Mercurial > repos > devteam > freebayes
changeset 40:0d8581534009 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d
| author | iuc |
|---|---|
| date | Tue, 05 Aug 2025 13:47:58 +0000 |
| parents | 85dc96ebc770 |
| children | |
| files | freebayes.xml leftalign.xml macros.xml test-data/freebayes-phix174.full.sample.gvcf test-data/freebayes-phix174.gvcf |
| diffstat | 5 files changed, 649 insertions(+), 37 deletions(-) [+] |
line wrap: on
line diff
--- a/freebayes.xml Tue Jun 10 07:59:51 2025 +0000 +++ b/freebayes.xml Tue Aug 05 13:47:58 2025 +0000 @@ -1,14 +1,15 @@ -<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0"> +<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1" profile="23.0"> <description>bayesian genetic variant detector</description> + <macros> + <import>macros.xml</import> + </macros> <xrefs> <xref type="bio.tools">freebayes</xref> </xrefs> - <macros> - <import>macros.xml</import> - </macros> <expand macro="requirements"> + <requirement type="package" version="3.11">grep</requirement> <requirement type="package" version="5.3.1">gawk</requirement> - <requirement type="package" version="20250422">parallel</requirement> + <requirement type="package" version="20250622">parallel</requirement> </expand> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ @@ -239,6 +240,18 @@ #end if #end if + #if str($output_options.flavor) == "gvcf": + --gvcf + #elif str($output_options.flavor) == "gvcf_custom": + --gvcf + #if $output_options.gvcf_block_size == 0: + ## special-casing the 0 case for performance + --gvcf-dont-use-chunk t + #else: + --gvcf-chunk $output_options.gvcf_block_size + #end if + #end if + "; done > freebayes_commands.sh && @@ -366,21 +379,21 @@ <when value="provide_vcf"> <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip" label="Use variants reported in this VCF dataset as input to the algorithm"/> - <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false" + <param argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> </when> </conditional> - <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true" + <param argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" /> - <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false" + <param argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes" /> - <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true" + <param argument="--observation-bias" type="data" format="tabular" optional="true" label="Load read length-dependent allele observation biases from" help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" /> - <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true" + <param argument="--contamination-estimates" type="data" format="tabular" optional="true" label="Upload per-sample estimates of contamination from" help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" /> - <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue="" + <param argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue="" label="Trim trailing reference matches" /> </when> <when value="do_not_set" /> @@ -432,7 +445,7 @@ <when value="set"> <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false" label="Include the reference allele in the analysis as if it is another sample from the same population" /> - <param name="reference_quality" argument="--reference-quality" type="text" value="100,60" + <param argument="--reference-quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" /> </when> <when value="do_not_set" /> @@ -457,13 +470,13 @@ <param name="n" argument="--use-best-n-alleles" type="integer" value="0" label="How many best SNP alleles to evaluate" help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" /> - <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3" + <param argument="--haplotype-length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" /> <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp" /> - <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1" + <param argument="--min-repeat-entropy" type="integer" value="1" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" /> - <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false" + <param argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false" label="Exclude observations which do not fully span the dynamically-determined detection window" help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" /> </when> @@ -508,7 +521,7 @@ help="default=~unbounded" /> <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" /> - <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000" + <param argument="--read-snp-limit" type="integer" value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)" help="default=~unbounded" /> </when> @@ -559,12 +572,12 @@ <option value="set">Set genotype likelihood options</option> </param> <when value="set"> - <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0" + <param argument="--base-quality-cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at" /> - <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false" + <param argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false" label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual" help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" /> - <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9" + <param argument="--prob-contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples" /> </when> <when value="do_not_set" /> @@ -578,17 +591,17 @@ <option value="set">Set algorithmic features</option> </param> <when value="set"> - <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false" + <param argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" /> <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000" label="Iterate no more than N times during genotyping step" /> - <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6" + <param argument="--genotyping-max-banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" /> <param name="W" argument="--posterior-integration-limits" type="text" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" /> <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false" label="Skip sample genotypings for which the sample has no supporting reads" /> - <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true" + <param argument="--genotype-variant-threshold" type="integer" value="" optional="true" label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample" help="default=~unbounded" /> <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false" @@ -598,7 +611,7 @@ help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" /> <param name="D" argument="--read-dependence-factor" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" /> - <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false" + <param argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false" label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" /> </when> <when value="do_not_set" /> @@ -609,6 +622,18 @@ <when value="naive" /> <when value="naive_w_filters" /> </conditional> + <conditional name="output_options"> + <param name="flavor" type="select" label="Type of main output to produce" help="The tool will, by default, produce VCF output with information about sites with called variants. If you want also information (such as depth of coverage) about non-called sites, you can use the gVCF or gVCF with custom block size options. The first collapses the stats of entire blocks of consecutive non-called sites into one non-call record. The second gives you control over how many consecutive non-called sites should be combined into a non-call record."> + <option value="vcf">VCF (default)</option> + <option value="gvcf">gVCF (--gvcf)</option> + <option value="gvcf_custom">gVCF with custom block size</option> + </param> + <when value="vcf" /> + <when value="gvcf" /> + <when value="gvcf_custom"> + <param name="gvcf_block_size" type="integer" value="0" min="0" max="2147483647" label="Maximal block size for consecutive non-called sites" help="Consolidate data from any non-called site together with the N next non-called sites into one gVCF record, i.e. produce gVCF block records of maximally N+1 sites. Blocks can be shorter if terminated by the end of a chromosome or a site with a called variant. Setting this parameter to 0 produces a separate record for every non-called site, but can result in very large output." /> + </when> + </conditional> </inputs> <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> @@ -620,7 +645,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> @@ -628,7 +653,31 @@ <param name="options_type_selector" value="simple"/> <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="1"> + <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> + <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" /> + <param name="input_bams" ftype="bam" value="freebayes-phix174.bam" /> + <param name="options_type_selector" value="simple" /> + <conditional name="output_options"> + <param name="flavor" value="gvcf" /> + </conditional> + <output name="output_vcf" file="freebayes-phix174.gvcf" lines_diff="4" /> + </test> + <test expect_num_outputs="1"> + <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> + <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" /> + <param name="input_bams" ftype="bam" value="freebayes-phix174.bam" /> + <param name="options_type_selector" value="simple" /> + <conditional name="output_options"> + <param name="flavor" value="gvcf_custom" /> + </conditional> + <!-- This test produces one record per reference position + so the test file only contains the first part of the expected output up to the second variant site --> + <output name="output_vcf" file="freebayes-phix174.full.sample.gvcf" compare="contains" lines_diff="2" /> + </test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> @@ -639,7 +688,7 @@ <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" /> </test> <!-- Test that user-provided (variant-input option) sites are included in output --> - <test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> @@ -658,7 +707,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> @@ -669,7 +718,7 @@ <param name="trim_complex_tail" value="--trim-complex-tail"/> <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/> @@ -679,7 +728,7 @@ <param name="min_coverage" value="250" /> <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/> @@ -689,7 +738,7 @@ <param name="limit_coverage" value="400" /> <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="1"> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/> @@ -699,7 +748,7 @@ <param name="skip_coverage" value="100" /> <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" /> </test> - <test> <!-- Test with CRAM --> + <test expect_num_outputs="1"> <!-- Test with CRAM --> <param name="reference_source_selector" value="history" /> <param name="processmode" value="individual" /> <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
--- a/leftalign.xml Tue Jun 10 07:59:51 2025 +0000 +++ b/leftalign.xml Tue Aug 05 13:47:58 2025 +0000 @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@+galaxy0"> <description> indels in BAM datasets</description> + <macros> + <import>macros.xml</import> + </macros> <xrefs> <xref type="bio.tools">freebayes</xref> </xrefs> - <macros> - <import>macros.xml</import> - </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[
--- a/macros.xml Tue Jun 10 07:59:51 2025 +0000 +++ b/macros.xml Tue Aug 05 13:47:58 2025 +0000 @@ -4,6 +4,7 @@ <requirements> <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement> <requirement type="package" version="1.22">samtools</requirement> + <requirement type="package" version="9.5">coreutils</requirement> <yield /> </requirements> </xml> @@ -52,8 +53,8 @@ --limit-coverage ${coverage_options.limit_coverage} </token> <xml name="par_min_cov"> - <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" /> - <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" /> - <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" /> + <param argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" /> + <param argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" /> + <param argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" /> </xml> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-phix174.full.sample.gvcf Tue Aug 05 13:47:58 2025 +0000 @@ -0,0 +1,436 @@ +##fileformat=VCFv4.2 +##fileDate=20250805 +##source=freeBayes v1.3.10 +##reference=localref.fa +##contig=<ID=phiX174,length=5386> +##phasing=none +##commandline="freebayes --region phiX174:0..5386 -f freebayes-phix174.fasta freebayes-phix174.bam --gvcf -& t" +##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=Float,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=Float,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +phiX174 1 . G <*> 0 . DP=0;END=1;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 2 . A <*> 0 . DP=0;END=2;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 3 . G <*> 0 . DP=0;END=3;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 4 . T <*> 0 . DP=0;END=4;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 5 . T <*> 0 . DP=0;END=5;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 6 . T <*> 0 . DP=0;END=6;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 7 . T <*> 0 . DP=0;END=7;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 8 . A <*> 0 . DP=0;END=8;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 9 . T <*> 0 . DP=0;END=9;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO -0:0:0:0:0:0:0 +phiX174 10 . C <*> 0 . DP=1;END=10;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 11 . G <*> 0 . DP=1;END=11;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 36:1:1:36:1:0:0 +phiX174 12 . C <*> 0 . DP=1;END=12;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 35:1:1:35:1:0:0 +phiX174 13 . T <*> 0 . DP=1;END=13;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 61:1:1:61:1:0:0 +phiX174 14 . T <*> 0 . DP=2;END=14;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 15 . C <*> 0 . DP=2;END=15;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 119:2:2:119:2:0:0 +phiX174 16 . C <*> 0 . DP=2;END=16;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 89:2:2:89:2:0:0 +phiX174 17 . A <*> 0 . DP=2;END=17;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 107:2:2:107:2:0:0 +phiX174 18 . T <*> 0 . DP=2;END=18;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 117:2:2:117:2:0:0 +phiX174 19 . G <*> 0 . DP=2;END=19;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 109:2:2:109:2:0:0 +phiX174 20 . A <*> 0 . DP=2;END=20;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 103:2:2:103:2:0:0 +phiX174 21 . C <*> 0 . DP=2;END=21;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 98:2:2:98:2:0:0 +phiX174 22 . G <*> 0 . DP=2;END=22;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 120:2:2:120:2:0:0 +phiX174 23 . C <*> 0 . DP=2;END=23;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 111:2:2:111:2:0:0 +phiX174 24 . A <*> 0 . DP=2;END=24;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 120:2:2:120:2:0:0 +phiX174 25 . G <*> 0 . DP=2;END=25;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 111:2:2:111:2:0:0 +phiX174 26 . A <*> 0 . DP=2;END=26;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 119:2:2:119:2:0:0 +phiX174 27 . A <*> 0 . DP=2;END=27;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 28 . G <*> 0 . DP=2;END=28;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 29 . T <*> 0 . DP=2;END=29;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 30 . T <*> 0 . DP=2;END=30;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 102:2:2:102:2:0:0 +phiX174 31 . A <*> 0 . DP=2;END=31;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 110:2:2:110:2:0:0 +phiX174 32 . A <*> 0 . DP=2;END=32;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 40:2:2:71:1:31:1 +phiX174 33 . C <*> 0 . DP=2;END=33;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 127:2:2:127:2:0:0 +phiX174 34 . A <*> 0 . DP=2;END=34;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 68:2:2:68:2:0:0 +phiX174 35 . C <*> 0 . DP=2;END=35;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 94:2:2:94:2:0:0 +phiX174 36 . T <*> 0 . DP=2;END=36;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 115:2:2:115:2:0:0 +phiX174 37 . T <*> 0 . DP=3;END=37;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 180:3:3:180:3:0:0 +phiX174 38 . T <*> 0 . DP=4;END=38;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 212:4:4:212:4:0:0 +phiX174 39 . C <*> 0 . DP=4;END=39;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 223:4:4:223:4:0:0 +phiX174 40 . G <*> 0 . DP=4;END=40;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 284:4:4:284:4:0:0 +phiX174 41 . G <*> 0 . DP=4;END=41;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 279:4:4:279:4:0:0 +phiX174 42 . A <*> 0 . DP=4;END=42;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 284:4:4:284:4:0:0 +phiX174 43 . T <*> 0 . DP=4;END=43;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 261:4:4:261:4:0:0 +phiX174 44 . A <*> 0 . DP=4;END=44;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 235:4:4:235:4:0:0 +phiX174 45 . T <*> 0 . DP=4;END=45;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 247:4:4:247:4:0:0 +phiX174 46 . T <*> 0 . DP=3;END=46;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 114:3:3:142:2:28:1 +phiX174 47 . T <*> 0 . DP=3;END=47;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 157:3:3:157:3:0:0 +phiX174 48 . C <*> 0 . DP=3;END=48;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 151:3:3:151:3:0:0 +phiX174 49 . T <*> 0 . DP=3;END=49;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 170:3:3:170:3:0:0 +phiX174 50 . G <*> 0 . DP=2;END=50;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 51 . A <*> 0 . DP=2;END=51;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 111:2:2:111:2:0:0 +phiX174 52 . T <*> 0 . DP=2;END=52;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 53 . G <*> 0 . DP=2;END=53;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 54 . A <*> 0 . DP=3;END=54;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 209:3:3:209:3:0:0 +phiX174 55 . G <*> 0 . DP=3;END=55;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 182:3:3:182:3:0:0 +phiX174 56 . T <*> 0 . DP=3;END=56;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 198:3:3:198:3:0:0 +phiX174 57 . C <*> 0 . DP=3;END=57;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 193:3:3:193:3:0:0 +phiX174 58 . G <*> 0 . DP=3;END=58;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 144:3:3:144:3:0:0 +phiX174 59 . A <*> 0 . DP=3;END=59;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 107:3:3:142:2:35:1 +phiX174 60 . A <*> 0 . DP=3;END=60;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 194:3:3:194:3:0:0 +phiX174 61 . A <*> 0 . DP=4;END=61;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 211:4:4:211:4:0:0 +phiX174 62 . A <*> 0 . DP=4;END=62;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 180:4:4:180:4:0:0 +phiX174 63 . A <*> 0 . DP=4;END=63;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 149:4:4:180:3:31:1 +phiX174 64 . T <*> 0 . DP=4;END=64;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 232:4:4:232:4:0:0 +phiX174 65 . T <*> 0 . DP=5;END=65;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 288:5:5:288:5:0:0 +phiX174 66 . A <*> 0 . DP=5;END=66;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 241:5:5:241:5:0:0 +phiX174 67 . T <*> 0 . DP=5;END=67;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 201:5:5:232:4:31:1 +phiX174 68 . C <*> 0 . DP=5;END=68;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 277:5:5:277:5:0:0 +phiX174 69 . T <*> 0 . DP=5;END=69;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 302:5:5:302:5:0:0 +phiX174 70 . T <*> 0 . DP=6;END=70;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 328:6:6:328:6:0:0 +phiX174 71 . G <*> 0 . DP=6;END=71;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 356:6:6:356:6:0:0 +phiX174 72 . A <*> 0 . DP=6;END=72;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 305:6:6:305:6:0:0 +phiX174 73 . T <*> 0 . DP=5;END=73;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 280:5:5:280:5:0:0 +phiX174 74 . A <*> 0 . DP=4;END=74;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 257:4:4:257:4:0:0 +phiX174 75 . A <*> 0 . DP=4;END=75;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 260:4:4:260:4:0:0 +phiX174 76 . A <*> 0 . DP=5;END=76;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 329:5:5:329:5:0:0 +phiX174 77 . G <*> 0 . DP=5;END=77;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 265:5:5:265:5:0:0 +phiX174 78 . C <*> 0 . DP=5;END=78;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 309:5:5:309:5:0:0 +phiX174 79 . A <*> 0 . DP=5;END=79;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 322:5:5:322:5:0:0 +phiX174 80 . G <*> 0 . DP=6;END=80;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 426:6:6:426:6:0:0 +phiX174 81 . G <*> 0 . DP=6;END=81;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 248:6:6:317:5:69:1 +phiX174 82 . A <*> 0 . DP=6;END=82;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 370:6:6:370:6:0:0 +phiX174 83 . A <*> 0 . DP=6;END=83;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 318:6:6:318:6:0:0 +phiX174 84 . T <*> 0 . DP=6;END=84;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 382:6:6:382:6:0:0 +phiX174 85 . T <*> 0 . DP=6;END=85;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 290:6:6:290:6:0:0 +phiX174 86 . A <*> 0 . DP=6;END=86;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 284:6:6:284:6:0:0 +phiX174 87 . C <*> 0 . DP=6;END=87;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 363:6:6:363:6:0:0 +phiX174 88 . T <*> 0 . DP=6;END=88;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 332:6:6:332:6:0:0 +phiX174 89 . A <*> 0 . DP=6;END=89;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 368:6:6:368:6:0:0 +phiX174 90 . C <*> 0 . DP=5;END=90;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 324:5:5:324:5:0:0 +phiX174 91 . T <*> 0 . DP=5;END=91;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 92 . G <*> 0 . DP=5;END=92;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 93 . C <*> 0 . DP=5;END=93;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 94 . T <*> 0 . DP=5;END=94;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 338:5:5:338:5:0:0 +phiX174 95 . T <*> 0 . DP=5;END=95;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 323:5:5:323:5:0:0 +phiX174 96 . G <*> 0 . DP=5;END=96;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 318:5:5:318:5:0:0 +phiX174 97 . T <*> 0 . DP=4;END=97;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 250:4:4:250:4:0:0 +phiX174 98 . T <*> 0 . DP=4;END=98;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 233:4:4:233:4:0:0 +phiX174 99 . T <*> 0 . DP=4;END=99;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 225:4:4:225:4:0:0 +phiX174 100 . A <*> 0 . DP=4;END=100;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 247:4:4:247:4:0:0 +phiX174 101 . C <*> 0 . DP=3;END=101;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 194:3:3:194:3:0:0 +phiX174 102 . G <*> 0 . DP=3;END=102;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 103 . A <*> 0 . DP=3;END=103;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 104 . A <*> 0 . DP=3;END=104;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 105 . T <*> 0 . DP=3;END=105;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 106 . T <*> 0 . DP=2;END=106;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 107 . A <*> 0 . DP=2;END=107;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 108 . A <*> 0 . DP=2;END=108;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 109 . A <*> 0 . DP=3;END=109;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 171:3:3:171:3:0:0 +phiX174 110 . T <*> 0 . DP=3;END=110;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 163:3:3:163:3:0:0 +phiX174 111 . C <*> 0 . DP=4;END=111;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 251:4:4:251:4:0:0 +phiX174 112 . G <*> 0 . DP=3;END=112;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 186:3:3:186:3:0:0 +phiX174 113 . A <*> 0 . DP=3;END=113;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 176:3:3:176:3:0:0 +phiX174 114 . A <*> 0 . DP=3;END=114;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 187:3:3:187:3:0:0 +phiX174 115 . G <*> 0 . DP=3;END=115;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 162:3:3:162:3:0:0 +phiX174 116 . T <*> 0 . DP=2;END=116;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 99:2:2:99:2:0:0 +phiX174 117 . G <*> 0 . DP=3;END=117;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 118 . G <*> 0 . DP=4;END=118;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 240:4:4:240:4:0:0 +phiX174 119 . A <*> 0 . DP=4;END=119;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 158:4:4:192:3:34:1 +phiX174 120 . C <*> 0 . DP=4;END=120;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 251:4:4:251:4:0:0 +phiX174 121 . T <*> 0 . DP=5;END=121;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 252:5:5:252:5:0:0 +phiX174 122 . G <*> 0 . DP=6;END=122;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 391:6:6:391:6:0:0 +phiX174 123 . C <*> 0 . DP=6;END=123;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 353:6:6:353:6:0:0 +phiX174 124 . T <*> 0 . DP=6;END=124;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 342:6:6:342:6:0:0 +phiX174 125 . G <*> 0 . DP=7;END=125;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 451:7:7:451:7:0:0 +phiX174 126 . G <*> 0 . DP=8;END=126;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 512:8:8:512:8:0:0 +phiX174 127 . C <*> 0 . DP=8;END=127;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 439:8:8:471:7:32:1 +phiX174 128 . G <*> 0 . DP=9;END=128;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 595:9:9:595:9:0:0 +phiX174 129 . G <*> 0 . DP=10;END=129;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 653:10:10:653:10:0:0 +phiX174 130 . A <*> 0 . DP=10;END=130;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 610:10:10:610:10:0:0 +phiX174 131 . A <*> 0 . DP=10;END=131;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 629:10:10:629:10:0:0 +phiX174 132 . A <*> 0 . DP=10;END=132;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 666:10:10:666:10:0:0 +phiX174 133 . A <*> 0 . DP=10;END=133;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 506:10:10:552:9:46:1 +phiX174 134 . T <*> 0 . DP=11;END=134;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 660:11:11:660:11:0:0 +phiX174 135 . G <*> 0 . DP=11;END=135;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 742:11:11:742:11:0:0 +phiX174 136 . A <*> 0 . DP=11;END=136;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 725:11:11:725:11:0:0 +phiX174 137 . G <*> 0 . DP=11;END=137;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 718:11:11:718:11:0:0 +phiX174 138 . A <*> 0 . DP=11;END=138;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 658:11:11:690:10:32:1 +phiX174 139 . A <*> 0 . DP=10;END=139;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 607:10:10:639:9:32:1 +phiX174 140 . A <*> 0 . DP=10;END=140;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 702:10:10:702:10:0:0 +phiX174 141 . A <*> 0 . DP=10;END=141;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 710:10:10:710:10:0:0 +phiX174 142 . T <*> 0 . DP=10;END=142;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 636:10:10:636:10:0:0 +phiX174 143 . T <*> 0 . DP=11;END=143;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 726:11:11:726:11:0:0 +phiX174 144 . C <*> 0 . DP=11;END=144;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 709:11:11:709:11:0:0 +phiX174 145 . G <*> 0 . DP=10;END=145;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 630:10:10:630:10:0:0 +phiX174 146 . A <*> 0 . DP=10;END=146;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 593:10:10:593:10:0:0 +phiX174 147 . C <*> 0 . DP=9;END=147;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 606:9:9:606:9:0:0 +phiX174 148 . C <*> 0 . DP=9;END=148;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 586:9:9:586:9:0:0 +phiX174 149 . T <*> 0 . DP=9;END=149;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 567:9:9:567:9:0:0 +phiX174 150 . A <*> 0 . DP=9;END=150;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 599:9:9:599:9:0:0 +phiX174 151 . T <*> 0 . DP=9;END=151;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 609:9:9:609:9:0:0 +phiX174 152 . C <*> 0 . DP=9;END=152;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 592:9:9:592:9:0:0 +phiX174 153 . C <*> 0 . DP=8;END=153;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 493:8:8:493:8:0:0 +phiX174 154 . T <*> 0 . DP=7;END=154;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 459:7:7:459:7:0:0 +phiX174 155 . T <*> 0 . DP=7;END=155;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 497:7:7:497:7:0:0 +phiX174 156 . G <*> 0 . DP=7;END=156;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 464:7:7:464:7:0:0 +phiX174 157 . C <*> 0 . DP=6;END=157;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 391:6:6:391:6:0:0 +phiX174 158 . G <*> 0 . DP=5;END=158;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 335:5:5:335:5:0:0 +phiX174 159 . C <*> 0 . DP=5;END=159;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 326:5:5:326:5:0:0 +phiX174 161 . G <*> 0 . DP=4;END=161;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 232:4:4:232:4:0:0 +phiX174 162 . C <*> 0 . DP=3;END=162;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 140:3:3:140:3:0:0 +phiX174 163 . T <*> 0 . DP=4;END=163;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 284:4:4:284:4:0:0 +phiX174 164 . C <*> 0 . DP=2;END=164;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 165 . G <*> 0 . DP=2;END=165;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 166 . A <*> 0 . DP=2;END=166;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 108:2:2:108:2:0:0 +phiX174 167 . G <*> 0 . DP=2;END=167;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 168 . A <*> 0 . DP=2;END=168;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 101:2:2:101:2:0:0 +phiX174 169 . A <*> 0 . DP=2;END=169;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 117:2:2:117:2:0:0 +phiX174 170 . G <*> 0 . DP=1;END=170;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 171 . C <*> 0 . DP=1;END=171;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 172 . T <*> 0 . DP=1;END=172;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 173 . C <*> 0 . DP=1;END=173;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 174 . T <*> 0 . DP=1;END=174;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 175 . T <*> 0 . DP=1;END=175;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 176 . A <*> 0 . DP=1;END=176;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 57:1:1:57:1:0:0 +phiX174 177 . C <*> 0 . DP=1;END=177;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 178 . T <*> 0 . DP=1;END=178;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 179 . T <*> 0 . DP=1;END=179;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 180 . T <*> 0 . DP=1;END=180;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 181 . G <*> 0 . DP=1;END=181;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 182 . C <*> 0 . DP=1;END=182;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 183 . G <*> 0 . DP=1;END=183;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 184 . A <*> 0 . DP=1;END=184;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 185 . C <*> 0 . DP=1;END=185;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 186 . C <*> 0 . DP=1;END=186;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 187 . T <*> 0 . DP=1;END=187;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 188 . T <*> 0 . DP=1;END=188;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 189 . T <*> 0 . DP=1;END=189;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 190 . C <*> 0 . DP=1;END=190;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 191 . G <*> 0 . DP=1;END=191;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 192 . C <*> 0 . DP=1;END=192;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 71:1:1:71:1:0:0 +phiX174 193 . C <*> 0 . DP=3;END=193;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 194 . A <*> 0 . DP=3;END=194;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 173:3:3:173:3:0:0 +phiX174 195 . T <*> 0 . DP=3;END=195;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 196 . C <*> 0 . DP=3;END=196;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 197 . A <*> 0 . DP=3;END=197;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 198 . A <*> 0 . DP=4;END=198;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 284:4:4:284:4:0:0 +phiX174 199 . C <*> 0 . DP=4;END=199;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 284:4:4:284:4:0:0 +phiX174 200 . T <*> 0 . DP=5;END=200;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 201 . A <*> 0 . DP=5;END=201;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 202 . A <*> 0 . DP=5;END=202;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 350:5:5:350:5:0:0 +phiX174 203 . C <*> 0 . DP=5;END=203;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 282:5:5:282:5:0:0 +phiX174 204 . G <*> 0 . DP=7;END=204;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 497:7:7:497:7:0:0 +phiX174 205 . A <*> 0 . DP=7;END=205;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 327:7:7:360:6:33:1 +phiX174 206 . T <*> 0 . DP=7;END=206;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 446:7:7:446:7:0:0 +phiX174 207 . T <*> 0 . DP=7;END=207;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 451:7:7:451:7:0:0 +phiX174 208 . C <*> 0 . DP=7;END=208;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 410:7:7:410:7:0:0 +phiX174 209 . T <*> 0 . DP=7;END=209;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 433:7:7:433:7:0:0 +phiX174 210 . G <*> 0 . DP=7;END=210;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 461:7:7:461:7:0:0 +phiX174 211 . T <*> 0 . DP=7;END=211;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 427:7:7:427:7:0:0 +phiX174 212 . C <*> 0 . DP=7;END=212;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 394:7:7:394:7:0:0 +phiX174 213 . A <*> 0 . DP=7;END=213;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 408:7:7:408:7:0:0 +phiX174 214 . A <*> 0 . DP=7;END=214;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 391:7:7:391:7:0:0 +phiX174 215 . A <*> 0 . DP=7;END=215;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 355:7:7:387:6:32:1 +phiX174 216 . A <*> 0 . DP=8;END=216;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 372:8:8:402:7:30:1 +phiX174 217 . A <*> 0 . DP=8;END=217;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 406:8:8:406:8:0:0 +phiX174 218 . C <*> 0 . DP=8;END=218;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 453:8:8:453:8:0:0 +phiX174 219 . T <*> 0 . DP=8;END=219;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 465:8:8:465:8:0:0 +phiX174 220 . G <*> 0 . DP=8;END=220;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 482:8:8:482:8:0:0 +phiX174 221 . A <*> 0 . DP=8;END=221;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 449:8:8:449:8:0:0 +phiX174 222 . C <*> 0 . DP=8;END=222;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 494:8:8:494:8:0:0 +phiX174 223 . G <*> 0 . DP=8;END=223;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 532:8:8:532:8:0:0 +phiX174 224 . C <*> 0 . DP=9;END=224;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 515:9:9:515:9:0:0 +phiX174 225 . G <*> 0 . DP=9;END=225;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 521:9:9:521:9:0:0 +phiX174 226 . T <*> 0 . DP=9;END=226;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 444:9:9:444:9:0:0 +phiX174 227 . T <*> 0 . DP=9;END=227;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 446:9:9:446:9:0:0 +phiX174 228 . G <*> 0 . DP=9;END=228;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 517:9:9:517:9:0:0 +phiX174 229 . G <*> 0 . DP=7;END=229;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 439:7:7:439:7:0:0 +phiX174 230 . A <*> 0 . DP=7;END=230;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 394:7:7:394:7:0:0 +phiX174 231 . T <*> 0 . DP=7;END=231;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 470:7:7:470:7:0:0 +phiX174 232 . G <*> 0 . DP=7;END=232;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 476:7:7:476:7:0:0 +phiX174 233 . A <*> 0 . DP=7;END=233;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 330:7:7:330:7:0:0 +phiX174 234 . G <*> 0 . DP=6;END=234;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 370:6:6:370:6:0:0 +phiX174 235 . G <*> 0 . DP=5;END=235;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 275:5:5:275:5:0:0 +phiX174 236 . A <*> 0 . DP=4;END=236;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 209:4:4:209:4:0:0 +phiX174 237 . G <*> 0 . DP=4;END=237;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 213:4:4:213:4:0:0 +phiX174 238 . A <*> 0 . DP=4;END=238;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 177:4:4:177:4:0:0 +phiX174 239 . A <*> 0 . DP=5;END=239;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 222:5:5:249:4:27:1 +phiX174 240 . G <*> 0 . DP=3;END=240;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 171:3:3:171:3:0:0 +phiX174 241 . T <*> 0 . DP=3;END=241;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 101:3:3:134:2:33:1 +phiX174 242 . G <*> 0 . DP=3;END=242;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 243 . G <*> 0 . DP=3;END=243;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 244 . C <*> 0 . DP=3;END=244;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 245 . T <*> 0 . DP=3;END=245;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 246 . T <*> 0 . DP=3;END=246;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 213:3:3:213:3:0:0 +phiX174 247 . A <*> 0 . DP=3;END=247;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 172:3:3:172:3:0:0 +phiX174 248 . A <*> 0 . DP=4;END=248;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 230:4:4:230:4:0:0 +phiX174 249 . T <*> 0 . DP=4;END=249;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 178:4:4:178:4:0:0 +phiX174 250 . A <*> 0 . DP=4;END=250;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 174:4:4:174:4:0:0 +phiX174 251 . T <*> 0 . DP=4;END=251;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 242:4:4:242:4:0:0 +phiX174 252 . G <*> 0 . DP=3;END=252;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 153:3:3:153:3:0:0 +phiX174 253 . C <*> 0 . DP=3;END=253;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 153:3:3:153:3:0:0 +phiX174 254 . T <*> 0 . DP=3;END=254;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 164:3:3:164:3:0:0 +phiX174 255 . T <*> 0 . DP=3;END=255;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 113:3:3:142:2:29:1 +phiX174 256 . G <*> 0 . DP=3;END=256;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 158:3:3:158:3:0:0 +phiX174 257 . G <*> 0 . DP=3;END=257;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 156:3:3:156:3:0:0 +phiX174 258 . C <*> 0 . DP=3;END=258;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 111:3:3:142:2:31:1 +phiX174 259 . A <*> 0 . DP=3;END=259;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 142:3:3:142:3:0:0 +phiX174 260 . C <*> 0 . DP=2;END=260;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 261 . G <*> 0 . DP=2;END=261;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 142:2:2:142:2:0:0 +phiX174 262 . T <*> 0 . DP=2;END=262;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 99:2:2:99:2:0:0 +phiX174 263 . T <*> 0 . DP=3;END=263;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 161:3:3:161:3:0:0 +phiX174 264 . C <*> 0 . DP=3;END=264;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 62:3:3:90:2:28:1 +phiX174 265 . G <*> 0 . DP=4;END=265;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 200:4:4:200:4:0:0 +phiX174 266 . T <*> 0 . DP=4;END=266;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 146:4:4:175:3:29:1 +phiX174 267 . C <*> 0 . DP=4;END=267;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 233:4:4:233:4:0:0 +phiX174 268 . A <*> 0 . DP=4;END=268;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 245:4:4:245:4:0:0 +phiX174 269 . A <*> 0 . DP=4;END=269;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 280:4:4:280:4:0:0 +phiX174 270 . G <*> 0 . DP=4;END=270;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 219:4:4:219:4:0:0 +phiX174 271 . G <*> 0 . DP=4;END=271;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 284:4:4:284:4:0:0 +phiX174 272 . A <*> 0 . DP=4;END=272;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 93:4:4:125:3:32:1 +phiX174 273 . C <*> 0 . DP=4;END=273;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 208:4:4:208:4:0:0 +phiX174 274 . T <*> 0 . DP=4;END=274;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 155:4:4:183:3:28:1 +phiX174 275 . G <*> 0 . DP=4;END=275;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 215:4:4:215:4:0:0 +phiX174 276 . G <*> 0 . DP=4;END=276;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 252:4:4:252:4:0:0 +phiX174 277 . T <*> 0 . DP=4;END=277;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 253:4:4:253:4:0:0 +phiX174 278 . T <*> 0 . DP=5;END=278;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 279 . T <*> 0 . DP=5;END=279;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 355:5:5:355:5:0:0 +phiX174 280 . A <*> 0 . DP=6;END=280;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 426:6:6:426:6:0:0 +phiX174 281 . G <*> 0 . DP=6;END=281;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 426:6:6:426:6:0:0 +phiX174 282 . A <*> 0 . DP=6;END=282;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 415:6:6:415:6:0:0 +phiX174 283 . T <*> 0 . DP=7;END=283;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 466:7:7:466:7:0:0 +phiX174 284 . A <*> 0 . DP=6;END=284;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 385:6:6:385:6:0:0 +phiX174 285 . T <*> 0 . DP=6;END=285;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 276:6:6:276:6:0:0 +phiX174 286 . G <*> 0 . DP=6;END=286;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 368:6:6:368:6:0:0 +phiX174 287 . A <*> 0 . DP=6;END=287;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 364:6:6:364:6:0:0 +phiX174 288 . G <*> 0 . DP=7;END=288;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 442:7:7:442:7:0:0 +phiX174 289 . T <*> 0 . DP=7;END=289;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 447:7:7:447:7:0:0 +phiX174 290 . C <*> 0 . DP=7;END=290;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 405:7:7:405:7:0:0 +phiX174 291 . A <*> 0 . DP=7;END=291;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 469:7:7:469:7:0:0 +phiX174 292 . C <*> 0 . DP=7;END=292;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 484:7:7:484:7:0:0 +phiX174 293 . A <*> 0 . DP=7;END=293;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 407:7:7:407:7:0:0 +phiX174 294 . T <*> 0 . DP=8;END=294;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 526:8:8:526:8:0:0 +phiX174 295 . T <*> 0 . DP=8;END=295;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 524:8:8:524:8:0:0 +phiX174 296 . T <*> 0 . DP=8;END=296;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 556:8:8:556:8:0:0 +phiX174 297 . T <*> 0 . DP=8;END=297;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 560:8:8:560:8:0:0 +phiX174 298 . G <*> 0 . DP=8;END=298;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 545:8:8:545:8:0:0 +phiX174 299 . T <*> 0 . DP=8;END=299;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 537:8:8:537:8:0:0 +phiX174 300 . T <*> 0 . DP=8;END=300;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 544:8:8:544:8:0:0 +phiX174 301 . C <*> 0 . DP=7;END=301;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 427:7:7:427:7:0:0 +phiX174 302 . A <*> 0 . DP=7;END=302;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 497:7:7:497:7:0:0 +phiX174 303 . T <*> 0 . DP=7;END=303;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 411:7:7:411:7:0:0 +phiX174 304 . G <*> 0 . DP=7;END=304;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 430:7:7:430:7:0:0 +phiX174 305 . G <*> 0 . DP=7;END=305;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 351:7:7:381:6:30:1 +phiX174 306 . T <*> 0 . DP=6;END=306;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 369:6:6:369:6:0:0 +phiX174 307 . A <*> 0 . DP=7;END=307;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 362:7:7:396:6:34:1 +phiX174 308 . G <*> 0 . DP=7;END=308;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 422:7:7:422:7:0:0 +phiX174 309 . A <*> 0 . DP=9;END=309;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 515:9:9:515:9:0:0 +phiX174 310 . G <*> 0 . DP=10;END=310;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 658:10:10:658:10:0:0 +phiX174 311 . A G 0.00392026 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=7.0097;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:478:2:70:-1.91487,0,-18.7749 +phiX174 312 . T <*> 0 . DP=9;END=312;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 612:9:9:612:9:0:0 +phiX174 313 . T <*> 0 . DP=9;END=313;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 589:9:9:589:9:0:0 +phiX174 314 . C <*> 0 . DP=8;END=314;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 493:8:8:493:8:0:0 +phiX174 315 . T <*> 0 . DP=8;END=315;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 568:8:8:568:8:0:0 +phiX174 316 . C <*> 0 . DP=7;END=316;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 497:7:7:497:7:0:0 +phiX174 317 . T <*> 0 . DP=7;END=317;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 485:7:7:485:7:0:0 +phiX174 318 . T <*> 0 . DP=7;END=318;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 469:7:7:469:7:0:0 +phiX174 319 . G <*> 0 . DP=6;END=319;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 384:6:6:384:6:0:0 +phiX174 320 . T <*> 0 . DP=7;END=320;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 449:7:7:449:7:0:0 +phiX174 321 . T <*> 0 . DP=8;END=321;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 490:8:8:490:8:0:0 +phiX174 322 . G <*> 0 . DP=9;END=322;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 496:9:9:496:9:0:0 +phiX174 323 . A <*> 0 . DP=9;END=323;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 446:9:9:446:9:0:0 +phiX174 324 . C <*> 0 . DP=9;END=324;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 498:9:9:498:9:0:0 +phiX174 325 . A <*> 0 . DP=10;END=325;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 640:10:10:640:10:0:0 +phiX174 326 . T <*> 0 . DP=10;END=326;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 654:10:10:654:10:0:0 +phiX174 327 . T <*> 0 . DP=11;END=327;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 587:11:11:587:11:0:0 +phiX174 328 . T <*> 0 . DP=11;END=328;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 567:11:11:597:10:30:1 +phiX174 329 . T <*> 0 . DP=11;END=329;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 637:11:11:637:11:0:0 +phiX174 330 . A <*> 0 . DP=10;END=330;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 633:10:10:633:10:0:0 +phiX174 331 . A <*> 0 . DP=10;END=331;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 542:10:10:573:9:31:1 +phiX174 332 . A <*> 0 . DP=10;END=332;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 480:10:10:507:9:27:1 +phiX174 333 . A <*> 0 . DP=10;END=333;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 582:10:10:582:10:0:0 +phiX174 334 . G <*> 0 . DP=11;END=334;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 558:11:11:558:11:0:0 +phiX174 335 . A <*> 0 . DP=10;END=335;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 451:10:10:487:9:36:1 +phiX174 336 . G <*> 0 . DP=10;END=336;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 561:10:10:588:9:27:1 +phiX174 337 . C <*> 0 . DP=10;END=337;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 565:10:10:592:9:27:1 +phiX174 338 . G <*> 0 . DP=11;END=338;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 697:11:11:697:11:0:0 +phiX174 339 . T <*> 0 . DP=11;END=339;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 694:11:11:694:11:0:0 +phiX174 340 . G <*> 0 . DP=11;END=340;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 729:11:11:729:11:0:0 +phiX174 341 . G <*> 0 . DP=11;END=341;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 700:11:11:700:11:0:0 +phiX174 342 . A <*> 0 . DP=11;END=342;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 539:11:11:567:10:28:1 +phiX174 343 . T <*> 0 . DP=11;END=343;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 639:11:11:639:11:0:0 +phiX174 344 . T <*> 0 . DP=11;END=344;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 655:11:11:655:11:0:0 +phiX174 345 . A <*> 0 . DP=9;END=345;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 473:9:9:473:9:0:0 +phiX174 346 . C <*> 0 . DP=8;END=346;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 527:8:8:527:8:0:0 +phiX174 347 . T <*> 0 . DP=8;END=347;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 356:8:8:384:7:28:1 +phiX174 348 . A <*> 0 . DP=8;END=348;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 478:8:8:478:8:0:0 +phiX174 349 . T <*> 0 . DP=8;END=349;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 468:8:8:468:8:0:0 +phiX174 350 . C <*> 0 . DP=9;END=350;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 601:9:9:601:9:0:0 +phiX174 351 . T <*> 0 . DP=9;END=351;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 586:9:9:586:9:0:0 +phiX174 352 . G <*> 0 . DP=9;END=352;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 568:9:9:568:9:0:0 +phiX174 353 . A <*> 0 . DP=9;END=353;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 588:9:9:588:9:0:0 +phiX174 354 . G <*> 0 . DP=10;END=354;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 577:10:10:615:9:38:1 +phiX174 355 . T <*> 0 . DP=11;END=355;MIN_DP=11 GQ:DP:MIN_DP:QR:RO:QA:AO 722:11:11:722:11:0:0 +phiX174 356 . C <*> 0 . DP=10;END=356;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 587:10:10:620:9:33:1 +phiX174 357 . C <*> 0 . DP=9;END=357;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 563:9:9:563:9:0:0 +phiX174 358 . G <*> 0 . DP=8;END=358;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 521:8:8:521:8:0:0 +phiX174 359 . A <*> 0 . DP=8;END=359;MIN_DP=8 GQ:DP:MIN_DP:QR:RO:QA:AO 542:8:8:542:8:0:0 +phiX174 360 . T <*> 0 . DP=7;END=360;MIN_DP=7 GQ:DP:MIN_DP:QR:RO:QA:AO 462:7:7:462:7:0:0 +phiX174 361 . G <*> 0 . DP=6;END=361;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 412:6:6:412:6:0:0 +phiX174 362 . C <*> 0 . DP=6;END=362;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 220:6:6:289:5:69:1 +phiX174 363 . T <*> 0 . DP=6;END=363;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 364:6:6:364:6:0:0 +phiX174 364 . G <*> 0 . DP=6;END=364;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 328:6:6:328:6:0:0 +phiX174 365 . T <*> 0 . DP=6;END=365;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 245:6:6:280:5:35:1 +phiX174 366 . T <*> 0 . DP=6;END=366;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 364:6:6:364:6:0:0 +phiX174 367 . C <*> 0 . DP=6;END=367;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 387:6:6:387:6:0:0 +phiX174 368 . A <*> 0 . DP=6;END=368;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 426:6:6:426:6:0:0 +phiX174 369 . A <*> 0 . DP=6;END=369;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 426:6:6:426:6:0:0 +phiX174 370 . C <*> 0 . DP=5;END=370;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 296:5:5:296:5:0:0 +phiX174 371 . C <*> 0 . DP=5;END=371;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 296:5:5:296:5:0:0 +phiX174 372 . A <*> 0 . DP=5;END=372;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 179:5:5:250:4:71:1 +phiX174 373 . C <*> 0 . DP=5;END=373;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 317:5:5:317:5:0:0 +phiX174 374 . T G 23.3387 . 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=37;MQMR=25;NS=1;NUMALT=1;ODDS=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:141:2:75:-5.19433,0,-3.54586 +phiX174 375 . A <*> 0 . DP=4;END=375;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 216:4:4:216:4:0:0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-phix174.gvcf Tue Aug 05 13:47:58 2025 +0000 @@ -0,0 +1,126 @@ +##fileformat=VCFv4.2 +##fileDate=20250805 +##source=freeBayes v1.3.10 +##reference=localref.fa +##contig=<ID=phiX174,length=5386> +##phasing=none +##commandline="freebayes --region phiX174:0..5386 -f freebayes-phix174.fasta freebayes-phix174.bam --gvcf" +##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=Float,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=Float,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown +phiX174 1 . G <*> 0 . DP=4;END=310;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 86804:4:0:87601:4:797:0 +phiX174 311 . A G 0.00392026 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=7.0097;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:478:2:70:-1.91487,0,-18.7749 +phiX174 312 . T <*> 0 . DP=8;END=373;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 31465:8:5:31945:8:480:0 +phiX174 374 . T G 23.3387 . 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=37;MQMR=25;NS=1;NUMALT=1;ODDS=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:141:2:75:-5.19433,0,-3.54586 +phiX174 375 . A <*> 0 . DP=6;END=912;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 227000:6:0:229264:6:2264:0 +phiX174 913 . A C 2.27318 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=0.380296;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:171:2:67:-3.54411,0,-6.47921 +phiX174 914 . G <*> 0 . DP=7;END=1204;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 129636:7:0:130843:7:1207:0 +phiX174 1205 . A C 0.00388031 . 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=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=7.01995;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:456:2:67:-2.11454,0,-21.3383 +phiX174 1206 . C <*> 0 . DP=9;END=1244;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 20203:9:0:20483:8:280:0 +phiX174 1245 . G T 0.0324554 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=4.8927;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:389:2:70:-2.83427,0,-14.5618 +phiX174 1246 . G <*> 0 . DP=9;END=1248;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 1576:9:9:1576:9:0:0 +phiX174 1249 . T G 0.0166698 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=5.56079;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:464:2:74:-1.94207,0,-16.5662 +phiX174 1250 . A <*> 0 . DP=9;END=1444;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 117232:9:0:118408:9:1176:0 +phiX174 1445 . C A 0.147157 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=3.36782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:273:2:76:-2.52649,0,-12.4911 +phiX174 1446 . C <*> 0 . DP=5;END=1576;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 40596:5:1:41046:5:450:0 +phiX174 1577 . A C 0.0123232 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=5.8634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:460:2:60:-1.81064,0,-19.8257 +phiX174 1578 . T <*> 0 . DP=11;END=1630;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 37187:11:0:37576:11:389:0 +phiX174 1631 . T G 0.00100612 . 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=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=8.3701;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:500:2:68:-1.52818,0,-17.3788 +phiX174 1632 . A <*> 0 . DP=10;END=1664;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 21423:10:0:21616:10:193:0 +phiX174 1665 . C A 0.0164128 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=5.57635;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:9,2:9:587:2:65:-2.35331,0,-21.269 +phiX174 1666 . A <*> 0 . DP=10;END=1771;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 62611:10:4:63430:9:819:0 +phiX174 1772 . T G 0.0180574 . 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=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=5.48067;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:7,2:7:425:2:59:-1.97686,0,-17.3816 +phiX174 1773 . T <*> 0 . DP=11;END=1785;MIN_DP=9 GQ:DP:MIN_DP:QR:RO:QA:AO 8476:11:9:8574:11:98:0 +phiX174 1786 . T G 7.94817e-05 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.9085;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:10,2:10:537:2:59:-0.861483,0,-25.1364 +phiX174 1787 . G <*> 0 . DP=4;END=1944;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 47842:4:1:48427:4:585:0 +phiX174 1945 . T G 1.01422 . 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=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.3354;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:263:2:59:-3.25425,0,-11.8637 +phiX174 1946 . G <*> 0 . DP=6;END=2229;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 106303:6:0:107388:5:1085:0 +phiX174 2230 . T G 0.00580188 . 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=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=6.61746;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:491:2:80:-2.28934,0,-22.3591 +phiX174 2231 . G <*> 0 . DP=5;END=2698;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 166680:5:1:168664:5:1984:0 +phiX174 2699 . C A 2.04855 . 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=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=0.517362;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:109:2:76:-3.4054,0,-5.58455 +phiX174 2700 . C <*> 0 . DP=3;END=2721;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 5193:3:2:5224:3:31:0 +phiX174 2722 . T G 1.01772 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.33197;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:150:2:67:-3.1308,0,-7.62253 +phiX174 2723 . A <*> 0 . DP=5;END=2813;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 29653:5:0:29924:5:271:0 +phiX174 2814 . T G 0.670623 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.79322;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=135;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=9.52472;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:135:2:57:-2.93048,0,-6.73807 +phiX174 2815 . T <*> 0 . DP=7;END=2827;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 5398:7:5:5428:6:30:0 +phiX174 2828 . T G 0.160629 . 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=31;MQMR=31;NS=1;NUMALT=1;ODDS=3.27866;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPL=0;RPP=7.35324;RPPR=4.45795;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:348:2:100:-3.34336,0,-13.6819 +phiX174 2829 . G <*> 0 . DP=4;END=2982;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 44584:4:0:45208:4:624:0 +phiX174 2983 . T G 1.55467 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=0.843116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:150:2:57:-3.34311,0,-7.61298 +phiX174 2984 . G <*> 0 . DP=5;END=3109;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 40846:5:0:41267:5:421:0 +phiX174 3110 . T C 1.16857 . AB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=1.17522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:6,3:6:361:3:94:-4.02963,0,-16.4039 +phiX174 3111 . G <*> 0 . DP=7;END=3154;MIN_DP=5 GQ:DP:MIN_DP:QR:RO:QA:AO 20734:7:5:20914:7:180:0 +phiX174 3155 . T G 5.42491 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=0.911202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:299:2:75:-4.38484,0,-11.5688 +phiX174 3156 . A <*> 0 . DP=11;END=3183;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 19187:11:0:19362:10:175:0 +phiX174 3184 . A C 0.000128182 . AB=0.153846;ABP=16.5402;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.0103;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.7273;NS=1;NUMALT=1;ODDS=10.4306;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=738;RO=11;RPL=1;RPP=3.0103;RPPR=4.78696;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:13:11,2:11:738:2:75:-0.695464,0,-29.8019 +phiX174 3185 . A <*> 0 . DP=7;END=3324;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 62297:7:0:63013:7:716:0 +phiX174 3325 . A C 0.0705175 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=4.11232;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:284:2:58:-2.65031,0,-9.66348 +phiX174 3326 . G <*> 0 . DP=7;END=3412;MIN_DP=4 GQ:DP:MIN_DP:QR:RO:QA:AO 42447:7:4:42832:7:385:0 +phiX174 3413 . T G 0.00284067 . 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=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=7.33194;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:537:2:57:-1.59087,0,-22.4183 +phiX174 3414 . C <*> 0 . DP=10;END=3417;MIN_DP=10 GQ:DP:MIN_DP:QR:RO:QA:AO 2435:10:10:2491:9:56:0 +phiX174 3418 . A C 0.000937887 . 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=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=8.44033;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:526:2:60:-1.49768,0,-21.0207 +phiX174 3419 . A <*> 0 . DP=7;END=3489;MIN_DP=3 GQ:DP:MIN_DP:QR:RO:QA:AO 32175:7:3:32478:7:303:0 +phiX174 3490 . A C 0.00226584 . 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=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=7.5581;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:543:2:66:-2.09471,0,-24.3433 +phiX174 3491 . T <*> 0 . DP=5;END=3728;MIN_DP=2 GQ:DP:MIN_DP:QR:RO:QA:AO 80198:5:2:80931:5:733:0 +phiX174 3729 . C T 0.295112 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.65478;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:232:2:63:-3.28331,0,-11.7007 +phiX174 3730 . A <*> 0 . DP=6;END=4030;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 108927:6:0:110100:5:1173:0 +phiX174 4031 . T G 0.0784807 . 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=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=4.00441;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:322:2:85:-3.02817,0,-11.6802 +phiX174 4032 . G <*> 0 . DP=6;END=4501;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 190881:6:0:192703:6:1822:0 +phiX174 4502 . A C 0.232919 . 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=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.89868;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:284:2:55:-2.57533,0,-11.8832 +phiX174 4503 . T <*> 0 . DP=6;END=4557;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 20294:6:0:20521:6:227:0 +phiX174 4558 . C G 0.076247 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=4.03372;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:204:2:59:-2.68445,0,-8.4362 +phiX174 4559 . T <*> 0 . DP=3;END=4654;MIN_DP=1 GQ:DP:MIN_DP:QR:RO:QA:AO 20927:3:1:21288:3:361:0 +phiX174 4655 . T G 0.399408 . 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=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.33999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:193:2:70:-2.81796,0,-11.1489 +phiX174 4656 . G <*> 0 . DP=8;END=4703;MIN_DP=6 GQ:DP:MIN_DP:QR:RO:QA:AO 26170:8:6:26393:8:223:0 +phiX174 4704 . T C 0.000171782 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.1378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:10,2:10:621:2:58:-1.1962,0,-26.2058 +phiX174 4705 . C <*> 0 . DP=7;END=5386;MIN_DP=0 GQ:DP:MIN_DP:QR:RO:QA:AO 291210:7:0:294344:6:3134:0