 1590 SampleB_freebayes_ann +NC_045512.2 18221 NC_045512.2;18221;A;C A C 95 94 1 ORF1b 17957A>C K5986T 0.0105263157894737 1594 SampleB_freebayes_ann +NC_045512.2 18242 NC_045512.2;18242;G;T G T 99 98 1 ORF1b 17978G>T G5993V 0.0101010101010101 1601 SampleB_freebayes_ann +NC_045512.2 18277 NC_045512.2;18277;A;T A T 103 101 2 ORF1b 18013A>T I6005L 0.0194174757281553 1612 SampleB_freebayes_ann +NC_045512.2 18288 NC_045512.2;18288;A;T A T 91 90 1 ORF1b 18024A>T V6008V 0.010989010989011 1616 SampleB_freebayes_ann +NC_045512.2 18335 NC_045512.2;18335;A;C A C 78 77 1 ORF1b 18071A>C E6024A 0.0128205128205128 1632 SampleB_freebayes_ann +NC_045512.2 18354 NC_045512.2;18354;A;C A C 40 39 1 ORF1b 18090A>C L6030F 0.025 1638 SampleB_freebayes_ann +NC_045512.2 18388 NC_045512.2;18388;C;T C T 64 63 1 ORF1b 18124C>T L6042L 0.015625 1649 SampleB_freebayes_ann +NC_045512.2 18471 NC_045512.2;18471;TCA;TA TCA TA 64 59 2 ORF1b 18208delC Q6070fs 0.03125 1677 SampleB_freebayes_ann +NC_045512.2 18471 NC_045512.2;18471;TCA;TAA TCA TAA 64 59 2 ORF1b 18208delC Q6070fs 0.03125 1677 SampleB_freebayes_ann +NC_045512.2 18471 NC_045512.2;18471;TCA;ACA TCA ACA 64 59 1 ORF1b 18208delC Q6070fs 0.015625 1677 SampleB_freebayes_ann +NC_045512.2 18492 NC_045512.2;18492;A;C A C 64 63 1 ORF1b 18228A>C P6076P 0.015625 1684 SampleB_freebayes_ann +NC_045512.2 18496 NC_045512.2;18496;A;C A C 64 62 1 ORF1b 18232A>C M6078L 0.015625 1685 SampleB_freebayes_ann +NC_045512.2 18496 NC_045512.2;18496;A;T A T 64 62 1 ORF1b 18232A>C M6078L 0.015625 1685 SampleB_freebayes_ann +NC_045512.2 18504 NC_045512.2;18504;A;C A C 64 63 1 ORF1b 18240A>C K6080N 0.015625 1688 SampleB_freebayes_ann +NC_045512.2 18511 NC_045512.2;18511;C;A C A 64 63 1 ORF1b 18247C>A P6083T 0.015625 1690 SampleB_freebayes_ann +NC_045512.2 18525 NC_045512.2;18525;G;T G T 61 59 2 ORF1b 18261G>T V6087V 0.0327868852459016 1695 SampleB_freebayes_ann +NC_045512.2 18545 NC_045512.2;18545;T;A T A 60 59 1 ORF1b 18281T>A M6094K 0.0166666666666667 1702 SampleB_freebayes_ann +NC_045512.2 18566 NC_045512.2;18566;A;G A G 34 24 10 ORF1b 18302A>G N6101S 0.294117647058824 1709 SampleB_freebayes_ann +NC_045512.2 18604 NC_045512.2;18604;G;T G T 69 68 1 ORF1b 18340G>T G6114C 0.0144927536231884 1721 SampleB_freebayes_ann +NC_045512.2 18617 NC_045512.2;18617;C;T C T 85 84 1 ORF1b 18353C>T T6118I 0.0117647058823529 1726 SampleB_freebayes_ann +NC_045512.2 18648 NC_045512.2;18648;T;C T C 84 82 2 ORF1b 18384T>C P6128P 0.0238095238095238 1736 SampleB_freebayes_ann +NC_045512.2 18675 NC_045512.2;18675;A;C A C 77 76 1 ORF1b 18411A>C R6137S 0.012987012987013 1745 SampleB_freebayes_ann +NC_045512.2 18701 NC_045512.2;18701;C;T C T 107 69 38 ORF1b 18437C>T S6146L 0.355140186915888 1754 SampleB_freebayes_ann +NC_045512.2 18717 NC_045512.2;18717;T;C T C 108 104 3 ORF1b 18453T>C C6151C 0.0277777777777778 1759 SampleB_freebayes_ann +NC_045512.2 18769 NC_045512.2;18769;G;A G A 108 106 2 ORF1b 18505G>A V6169I 0.0185185185185185 1776 SampleB_freebayes_ann +NC_045512.2 18798 NC_045512.2;18798;A;G A G 108 106 2 ORF1b 18534A>G L6178L 0.0185185185185185 1786 SampleB_freebayes_ann +NC_045512.2 18842 NC_045512.2;18842;A;G A G 108 106 2 ORF1b 18578A>G H6193R 0.0185185185185185 1801 SampleB_freebayes_ann +NC_045512.2 18883 NC_045512.2;18883;G;A G A 108 106 2 ORF1b 18619G>A V6207I 0.0185185185185185 1814 SampleB_freebayes_ann +NC_045512.2 18896 NC_045512.2;18896;T;C T C 106 104 2 ORF1b 18632T>C F6211S 0.0188679245283019 1819 SampleB_freebayes_ann +NC_045512.2 18902 NC_045512.2;18902;A;T A T 85 84 1 ORF1b 18638A>T K6213M 0.0117647058823529 1821 SampleB_freebayes_ann +NC_045512.2 18936 NC_045512.2;18936;T;C T C 79 70 9 ORF1b 18672T>C I6224I 0.113924050632911 1832 SampleB_freebayes_ann +NC_045512.2 18945 NC_045512.2;18945;A;G A G 79 78 1 ORF1b 18681A>G E6227E 0.0126582278481013 1835 SampleB_freebayes_ann +NC_045512.2 18970 NC_045512.2;18970;A;G A G 64 63 1 ORF1b 18706A>G K6236E 0.015625 1843 SampleB_freebayes_ann +NC_045512.2 18976 NC_045512.2;18976;C;T C T 59 58 1 ORF1b 18712C>T Q6238* 0.0169491525423729 1845 SampleB_freebayes_ann +NC_045512.2 18978 NC_045512.2;18978;A;C A C 56 53 1 ORF1b 18714A>C Q6238H 0.0178571428571429 1846 SampleB_freebayes_ann +NC_045512.2 18978 NC_045512.2;18978;A;G A G 56 53 2 ORF1b 18714A>C Q6238H 0.0357142857142857 1846 SampleB_freebayes_ann +NC_045512.2 19150 NC_045512.2;19150;G;T G T 56 54 2 ORF1b 18886G>T A6296S 0.0357142857142857 1903 SampleB_freebayes_ann +NC_045512.2 19164 NC_045512.2;19164;C;A C A 57 56 1 ORF1b 18900C>A D6300E 0.0175438596491228 1908 SampleB_freebayes_ann +NC_045512.2 19166 NC_045512.2;19166;A;C A C 57 56 1 ORF1b 18902A>C K6301T 0.0175438596491228 1909 SampleB_freebayes_ann +NC_045512.2 19193 NC_045512.2;19193;G;T G T 55 54 1 ORF1b 18929G>T W6310L 0.0181818181818182 1918 SampleB_freebayes_ann +NC_045512.2 19239 NC_045512.2;19239;ATTTGA;ATTGA ATTTGA ATTGA 33 32 1 ORF1b 18978delT F6326fs 0.0303030303030303 1933 SampleB_freebayes_ann +NC_045512.2 19267 NC_045512.2;19267;A;C A C 30 29 1 ORF1b 19003A>C N6335H 0.0333333333333333 1942 SampleB_freebayes_ann +NC_045512.2 19342 NC_045512.2;19342;G;T G T 4 3 1 ORF1b 19078G>T A6360S 0.25 1967 SampleB_freebayes_ann +NC_045512.2 19450 NC_045512.2;19450;G;T G T 4 3 1 ORF1b 19186G>T A6396S 0.25 2003 SampleB_freebayes_ann +NC_045512.2 19457 NC_045512.2;19457;G;T G T 4 3 1 ORF1b 19193G>T C6398F 0.25 2006 SampleB_freebayes_ann +NC_045512.2 19493 NC_045512.2;19493;G;A G A 4 3 1 ORF1b 19229G>A R6410K 0.25 2018 SampleB_freebayes_ann +NC_045512.2 19495 NC_045512.2;19495;C;A C A 4 3 1 ORF1b 19231C>A H6411N 0.25 2018 SampleB_freebayes_ann +NC_045512.2 19685 NC_045512.2;19685;T;G T G 4 3 1 ORF1b 19421T>G V6474G 0.25 2082 SampleB_freebayes_ann +NC_045512.2 19854 NC_045512.2;19854;C;G C G 4 3 1 ORF1b 19590C>G D6530E 0.25 2138 SampleB_freebayes_ann +NC_045512.2 19984 NC_045512.2;19984;T;G T G 4 3 1 ORF1b 19720T>G F6574V 0.25 2181 SampleB_freebayes_ann +NC_045512.2 20011 NC_045512.2;20011;G;T G T 4 3 1 ORF1b 19747G>T V6583L 0.25 2190 SampleB_freebayes_ann +NC_045512.2 20044 NC_045512.2;20044;C;T C T 4 2 2 ORF1b 19780C>T L6594F 0.5 2201 SampleB_freebayes_ann +NC_045512.2 20178 NC_045512.2;20178;C;T C T 3 2 1 ORF1b 19914C>T V6638V 0.333333333333333 2246 SampleB_freebayes_ann +NC_045512.2 20284 NC_045512.2;20284;A;T A T 2 1 1 ORF1b 20020A>T I6674F 0.5 2281 SampleB_freebayes_ann +NC_045512.2 20823 NC_045512.2;20823;C;T C T 17 15 2 ORF1b 20559C>T N6853N 0.117647058823529 2461 SampleB_freebayes_ann +NC_045512.2 20889 NC_045512.2;20889;A;G A G 33 32 1 ORF1b 20625A>G G6875G 0.0303030303030303 2483 SampleB_freebayes_ann +NC_045512.2 20908 NC_045512.2;20908;G;T G T 32 31 1 ORF1b 20644G>T V6882F 0.03125 2489 SampleB_freebayes_ann +NC_045512.2 20921 NC_045512.2;20921;G;T G T 32 31 1 ORF1b 20657G>T W6886L 0.03125 2494 SampleB_freebayes_ann +NC_045512.2 20923 NC_045512.2;20923;T;C T C 32 30 2 ORF1b 20659T>C L6887L 0.0625 2494 SampleB_freebayes_ann +NC_045512.2 20934 NC_045512.2;20934;T;C T C 32 31 1 ORF1b 20670T>C G6890G 0.03125 2498 SampleB_freebayes_ann +NC_045512.2 20960 NC_045512.2;20960;A;C A C 32 31 1 ORF1b 20696A>C N6899T 0.03125 2507 SampleB_freebayes_ann +NC_045512.2 20982 NC_045512.2;20982;T;A T A 32 31 1 ORF1b 20718T>A D6906E 0.03125 2514 SampleB_freebayes_ann +NC_045512.2 20996 NC_045512.2;20996;G;A G A 32 30 1 ORF1b 20732G>A G6911D 0.03125 2519 SampleB_freebayes_ann +NC_045512.2 20996 NC_045512.2;20996;G;C G C 32 30 1 ORF1b 20732G>A G6911D 0.03125 2519 SampleB_freebayes_ann +NC_045512.2 21003 NC_045512.2;21003;T;A T A 32 30 2 ORF1b 20739T>A C6913* 0.0625 2521 SampleB_freebayes_ann +NC_045512.2 21038 NC_045512.2;21038;T;A T A 32 31 1 ORF1b 20774T>A I6925N 0.03125 2533 SampleB_freebayes_ann +NC_045512.2 21077 NC_045512.2;21077;C;A C A 38 37 1 ORF1b 20813C>A T6938K 0.0263157894736842 2546 SampleB_freebayes_ann +NC_045512.2 21115 NC_045512.2;21115;A;G A G 33 32 1 ORF1b 20851A>G I6951V 0.0303030303030303 2558 SampleB_freebayes_ann +NC_045512.2 21125 NC_045512.2;21125;T;C T C 33 32 1 ORF1b 20861T>C F6954S 0.0303030303030303 2562 SampleB_freebayes_ann +NC_045512.2 21141 NC_045512.2;21141;A;C A C 33 32 1 ORF1b 20877A>C L6959L 0.0303030303030303 2567 SampleB_freebayes_ann +NC_045512.2 21159 NC_045512.2;21159;G;A G A 39 37 2 ORF1b 20895G>A V6965V 0.0512820512820513 2573 SampleB_freebayes_ann +NC_045512.2 21183 NC_045512.2;21183;T;G T G 33 32 1 ORF1b 20919T>G S6973S 0.0303030303030303 2581 SampleB_freebayes_ann +NC_045512.2 21201 NC_045512.2;21201;T;A T A 28 26 1 ORF1b 20937T>A Y6979* 0.0357142857142857 2587 SampleB_freebayes_ann +NC_045512.2 21201 NC_045512.2;21201;T;G T G 28 26 1 ORF1b 20937T>A Y6979* 0.0357142857142857 2587 SampleB_freebayes_ann +NC_045512.2 21217 NC_045512.2;21217;T;A T A 33 32 1 ORF1b 20953T>A F6985I 0.0303030303030303 2592 SampleB_freebayes_ann +NC_045512.2 21253 NC_045512.2;21253;G;T G T 33 32 1 ORF1b 20989G>T A6997S 0.0303030303030303 2604 SampleB_freebayes_ann +NC_045512.2 21294 NC_045512.2;21294;T;A T A 33 32 1 ORF1b 21030T>A L7010L 0.0303030303030303 2618 SampleB_freebayes_ann +NC_045512.2 21334 NC_045512.2;21334;G;T G T 33 32 1 ORF1b 21070G>T A7024S 0.0303030303030303 2631 SampleB_freebayes_ann +NC_045512.2 21359 NC_045512.2;21359;CAAATC;CAATC CAAATC CAATC 33 31 2 ORF1b 21098delA N7033fs 0.0606060606060606 2640 SampleB_freebayes_ann +NC_045512.2 21380 NC_045512.2;21380;C;T C T 26 25 1 ORF1b 21116C>T S7039F 0.0384615384615385 2647 SampleB_freebayes_ann +NC_045512.2 21394 NC_045512.2;21394;G;C G C 22 21 1 ORF1b 21130G>C D7044H 0.0454545454545455 2651 SampleB_freebayes_ann +NC_045512.2 21401 NC_045512.2;21401;G;C G C 18 17 1 ORF1b 21137G>C S7046T 0.0555555555555556 2654 SampleB_freebayes_ann +NC_045512.2 21441 NC_045512.2;21441;T;G T G 17 16 1 ORF1b 21177T>G S7059S 0.0588235294117647 2667 SampleB_freebayes_ann +NC_045512.2 21718 NC_045512.2;21718;G;A G A 2 1 1 S 156G>A Q52Q 0.5 52 SampleB_freebayes_ann +NC_045512.2 21764 NC_045512.2;21764;ATACATGT;AT ATACATGT AT 2 0 2 S 204_209delACATGT H69_V70del 1 68 SampleB_freebayes_ann +NC_045512.2 21961 NC_045512.2;21961;T;G T G 2 1 1 S 399T>G F133L 0.5 133 SampleB_freebayes_ann +NC_045512.2 21990 NC_045512.2;21990;TTTATTAC;TTTAC TTTATTAC TTTAC 4 0 4 S 432_434delTTA Y145del 1 143 SampleB_freebayes_ann +NC_045512.2 22050 NC_045512.2;22050;C;G C G 6 5 1 S 488C>G A163G 0.166666666666667 163 SampleB_freebayes_ann +NC_045512.2 22520 NC_045512.2;22520;G;T G T 6 5 1 S 958G>T V320F 0.166666666666667 320 SampleB_freebayes_ann +NC_045512.2 22754 NC_045512.2;22754;G;T G T 4 3 1 S 1192G>T D398Y 0.25 398 SampleB_freebayes_ann +NC_045512.2 22938 NC_045512.2;22938;C;T C T 4 3 1 S 1376C>T S459F 0.25 459 SampleB_freebayes_ann +NC_045512.2 23063 NC_045512.2;23063;A;T A T 4 0 4 S 1501A>T N501Y 1 501 SampleB_freebayes_ann +NC_045512.2 23271 NC_045512.2;23271;C;A C A 16 0 16 S 1709C>A A570D 1 570 SampleB_freebayes_ann +NC_045512.2 23314 NC_045512.2;23314;T;A T A 16 14 2 S 1752T>A I584I 0.125 584 SampleB_freebayes_ann +NC_045512.2 23396 NC_045512.2;23396;T;G T G 15 14 1 S 1834T>G Y612D 0.0666666666666667 612 SampleB_freebayes_ann +NC_045512.2 23403 NC_045512.2;23403;A;G A G 15 0 15 S 1841A>G D614G 1 614 SampleB_freebayes_ann +NC_045512.2 23417 NC_045512.2;23417;G;A G A 13 12 1 S 1855G>A E619K 0.0769230769230769 619 SampleB_freebayes_ann +NC_045512.2 23420 NC_045512.2;23420;G;A G A 13 12 1 S 1858G>A V620I 0.0769230769230769 620 SampleB_freebayes_ann +NC_045512.2 23421 NC_045512.2;23421;T;A T A 13 12 1 S 1859T>A V620D 0.0769230769230769 620 SampleB_freebayes_ann +NC_045512.2 23592 NC_045512.2;23592;A;G A G 8 6 2 S 2030A>G Q677R 0.25 677 SampleB_freebayes_ann +NC_045512.2 23604 NC_045512.2;23604;C;A C A 8 0 8 S 2042C>A P681H 1 681 SampleB_freebayes_ann +NC_045512.2 23709 NC_045512.2;23709;C;T C T 8 0 8 S 2147C>T T716I 1 716 SampleB_freebayes_ann +NC_045512.2 23791 NC_045512.2;23791;T;G T G 7 6 1 S 2229T>G C743W 0.142857142857143 743 SampleB_freebayes_ann +NC_045512.2 24004 NC_045512.2;24004;G;T G T 10 9 1 S 2442G>T K814N 0.1 814 SampleB_freebayes_ann +NC_045512.2 24035 NC_045512.2;24035;A;C A C 10 9 1 S 2473A>C K825Q 0.1 825 SampleB_freebayes_ann +NC_045512.2 24076 NC_045512.2;24076;T;C T C 9 8 1 S 2514T>C G838G 0.111111111111111 838 SampleB_freebayes_ann +NC_045512.2 24077 NC_045512.2;24077;G;T G T 9 8 1 S 2515G>T D839Y 0.111111111111111 839 SampleB_freebayes_ann +NC_045512.2 24134 NC_045512.2;24134;C;A C A 8 7 1 S 2572C>A L858I 0.125 858 SampleB_freebayes_ann +NC_045512.2 24369 NC_045512.2;24369;A;C A C 8 7 1 S 2807A>C D936A 0.125 936 SampleB_freebayes_ann +NC_045512.2 24417 NC_045512.2;24417;T;A T A 36 35 1 S 2855T>A V952D 0.0277777777777778 952 SampleB_freebayes_ann +NC_045512.2 24494 NC_045512.2;24494;AATGA;CATGT AATGA CATGT 60 59 1 S 2932_2936delAATGAinsCATGT ND978HV 0.0166666666666667 978 SampleB_freebayes_ann +NC_045512.2 24506 NC_045512.2;24506;T;G T G 62 0 62 S 2944T>G S982A 1 982 SampleB_freebayes_ann +NC_045512.2 24513 NC_045512.2;24513;T;A T A 62 61 1 S 2951T>A L984H 0.0161290322580645 984 SampleB_freebayes_ann +NC_045512.2 24517 NC_045512.2;24517;C;A C A 63 62 1 S 2955C>A D985E 0.0158730158730159 985 SampleB_freebayes_ann +NC_045512.2 24535 NC_045512.2;24535;G;T G T 61 60 1 S 2973G>T V991V 0.0163934426229508 991 SampleB_freebayes_ann +NC_045512.2 24543 NC_045512.2;24543;A;C A C 63 62 1 S 2981A>C D994A 0.0158730158730159 994 SampleB_freebayes_ann +NC_045512.2 24553 NC_045512.2;24553;C;A C A 63 62 1 S 2991C>A I997I 0.0158730158730159 997 SampleB_freebayes_ann +NC_045512.2 24575 NC_045512.2;24575;C;A C A 63 62 1 S 3013C>A Q1005K 0.0158730158730159 1005 SampleB_freebayes_ann +NC_045512.2 24654 NC_045512.2;24654;A;C A C 63 62 1 S 3092A>C E1031A 0.0158730158730159 1031 SampleB_freebayes_ann +NC_045512.2 24682 NC_045512.2;24682;T;G T G 63 62 1 S 3120T>G V1040V 0.0158730158730159 1040 SampleB_freebayes_ann +NC_045512.2 24693 NC_045512.2;24693;G;C G C 42 41 1 S 3131G>C G1044A 0.0238095238095238 1044 SampleB_freebayes_ann +NC_045512.2 24705 NC_045512.2;24705;A;C A C 85 84 1 S 3143A>C H1048P 0.0117647058823529 1048 SampleB_freebayes_ann +NC_045512.2 24706 NC_045512.2;24706;T;C T C 86 85 1 S 3144T>C H1048H 0.0116279069767442 1048 SampleB_freebayes_ann +NC_045512.2 24709 NC_045512.2;24709;TAT;TAAT TAT TAAT 90 88 1 S 3148dupA M1050fs 0.0111111111111111 1049 SampleB_freebayes_ann +NC_045512.2 24709 NC_045512.2;24709;TAT;GAT TAT GAT 90 88 1 S 3148dupA M1050fs 0.0111111111111111 1049 SampleB_freebayes_ann +NC_045512.2 24719 NC_045512.2;24719;C;A C A 99 97 1 S 3157C>A P1053T 0.0101010101010101 1053 SampleB_freebayes_ann +NC_045512.2 24719 NC_045512.2;24719;C;G C G 99 97 1 S 3157C>A P1053T 0.0101010101010101 1053 SampleB_freebayes_ann +NC_045512.2 24776 NC_045512.2;24776;G;A G A 127 125 2 S 3214G>A E1072K 0.015748031496063 1072 SampleB_freebayes_ann +NC_045512.2 24821 NC_045512.2;24821;G;C G C 131 129 2 S 3259G>C A1087P 0.0152671755725191 1087 SampleB_freebayes_ann +NC_045512.2 24867 NC_045512.2;24867;G;T G T 134 132 2 S 3305G>T W1102L 0.0149253731343284 1102 SampleB_freebayes_ann +NC_045512.2 24914 NC_045512.2;24914;GACA;CACT GACA CACT 134 0 2 S 3352G>C D1118H 0.0149253731343284 1118 SampleB_freebayes_ann +NC_045512.2 24914 NC_045512.2;24914;GACA;CACA GACA CACA 134 0 131 S 3352G>C D1118H 0.977611940298507 1118 SampleB_freebayes_ann +NC_045512.2 24958 NC_045512.2;24958;T;C T C 133 131 2 S 3396T>C I1132I 0.0150375939849624 1132 SampleB_freebayes_ann +NC_045512.2 25001 NC_045512.2;25001;T;C T C 149 147 2 S 3439T>C S1147P 0.0134228187919463 1147 SampleB_freebayes_ann +NC_045512.2 25132 NC_045512.2;25132;C;T C T 132 130 2 S 3570C>T A1190A 0.0151515151515152 1190 SampleB_freebayes_ann +NC_045512.2 25241 NC_045512.2;25241;A;G A G 131 129 2 S 3679A>G I1227V 0.0152671755725191 1227 SampleB_freebayes_ann +NC_045512.2 25304 NC_045512.2;25304;T;C T C 113 109 4 S 3742T>C C1248R 0.0353982300884956 1248 SampleB_freebayes_ann +NC_045512.2 25394 NC_045512.2;25394;T;C T C 116 113 2 ORF3a 2T>C M1? 0.0172413793103448 1 SampleB_freebayes_ann +NC_045512.2 25446 NC_045512.2;25446;T;A T A 116 114 2 ORF3a 54T>A G18G 0.0172413793103448 18 SampleB_freebayes_ann +NC_045512.2 25479 NC_045512.2;25479;T;C T C 116 114 2 ORF3a 87T>C V29V 0.0172413793103448 29 SampleB_freebayes_ann +NC_045512.2 25515 NC_045512.2;25515;C;A C A 116 114 2 ORF3a 123C>A L41L 0.0172413793103448 41 SampleB_freebayes_ann +NC_045512.2 25549 NC_045512.2;25549;CTTGC;CTGC CTTGC CTGC 112 110 2 ORF3a 159delT A54fs 0.0178571428571429 53 SampleB_freebayes_ann +NC_045512.2 25586 NC_045512.2;25586;T;C T C 82 80 2 ORF3a 194T>C L65P 0.024390243902439 65 SampleB_freebayes_ann +NC_045512.2 25611 NC_045512.2;25611;CT;AC CT AC 65 64 1 ORF3a 219_220delCTinsAC S74P 0.0153846153846154 73 SampleB_freebayes_ann +NC_045512.2 25620 NC_045512.2;25620;T;G T G 70 69 1 ORF3a 228T>G G76G 0.0142857142857143 76 SampleB_freebayes_ann +NC_045512.2 25624 NC_045512.2;25624;C;T C T 72 64 8 ORF3a 232C>T H78Y 0.111111111111111 78 SampleB_freebayes_ann +NC_045512.2 25630 NC_045512.2;25630;G;T G T 72 71 1 ORF3a 238G>T V80F 0.0138888888888889 80 SampleB_freebayes_ann +NC_045512.2 25635 NC_045512.2;25635;C;G C G 72 71 1 ORF3a 243C>G C81W 0.0138888888888889 81 SampleB_freebayes_ann +NC_045512.2 25638 NC_045512.2;25638;C;T C T 72 63 9 ORF3a 246C>T N82N 0.125 82 SampleB_freebayes_ann +NC_045512.2 25643 NC_045512.2;25643;T;G T G 71 70 1 ORF3a 251T>G L84R 0.0140845070422535 84 SampleB_freebayes_ann +NC_045512.2 25673 NC_045512.2;25673;T;A T A 42 41 1 ORF3a 281T>A L94H 0.0238095238095238 94 SampleB_freebayes_ann +NC_045512.2 25687 NC_045512.2;25687;G;A G A 9 8 1 ORF3a 295G>A A99T 0.111111111111111 99 SampleB_freebayes_ann +NC_045512.2 25698 NC_045512.2;25698;A;C A C 15 14 1 ORF3a 306A>C E102D 0.0666666666666667 102 SampleB_freebayes_ann +NC_045512.2 25716 NC_045512.2;25716;T;C T C 18 16 2 ORF3a 324T>C L108L 0.111111111111111 108 SampleB_freebayes_ann +NC_045512.2 25718 NC_045512.2;25718;A;T A T 18 17 1 ORF3a 326A>T Y109F 0.0555555555555556 109 SampleB_freebayes_ann +NC_045512.2 25740 NC_045512.2;25740;G;T G T 17 15 2 ORF3a 348G>T Q116H 0.117647058823529 116 SampleB_freebayes_ann +NC_045512.2 25795 NC_045512.2;25795;T;C T C 18 17 1 ORF3a 403T>C S135P 0.0555555555555556 135 SampleB_freebayes_ann +NC_045512.2 25855 NC_045512.2;25855;G;T G T 18 17 1 ORF3a 463G>T D155Y 0.0555555555555556 155 SampleB_freebayes_ann +NC_045512.2 25862 NC_045512.2;25862;G;T G T 18 17 1 ORF3a 470G>T C157F 0.0555555555555556 157 SampleB_freebayes_ann +NC_045512.2 26010 NC_045512.2;26010;C;T C T 4 3 1 ORF3a 618C>T Y206Y 0.25 206 SampleB_freebayes_ann +NC_045512.2 26064 NC_045512.2;26064;T;G T G 8 7 1 ORF3a 672T>G G224G 0.125 224 SampleB_freebayes_ann +NC_045512.2 26171 NC_045512.2;26171;T;C T C 8 4 4 ORF3a 779T>C M260T 0.5 260 SampleB_freebayes_ann +NC_045512.2 26187 NC_045512.2;26187;T;C T C 8 6 2 ORF3a 795T>C D265D 0.25 265 SampleB_freebayes_ann +NC_045512.2 26213 NC_045512.2;26213;CTTTGTA;CTTGTA CTTTGTA CTTGTA 18 17 1 ORF3a 824delT L275fs 0.0555555555555556 274 SampleB_freebayes_ann +NC_045512.2 26271 NC_045512.2;26271;A;C A C 24 23 1 E 27A>C T9T 0.0416666666666667 9 SampleB_freebayes_ann +NC_045512.2 26308 NC_045512.2;26308;G;T G T 33 32 1 E 64G>T A22S 0.0303030303030303 22 SampleB_freebayes_ann +NC_045512.2 26312 NC_045512.2;26312;T;A T A 32 30 2 E 68T>A F23Y 0.0625 23 SampleB_freebayes_ann +NC_045512.2 26450 NC_045512.2;26450;G;A G A 29 28 1 E 206G>A R69K 0.0344827586206897 69 SampleB_freebayes_ann +NC_045512.2 26451 NC_045512.2;26451;A;C A C 26 25 1 E 207A>C R69S 0.0384615384615385 69 SampleB_freebayes_ann +NC_045512.2 26602 NC_045512.2;26602;T;A T A 39 38 1 M 80T>A L27Q 0.0256410256410256 27 SampleB_freebayes_ann +NC_045512.2 26612 NC_045512.2;26612;A;G A G 50 48 1 M 90A>G T30T 0.02 30 SampleB_freebayes_ann +NC_045512.2 26612 NC_045512.2;26612;A;T A T 50 48 1 M 90A>G T30T 0.02 30 SampleB_freebayes_ann +NC_045512.2 26669 NC_045512.2;26669;T;G T G 58 57 1 M 147T>G I49M 0.0172413793103448 49 SampleB_freebayes_ann +NC_045512.2 26718 NC_045512.2;26718;G;T G T 59 57 2 M 196G>T V66L 0.0338983050847458 66 SampleB_freebayes_ann +NC_045512.2 26720 NC_045512.2;26720;G;T G T 59 57 2 M 198G>T V66V 0.0338983050847458 66 SampleB_freebayes_ann +NC_045512.2 26731 NC_045512.2;26731;T;C T C 59 57 2 M 209T>C V70A 0.0338983050847458 70 SampleB_freebayes_ann +NC_045512.2 26766 NC_045512.2;26766;A;C A C 58 57 1 M 244A>C I82L 0.0172413793103448 82 SampleB_freebayes_ann +NC_045512.2 26785 NC_045512.2;26785;T;C T C 58 56 2 M 263T>C V88A 0.0344827586206897 88 SampleB_freebayes_ann +NC_045512.2 26810 NC_045512.2;26810;C;A C A 59 58 1 M 288C>A F96L 0.0169491525423729 96 SampleB_freebayes_ann +NC_045512.2 26816 NC_045512.2;26816;TT;GG TT GG 56 55 1 M 294_295delTTinsGG S99A 0.0178571428571429 98 SampleB_freebayes_ann +NC_045512.2 26827 NC_045512.2;26827;T;C T C 33 32 1 M 305T>C L102P 0.0303030303030303 102 SampleB_freebayes_ann +NC_045512.2 26832 NC_045512.2;26832;G;T G T 32 31 1 M 310G>T A104S 0.03125 104 SampleB_freebayes_ann +NC_045512.2 26890 NC_045512.2;26890;C;T C T 138 136 2 M 368C>T P123L 0.0144927536231884 123 SampleB_freebayes_ann +NC_045512.2 27142 NC_045512.2;27142;A;C A C 156 154 2 M 620A>C N207T 0.0128205128205128 207 SampleB_freebayes_ann +NC_045512.2 27163 NC_045512.2;27163;G;T G T 140 127 13 M 641G>T S214I 0.0928571428571429 214 SampleB_freebayes_ann +NC_045512.2 27214 NC_045512.2;27214;G;T G T 95 94 1 ORF6 13G>T V5F 0.0105263157894737 5 SampleB_freebayes_ann +NC_045512.2 27215 NC_045512.2;27215;T;G T G 85 83 2 ORF6 14T>G V5G 0.0235294117647059 5 SampleB_freebayes_ann +NC_045512.2 27217 NC_045512.2;27217;G;C G C 37 36 1 ORF6 16G>C D6H 0.027027027027027 6 SampleB_freebayes_ann +NC_045512.2 27224 NC_045512.2;27224;A;G A G 37 36 1 ORF6 23A>G Q8R 0.027027027027027 8 SampleB_freebayes_ann +NC_045512.2 27237 NC_045512.2;27237;A;C A C 40 39 1 ORF6 36A>C A12A 0.025 12 SampleB_freebayes_ann +NC_045512.2 27240 NC_045512.2;27240;G;A G A 41 40 1 ORF6 39G>A E13E 0.024390243902439 13 SampleB_freebayes_ann +NC_045512.2 27279 NC_045512.2;27279;T;G T G 41 40 1 ORF6 78T>G I26M 0.024390243902439 26 SampleB_freebayes_ann +NC_045512.2 27285 NC_045512.2;27285;T;G T G 42 41 1 ORF6 84T>G N28K 0.0238095238095238 28 SampleB_freebayes_ann +NC_045512.2 27289 NC_045512.2;27289;G;T G T 42 41 1 ORF6 88G>T D30Y 0.0238095238095238 30 SampleB_freebayes_ann +NC_045512.2 27366 NC_045512.2;27366;G;T G T 42 38 4 ORF6 165G>T E55D 0.0952380952380952 55 SampleB_freebayes_ann +NC_045512.2 27386 NC_045512.2;27386;A;C A C 41 40 1 ORF6 185A>C Ter62Sext*? 0.024390243902439 62 SampleB_freebayes_ann +NC_045512.2 27447 NC_045512.2;27447;T;G T G 57 56 1 ORF7a 54T>G Y18* 0.0175438596491228 18 SampleB_freebayes_ann +NC_045512.2 27460 NC_045512.2;27460;T;G T G 67 66 1 ORF7a 67T>G C23G 0.0149253731343284 23 SampleB_freebayes_ann +NC_045512.2 27468 NC_045512.2;27468;A;G A G 66 65 1 ORF7a 75A>G R25R 0.0151515151515152 25 SampleB_freebayes_ann +NC_045512.2 27472 NC_045512.2;27472;A;T A T 69 68 1 ORF7a 79A>T T27S 0.0144927536231884 27 SampleB_freebayes_ann +NC_045512.2 27478 NC_045512.2;27478;G;A G A 69 68 1 ORF7a 85G>A V29I 0.0144927536231884 29 SampleB_freebayes_ann +NC_045512.2 27484 NC_045512.2;27484;T;C T C 69 67 2 ORF7a 91T>C L31L 0.0289855072463768 31 SampleB_freebayes_ann +NC_045512.2 27542 NC_045512.2;27542;C;A C A 68 67 1 ORF7a 149C>A A50D 0.0147058823529412 50 SampleB_freebayes_ann +NC_045512.2 27557 NC_045512.2;27557;C;A C A 94 93 1 ORF7a 164C>A A55E 0.0106382978723404 55 SampleB_freebayes_ann +NC_045512.2 27558 NC_045512.2;27558;A;C A C 95 94 1 ORF7a 165A>C A55A 0.0105263157894737 55 SampleB_freebayes_ann +NC_045512.2 27621 NC_045512.2;27621;G;T G T 101 89 12 ORF7a 228G>T Q76H 0.118811881188119 76 SampleB_freebayes_ann +NC_045512.2 27647 NC_045512.2;27647;A;C A C 101 99 2 ORF7a 254A>C K85T 0.0198019801980198 85 SampleB_freebayes_ann +NC_045512.2 27690 NC_045512.2;27690;A;C A C 99 98 1 ORF7a 297A>C P99P 0.0101010101010101 99 SampleB_freebayes_ann +NC_045512.2 27691 NC_045512.2;27691;A;C A C 98 97 1 ORF7a 298A>C I100L 0.0102040816326531 100 SampleB_freebayes_ann +NC_045512.2 27700 NC_045512.2;27700;A;T A T 99 97 2 ORF7a 307A>T I103F 0.0202020202020202 103 SampleB_freebayes_ann +NC_045512.2 27703 NC_045512.2;27703;G;T G T 97 96 1 ORF7a 310G>T V104F 0.0103092783505155 104 SampleB_freebayes_ann +NC_045512.2 27722 NC_045512.2;27722;T;G T G 97 96 1 ORF7a 329T>G I110R 0.0103092783505155 110 SampleB_freebayes_ann +NC_045512.2 27741 NC_045512.2;27741;C;A C A 96 95 1 ORF7a 348C>A L116L 0.0104166666666667 116 SampleB_freebayes_ann +NC_045512.2 27742 NC_045512.2;27742;A;C A C 95 94 1 ORF7a 349A>C K117Q 0.0105263157894737 117 SampleB_freebayes_ann +NC_045512.2 27779 NC_045512.2;27779;C;T C T 54 53 1 ORF7b 24C>T D8D 0.0185185185185185 8 SampleB_freebayes_ann +NC_045512.2 27837 NC_045512.2;27837;T;C T C 93 92 1 ORF7b 82T>C F28L 0.010752688172043 28 SampleB_freebayes_ann +NC_045512.2 27848 NC_045512.2;27848;A;G A G 83 82 1 ORF7b 93A>G S31S 0.0120481927710843 31 SampleB_freebayes_ann +NC_045512.2 27853 NC_045512.2;27853;A;T A T 87 86 1 ORF7b 98A>T E33V 0.0114942528735632 33 SampleB_freebayes_ann +NC_045512.2 27860 NC_045512.2;27860;A;C A C 72 70 1 ORF7b 105A>C Q35H 0.0138888888888889 35 SampleB_freebayes_ann +NC_045512.2 27860 NC_045512.2;27860;A;G A G 72 70 1 ORF7b 105A>C Q35H 0.0138888888888889 35 SampleB_freebayes_ann +NC_045512.2 27865 NC_045512.2;27865;A;G A G 78 77 1 ORF7b 110A>G H37R 0.0128205128205128 37 SampleB_freebayes_ann +NC_045512.2 27867 NC_045512.2;27867;A;C A C 80 79 1 ORF7b 112A>C N38H 0.0125 38 SampleB_freebayes_ann +NC_045512.2 27945 NC_045512.2;27945;C;T C T 114 112 2 ORF8 52C>T Q18* 0.0175438596491228 18 SampleB_freebayes_ann +NC_045512.2 27972 NC_045512.2;27972;C;T C T 114 0 114 ORF8 79C>T Q27* 1 27 SampleB_freebayes_ann +NC_045512.2 27989 NC_045512.2;27989;A;T A T 114 112 2 ORF8 96A>T V32V 0.0175438596491228 32 SampleB_freebayes_ann +NC_045512.2 28011 NC_045512.2;28011;C;T C T 114 104 10 ORF8 118C>T H40Y 0.087719298245614 40 SampleB_freebayes_ann +NC_045512.2 28040 NC_045512.2;28040;A;C A C 114 112 2 ORF8 147A>C V49V 0.0175438596491228 49 SampleB_freebayes_ann +NC_045512.2 28048 NC_045512.2;28048;G;T G T 114 0 114 ORF8 155G>T R52I 1 52 SampleB_freebayes_ann +NC_045512.2 28076 NC_045512.2;28076;C;T C T 113 109 4 ORF8 183C>T C61C 0.0353982300884956 61 SampleB_freebayes_ann +NC_045512.2 28095 NC_045512.2;28095;A;T A T 152 138 14 ORF8 202A>T K68* 0.0921052631578947 68 SampleB_freebayes_ann +NC_045512.2 28111 NC_045512.2;28111;A;G A G 155 0 155 ORF8 218A>G Y73C 1 73 SampleB_freebayes_ann +NC_045512.2 28178 NC_045512.2;28178;G;A G A 197 195 2 ORF8 285G>A L95L 0.0101522842639594 95 SampleB_freebayes_ann +NC_045512.2 28217 NC_045512.2;28217;T;C T C 199 196 2 ORF8 324T>C F108F 0.0100502512562814 108 SampleB_freebayes_ann +NC_045512.2 28250 NC_045512.2;28250;TTTCAT;TCTGTTCT TTTCAT TCTGTTCT 201 195 3 ORF8 358_361delTTCAinsCTGTTC F120fs 0.0149253731343284 119 SampleB_freebayes_ann +NC_045512.2 28280 NC_045512.2;28280;GAT;CTA GAT CTA 200 0 200 N 7_9delGATinsCTA D3L 1 3 SampleB_freebayes_ann +NC_045512.2 28295 NC_045512.2;28295;A;G A G 201 192 8 N 22A>G N8D 0.0398009950248756 8 SampleB_freebayes_ann +NC_045512.2 28338 NC_045512.2;28338;A;C A C 198 195 3 N 65A>C D22A 0.0151515151515152 22 SampleB_freebayes_ann +NC_045512.2 28434 NC_045512.2;28434;C;T C T 148 146 2 N 161C>T T54I 0.0135135135135135 54 SampleB_freebayes_ann +NC_045512.2 28477 NC_045512.2;28477;A;G A G 65 64 1 N 204A>G R68R 0.0153846153846154 68 SampleB_freebayes_ann +NC_045512.2 28487 NC_045512.2;28487;G;A G A 110 107 3 N 214G>A V72I 0.0272727272727273 72 SampleB_freebayes_ann +NC_045512.2 28524 NC_045512.2;28524;T;G T G 111 109 2 N 251T>G I84S 0.018018018018018 84 SampleB_freebayes_ann +NC_045512.2 28525 NC_045512.2;28525;T;G T G 107 103 4 N 252T>G I84M 0.0373831775700935 84 SampleB_freebayes_ann +NC_045512.2 28539 NC_045512.2;28539;G;T G T 113 107 6 N 266G>T R89I 0.0530973451327434 89 SampleB_freebayes_ann +NC_045512.2 28549 NC_045512.2;28549;ACGA;AA ACGA AA 113 101 12 N 277_278delCG R93fs 0.106194690265487 92 SampleB_freebayes_ann +NC_045512.2 28568 NC_045512.2;28568;G;C G C 113 111 2 N 295G>C G99R 0.0176991150442478 99 SampleB_freebayes_ann +NC_045512.2 28653 NC_045512.2;28653;A;C A C 113 111 2 N 380A>C K127T 0.0176991150442478 127 SampleB_freebayes_ann +NC_045512.2 28657 NC_045512.2;28657;C;T C T 113 101 12 N 384C>T D128D 0.106194690265487 128 SampleB_freebayes_ann +NC_045512.2 28718 NC_045512.2;28718;C;T C T 92 91 1 N 445C>T R149C 0.0108695652173913 149 SampleB_freebayes_ann +NC_045512.2 28719 NC_045512.2;28719;G;T G T 92 87 5 N 446G>T R149L 0.0543478260869565 149 SampleB_freebayes_ann +NC_045512.2 28725 NC_045512.2;28725;C;T C T 92 90 2 N 452C>T P151L 0.0217391304347826 151 SampleB_freebayes_ann +NC_045512.2 28739 NC_045512.2;28739;G;T G T 91 88 3 N 466G>T A156S 0.032967032967033 156 SampleB_freebayes_ann +NC_045512.2 28746 NC_045512.2;28746;T;A T A 93 92 1 N 473T>A V158E 0.010752688172043 158 SampleB_freebayes_ann +NC_045512.2 28750 NC_045512.2;28750;A;G A G 94 93 1 N 477A>G L159L 0.0106382978723404 159 SampleB_freebayes_ann +NC_045512.2 28753 NC_045512.2;28753;A;C A C 97 95 1 N 480A>C Q160H 0.0103092783505155 160 SampleB_freebayes_ann +NC_045512.2 28753 NC_045512.2;28753;A;G A G 97 95 1 N 480A>C Q160H 0.0103092783505155 160 SampleB_freebayes_ann +NC_045512.2 28782 NC_045512.2;28782;G;T G T 64 63 1 N 509G>T G170V 0.015625 170 SampleB_freebayes_ann +NC_045512.2 28786 NC_045512.2;28786;C;A C A 64 63 1 N 513C>A F171L 0.015625 171 SampleB_freebayes_ann +NC_045512.2 28802 NC_045512.2;28802;A;G A G 64 63 1 N 529A>G R177G 0.015625 177 SampleB_freebayes_ann +NC_045512.2 28827 NC_045512.2;28827;G;T G T 69 68 1 N 554G>T R185L 0.0144927536231884 185 SampleB_freebayes_ann +NC_045512.2 28835 NC_045512.2;28835;T;G T G 69 68 1 N 562T>G S188A 0.0144927536231884 188 SampleB_freebayes_ann +NC_045512.2 28847 NC_045512.2;28847;A;G A G 69 68 1 N 574A>G N192D 0.0144927536231884 192 SampleB_freebayes_ann +NC_045512.2 28853 NC_045512.2;28853;T;G T G 69 68 1 N 580T>G S194A 0.0144927536231884 194 SampleB_freebayes_ann +NC_045512.2 28858 NC_045512.2;28858;AAA;CAT AAA CAT 69 68 1 N 585_587delAAAinsCAT RN195SI 0.0144927536231884 195 SampleB_freebayes_ann +NC_045512.2 28865 NC_045512.2;28865;A;C A C 69 68 1 N 592A>C T198P 0.0144927536231884 198 SampleB_freebayes_ann +NC_045512.2 28874 NC_045512.2;28874;A;G A G 69 68 1 N 601A>G S201G 0.0144927536231884 201 SampleB_freebayes_ann +NC_045512.2 28881 NC_045512.2;28881;GGGGAAC;AACGAAT GGGGAAC AACGAAT 69 0 2 N 608_610delGGGinsAAC RG203KR 0.0289855072463768 203 SampleB_freebayes_ann +NC_045512.2 28881 NC_045512.2;28881;GGGGAAC;AACGAAC GGGGAAC AACGAAC 69 0 66 N 608_610delGGGinsAAC RG203KR 0.956521739130435 203 SampleB_freebayes_ann +NC_045512.2 28889 NC_045512.2;28889;T;A T A 69 68 1 N 616T>A S206T 0.0144927536231884 206 SampleB_freebayes_ann +NC_045512.2 28895 NC_045512.2;28895;GCTAG;GG GCTAG GG 69 64 4 N 623_625delCTA A208_R209delinsG 0.0579710144927536 208 SampleB_freebayes_ann +NC_045512.2 28895 NC_045512.2;28895;GCTAG;GCAAG GCTAG GCAAG 69 64 1 N 623_625delCTA A208_R209delinsG 0.0144927536231884 208 SampleB_freebayes_ann +NC_045512.2 28900 NC_045512.2;28900;A;G A G 69 68 1 N 627A>G R209R 0.0144927536231884 209 SampleB_freebayes_ann +NC_045512.2 28905 NC_045512.2;28905;C;T C T 69 67 2 N 632C>T A211V 0.0289855072463768 211 SampleB_freebayes_ann +NC_045512.2 28960 NC_045512.2;28960;G;T G T 65 63 2 N 687G>T Q229H 0.0307692307692308 229 SampleB_freebayes_ann +NC_045512.2 28963 NC_045512.2;28963;T;G T G 65 64 1 N 690T>G L230L 0.0153846153846154 230 SampleB_freebayes_ann +NC_045512.2 28975 NC_045512.2;28975;G;T G T 65 61 4 N 702G>T M234I 0.0615384615384615 234 SampleB_freebayes_ann +NC_045512.2 28977 NC_045512.2;28977;C;T C T 65 4 61 N 704C>T S235F 0.938461538461539 235 SampleB_freebayes_ann +NC_045512.2 28984 NC_045512.2;28984;A;C A C 44 43 1 N 711A>C K237N 0.0227272727272727 237 SampleB_freebayes_ann +NC_045512.2 28988 NC_045512.2;28988;C;T C T 74 73 1 N 715C>T Q239* 0.0135135135135135 239 SampleB_freebayes_ann +NC_045512.2 28991 NC_045512.2;28991;C;A C A 80 79 1 N 718C>A Q240K 0.0125 240 SampleB_freebayes_ann +NC_045512.2 29030 NC_045512.2;29030;G;A G A 91 90 1 N 757G>A E253K 0.010989010989011 253 SampleB_freebayes_ann +NC_045512.2 29034 NC_045512.2;29034;C;T C T 91 90 1 N 761C>T A254V 0.010989010989011 254 SampleB_freebayes_ann +NC_045512.2 29071 NC_045512.2;29071;A;G A G 61 60 1 N 798A>G K266K 0.0163934426229508 266 SampleB_freebayes_ann +NC_045512.2 29081 NC_045512.2;29081;G;T G T 98 86 12 N 808G>T V270L 0.122448979591837 270 SampleB_freebayes_ann +NC_045512.2 29149 NC_045512.2;29149;C;T C T 106 104 2 N 876C>T I292I 0.0188679245283019 292 SampleB_freebayes_ann +NC_045512.2 29170 NC_045512.2;29170;A;C A C 106 104 2 N 897A>C K299N 0.0188679245283019 299 SampleB_freebayes_ann +NC_045512.2 29219 NC_045512.2;29219;G;T G T 106 104 2 N 946G>T G316* 0.0188679245283019 316 SampleB_freebayes_ann +NC_045512.2 29240 NC_045512.2;29240;G;C G C 98 97 1 N 967G>C E323Q 0.0102040816326531 323 SampleB_freebayes_ann +NC_045512.2 29277 NC_045512.2;29277;G;T G T 99 98 1 N 1004G>T G335V 0.0101010101010101 335 SampleB_freebayes_ann +NC_045512.2 29278 NC_045512.2;29278;T;A T A 99 98 1 N 1005T>A G335G 0.0101010101010101 335 SampleB_freebayes_ann +NC_045512.2 29279 NC_045512.2;29279;G;T G T 98 97 1 N 1006G>T A336S 0.0102040816326531 336 SampleB_freebayes_ann +NC_045512.2 29283 NC_045512.2;29283;T;C T C 95 94 1 N 1010T>C I337T 0.0105263157894737 337 SampleB_freebayes_ann +NC_045512.2 29300 NC_045512.2;29300;G;A G A 58 57 1 N 1027G>A D343N 0.0172413793103448 343 SampleB_freebayes_ann +NC_045512.2 29304 NC_045512.2;29304;C;A C A 58 57 1 N 1031C>A P344Q 0.0172413793103448 344 SampleB_freebayes_ann +NC_045512.2 29344 NC_045512.2;29344;T;G T G 59 58 1 N 1071T>G I357M 0.0169491525423729 357 SampleB_freebayes_ann +NC_045512.2 29369 NC_045512.2;29369;A;C A C 52 50 1 N 1096A>C T366P 0.0192307692307692 366 SampleB_freebayes_ann +NC_045512.2 29369 NC_045512.2;29369;A;G A G 52 50 1 N 1096A>C T366P 0.0192307692307692 366 SampleB_freebayes_ann +NC_045512.2 29401 NC_045512.2;29401;T;A T A 14 13 1 N 1128T>A A376A 0.0714285714285714 376 SampleB_freebayes_ann +NC_045512.2 29420 NC_045512.2;29420;C;A C A 14 13 1 N 1147C>A P383T 0.0714285714285714 383 SampleB_freebayes_ann +NC_045512.2 29431 NC_045512.2;29431;G;A G A 14 13 1 N 1158G>A Q386Q 0.0714285714285714 386 SampleB_freebayes_ann +NC_045512.2 29433 NC_045512.2;29433;A;G A G 14 13 1 N 1160A>G K387R 0.0714285714285714 387 SampleB_freebayes_ann +NC_045512.2 29570 NC_045512.2;29570;A;C A C 53 51 2 ORF10 13A>C N5H 0.0377358490566038 5 SampleB_freebayes_ann +NC_045512.2 29580 NC_045512.2;29580;CTTTTCCG;CTTTCCG CTTTTCCG CTTTCCG 53 47 2 ORF10 27delT P10fs 0.0377358490566038 8 SampleB_freebayes_ann +NC_045512.2 29580 NC_045512.2;29580;CTTTTCCG;TTTTTCCG CTTTTCCG TTTTTCCG 53 47 4 ORF10 27delT P10fs 0.0754716981132076 8 SampleB_freebayes_ann +NC_045512.2 29594 NC_045512.2;29594;A;T A T 52 51 1 ORF10 37A>T I13L 0.0192307692307692 13 SampleB_freebayes_ann +NC_045512.2 29607 NC_045512.2;29607;T;C T C 51 50 1 ORF10 50T>C L17P 0.0196078431372549 17 SampleB_freebayes_ann +NC_045512.2 280 NC_045512.2;280;CC;TT CC TT 495 302 192 ORF1a 15_16delCCinsTT P6S 0.387878787878788 5 SampleC_freebayes_ann +NC_045512.2 335 NC_045512.2;335;CGC;TGT CGC TGT 783 609 170 ORF1a 70_72delCGCinsTGT R24C 0.217113665389527 24 SampleC_freebayes_ann +NC_045512.2 346 NC_045512.2;346;C;T C T 914 904 10 ORF1a 81C>T L27L 0.0109409190371991 27 SampleC_freebayes_ann +NC_045512.2 396 NC_045512.2;396;A;G A G 1364 1344 19 ORF1a 131A>G Q44R 0.0139296187683284 44 SampleC_freebayes_ann +NC_045512.2 613 NC_045512.2;613;G;A G A 1438 247 1191 ORF1a 348G>A V116V 0.828233657858136 116 SampleC_freebayes_ann +NC_045512.2 682 NC_045512.2;682;T;C T C 1852 1771 79 ORF1a 417T>C D139D 0.0426565874730022 139 SampleC_freebayes_ann +NC_045512.2 823 NC_045512.2;823;C;T C T 1547 1524 22 ORF1a 558C>T V186V 0.0142210730446025 186 SampleC_freebayes_ann +NC_045512.2 895 NC_045512.2;895;A;T A T 1742 1653 89 ORF1a 630A>T K210N 0.0510907003444317 210 SampleC_freebayes_ann +NC_045512.2 913 NC_045512.2;913;C;T C T 1739 1471 262 ORF1a 648C>T S216S 0.15066129959747 216 SampleC_freebayes_ann +NC_045512.2 1048 NC_045512.2;1048;G;T G T 3251 938 2313 ORF1a 783G>T K261N 0.711473392802215 261 SampleC_freebayes_ann +NC_045512.2 1259 NC_045512.2;1259;C;T C T 2654 2459 194 ORF1a 994C>T Q332* 0.0730972117558402 332 SampleC_freebayes_ann +NC_045512.2 1441 NC_045512.2;1441;C;T C T 1222 1203 18 ORF1a 1176C>T G392G 0.0147299509001637 392 SampleC_freebayes_ann +NC_045512.2 1469 NC_045512.2;1469;C;T C T 1145 1036 109 ORF1a 1204C>T R402C 0.0951965065502183 402 SampleC_freebayes_ann +NC_045512.2 1485 NC_045512.2;1485;GAG;GG GAG GG 1076 867 206 ORF1a 1221delA G408fs 0.191449814126394 407 SampleC_freebayes_ann +NC_045512.2 1644 NC_045512.2;1644;ACAT;CCAA ACAT CCAA 3724 3669 43 ORF1a 1379_1382delACATinsCCAA NI460TN 0.011546723952739 460 SampleC_freebayes_ann +NC_045512.2 1656 NC_045512.2;1656;TTGG;ATGT TTGG ATGT 3885 3811 61 ORF1a 1391_1394delTTGGinsATGT VG464DV 0.0157014157014157 464 SampleC_freebayes_ann +NC_045512.2 1700 NC_045512.2;1700;T;C T C 4549 4481 66 ORF1a 1435T>C S479P 0.0145086832270829 479 SampleC_freebayes_ann +NC_045512.2 1820 NC_045512.2;1820;G;A G A 4790 4561 225 ORF1a 1555G>A G519S 0.046972860125261 519 SampleC_freebayes_ann +NC_045512.2 2095 NC_045512.2;2095;G;A G A 1292 1273 16 ORF1a 1830G>A S610S 0.0123839009287926 610 SampleC_freebayes_ann +NC_045512.2 2155 NC_045512.2;2155;G;A G A 1466 1443 20 ORF1a 1890G>A W630* 0.0136425648021828 630 SampleC_freebayes_ann +NC_045512.2 2763 NC_045512.2;2763;TGC;TC TGC TC 2954 2410 532 ORF1a 2499delG Q834fs 0.180094786729858 833 SampleC_freebayes_ann +NC_045512.2 3037 NC_045512.2;3037;CTAC;TTAT CTAC TTAT 2053 0 326 ORF1a 2772C>T F924F 0.158792011690209 924 SampleC_freebayes_ann +NC_045512.2 3037 NC_045512.2;3037;CTAC;TTAC CTAC TTAC 2053 0 1726 ORF1a 2772C>T F924F 0.840720896249391 924 SampleC_freebayes_ann +NC_045512.2 3244 NC_045512.2;3244;C;T C T 3062 3019 43 ORF1a 2979C>T G993G 0.0140431090790333 993 SampleC_freebayes_ann +NC_045512.2 3267 NC_045512.2;3267;C;T C T 3354 524 2829 ORF1a 3002C>T T1001I 0.843470483005367 1001 SampleC_freebayes_ann +NC_045512.2 3290 NC_045512.2;3290;C;G C G 3816 3719 92 ORF1a 3025C>G Q1009E 0.0241090146750524 1009 SampleC_freebayes_ann +NC_045512.2 3327 NC_045512.2;3327;AGA;AA AGA AA 3813 3293 509 ORF1a 3063delG T1022fs 0.133490689745607 1021 SampleC_freebayes_ann +NC_045512.2 3483 NC_045512.2;3483;G;T G T 2793 2753 35 ORF1a 3218G>T G1073V 0.012531328320802 1073 SampleC_freebayes_ann +NC_045512.2 3491 NC_045512.2;3491;AA;TT AA TT 2589 2540 47 ORF1a 3226_3227delAAinsTT N1076F 0.0181537273078409 1076 SampleC_freebayes_ann +NC_045512.2 3500 NC_045512.2;3500;A;C A C 2368 2319 49 ORF1a 3235A>C T1079P 0.0206925675675676 1079 SampleC_freebayes_ann +NC_045512.2 3522 NC_045512.2;3522;A;T A T 1893 1737 156 ORF1a 3257A>T E1086V 0.0824088748019018 1086 SampleC_freebayes_ann +NC_045512.2 3668 NC_045512.2;3668;T;G T G 1674 1656 17 ORF1a 3403T>G Y1135D 0.0101553166069295 1135 SampleC_freebayes_ann +NC_045512.2 3961 NC_045512.2;3961;C;T C T 455 450 5 ORF1a 3696C>T I1232I 0.010989010989011 1232 SampleC_freebayes_ann +NC_045512.2 4038 NC_045512.2;4038;A;C A C 363 357 6 ORF1a 3773A>C D1258A 0.0165289256198347 1258 SampleC_freebayes_ann +NC_045512.2 4102 NC_045512.2;4102;A;T A T 1952 1932 20 ORF1a 3837A>T L1279F 0.0102459016393443 1279 SampleC_freebayes_ann +NC_045512.2 4162 NC_045512.2;4162;G;T G T 2283 2001 282 ORF1a 3897G>T V1299V 0.123521681997372 1299 SampleC_freebayes_ann +NC_045512.2 4181 NC_045512.2;4181;G;T G T 2202 934 1267 ORF1a 3916G>T A1306S 0.575386012715713 1306 SampleC_freebayes_ann +NC_045512.2 4268 NC_045512.2;4268;A;G A G 2364 2332 32 ORF1a 4003A>G N1335D 0.0135363790186125 1335 SampleC_freebayes_ann +NC_045512.2 4435 NC_045512.2;4435;T;C T C 1857 1831 25 ORF1a 4170T>C P1390P 0.0134625740441572 1390 SampleC_freebayes_ann +NC_045512.2 4747 NC_045512.2;4747;T;C T C 644 627 16 ORF1a 4482T>C S1494S 0.0248447204968944 1494 SampleC_freebayes_ann +NC_045512.2 4752 NC_045512.2;4752;C;T C T 643 553 89 ORF1a 4487C>T T1496I 0.138413685847589 1496 SampleC_freebayes_ann +NC_045512.2 4839 NC_045512.2;4839;T;C T C 596 590 6 ORF1a 4574T>C I1525T 0.0100671140939597 1525 SampleC_freebayes_ann +NC_045512.2 4850 NC_045512.2;4850;A;G A G 650 642 8 ORF1a 4585A>G K1529E 0.0123076923076923 1529 SampleC_freebayes_ann +NC_045512.2 4955 NC_045512.2;4955;GAAGT;GAGT GAAGT GAGT 1155 1091 13 ORF1a 4692delA V1565fs 0.0112554112554113 1564 SampleC_freebayes_ann +NC_045512.2 4955 NC_045512.2;4955;GAAGT;GACGT GAAGT GACGT 1155 1091 48 ORF1a 4692delA V1565fs 0.0415584415584416 1564 SampleC_freebayes_ann +NC_045512.2 5118 NC_045512.2;5118;TTT;AAA TTT AAA 2311 2265 43 ORF1a 4853_4855delTTTinsAAA FY1618* 0.0186066637819126 1618 SampleC_freebayes_ann +NC_045512.2 5182 NC_045512.2;5182;T;C T C 1991 1486 503 ORF1a 4917T>C D1639D 0.252636865896534 1639 SampleC_freebayes_ann +NC_045512.2 5184 NC_045512.2;5184;C;T C T 1997 1661 332 ORF1a 4919C>T P1640L 0.166249374061092 1640 SampleC_freebayes_ann +NC_045512.2 5239 NC_045512.2;5239;C;T C T 1769 1265 502 ORF1a 4974C>T Y1658Y 0.283776144714528 1658 SampleC_freebayes_ann +NC_045512.2 5283 NC_045512.2;5283;AC;GT AC GT 1943 1901 36 ORF1a 5018_5019delACinsGT N1673S 0.0185280494081318 1673 SampleC_freebayes_ann +NC_045512.2 5388 NC_045512.2;5388;C;A C A 1638 945 691 ORF1a 5123C>A A1708D 0.421855921855922 1708 SampleC_freebayes_ann +NC_045512.2 5584 NC_045512.2;5584;A;G A G 1403 1043 359 ORF1a 5319A>G T1773T 0.255880256593015 1773 SampleC_freebayes_ann +NC_045512.2 5765 NC_045512.2;5765;GG;AC GG AC 638 621 11 ORF1a 5500_5501delGGinsAC G1834T 0.0172413793103448 1834 SampleC_freebayes_ann +NC_045512.2 5818 NC_045512.2;5818;T;C T C 650 390 260 ORF1a 5553T>C A1851A 0.4 1851 SampleC_freebayes_ann +NC_045512.2 5909 NC_045512.2;5909;TAT;TT TAT TT 1363 1149 213 ORF1a 5645delA Y1882fs 0.156272927366104 1882 SampleC_freebayes_ann +NC_045512.2 5944 NC_045512.2;5944;C;T C T 1712 1315 395 ORF1a 5679C>T D1893D 0.230724299065421 1893 SampleC_freebayes_ann +NC_045512.2 5986 NC_045512.2;5986;CACAG;TACAA CACAG TACAA 1749 655 576 ORF1a 5721_5725delCACAGinsTACAA E1909K 0.329331046312178 1907 SampleC_freebayes_ann +NC_045512.2 5986 NC_045512.2;5986;CACAG;TACAG CACAG TACAG 1749 655 504 ORF1a 5721_5725delCACAGinsTACAA E1909K 0.288164665523156 1907 SampleC_freebayes_ann +NC_045512.2 6401 NC_045512.2;6401;CC;GT CC GT 2996 1228 40 ORF1a 6137C>T P2046L 0.013351134846462 2046 SampleC_freebayes_ann +NC_045512.2 6401 NC_045512.2;6401;CC;CT CC CT 2996 1228 1723 ORF1a 6137C>T P2046L 0.575100133511349 2046 SampleC_freebayes_ann +NC_045512.2 6459 NC_045512.2;6459;A;G A G 2778 2731 47 ORF1a 6194A>G N2065S 0.0169186465082793 2065 SampleC_freebayes_ann +NC_045512.2 6581 NC_045512.2;6581;A;G A G 3950 3899 42 ORF1a 6316A>G T2106A 0.0106329113924051 2106 SampleC_freebayes_ann +NC_045512.2 6654 NC_045512.2;6654;TTAATAGTGTCCCTTGGGATACTATAGCT;TT TTAATAGTGTCCCTTGGGATACTATAGCT TT 2584 2411 90 ORF1a 6394_6420delAGTGTCCCTTGGGATACTATAGCTAAT S2132_N2140del 0.0348297213622291 2130 SampleC_freebayes_ann +NC_045512.2 6728 NC_045512.2;6728;A;G A G 4495 4361 131 ORF1a 6463A>G N2155D 0.0291434927697442 2155 SampleC_freebayes_ann +NC_045512.2 6772 NC_045512.2;6772;G;A G A 5961 5882 72 ORF1a 6507G>A M2169I 0.0120785103170609 2169 SampleC_freebayes_ann +NC_045512.2 6954 NC_045512.2;6954;T;C T C 4348 1098 3244 ORF1a 6689T>C I2230T 0.746090156393744 2230 SampleC_freebayes_ann +NC_045512.2 7124 NC_045512.2;7124;C;T C T 2633 1069 1563 ORF1a 6859C>T P2287S 0.59361944549943 2287 SampleC_freebayes_ann +NC_045512.2 7262 NC_045512.2;7262;C;A C A 2907 2866 36 ORF1a 6997C>A L2333I 0.0123839009287926 2333 SampleC_freebayes_ann +NC_045512.2 7363 NC_045512.2;7363;G;C G C 3189 2796 387 ORF1a 7098G>C W2366C 0.121354656632173 2366 SampleC_freebayes_ann +NC_045512.2 7429 NC_045512.2;7429;A;G A G 2042 1204 835 ORF1a 7164A>G A2388A 0.408912830558276 2388 SampleC_freebayes_ann +NC_045512.2 8172 NC_045512.2;8172;C;T C T 841 824 17 ORF1a 7907C>T A2636V 0.0202140309155767 2636 SampleC_freebayes_ann +NC_045512.2 8364 NC_045512.2;8364;A;G A G 897 530 366 ORF1a 8099A>G N2700S 0.408026755852843 2700 SampleC_freebayes_ann +NC_045512.2 8557 NC_045512.2;8557;A;G A G 1033 660 373 ORF1a 8292A>G K2764K 0.36108422071636 2764 SampleC_freebayes_ann +NC_045512.2 8565 NC_045512.2;8565;ATAA;GTAG ATAA GTAG 903 592 310 ORF1a 8300_8303delATAAinsGTAG NN2767SS 0.343300110741971 2767 SampleC_freebayes_ann +NC_045512.2 8634 NC_045512.2;8634;T;C T C 694 622 71 ORF1a 8369T>C I2790T 0.102305475504323 2790 SampleC_freebayes_ann +NC_045512.2 8716 NC_045512.2;8716;TC;GA TC GA 265 260 5 ORF1a 8451_8452delTCinsGA R2818S 0.0188679245283019 2817 SampleC_freebayes_ann +NC_045512.2 8782 NC_045512.2;8782;C;A C A 295 291 4 ORF1a 8517C>A S2839R 0.0135593220338983 2839 SampleC_freebayes_ann +NC_045512.2 8844 NC_045512.2;8844;G;A G A 330 318 12 ORF1a 8579G>A R2860K 0.0363636363636364 2860 SampleC_freebayes_ann +NC_045512.2 8873 NC_045512.2;8873;C;T C T 293 289 3 ORF1a 8608C>T P2870S 0.0102389078498294 2870 SampleC_freebayes_ann +NC_045512.2 8986 NC_045512.2;8986;C;T C T 920 114 804 ORF1a 8721C>T D2907D 0.873913043478261 2907 SampleC_freebayes_ann +NC_045512.2 9026 NC_045512.2;9026;A;T A T 1113 1042 71 ORF1a 8761A>T I2921F 0.0637915543575921 2921 SampleC_freebayes_ann +NC_045512.2 9053 NC_045512.2;9053;G;T G T 1082 169 913 ORF1a 8788G>T V2930L 0.843807763401109 2930 SampleC_freebayes_ann +NC_045512.2 9241 NC_045512.2;9241;A;T A T 1557 1495 60 ORF1a 8976A>T S2992S 0.0385356454720617 2992 SampleC_freebayes_ann +NC_045512.2 9445 NC_045512.2;9445;T;C T C 1927 1836 91 ORF1a 9180T>C L3060L 0.047223663725999 3060 SampleC_freebayes_ann +NC_045512.2 9511 NC_045512.2;9511;T;C T C 2576 2355 220 ORF1a 9246T>C T3082T 0.0854037267080745 3082 SampleC_freebayes_ann +NC_045512.2 9521 NC_045512.2;9521;C;T C T 2683 2625 56 ORF1a 9256C>T L3086F 0.0208721580320537 3086 SampleC_freebayes_ann +NC_045512.2 9627 NC_045512.2;9627;CTTTTTTAG;CTTTTTAG CTTTTTTAG CTTTTTAG 2471 2424 30 ORF1a 9368delT L3123fs 0.0121408336705787 3121 SampleC_freebayes_ann +NC_045512.2 9734 NC_045512.2;9734;T;C T C 2465 1803 659 ORF1a 9469T>C F3157L 0.267342799188641 3157 SampleC_freebayes_ann +NC_045512.2 9865 NC_045512.2;9865;T;C T C 945 934 11 ORF1a 9600T>C P3200P 0.0116402116402116 3200 SampleC_freebayes_ann +NC_045512.2 9891 NC_045512.2;9891;C;T C T 1065 691 373 ORF1a 9626C>T A3209V 0.350234741784038 3209 SampleC_freebayes_ann +NC_045512.2 10029 NC_045512.2;10029;C;T C T 857 419 437 ORF1a 9764C>T T3255I 0.509918319719953 3255 SampleC_freebayes_ann +NC_045512.2 10228 NC_045512.2;10228;C;T C T 3020 2170 847 ORF1a 9963C>T L3321L 0.28046357615894 3321 SampleC_freebayes_ann +NC_045512.2 10408 NC_045512.2;10408;C;T C T 2339 1750 587 ORF1a 10143C>T Y3381Y 0.25096194955109 3381 SampleC_freebayes_ann +NC_045512.2 10487 NC_045512.2;10487;T;C T C 1268 1208 60 ORF1a 10222T>C C3408R 0.0473186119873817 3408 SampleC_freebayes_ann +NC_045512.2 11074 NC_045512.2;11074;CTTTTTTTTGTATGA;CTTTTTTTGTATGA CTTTTTTTTGTATGA CTTTTTTTGTATGA 552 518 13 ORF1a 10817delT L3606fs 0.0235507246376812 3603 SampleC_freebayes_ann +NC_045512.2 11074 NC_045512.2;11074;CTTTTTTTTGTATGA;CTTTTTTTTTGTATGA CTTTTTTTTGTATGA CTTTTTTTTTGTATGA 552 518 12 ORF1a 10817delT L3606fs 0.0217391304347826 3603 SampleC_freebayes_ann +NC_045512.2 11151 NC_045512.2;11151;T;A T A 800 788 12 ORF1a 10886T>A V3629D 0.015 3629 SampleC_freebayes_ann +NC_045512.2 11201 NC_045512.2;11201;A;G A G 801 56 744 ORF1a 10936A>G T3646A 0.928838951310862 3646 SampleC_freebayes_ann +NC_045512.2 11332 NC_045512.2;11332;A;G A G 1472 674 797 ORF1a 11067A>G V3689V 0.541440217391304 3689 SampleC_freebayes_ann +NC_045512.2 11418 NC_045512.2;11418;T;C T C 2727 2269 444 ORF1a 11153T>C V3718A 0.162816281628163 3718 SampleC_freebayes_ann +NC_045512.2 11514 NC_045512.2;11514;C;T C T 2189 1839 349 ORF1a 11249C>T T3750I 0.159433531292828 3750 SampleC_freebayes_ann +NC_045512.2 11522 NC_045512.2;11522;T;G T G 2266 1963 301 ORF1a 11257T>G F3753V 0.132833186231245 3753 SampleC_freebayes_ann +NC_045512.2 11593 NC_045512.2;11593;TC;GA TC GA 2530 2495 31 ORF1a 11328_11329delTCinsGA Q3777K 0.0122529644268775 3776 SampleC_freebayes_ann +NC_045512.2 11952 NC_045512.2;11952;A;T A T 3760 3720 40 ORF1a 11687A>T N3896I 0.0106382978723404 3896 SampleC_freebayes_ann +NC_045512.2 12165 NC_045512.2;12165;C;T C T 4731 4675 48 ORF1a 11900C>T A3967V 0.010145846544071 3967 SampleC_freebayes_ann +NC_045512.2 12395 NC_045512.2;12395;G;A G A 2722 2692 28 ORF1a 12130G>A A4044T 0.0102865540044085 4044 SampleC_freebayes_ann +NC_045512.2 12421 NC_045512.2;12421;A;G A G 2716 2679 34 ORF1a 12156A>G A4052A 0.0125184094256259 4052 SampleC_freebayes_ann +NC_045512.2 12543 NC_045512.2;12543;C;T C T 3019 2977 41 ORF1a 12278C>T S4093L 0.0135806558463067 4093 SampleC_freebayes_ann +NC_045512.2 13061 NC_045512.2;13061;G;A G A 3822 3763 53 ORF1a 12796G>A V4266I 0.0138670852956567 4266 SampleC_freebayes_ann +NC_045512.2 13105 NC_045512.2;13105;C;T C T 3664 3555 105 ORF1a 12840C>T Y4280Y 0.0286572052401747 4280 SampleC_freebayes_ann +NC_045512.2 13162 NC_045512.2;13162;TACACACACT;TACACACT TACACACACT TACACACT 2963 2599 334 ORF1a 12904_12905delAC T4302fs 0.112723590955113 4299 SampleC_freebayes_ann +NC_045512.2 13514 NC_045512.2;13514;G;A G A 729 713 16 ORF1b 13250G>A G4417D 0.0219478737997256 25 SampleC_freebayes_ann +NC_045512.2 13617 NC_045512.2;13617;G;A G A 1856 1161 681 ORF1b 13353G>A K4451K 0.366918103448276 59 SampleC_freebayes_ann +NC_045512.2 13625 NC_045512.2;13625;ATG;AG ATG AG 1903 1859 43 ORF1b 13362delT D4454fs 0.022595901208618 62 SampleC_freebayes_ann +NC_045512.2 13837 NC_045512.2;13837;C;T C T 3272 3183 88 ORF1b 13573C>T H4525Y 0.0268948655256724 132 SampleC_freebayes_ann +NC_045512.2 13884 NC_045512.2;13884;ATA;AA ATA AA 3158 3117 38 ORF1b 13621delT Y4541fs 0.0120329322355921 148 SampleC_freebayes_ann +NC_045512.2 13948 NC_045512.2;13948;G;T G T 2345 1889 452 ORF1b 13684G>T D4562Y 0.192750533049041 169 SampleC_freebayes_ann +NC_045512.2 14343 NC_045512.2;14343;T;C T C 3163 2919 243 ORF1b 14079T>C C4693C 0.07682579829276 301 SampleC_freebayes_ann +NC_045512.2 14408 NC_045512.2;14408;C;T C T 2866 3 2863 ORF1b 14144C>T P4715L 0.998953244940684 323 SampleC_freebayes_ann +NC_045512.2 14599 NC_045512.2;14599;C;T C T 1918 1293 624 ORF1b 14335C>T L4779L 0.32533889468196 386 SampleC_freebayes_ann +NC_045512.2 14676 NC_045512.2;14676;C;T C T 2867 2494 371 ORF1b 14412C>T P4804P 0.129403557725846 412 SampleC_freebayes_ann +NC_045512.2 14925 NC_045512.2;14925;C;T C T 1720 1651 68 ORF1b 14661C>T V4887V 0.0395348837209302 495 SampleC_freebayes_ann +NC_045512.2 14960 NC_045512.2;14960;A;T A T 1845 1803 42 ORF1b 14696A>T N4899I 0.0227642276422764 507 SampleC_freebayes_ann +NC_045512.2 15081 NC_045512.2;15081;C;A C A 1823 1800 19 ORF1b 14817C>A A4939A 0.0104223806911684 547 SampleC_freebayes_ann +NC_045512.2 15099 NC_045512.2;15099;A;G A G 1724 1702 20 ORF1b 14835A>G R4945R 0.0116009280742459 553 SampleC_freebayes_ann +NC_045512.2 15112 NC_045512.2;15112;G;A G A 1742 1719 22 ORF1b 14848G>A A4950T 0.0126291618828932 557 SampleC_freebayes_ann +NC_045512.2 15279 NC_045512.2;15279;C;T C T 1355 672 679 ORF1b 15015C>T H5005H 0.501107011070111 613 SampleC_freebayes_ann +NC_045512.2 15451 NC_045512.2;15451;G;A G A 1065 639 426 ORF1b 15187G>A G5063S 0.4 670 SampleC_freebayes_ann +NC_045512.2 15610 NC_045512.2;15610;C;T C T 2649 2587 61 ORF1b 15346C>T Q5116* 0.0230275575688939 723 SampleC_freebayes_ann +NC_045512.2 15682 NC_045512.2;15682;TATT;AATA TATT AATA 3135 3065 62 ORF1b 15418_15421delTATTinsAATA YL5140NM 0.0197767145135566 747 SampleC_freebayes_ann +NC_045512.2 15765 NC_045512.2;15765;A;G A G 2620 2591 29 ORF1b 15501A>G L5167L 0.0110687022900763 775 SampleC_freebayes_ann +NC_045512.2 15924 NC_045512.2;15924;C;T C T 3061 3024 37 ORF1b 15660C>T Y5220Y 0.0120875530872264 828 SampleC_freebayes_ann +NC_045512.2 16047 NC_045512.2;16047;T;C T C 3555 3144 409 ORF1b 15783T>C L5261L 0.115049226441632 869 SampleC_freebayes_ann +NC_045512.2 16176 NC_045512.2;16176;T;C T C 2173 1925 247 ORF1b 15912T>C T5304T 0.113667740450989 912 SampleC_freebayes_ann +NC_045512.2 16466 NC_045512.2;16466;C;T C T 1646 33 1613 ORF1b 16202C>T P5401L 0.979951397326853 1009 SampleC_freebayes_ann +NC_045512.2 16816 NC_045512.2;16816;C;T C T 1179 878 301 ORF1b 16552C>T Q5518* 0.255301102629347 1125 SampleC_freebayes_ann +NC_045512.2 17218 NC_045512.2;17218;G;C G C 2615 2579 35 ORF1b 16954G>C D5652H 0.0133843212237094 1259 SampleC_freebayes_ann +NC_045512.2 17814 NC_045512.2;17814;G;A G A 1401 1158 241 ORF1b 17550G>A L5850L 0.172019985724483 1458 SampleC_freebayes_ann +NC_045512.2 18564 NC_045512.2;18564;A;C A C 2012 1986 26 ORF1b 18300A>C K6100N 0.0129224652087475 1708 SampleC_freebayes_ann +NC_045512.2 18585 NC_045512.2;18585;A;G A G 1713 1666 34 ORF1b 18321A>G V6107V 0.0198482194979568 1715 SampleC_freebayes_ann +NC_045512.2 18589 NC_045512.2;18589;G;T G T 1666 1595 68 ORF1b 18325G>T V6109F 0.0408163265306122 1716 SampleC_freebayes_ann +NC_045512.2 18591 NC_045512.2;18591;C;A C A 1626 1549 22 ORF1b 18327C>A V6109V 0.013530135301353 1717 SampleC_freebayes_ann +NC_045512.2 18591 NC_045512.2;18591;C;G C G 1626 1549 53 ORF1b 18327C>A V6109V 0.0325953259532595 1717 SampleC_freebayes_ann +NC_045512.2 18596 NC_045512.2;18596;G;T G T 1560 1519 36 ORF1b 18332G>T W6111L 0.0230769230769231 1719 SampleC_freebayes_ann +NC_045512.2 18607 NC_045512.2;18607;T;G T G 2032 1989 37 ORF1b 18343T>G F6115V 0.0182086614173228 1722 SampleC_freebayes_ann +NC_045512.2 18634 NC_045512.2;18634;G;T G T 2484 2453 30 ORF1b 18370G>T V6124L 0.0120772946859903 1731 SampleC_freebayes_ann +NC_045512.2 18977 NC_045512.2;18977;A;G A G 3941 3433 507 ORF1b 18713A>G Q6238R 0.128647551382898 1846 SampleC_freebayes_ann +NC_045512.2 19132 NC_045512.2;19132;G;T G T 5691 5556 135 ORF1b 18868G>T E6290* 0.0237216657880865 1897 SampleC_freebayes_ann +NC_045512.2 19137 NC_045512.2;19137;A;C A C 5642 5525 114 ORF1b 18873A>C L6291F 0.0202056008507621 1899 SampleC_freebayes_ann +NC_045512.2 19165 NC_045512.2;19165;A;G A G 5857 5683 172 ORF1b 18901A>G K6301E 0.0293665699163394 1908 SampleC_freebayes_ann +NC_045512.2 19220 NC_045512.2;19220;C;T C T 5406 1886 3517 ORF1b 18956C>T A6319V 0.650573436921939 1927 SampleC_freebayes_ann +NC_045512.2 19245 NC_045512.2;19245;C;T C T 5068 4668 399 ORF1b 18981C>T D6327D 0.0787292817679558 1935 SampleC_freebayes_ann +NC_045512.2 19333 NC_045512.2;19333;G;T G T 4077 2976 1101 ORF1b 19069G>T D6357Y 0.270051508462104 1964 SampleC_freebayes_ann +NC_045512.2 19452 NC_045512.2;19452;T;A T A 3420 3372 42 ORF1b 19188T>A A6396A 0.012280701754386 2004 SampleC_freebayes_ann +NC_045512.2 19751 NC_045512.2;19751;A;T A T 917 904 12 ORF1b 19487A>T E6496V 0.0130861504907306 2104 SampleC_freebayes_ann +NC_045512.2 19887 NC_045512.2;19887;A;G A G 1166 1133 33 ORF1b 19623A>G K6541K 0.0283018867924528 2149 SampleC_freebayes_ann +NC_045512.2 19895 NC_045512.2;19895;C;T C T 1174 1155 18 ORF1b 19631C>T A6544V 0.0153321976149915 2152 SampleC_freebayes_ann +NC_045512.2 19983 NC_045512.2;19983;CTTTTTTGA;CTTTTTGA CTTTTTTGA CTTTTTGA 941 897 24 ORF1b 19725delT F6575fs 0.0255047821466525 2181 SampleC_freebayes_ann +NC_045512.2 20088 NC_045512.2;20088;T;C T C 976 966 10 ORF1b 19824T>C G6608G 0.0102459016393443 2216 SampleC_freebayes_ann +NC_045512.2 20633 NC_045512.2;20633;T;C T C 2089 1923 166 ORF1b 20369T>C V6790A 0.0794638583054093 2398 SampleC_freebayes_ann +NC_045512.2 20686 NC_045512.2;20686;G;A G A 1937 1901 36 ORF1b 20422G>A A6808T 0.0185854414042334 2415 SampleC_freebayes_ann +NC_045512.2 20897 NC_045512.2;20897;C;A C A 1649 1609 40 ORF1b 20633C>A P6878Q 0.0242571255306246 2486 SampleC_freebayes_ann +NC_045512.2 20912 NC_045512.2;20912;T;A T A 1786 1762 20 ORF1b 20648T>A L6883* 0.0111982082866741 2491 SampleC_freebayes_ann +NC_045512.2 21004 NC_045512.2;21004;G;T G T 2194 2124 68 ORF1b 20740G>T A6914S 0.0309936189608022 2521 SampleC_freebayes_ann +NC_045512.2 21137 NC_045512.2;21137;A;G A G 3005 2941 62 ORF1b 20873A>G K6958R 0.0206322795341098 2566 SampleC_freebayes_ann +NC_045512.2 21357 NC_045512.2;21357;T;C T C 3104 3026 76 ORF1b 21093T>C N7031N 0.0244845360824742 2639 SampleC_freebayes_ann +NC_045512.2 21408 NC_045512.2;21408;T;A T A 3187 3152 33 ORF1b 21144T>A F7048L 0.010354565422027 2656 SampleC_freebayes_ann +NC_045512.2 21417 NC_045512.2;21417;A;T A T 3209 3108 101 ORF1b 21153A>T K7051N 0.0314739794328451 2659 SampleC_freebayes_ann +NC_045512.2 21575 NC_045512.2;21575;C;T C T 2364 1871 489 S 13C>T L5F 0.206852791878173 5 SampleC_freebayes_ann +NC_045512.2 21618 NC_045512.2;21618;C;G C G 2058 609 1448 S 56C>G T19R 0.703595724003887 19 SampleC_freebayes_ann +NC_045512.2 21650 NC_045512.2;21650;A;C A C 1834 1636 198 S 88A>C N30H 0.107960741548528 30 SampleC_freebayes_ann +NC_045512.2 21656 NC_045512.2;21656;TTCACACG;TACC TTCACACG TACC 1573 1501 51 S 95_101delTCACACGinsACC F32fs 0.0324221233312142 32 SampleC_freebayes_ann +NC_045512.2 21764 NC_045512.2;21764;ATACATGT;AT ATACATGT AT 744 0 744 S 204_209delACATGT H69_V70del 1 68 SampleC_freebayes_ann +NC_045512.2 21855 NC_045512.2;21855;C;T C T 784 351 433 S 293C>T S98F 0.552295918367347 98 SampleC_freebayes_ann +NC_045512.2 21974 NC_045512.2;21974;G;C G C 739 390 348 S 412G>C D138H 0.470906630581867 138 SampleC_freebayes_ann +NC_045512.2 21979 NC_045512.2;21979;ATTTTTGGGTGTTTATTAC;ATTTTGGGTGTTTAC ATTTTTGGGTGTTTATTAC ATTTTGGGTGTTTAC 548 47 12 S 422_431delTGGGTGTTTAinsGGGTGT L141fs 0.0218978102189781 139 SampleC_freebayes_ann +NC_045512.2 21979 NC_045512.2;21979;ATTTTTGGGTGTTTATTAC;ATTTTTGGGTGTTTAC ATTTTTGGGTGTTTATTAC ATTTTTGGGTGTTTAC 548 47 482 S 422_431delTGGGTGTTTAinsGGGTGT L141fs 0.87956204379562 139 SampleC_freebayes_ann +NC_045512.2 22028 NC_045512.2;22028;GAGTTCAG;GG GAGTTCAG GG 505 444 60 S 467_472delAGTTCA E156_R158delinsG 0.118811881188119 156 SampleC_freebayes_ann +NC_045512.2 22070 NC_045512.2;22070;T;G T G 415 404 11 S 508T>G Y170D 0.0265060240963855 170 SampleC_freebayes_ann +NC_045512.2 22218 NC_045512.2;22218;GTTTTTCG;GTTTTCG GTTTTTCG GTTTTCG 973 946 12 S 661delT S221fs 0.0123329907502569 219 SampleC_freebayes_ann +NC_045512.2 22282 NC_045512.2;22282;TTTACTTGCT;TT TTTACTTGCT TT 2520 2139 370 S 723_730delACTTGCTT L241fs 0.146825396825397 240 SampleC_freebayes_ann +NC_045512.2 22315 NC_045512.2;22315;T;G T G 4311 3944 357 S 753T>G P251P 0.0828114126652749 251 SampleC_freebayes_ann +NC_045512.2 22600 NC_045512.2;22600;ATTTGC;ATTGC ATTTGC ATTGC 5420 5113 275 S 1041delT F347fs 0.0507380073800738 346 SampleC_freebayes_ann +NC_045512.2 22643 NC_045512.2;22643;TGT;ACA TGT ACA 3250 3179 66 S 1081_1083delTGTinsACA C361T 0.0203076923076923 361 SampleC_freebayes_ann +NC_045512.2 22852 NC_045512.2;22852;A;G A G 2894 2473 416 S 1290A>G T430T 0.143745680718728 430 SampleC_freebayes_ann +NC_045512.2 22917 NC_045512.2;22917;T;G T G 1753 604 1147 S 1355T>G L452R 0.654306902452938 452 SampleC_freebayes_ann +NC_045512.2 22995 NC_045512.2;22995;C;A C A 1708 619 1088 S 1433C>A T478K 0.637002341920375 478 SampleC_freebayes_ann +NC_045512.2 23063 NC_045512.2;23063;A;T A T 1592 1014 578 S 1501A>T N501Y 0.363065326633166 501 SampleC_freebayes_ann +NC_045512.2 23271 NC_045512.2;23271;C;A C A 3990 3879 99 S 1709C>A A570D 0.024812030075188 570 SampleC_freebayes_ann +NC_045512.2 23302 NC_045512.2;23302;G;C G C 4207 3556 649 S 1740G>C Q580H 0.154266698359876 580 SampleC_freebayes_ann +NC_045512.2 23403 NC_045512.2;23403;A;G A G 3572 2 3570 S 1841A>G D614G 0.999440089585666 614 SampleC_freebayes_ann +NC_045512.2 23472 NC_045512.2;23472;C;A C A 2386 2346 35 S 1910C>A S637Y 0.0146689019279128 637 SampleC_freebayes_ann +NC_045512.2 23492 NC_045512.2;23492;C;A C A 1868 1835 22 S 1930C>A Q644K 0.0117773019271949 644 SampleC_freebayes_ann +NC_045512.2 23575 NC_045512.2;23575;C;T C T 456 448 6 S 2013C>T C671C 0.0131578947368421 671 SampleC_freebayes_ann +NC_045512.2 23604 NC_045512.2;23604;C;G C G 536 0 536 S 2042C>G P681R 1 681 SampleC_freebayes_ann +NC_045512.2 23746 NC_045512.2;23746;A;G A G 618 559 59 S 2184A>G P728P 0.0954692556634304 728 SampleC_freebayes_ann +NC_045512.2 23865 NC_045512.2;23865;C;T C T 325 319 6 S 2303C>T T768I 0.0184615384615385 768 SampleC_freebayes_ann +NC_045512.2 23887 NC_045512.2;23887;CAAAAACACCCAAG;CAAAACACCCAAG CAAAAACACCCAAG CAAAACACCCAAG 304 300 4 S 2330delA N777fs 0.0131578947368421 775 SampleC_freebayes_ann +NC_045512.2 23910 NC_045512.2;23910;C;T C T 401 395 6 S 2348C>T A783V 0.0149625935162095 783 SampleC_freebayes_ann +NC_045512.2 23996 NC_045512.2;23996;C;T C T 555 548 6 S 2434C>T P812S 0.0108108108108108 812 SampleC_freebayes_ann +NC_045512.2 24110 NC_045512.2;24110;A;C A C 569 512 57 S 2548A>C I850L 0.100175746924429 850 SampleC_freebayes_ann +NC_045512.2 24201 NC_045512.2;24201;G;A G A 542 529 12 S 2639G>A G880D 0.022140221402214 880 SampleC_freebayes_ann +NC_045512.2 24320 NC_045512.2;24320;CAAAAATTG;CAAAATTG CAAAAATTG CAAAATTG 537 358 172 S 2763delA K921fs 0.320297951582868 920 SampleC_freebayes_ann +NC_045512.2 24329 NC_045512.2;24329;A;G A G 563 557 6 S 2767A>G I923V 0.0106571936056838 923 SampleC_freebayes_ann +NC_045512.2 24410 NC_045512.2;24410;G;A G A 949 580 368 S 2848G>A D950N 0.387776606954689 950 SampleC_freebayes_ann +NC_045512.2 24506 NC_045512.2;24506;T;G T G 2224 1519 704 S 2944T>G S982A 0.316546762589928 982 SampleC_freebayes_ann +NC_045512.2 24626 NC_045512.2;24626;G;A G A 2469 2418 45 S 3064G>A A1022T 0.0182260024301337 1022 SampleC_freebayes_ann +NC_045512.2 24794 NC_045512.2;24794;G;C G C 3784 3110 668 S 3232G>C A1078P 0.176532769556025 1078 SampleC_freebayes_ann +NC_045512.2 24914 NC_045512.2;24914;G;C G C 4900 3738 1158 S 3352G>C D1118H 0.236326530612245 1118 SampleC_freebayes_ann +NC_045512.2 24952 NC_045512.2;24952;A;G A G 4842 4770 70 S 3390A>G I1130M 0.0144568360181743 1130 SampleC_freebayes_ann +NC_045512.2 25047 NC_045512.2;25047;C;T C T 4648 4309 333 S 3485C>T P1162L 0.0716437177280551 1162 SampleC_freebayes_ann +NC_045512.2 25243 NC_045512.2;25243;A;G A G 3225 3152 69 S 3681A>G I1227M 0.0213953488372093 1227 SampleC_freebayes_ann +NC_045512.2 25244 NC_045512.2;25244;G;T G T 3243 2802 439 S 3682G>T V1228L 0.135368485969781 1228 SampleC_freebayes_ann +NC_045512.2 25277 NC_045512.2;25277;A;T A T 2415 2353 49 S 3715A>T S1239C 0.0202898550724638 1239 SampleC_freebayes_ann +NC_045512.2 25286 NC_045512.2;25286;A;T A T 2593 2498 74 S 3724A>T S1242C 0.0285383725414578 1242 SampleC_freebayes_ann +NC_045512.2 25296 NC_045512.2;25296;A;C A C 2571 2375 141 S 3734A>C K1245T 0.0548424737456243 1245 SampleC_freebayes_ann +NC_045512.2 25296 NC_045512.2;25296;A;T A T 2571 2375 54 S 3734A>C K1245T 0.0210035005834306 1245 SampleC_freebayes_ann +NC_045512.2 25297 NC_045512.2;25297;GGGC;GGGG GGGC GGGG 2484 2410 63 S 3738C>G G1246G 0.0253623188405797 1245 SampleC_freebayes_ann +NC_045512.2 25308 NC_045512.2;25308;C;G C G 2591 2521 27 S 3746C>G S1249C 0.0104206869934388 1249 SampleC_freebayes_ann +NC_045512.2 25308 NC_045512.2;25308;C;T C T 2591 2521 37 S 3746C>G S1249C 0.0142802006947125 1249 SampleC_freebayes_ann +NC_045512.2 25312 NC_045512.2;25312;T;G T G 2594 2563 29 S 3750T>G C1250W 0.0111796453353894 1250 SampleC_freebayes_ann +NC_045512.2 25314 NC_045512.2;25314;G;T G T 2511 2398 98 S 3752G>T G1251V 0.0390282755874154 1251 SampleC_freebayes_ann +NC_045512.2 25316 NC_045512.2;25316;T;C T C 2470 2408 38 S 3754T>C S1252P 0.0153846153846154 1252 SampleC_freebayes_ann +NC_045512.2 25323 NC_045512.2;25323;GCAAA;GAAAT GCAAA GAAAT 2463 1957 71 S 3762C>A C1254* 0.0288266341859521 1254 SampleC_freebayes_ann +NC_045512.2 25323 NC_045512.2;25323;GCAAA;CAAAA GCAAA CAAAA 2463 1957 67 S 3762C>A C1254* 0.0272025984571661 1254 SampleC_freebayes_ann +NC_045512.2 25323 NC_045512.2;25323;GCAAA;GAAAA GCAAA GAAAA 2463 1957 284 S 3762C>A C1254* 0.115306536743808 1254 SampleC_freebayes_ann +NC_045512.2 25331 NC_045512.2;25331;G;T G T 2694 2510 167 S 3769G>T D1257Y 0.0619896065330364 1257 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;CACG GAAG CACG 2461 1948 70 S 3772G>T E1258* 0.0284437220642015 1258 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;CACC GAAG CACC 2461 1948 48 S 3772G>T E1258* 0.0195042665583096 1258 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;GACC GAAG GACC 2461 1948 48 S 3772G>T E1258* 0.0195042665583096 1258 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;CAAG GAAG CAAG 2461 1948 67 S 3772G>T E1258* 0.0272247054043072 1258 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;TAAG GAAG TAAG 2461 1948 57 S 3772G>T E1258* 0.0231613165379927 1258 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;GACG GAAG GACG 2461 1948 133 S 3772G>T E1258* 0.0540430719219829 1258 SampleC_freebayes_ann +NC_045512.2 25334 NC_045512.2;25334;GAAG;GAAC GAAG GAAC 2461 1948 35 S 3772G>T E1258* 0.0142218610321008 1258 SampleC_freebayes_ann +NC_045512.2 25350 NC_045512.2;25350;CAGT;CT CAGT CT 3349 2991 349 S 3789_3790delAG V1264fs 0.104210212003583 1263 SampleC_freebayes_ann +NC_045512.2 25439 NC_045512.2;25439;A;C A C 4980 4568 409 ORF3a 47A>C K16T 0.0821285140562249 16 SampleC_freebayes_ann +NC_045512.2 25469 NC_045512.2;25469;C;T C T 4510 684 3826 ORF3a 77C>T S26L 0.848337028824834 26 SampleC_freebayes_ann +NC_045512.2 25696 NC_045512.2;25696;G;A G A 54 52 2 ORF3a 304G>A E102K 0.037037037037037 102 SampleC_freebayes_ann +NC_045512.2 25702 NC_045512.2;25702;C;A C A 62 61 1 ORF3a 310C>A P104T 0.0161290322580645 104 SampleC_freebayes_ann +NC_045512.2 25734 NC_045512.2;25734;C;A C A 68 67 1 ORF3a 342C>A F114L 0.0147058823529412 114 SampleC_freebayes_ann +NC_045512.2 25750 NC_045512.2;25750;T;C T C 74 72 2 ORF3a 358T>C F120L 0.027027027027027 120 SampleC_freebayes_ann +NC_045512.2 25785 NC_045512.2;25785;G;T G T 90 80 10 ORF3a 393G>T W131C 0.111111111111111 131 SampleC_freebayes_ann +NC_045512.2 25797 NC_045512.2;25797;CAAAAACCCAT;CAAAAAACCCAT CAAAAACCCAT CAAAAAACCCAT 96 76 18 ORF3a 410dupA N137fs 0.1875 135 SampleC_freebayes_ann +NC_045512.2 25797 NC_045512.2;25797;CAAAAACCCAT;CAAAAACCCAC CAAAAACCCAT CAAAAACCCAC 96 76 2 ORF3a 410dupA N137fs 0.0208333333333333 135 SampleC_freebayes_ann +NC_045512.2 25811 NC_045512.2;25811;T;A T A 97 95 2 ORF3a 419T>A L140H 0.0206185567010309 140 SampleC_freebayes_ann +NC_045512.2 25831 NC_045512.2;25831;C;T C T 79 75 4 ORF3a 439C>T L147F 0.0506329113924051 147 SampleC_freebayes_ann +NC_045512.2 26042 NC_045512.2;26042;CTCAA;TTGAG CTCAA TTGAG 1484 1433 44 ORF3a 650_654delCTCAAinsTTGAG TQ217IE 0.0296495956873315 217 SampleC_freebayes_ann +NC_045512.2 26057 NC_045512.2;26057;A;C A C 1482 1465 15 ORF3a 665A>C D222A 0.0101214574898785 222 SampleC_freebayes_ann +NC_045512.2 26069 NC_045512.2;26069;A;G A G 1483 1467 16 ORF3a 677A>G E226G 0.0107889413351315 226 SampleC_freebayes_ann +NC_045512.2 26089 NC_045512.2;26089;T;A T A 1477 1460 17 ORF3a 697T>A Y233N 0.011509817197021 233 SampleC_freebayes_ann +NC_045512.2 26108 NC_045512.2;26108;A;T A T 1558 1542 16 ORF3a 716A>T E239V 0.0102695763799743 239 SampleC_freebayes_ann +NC_045512.2 26141 NC_045512.2;26141;A;T A T 1542 1522 17 ORF3a 749A>T D250V 0.0110246433203632 250 SampleC_freebayes_ann +NC_045512.2 26145 NC_045512.2;26145;T;C T C 1538 1516 20 ORF3a 753T>C G251G 0.0130039011703511 251 SampleC_freebayes_ann +NC_045512.2 26533 NC_045512.2;26533;C;T C T 2958 2905 52 M 11C>T S4F 0.017579445571332 4 SampleC_freebayes_ann +NC_045512.2 26542 NC_045512.2;26542;CTAT;ATAG CTAT ATAG 2947 2808 131 M 20_23delCTATinsATAG TI7NS 0.0444519850695623 7 SampleC_freebayes_ann +NC_045512.2 26554 NC_045512.2;26554;A;G A G 3289 3248 40 M 32A>G E11G 0.0121617512921861 11 SampleC_freebayes_ann +NC_045512.2 26611 NC_045512.2;26611;C;G C G 4179 3615 561 M 89C>G T30R 0.13424264178033 30 SampleC_freebayes_ann +NC_045512.2 26705 NC_045512.2;26705;T;C T C 4508 4311 193 M 183T>C T61T 0.042812777284827 61 SampleC_freebayes_ann +NC_045512.2 26767 NC_045512.2;26767;T;C T C 3984 1212 2770 M 245T>C I82T 0.695281124497992 82 SampleC_freebayes_ann +NC_045512.2 26837 NC_045512.2;26837;T;C T C 3100 3055 44 M 315T>C R105R 0.0141935483870968 105 SampleC_freebayes_ann +NC_045512.2 27059 NC_045512.2;27059;C;T C T 5267 4956 299 M 537C>T Y179Y 0.0567685589519651 179 SampleC_freebayes_ann +NC_045512.2 27115 NC_045512.2;27115;G;A G A 4546 4357 184 M 593G>A R198H 0.0404751429828421 198 SampleC_freebayes_ann +NC_045512.2 27143 NC_045512.2;27143;C;T C T 4401 4125 272 M 621C>T N207N 0.0618041354237673 207 SampleC_freebayes_ann +NC_045512.2 27285 NC_045512.2;27285;T;A T A 2885 2852 31 ORF6 84T>A N28K 0.0107452339688042 28 SampleC_freebayes_ann +NC_045512.2 27291 NC_045512.2;27291;TTACA;TA TTACA TA 2674 2606 61 ORF6 91_93delTAC Y31del 0.0228122662677637 30 SampleC_freebayes_ann +NC_045512.2 27335 NC_045512.2;27335;C;T C T 3108 3027 78 ORF6 134C>T T45I 0.0250965250965251 45 SampleC_freebayes_ann +NC_045512.2 27344 NC_045512.2;27344;AA;TT AA TT 3040 2943 95 ORF6 143_144delAAinsTT K48I 0.03125 48 SampleC_freebayes_ann +NC_045512.2 27354 NC_045512.2;27354;A;G A G 3037 2967 68 ORF6 153A>G Q51Q 0.0223905169575239 51 SampleC_freebayes_ann +NC_045512.2 27527 NC_045512.2;27527;C;T C T 3598 2439 1157 ORF7a 134C>T P45L 0.321567537520845 45 SampleC_freebayes_ann +NC_045512.2 27566 NC_045512.2;27566;G;T G T 3845 3117 727 ORF7a 173G>T C58F 0.189076723016905 58 SampleC_freebayes_ann +NC_045512.2 27607 NC_045512.2;27607;A;T A T 4113 3369 744 ORF7a 214A>T K72* 0.180889861415026 72 SampleC_freebayes_ann +NC_045512.2 27625 NC_045512.2;27625;C;T C T 4049 3973 75 ORF7a 232C>T R78C 0.0185230921215115 78 SampleC_freebayes_ann +NC_045512.2 27629 NC_045512.2;27629;C;A C A 4112 3313 788 ORF7a 236C>A A79D 0.191634241245136 79 SampleC_freebayes_ann +NC_045512.2 27638 NC_045512.2;27638;T;C T C 4141 1838 2302 ORF7a 245T>C V82A 0.555904370924897 82 SampleC_freebayes_ann +NC_045512.2 27652 NC_045512.2;27652;T;A T A 4346 4299 46 ORF7a 259T>A F87I 0.0105844454670962 87 SampleC_freebayes_ann +NC_045512.2 27696 NC_045512.2;27696;T;C T C 5194 5136 57 ORF7a 303T>C F101F 0.0109742010011552 101 SampleC_freebayes_ann +NC_045512.2 27752 NC_045512.2;27752;C;T C T 4981 2247 2730 ORF7a 359C>T T120I 0.548082714314395 120 SampleC_freebayes_ann +NC_045512.2 27777 NC_045512.2;27777;G;A G A 4362 4286 74 ORF7b 22G>A D8N 0.0169646950939936 8 SampleC_freebayes_ann +NC_045512.2 27857 NC_045512.2;27857;G;A G A 1159 1139 16 ORF7b 102G>A L34L 0.0138050043140639 34 SampleC_freebayes_ann +NC_045512.2 27864 NC_045512.2;27864;C;A C A 1237 1169 66 ORF7b 109C>A H37N 0.053354890864996 37 SampleC_freebayes_ann +NC_045512.2 27870 NC_045512.2;27870;GAAAC;TAAAT GAAAC TAAAT 1272 136 17 ORF7b 115G>T E39* 0.0133647798742138 39 SampleC_freebayes_ann +NC_045512.2 27870 NC_045512.2;27870;GAAAC;TAAAC GAAAC TAAAC 1272 136 25 ORF7b 115G>T E39* 0.0196540880503145 39 SampleC_freebayes_ann +NC_045512.2 27870 NC_045512.2;27870;GAAAC;GAAAT GAAAC GAAAT 1272 136 1088 ORF7b 115G>T E39* 0.855345911949686 39 SampleC_freebayes_ann +NC_045512.2 27942 NC_045512.2;27942;C;T C T 1411 1229 182 ORF8 49C>T H17Y 0.128986534372785 17 SampleC_freebayes_ann +NC_045512.2 27972 NC_045512.2;27972;C;T C T 1308 1152 150 ORF8 79C>T Q27* 0.114678899082569 27 SampleC_freebayes_ann +NC_045512.2 27981 NC_045512.2;27981;CCA;CTACA CCA CTACA 1259 1239 15 ORF8 88_89insTA P30fs 0.0119142176330421 30 SampleC_freebayes_ann +NC_045512.2 27987 NC_045512.2;27987;GTAG;GG GTAG GG 1259 1238 17 ORF8 95_96delTA V32fs 0.0135027799841144 32 SampleC_freebayes_ann +NC_045512.2 28048 NC_045512.2;28048;G;T G T 1234 1101 133 ORF8 155G>T R52I 0.107779578606159 52 SampleC_freebayes_ann +NC_045512.2 28095 NC_045512.2;28095;A;T A T 2258 2163 95 ORF8 202A>T K68* 0.0420726306465899 68 SampleC_freebayes_ann +NC_045512.2 28111 NC_045512.2;28111;A;G A G 2841 1357 1482 ORF8 218A>G Y73C 0.521647307286167 73 SampleC_freebayes_ann +NC_045512.2 28242 NC_045512.2;28242;GTTTTAGATTTCA;GTTTTAA GTTTTAGATTTCA GTTTTAA 6286 4147 1587 ORF8 353dupT L118fs 0.252465797009227 117 SampleC_freebayes_ann +NC_045512.2 28242 NC_045512.2;28242;GTTTTAGATTTCA;GTTTTTAGATTTCA GTTTTAGATTTCA GTTTTTAGATTTCA 6286 4147 509 ORF8 353dupT L118fs 0.0809735921094496 117 SampleC_freebayes_ann +NC_045512.2 28280 NC_045512.2;28280;GAT;CTA GAT CTA 6314 2875 3423 N 7_9delGATinsCTA D3L 0.542128603104213 3 SampleC_freebayes_ann +NC_045512.2 28295 NC_045512.2;28295;A;G A G 7561 6578 980 N 22A>G N8D 0.129612485121016 8 SampleC_freebayes_ann +NC_045512.2 28461 NC_045512.2;28461;A;G A G 2180 1392 787 N 188A>G D63G 0.361009174311927 63 SampleC_freebayes_ann +NC_045512.2 28567 NC_045512.2;28567;C;T C T 2372 2344 26 N 294C>T D98D 0.0109612141652614 98 SampleC_freebayes_ann +NC_045512.2 28579 NC_045512.2;28579;A;T A T 2340 2254 86 N 306A>T K102N 0.0367521367521368 102 SampleC_freebayes_ann +NC_045512.2 28598 NC_045512.2;28598;T;C T C 2328 2299 27 N 325T>C Y109H 0.0115979381443299 109 SampleC_freebayes_ann +NC_045512.2 28881 NC_045512.2;28881;GGGG;AACC GGGG AACC 4147 1 414 N 608G>T R203M 0.0998312032794791 203 SampleC_freebayes_ann +NC_045512.2 28881 NC_045512.2;28881;GGGG;AACG GGGG AACG 4147 1 1062 N 608G>T R203M 0.25608873884736 203 SampleC_freebayes_ann +NC_045512.2 28881 NC_045512.2;28881;GGGG;TGGG GGGG TGGG 4147 1 2649 N 608G>T R203M 0.638775018085363 203 SampleC_freebayes_ann +NC_045512.2 28915 NC_045512.2;28915;CG;TT CG TT 4477 1892 125 N 643G>T G215C 0.027920482465937 214 SampleC_freebayes_ann +NC_045512.2 28915 NC_045512.2;28915;CG;CT CG CT 4477 1892 2449 N 643G>T G215C 0.547018092472638 214 SampleC_freebayes_ann +NC_045512.2 28972 NC_045512.2;28972;A;G A G 4047 3939 108 N 699A>G K233K 0.0266864343958488 233 SampleC_freebayes_ann +NC_045512.2 28977 NC_045512.2;28977;C;T C T 3909 2408 1501 N 704C>T S235F 0.383985674085444 235 SampleC_freebayes_ann +NC_045512.2 29000 NC_045512.2;29000;G;T G T 3760 3028 732 N 727G>T G243C 0.19468085106383 243 SampleC_freebayes_ann +NC_045512.2 29029 NC_045512.2;29029;T;C T C 3572 3497 74 N 756T>C A252A 0.0207166853303471 252 SampleC_freebayes_ann +NC_045512.2 29039 NC_045512.2;29039;A;T A T 3516 3367 149 N 766A>T K256* 0.0423777019340159 256 SampleC_freebayes_ann +NC_045512.2 29049 NC_045512.2;29049;G;A G A 3347 3243 101 N 776G>A R259Q 0.0301762772632208 259 SampleC_freebayes_ann +NC_045512.2 29067 NC_045512.2;29067;CTAAAGCATACAATGT;CT CTAAAGCATACAATGT CT 2118 1911 187 N 798_811delAGCATACAATGTAA K266fs 0.0882908404154863 265 SampleC_freebayes_ann +NC_045512.2 29402 NC_045512.2;29402;G;T G T 4271 2642 1623 N 1129G>T D377Y 0.380004682744088 377 SampleC_freebayes_ann
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pangolin_constellations.loc.sample Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,10 @@ +# this is a tab separated file describing the location of constellations databases used for the +# scorpio part of the pangolin SARS-CoV-2 lineage typing tool +# +# the columns are: +# value description min_scorpio_version date path +# +# min_scorpio_version is the minimum scorpio tool major version that is needed to read the constellations data +# +# for example +#v0.1.10 constellations release v0.1.10 0 2022-05-05T13:14:56 /srv/galaxy/tool-data/pangolin_constellations/v0.1.10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,7 @@ +<tables> + <table name="pangolin_constellations" comment_char="#" allow_duplicate_entries="False"> + <!-- min_scorpio_version is the minimum scorpio tool major version that is needed to read the constellations data --> + <columns>value, description, min_scorpio_version, date, path</columns> + <file path="tool-data/pangolin_constellations.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Aug 08 15:12:08 2023 +0000 @@ -0,0 +1,7 @@ +<tables> + <table name="pangolin_constellations" comment_char="#" allow_duplicate_entries="False"> + <!-- min_scorpio_version is the minimum scorpio tool major version that is needed to read the constellations data --> + <columns>value, description, min_scorpio_version, date, path</columns> + <file path="${__HERE__}/test-data/pangolin_constellations.loc" /> + </table> +</tables>