Mercurial > repos > ulfschaefer > filter_vcf
changeset 9:2e3115b4df74 draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Mon, 21 Dec 2015 10:49:48 -0500 |
| parents | 5932a130395e |
| children | c2f8e7580133 |
| files | LICENSE filter_vcf.py filter_vcf.sh filter_vcf.xml phe/__init__.py phe/metadata/__init__.py phe/variant/GATKVariantCaller.py phe/variant/MPileupVariantCaller.py phe/variant/__init__.py phe/variant/variant_factory.py phe/variant_filters/ADFilter.py phe/variant_filters/DP4Filter.py phe/variant_filters/DepthFilter.py phe/variant_filters/GQFilter.py phe/variant_filters/GTFilter.py phe/variant_filters/MQ0FFilter.py phe/variant_filters/MQ0Filter.py phe/variant_filters/MQFilter.py phe/variant_filters/QualFilter.py phe/variant_filters/__init__.py test-data/test_input.vcf test-data/test_output.vcf tool_dependencies.xml |
| diffstat | 23 files changed, 0 insertions(+), 4275 deletions(-) [+] |
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--- a/LICENSE Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,676 +0,0 @@ - - - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. By contrast, -the GNU General Public License is intended to guarantee your freedom to -share and change all versions of a program--to make sure it remains free -software for all its users. We, the Free Software Foundation, use the -GNU General Public License for most of our software; it applies also to -any other work released this way by its authors. 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--- a/filter_vcf.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -#!/usr/bin/env python -'''Simple VCF parser using custom filters. - -Created on 6 Oct 2015 - -@author: alex -''' -import argparse - -from phe.variant import VariantSet - - -def get_args(): - - args = argparse.ArgumentParser() - - args.add_argument("--vcf", "-v", required=True, help="VCF file to (re)filter.") - args.add_argument("--filters", "-f", required=True, help="Filter(s) to apply as key:threshold pairs, separated by comma.") - args.add_argument("--output", "-o", required=True, help="Location for filtered VCF to be written.") - - return args.parse_args() - - -def main(): - args = get_args() - - var_set = VariantSet(args.vcf, filters=args.filters) - - var_set.filter_variants() - - var_set.serialise(args.output) - -if __name__ == '__main__': - exit(main())
--- a/filter_vcf.sh Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#!/bin/bash - -OUTPUT=$1 -shift -VCF=$1 -shift -FILTERS=$@ - -FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -export PATH=$PATH:$DIR -CMD="filter_vcf.py --vcf $VCF --filters $FILTERS --output $OUTPUT" - -echo "CMD: "$CMD -eval $CMD
--- a/filter_vcf.xml Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -<tool id="filter_vcf" name="Filter VCF" version="1.0"> - <description>filters a VCF file</description> - <requirements> - <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="0.6.8dev">pyvcf</requirement> - <requirement type="package" version="3.11">pyyaml</requirement> - </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <command interpreter="bash"> - filter_vcf.sh - $output - $input - #for $sf in $snp_filter: - #for $name, $param in $sf.snp_filter_type.iteritems(): - #if $name not in [ "__current_case__", "snp_filter_type_selector" ]: - ${name}:"${param}" - #end if - #end for - #end for - </command> - - <inputs> - <param name="input" type="data" format="vcf" label="VCF File to filter" /> - - <repeat name="snp_filter" title="SNP Filter" help=""> - <conditional name="snp_filter_type"> - <param name="snp_filter_type_selector" type="select" label="SNP Filter Type"> - <option value="gq_score_option">GQ score</option> - <option value="dp4_ratio_option">DP4 ratio</option> - <option value="ad_ratio_option">AD ratio</option> - <option value="mq_score_option">MQ score</option> - <option value="min_depth_option">Minimum depth</option> - <option value="uncall_gt_option">Uncall GT</option> - <option value="mq0_ratio_option">MQ0 ratio</option> - <option value="qual_score_option">Quality score</option> - <option value="mq0f_ratio_option">MQ0F ratio</option> - </param> - <when value="gq_score_option"> - <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/> - </when> - <when value="dp4_ratio_option"> - <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/> - </when> - <when value="ad_ratio_option"> - <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/> - </when> - <when value="mq_score_option"> - <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/> - </when> - <when value="min_depth_option"> - <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/> - </when> - <when value="uncall_gt_option"> - <param name="uncall_gt" type="text" value="" hidden="True"/> - </when> - <when value="mq0_ratio_option"> - <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/> - </when> - <when value="qual_score_option"> - <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/> - </when> - <when value="mq0f_ratio_option"> - <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/> - </when> - </conditional> - </repeat> - - </inputs> - - <outputs> - <data format="vcf" name="output" label="${tool.name} on ${on_string}: filtered VCF" /> - </outputs> - <tests> - <test> - <param name="input" value="test_input.vcf" ftype="vcf" /> - <param name="min_depth" value="100" /> - <output name="output" file="test_output.vcf" ftype="vcf" /> - </test> - </tests> - <help> - -usage: filter_vcf.py [-h] \-\-vcf VCF \-\-filters FILTERS \-\-output OUTPUT - -optional arguments: - --h, \-\-help show this help message and exit - -\-\-vcf VCF, -v VCF VCF file to (re)filter. - -\-\-filters FILTERS, -f FILTERS Filter(s) to apply as key:threshold pairs, separated by comma. - -\-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written. - - </help> -</tool>
--- a/phe/__init__.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -if __name__ == "phe": - # If this package is added as library, append extended path. - from pkgutil import extend_path - __path__ = extend_path(__path__, __name__) \ No newline at end of file
--- a/phe/metadata/__init__.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -"""Metadata related information.""" - -import abc - -class PHEMetaData(object): - """Abstract class to provide interface for meta-data creation.""" - - __metaclass__ = abc.ABCMeta - - def __init__(self): - pass - - @abc.abstractmethod - def get_meta(self): - """Get the metadata.""" - raise NotImplementedError("get meta has not been implemented yet.")
--- a/phe/variant/GATKVariantCaller.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -''' -Created on 22 Sep 2015 - -@author: alex -''' -from collections import OrderedDict -import logging -import os -import subprocess - -from phe.variant import VariantCaller - - -class GATKVariantCaller(VariantCaller): - """Implemetation of the Broad institute's variant caller.""" - - name = "gatk" - """Plain text name of the variant caller.""" - - _default_options = "--sample_ploidy 2 --genotype_likelihoods_model BOTH -rf BadCigar -out_mode EMIT_ALL_SITES -nt 1" - """Default options for the variant caller.""" - - def __init__(self, cmd_options=None): - """Constructor""" - if cmd_options is None: - cmd_options = self._default_options - - super(GATKVariantCaller, self).__init__(cmd_options=cmd_options) - - self.last_command = None - - def get_info(self, plain=False): - d = {"name": "gatk", "version": self.get_version(), "command": self.last_command} - - if plain: - result = "GATK(%(version)s): %(command)s" % d - else: - result = OrderedDict(d) - - return result - - def get_version(self): - - p = subprocess.Popen(["java", "-jar", os.environ["GATK_JAR"], "-version"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) - (output, _) = p.communicate() - - # last character is EOL. - version = output.split("\n")[-2] - - return version - - def make_vcf(self, *args, **kwargs): - ref = kwargs.get("ref") - bam = kwargs.get("bam") - - if kwargs.get("vcf_file") is None: - kwargs["vcf_file"] = "variants.vcf" - - opts = {"ref": os.path.abspath(ref), - "bam": os.path.abspath(bam), - "gatk_jar": os.environ["GATK_JAR"], - "all_variants_file": os.path.abspath(kwargs.get("vcf_file")), - "extra_cmd_options": self.cmd_options} - -# if not self.create_aux_files(ref): -# logging.warn("Auxiliary files were not created.") -# return False - - # Call variants - # FIXME: Sample ploidy = 2? - os.environ["GATK_JAR"] - cmd = "java -XX:+UseSerialGC -jar %(gatk_jar)s -T UnifiedGenotyper -R %(ref)s -I %(bam)s -o %(all_variants_file)s %(extra_cmd_options)s" % opts - success = os.system(cmd) - - if success != 0: - logging.warn("Calling variants returned non-zero exit status.") - return False - - self.last_command = cmd - - return True - - def create_aux_files(self, ref): - """Create auxiliary files needed for this variant. - - Tools needed: samtools and picard tools. Picard tools is a Java - library that can be defined using environment variable: PICARD_JAR - specifying path to picard.jar or PICARD_TOOLS_PATH specifying path - to the directory where separate jars are (older version before jars - were merged into a single picard.jar). - Parameters: - ----------- - ref: str - Path to the reference file. - - Returns: - -------- - bool: - True if auxiliary files were created, False otherwise. - """ - - ref_name, _ = os.path.splitext(ref) - - success = os.system("samtools faidx %s" % ref) - - if success != 0: - logging.warn("Fasta index could not be created.") - return False - - d = {"ref": ref, "ref_name": ref_name} - - if os.environ.get("PICARD_TOOLS_PATH"): - d["picard_tools_path"] = os.path.join(os.environ["PICARD_TOOLS_PATH"], "CreateSequenceDictionary.jar") - elif os.environ.get("PICARD_JAR"): - # This is used in newer version of PICARD tool where multiple - # jars were merged into a single jar file. - d["picard_tools_path"] = "%s %s" % (os.environ["PICARD_JAR"], "CreateSequenceDictionary") - else: - logging.error("Picard tools are not present in the path.") - return False - - success = os.system("java -jar %(picard_tools_path)s R=%(ref)s O=%(ref_name)s.dict" % d) - - if success != 0: - logging.warn("Dictionary for the %s reference could not be created", ref) - return False
--- a/phe/variant/MPileupVariantCaller.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -''' -Created on 22 Sep 2015 - -@author: alex -''' -from collections import OrderedDict -import logging -import os -import subprocess -import tempfile - -from phe.variant import VariantCaller - - -class MPileupVariantCaller(VariantCaller): - """Implemetation of the Broad institute's variant caller.""" - - name = "mpileup" - """Plain text name of the variant caller.""" - - _default_options = "-m -f GQ" - """Default options for the variant caller.""" - - def __init__(self, cmd_options=None): - """Constructor""" - if cmd_options is None: - cmd_options = self._default_options - - super(MPileupVariantCaller, self).__init__(cmd_options=cmd_options) - - self.last_command = None - - def get_info(self, plain=False): - d = {"name": self.name, "version": self.get_version(), "command": self.last_command} - - if plain: - result = "mpileup(%(version)s): %(command)s" % d - else: - result = OrderedDict(d) - - return result - - def get_version(self): - - p = subprocess.Popen(["samtools", "--version"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) - (output, _) = p.communicate() - - # first line is the version of the samtools - version = output.split("\n")[0].split(" ")[1] - - return version - - def make_vcf(self, *args, **kwargs): - ref = kwargs.get("ref") - bam = kwargs.get("bam") - - if kwargs.get("vcf_file") is None: - kwargs["vcf_file"] = "variants.vcf" - - opts = {"ref": os.path.abspath(ref), - "bam": os.path.abspath(bam), - "all_variants_file": os.path.abspath(kwargs.get("vcf_file")), - "extra_cmd_options": self.cmd_options} - - with tempfile.NamedTemporaryFile(suffix=".pileup") as tmp: - opts["pileup_file"] = tmp.name - cmd = "samtools mpileup -t DP,DV,DP4,DPR,SP -Auf %(ref)s %(bam)s | bcftools call %(extra_cmd_options)s > %(all_variants_file)s" % opts - print cmd - self.last_command = cmd - if os.system(cmd) != 0: - logging.warn("Pileup creation was not successful.") - return False - - return True - - def create_aux_files(self, ref): - """Index reference with faidx from samtools. - - Parameters: - ----------- - ref: str - Path to the reference file. - - Returns: - -------- - bool: - True if auxiliary files were created, False otherwise. - """ - - success = os.system("samtools faidx %s" % ref) - - if success != 0: - logging.warn("Fasta index could not be created.") - return False - - return True
--- a/phe/variant/__init__.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,288 +0,0 @@ -"""Classes and methods to work with variants and such.""" -import abc -#ulf -# from collections import OrderedDict -try: - from collections import OrderedDict -except ImportError: - from ordereddict import OrderedDict - -import logging -import pickle - -from vcf import filters -import vcf -from vcf.parser import _Filter - -from phe.metadata import PHEMetaData -from phe.variant_filters import make_filters, PHEFilterBase, str_to_filters - - -class VCFTemplate(object): - """This is a small hack class for the Template used in generating - VCF file.""" - - def __init__(self, vcf_reader): - self.infos = vcf_reader.infos - self.formats = vcf_reader.formats - self.filters = vcf_reader.filters - self.alts = vcf_reader.alts - self.contigs = vcf_reader.contigs - self.metadata = vcf_reader.metadata - self._column_headers = vcf_reader._column_headers - self.samples = vcf_reader.samples - -class VariantSet(object): - """A convenient representation of set of variants. - TODO: Implement iterator and generator for the variant set. - """ - - _reader = None - - def __init__(self, vcf_in, filters=None): - """Constructor of variant set. - - Parameters: - ----------- - vcf_in: str - Path to the VCF file for loading information. - filters: str or dict, optional - Dictionary or string of the filter:threshold key value pairs. - """ - self.vcf_in = vcf_in - self._reader = vcf.Reader(filename=vcf_in) - self.out_template = VCFTemplate(self._reader) - - self.filters = [] - if filters is not None: - if isinstance(filters, str): - self.filters = str_to_filters(filters) - elif isinstance(filters, dict): - self.filters = make_filters(config=filters) - elif isinstance(filters, list): - self.filters = filters - else: - logging.warn("Could not create filters from %s", filters) - else: - reader = vcf.Reader(filename=self.vcf_in) - filters = {} - for filter_id in reader.filters: - filters.update(PHEFilterBase.decode(filter_id)) - - if filters: - self.filters = make_filters(config=filters) - - self.variants = [] - - def filter_variants(self, keep_only_snps=True): - """Create a variant """ - - if self._reader is None: - # Create a reader class from input VCF. - self._reader = vcf.Reader(filename=self.vcf_in) - - # get list of existing filters. - existing_filters = {} - removed_filters = [] - - for filter_id in self._reader.filters: - conf = PHEFilterBase.decode(filter_id) - tuple(conf.keys()) - existing_filters.update({tuple(conf.keys()):filter_id}) - - # Add each filter we are going to use to the record. - # This is needed for writing out proper #FILTER header in VCF. - for record_filter in self.filters: - # We know that each filter has short description method. - short_doc = record_filter.short_desc() - short_doc = short_doc.split('\n')[0].lstrip() - - filter_name = PHEFilterBase.decode(record_filter.filter_name()) - - # Check if the sample has been filtered for this type of filter - # in the past. If so remove is, because it is going to be refiltered. - if tuple(filter_name) in existing_filters: - logging.info("Removing existing filter: %s", existing_filters[tuple(filter_name)]) - removed_filters.append(existing_filters[tuple(filter_name)]) - del self._reader.filters[existing_filters[tuple(filter_name)]] - - self._reader.filters[record_filter.filter_name()] = _Filter(record_filter.filter_name(), short_doc) - - # For each record (POSITION) apply set of filters. - for record in self._reader: - - # If this record failed filters and we removed some, - # check is they need to be removed from record. - if isinstance(record.FILTER, list) and len(record.FILTER) > 0: - for filter_id in removed_filters: - if filter_id in record.FILTER: - record.FILTER.remove(filter_id) - - for record_filter in self.filters: - - # Call to __call__ method in each filter. - result = record_filter(record) - - # Record is KEPT if filter returns None - if result == None: - continue - - # If we got this far, then record is filtered OUT. - record.add_filter(record_filter.filter_name()) - - # After applying all filters, check if FILTER is None. - # If it is, then record PASSED all filters. - if record.FILTER is None or record.FILTER == []: - record.FILTER = 'PASS' - # FIXME: Does this work for indels? - if keep_only_snps and record.is_snp: - self.variants.append(record) - else: - self.variants.append(record) - - self.update_filters(self._reader.filters) - - return [ variant for variant in self.variants if variant.FILTER == "PASS"] - - def add_metadata(self, info): - """Add metadata to the variant set. - - Parameters: - ----------- - info: dict - Dictionary of key value pairs to be inserted into metadata. - """ - for info_key, metadata in info.items(): - self.out_template.metadata[info_key] = metadata - - def write_variants(self, vcf_out, only_snps=False, only_good=False): - """Write variants to a VCF file. - - Parameters: - ----------- - vcf_out: str - Path to the file where VCF data is written. - only_snps: bool, optional - True is *only* SNP are to be written to the output (default: False). - only_good: bool, optional - True if only those records that PASS all filters should be written - (default: False). - - Returns: - int: - Number of records written. - """ - written_variants = 0 - with open(vcf_out, "w") as out_vcf: - writer = vcf.Writer(out_vcf, self.out_template) - for record in self.variants: - - if only_snps and not record.is_snp: - continue - - if only_good and record.FILTER != "PASS" or record.FILTER is None: - continue - - writer.write_record(record) - written_variants += 1 - - return written_variants - - def _write_bad_variants(self, vcf_out): - """**PRIVATE:** Write only those records that **haven't** passed.""" - written_variants = 0 - with open(vcf_out, "w") as out_vcf: - writer = vcf.Writer(out_vcf, self.out_template) - for record in self.variants: - if record.FILTER != "PASS" and record.FILTER is not None: - writer.write_record(record) - written_variants += 1 - return written_variants - - def serialise(self, out_file): - """Save the data in this class to a file for future use/reload. - - Parameters: - ----------- - out_file: str - path to file where the data should be written to. - - Returns: - -------- - int: - Number of variants written. - """ - written_variants = 0 - with open(out_file, "w") as out_vcf: - writer = vcf.Writer(out_vcf, self.out_template) - for record in self.variants: - writer.write_record(record) - written_variants += 1 - - return written_variants - - def update_filters(self, new_filters): - """Update internal filters in the output template.""" - for new_filter, filter_data in new_filters.items(): - self.out_template.filters[new_filter] = filter_data - - -class VariantCaller(PHEMetaData): - """Abstract class used for access to the implemented variant callers.""" - - __metaclass__ = abc.ABCMeta - - def __init__(self, cmd_options=None): - """Constructor for variant caller. - - Parameters: - ----------- - cmd_options: str, optional - Command options to pass to the variant command. - """ - self.cmd_options = cmd_options - - super(VariantCaller, self).__init__() - - @abc.abstractmethod - def make_vcf(self, *args, **kwargs): - """Create a VCF from **BAM** file. - - Parameters: - ----------- - ref: str - Path to the reference file. - bam: str - Path to the indexed **BAM** file for calling variants. - vcf_file: str - path to the VCF file where data will be written to. - - Returns: - -------- - bool: - True if variant calling was successful, False otherwise. - """ - raise NotImplementedError("make_vcf is not implemented yet.") - - @abc.abstractmethod - def create_aux_files(self, ref): - """Create needed (if any) auxiliary files. - These files are required for proper functioning of the variant caller. - """ - raise NotImplementedError("create_aux_files is not implemeted.") - - @abc.abstractmethod - def get_info(self, plain=False): - """Get information about this variant caller.""" - raise NotImplementedError("Get info has not been implemented yet." - ) - def get_meta(self): - """Get the metadata about this variant caller.""" - od = self.get_info() - od["ID"] = "VariantCaller" - return OrderedDict({"PHEVariantMetaData": [od]}) - - @abc.abstractmethod - def get_version(self): - """Get the version of the underlying command used.""" - raise NotImplementedError("Get version has not been implemented yet.")
--- a/phe/variant/variant_factory.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -'''Classes and functions for working with variant callers. - -Created on 22 Sep 2015 - -@author: alex -''' -import glob -import inspect -import logging -import os -import sys - -from phe.variant import VariantCaller - -def dynamic_caller_loader(): - """Fancy way of dynamically importing existing variant callers. - - Returns - ------- - dict: - Available variant callers dictionary. Keys are parameters that - can be used to call variants. - """ - - # We assume the caller are in the same directory as THIS file. - variants_dir = os.path.dirname(__file__) - variants_dir = os.path.abspath(variants_dir) - - # This is populated when the module is first imported. - avail_callers = {} - - # Add this directory to the syspath. - sys.path.insert(0, variants_dir) - - # Find all "py" files. - for caller_mod in glob.glob(os.path.join(variants_dir, "*.py")): - - # Derive name of the module where caller is. - caller_mod_file = os.path.basename(caller_mod) - - # Ignore __init__ file, only base class is there. - if caller_mod_file.startswith("__init__"): - continue - - # Import the module with a caller. - mod = __import__(caller_mod_file.replace(".pyc", "").replace(".py", "")) - - # Find all the classes contained in this module. - classes = inspect.getmembers(mod, inspect.isclass) - for cls_name, cls in classes: - # For each class, if it is a sublass of VariantCaller, add it. - if cls_name != "VariantCaller" and issubclass(cls, VariantCaller): - # The name is inherited and defined within each caller. - avail_callers[cls.name] = cls - - sys.path.remove(variants_dir) - - return avail_callers - -_avail_variant_callers = dynamic_caller_loader() - -def available_callers(): - """Return list of available variant callers.""" - return _avail_variant_callers.keys() - -def factory(variant=None, custom_options=None): - """Make an instance of a variant class. - - Parameters: - ----------- - variant: str, optional - Name of the variant class to instantiate. - custom_options: str, optional - Custom options to be passed directly to the implementing class. - - Returns: - -------- - :py:class:`phe.variant.VariantCaller`: - Instance of the :py:class:`phe.variant.VariantCaller` for given - variant name, or None if one couldn't be found. - """ - if variant is not None and isinstance(variant, str): - - variant = variant.lower() - if variant in _avail_variant_callers: - return _avail_variant_callers[variant](cmd_options=custom_options) - else: - logging.error("No implementation for %s mapper.") - return None - - logging.warn("Unknown parameters. Mapper could not be initialised.") - return None
--- a/phe/variant_filters/ADFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ -'''Filter VCFs on AD ratio. - -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class ADFilter(PHEFilterBase): - '''Filter sites by AD ratio.''' - - - name = "ADRatio" - _default_threshold = 0.9 - parameter = "ad_ratio" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold, - help="Filter sites below minimum ad ratio (default: %s)" % self._default_threshold) - - def __init__(self, args): - """AD Ratio constructor.""" - # This needs to happen first, because threshold is initialised here. - super(ADFilter, self).__init__(args) - - # Change the threshold to custom dp value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.ad_ratio - elif isinstance(args, dict): - try: - self.threshold = float(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - if not record.is_snp: - return None - - if len(record.samples) > 1: - logging.warn("More than 1 sample detected. Only first is considered.") - - try: - record_ad = record.samples[0].data.AD - - # FIXME: when record length is > 2, what do you do? - assert len(record_ad) == 2, "AD data is incomplete POS: %i" % record.POS - - depth = sum(record.samples[0].data.AD) - - ratio = float(record_ad[1]) / depth - except Exception: - logging.error("Could not calculate AD ratio from %s POS: %s", record_ad, record.POS) - ratio = None - - if ratio is None or ratio < self.threshold: - # FIXME: When ratio is None, i.e. error, what do you do? - return ratio or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (AD ratio > %s )" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/DP4Filter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -'''Filter VCFs on AD ratio. - -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class DP4Filter(PHEFilterBase): - '''Filter sites by AD ratio.''' - - - name = "DP4" - _default_threshold = 0.9 - parameter = "dp4_ratio" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold, - help="Filter sites below minimum dp4 ratio (default: %s)" % self._default_threshold) - - def __init__(self, args): - """AD Ratio constructor.""" - # This needs to happen first, because threshold is initialised here. - super(DP4Filter, self).__init__(args) - - # Change the threshold to custom dp value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.ad_ratio - elif isinstance(args, dict): - try: - self.threshold = float(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - if not record.is_snp: - return None - - try: - record_dp = record.INFO.get("DP4") - - # FIXME: when record length is > 2, what do you do? - assert len(record_dp) == 4, "DP4 data should have 4 datum POS: %i" % record.POS - - depth = sum(record_dp) - - ratio = float(sum(record_dp[2:])) / depth - except Exception: - logging.error("Could not calculate DP4 ratio from %s POS: %s", record_dp, record.POS) - ratio = None - - if ratio is None or ratio < self.threshold: - # FIXME: When ratio is None, i.e. error, what do you do? - return ratio or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (DP4 ratio > %s )" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/DepthFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -'''Filter VCF on depth of coverage. - -Created on 24 Sep 2015 - -@author: alex -''' -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class DepthFilter(PHEFilterBase): - """Filter sites by depth.""" - - name = "MinDepth" - _default_threshold = 5 - parameter = "min_depth" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--" % arg_name, type=int, default=self._default_threshold, - help="Filter sites below minimum depth (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Depth constructor.""" - # This needs to happen first, because threshold is initialised here. - super(DepthFilter, self).__init__(args) - - # Change the threshold to custom dp value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.min_depth - elif isinstance(args, dict): - try: - self.threshold = int(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - if len(record.samples) > 1: - logging.warn("Currently we only filter VCFs with 1 sample. Only first sample will be used.") - - try: - record_dp = record.samples[0].data.DP - except AttributeError: - record_dp = None - - if record_dp is None: -# logging.debug("Falling back to INFO DP") - record_dp = record.INFO.get("DP") - - if record_dp is None or record_dp < self.threshold: - return record_dp or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (DP > %i)" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/GQFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -'''Filter VCF on GQ parameter. -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class GQFilter(PHEFilterBase): - '''Filter sites by GQ score.''' - - name = "MinGQ" - _default_threshold = 0 - parameter = "gq_score" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=int, default=self._default_threshold, - help="Filter sites below given GQ score (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Depth constructor.""" - # This needs to happen first, because threshold is initialised here. - super(GQFilter, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.gq_score - elif isinstance(args, dict): - try: - self.threshold = int(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - if not record.is_snp: - return None - - if len(record.samples) > 1: - logging.warn("More than 1 sample detected. Only first is considered.") - - try: - record_gq = record.samples[0].data.GQ - except AttributeError: - logging.error("Could not retrieve GQ score POS %i", record.POS) - record_gq = None - - if record_gq is None or record_gq < self.threshold: - # FIXME: when record_gq is None, i,e, error, what do you do? - return record_gq or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (GQ > %s)" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/GTFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -'''Filter VCF on GT filter parameter. - -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class UncallableGTFilter(PHEFilterBase): - '''Filter uncallable genotypes''' - - name = "UncallGT" - _default_threshold = None - parameter = "uncall_gt" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=str, default=self._default_threshold, - help="Filter sites below given GQ score (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Depth constructor.""" - # This needs to happen first, because threshold is initialised here. - super(UncallableGTFilter, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.gq_score - elif isinstance(args, dict): - try: - self.threshold = str(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - if len(record.samples) > 1: - logging.warn("More than 1 sample detected. Only first is considered.") - - try: - record_gt = record.samples[0].data.GT - except AttributeError: - logging.error("Could not retrieve GQ score POS %i", record.POS) - record_gt = None - - if record_gt is None: - return "./." - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (GT != ./. )" % (short_desc) - - return short_desc - - def is_gap(self): - return True - - def is_n(self): - return False
--- a/phe/variant_filters/MQ0FFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -'''Filter VCF on MQ filter. -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class MQ0Filter(PHEFilterBase): - '''Filter sites by MQ0 (Total Mapping Quality Zero Reads) to DP ratio.''' - - name = "MinMQ0F" - _default_threshold = 0.05 - parameter = "mq0f_ratio" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold, - help="Filter sites below given MQ0F ratio (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Mapping Quality Zero constructor.""" - # This needs to happen first, because threshold is initialised here. - super(MQ0Filter, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.mq_score - elif isinstance(args, dict): - try: - self.threshold = float(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - - record_mq = record.INFO.get("MQ0F") - - if record_mq is None or record_mq > self.threshold: - # FIXME: when record_mq is None, i,e, error/missing, what do you do? - return record_mq or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (MQ0F > %s)" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/MQ0Filter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -'''Filter VCF on MQ filter. -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class MQ0Filter(PHEFilterBase): - '''Filter sites by MQ0 (Total Mapping Quality Zero Reads) to DP ratio.''' - - name = "MinMQ0" - _default_threshold = 0.05 - parameter = "mq0_ratio" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold, - help="Filter sites below given MQ score (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Mapping Quality Zero constructor.""" - # This needs to happen first, because threshold is initialised here. - super(MQ0Filter, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.mq_score - elif isinstance(args, dict): - try: - self.threshold = float(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - - record_mq = record.INFO.get("MQ0") - - if record_mq: - # We consider DO from INFO not samples because MQ0 is also from INFO. - record_mq /= float(record.INFO.get("DP")) - - if record_mq is None or record_mq > self.threshold: - # FIXME: when record_mq is None, i,e, error/missing, what do you do? - return record_mq or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (MQ0 > %s)" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/MQFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -'''Filter VCF on MQ filter. -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class MQFilter(PHEFilterBase): - '''Filter sites by Mapping Quality (MQ) score.''' - - name = "MinMQ" - _default_threshold = 30 - parameter = "mq_score" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=int, default=self._default_threshold, - help="Filter sites below given MQ score (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Mapping Quality constructor.""" - # This needs to happen first, because threshold is initialised here. - super(MQFilter, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.mq_score - elif isinstance(args, dict): - try: - self.threshold = int(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - record_mq = record.INFO.get("MQ") - - if record_mq is None or record_mq < self.threshold: - # FIXME: when record_mq is None, i,e, error/missing, what do you do? - return record_mq or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (MQ > %s)" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/QualFilter.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -'''Filter VCF on GQ parameter. -Created on 24 Sep 2015 - -@author: alex -''' - -import argparse -import logging - -from phe.variant_filters import PHEFilterBase - - -class QualFilter(PHEFilterBase): - '''Filter sites by QUAL score.''' - - name = "LowSNPQual" - _default_threshold = 40.0 - parameter = "qual_score" - - @classmethod - def customize_parser(self, parser): - arg_name = self.parameter.replace("_", "-") - parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold, - help="Filter sites below given GQ score (default: %s)" % self._default_threshold) - - def __init__(self, args): - """Min Depth constructor.""" - # This needs to happen first, because threshold is initialised here. - super(QualFilter, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - if isinstance(args, argparse.Namespace): - self.threshold = args.gq_score - elif isinstance(args, dict): - try: - self.threshold = float(args.get(self.parameter)) - except TypeError: - logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) - self.threshold = None - - def __call__(self, record): - """Filter a :py:class:`vcf.model._Record`.""" - - - record_qual = record.QUAL - - if record_qual is None or record_qual < self.threshold: - # FIXME: when record_gq is None, i,e, error, what do you do? - return record_qual or False - else: - return None - - def short_desc(self): - short_desc = self.__doc__ or '' - - if short_desc: - short_desc = "%s (QUAL > %s)" % (short_desc, self.threshold) - - return short_desc
--- a/phe/variant_filters/__init__.py Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,209 +0,0 @@ -"""Classes and functions for working with variant filters.""" - -from __builtin__ import __import__ -from abc import abstractproperty -import abc -import argparse -import glob -import inspect -import logging -import os -import re -import sys - -import vcf -import vcf.filters -from vcf.parser import _Filter - -IUPAC_CODES = {frozenset(["A", "G"]): "R", - frozenset(["C", "T"]): "Y", - frozenset(["G", "C"]): "S", - frozenset(["A", "T"]): "W", - frozenset(["G", "T"]): "K", - frozenset(["A", "C"]): "M", - frozenset(["C", "G", "T"]): "B", - frozenset(["A", "G", "T"]): "D", - frozenset(["A", "C", "T"]): "H", - frozenset(["A", "C", "G"]): "V" - } - -class PHEFilterBase(vcf.filters.Base): - """Base class for VCF filters.""" - __meta__ = abc.ABCMeta - - magic_sep = ":" - decoder_pattern = re.compile(magic_sep) - - @abc.abstractproperty - def parameter(self): - """Short name of parameter being filtered.""" - return self.parameter - - @abc.abstractproperty - def _default_threshold(self): - """Default threshold for filtering.""" - return self._default_threshold - - def __init__(self, args): - super(PHEFilterBase, self).__init__(args) - - # Change the threshold to custom gq value. - self.threshold = self._default_threshold - - if isinstance(args, dict): - self.threshold = args.get(self.parameter) - - def __str__(self): - return self.filter_name() - - @abc.abstractmethod - def short_desc(self): - """Short description of the filter (included in VCF).""" - raise NotImplementedError("Get short description is not implemented.") - - def get_config(self): - """This is used for reconstructing filter.""" - return {self.parameter: self.threshold} - - def filter_name(self): - """Create filter names by their parameter separated by magic. - E.g. if filter parameter is ad_ratio and threshold is 0.9 then - ad_ratio:0.9 if the filter name. - """ - return "%s%s%s" % (self.parameter, self.magic_sep, self.threshold) - - @staticmethod - def decode(filter_id): - """Decode name of filter.""" - conf = {} - - if PHEFilterBase.magic_sep in filter_id: - info = PHEFilterBase.decoder_pattern.split(filter_id) - assert len(info) == 2 - conf[info[0]] = info[1] - return conf - - def is_gap(self): - return False - - def is_n(self): - return True - - @staticmethod - def call_concensus(record): - extended_code = "N" - try: - sample_ad = set([str(c) for c in record.ALT] + [record.REF]) - - - for code, cov in IUPAC_CODES.items(): - if sample_ad == cov: - extended_code = code - break - except AttributeError: - extended_code = "N" - - return extended_code - -def dynamic_filter_loader(): - """Fancy way of dynamically importing existing filters. - - Returns - ------- - dict: - Available filters dictionary. Keys are parameters that - can be supplied to the filters. - """ - - # We assume the filters are in the same directory as THIS file. - filter_dir = os.path.dirname(__file__) - filter_dir = os.path.abspath(filter_dir) - - # This is populated when the module is first imported. - avail_filters = {} - - # Add this directory to the syspath. - sys.path.insert(0, filter_dir) - - # Find all "py" files. - for filter_mod in glob.glob(os.path.join(filter_dir, "*.py")): - - # Derive name of the module where filter is. - filter_mod_file = os.path.basename(filter_mod) - - # Ignore this file, obviously. - if filter_mod_file.startswith("__init__"): - continue - - # Import the module with a filter. - mod = __import__(filter_mod_file.replace(".pyc", "").replace(".py", "")) - - # Find all the classes contained in this module. - classes = inspect.getmembers(mod, inspect.isclass) - for cls_name, cls in classes: - # For each class, if it is a sublass of PHEFilterBase, add it. - if cls_name != "PHEFilterBase" and issubclass(cls, PHEFilterBase): - # The parameters are inherited and defined within each filter. - avail_filters[cls.parameter] = cls - - sys.path.remove(filter_dir) - - return avail_filters - -_avail_filters = dynamic_filter_loader() - -def available_filters(): - """Return list of available filters.""" - return _avail_filters.keys() - -def str_to_filters(filters): - """Convert from filter string to array of filters. - E.g. ad_ration:0.9,min_depth:5 - - Parameters: - ----------- - filters: str - String version of filters, separated by comma. - - Returns: - -------- - list: - List of :py:class:`phe.variant_filters.PHEFilterBase` instances. - """ - - config = {} - for kv_pair in filters.split(","): - pair = kv_pair.split(":") - assert len(pair) == 2, "Filters should be separated by ':' %s" % kv_pair - - # We don't care about casting them to correct type because Filters - # will do it for us. - config[pair[0]] = pair[1] - - return make_filters(config) - -def make_filters(config): - """Create a list of filters from *config*. - - Parameters: - ----------- - config: dict, optional - Dictionary with parameter: value pairs. For each parameter, an - appropriate Filter will be found and instanciated. - - Returns: - -------- - list: - List of :py:class:`PHEFilterBase` filters. - """ - filters = [] - - if config: - for custom_filter in config: - if custom_filter in _avail_filters: - filters.append(_avail_filters[custom_filter](config)) - else: - logging.warn("Could not find appropriate filter for %s", - custom_filter) - - return filters
--- a/test-data/test_input.vcf Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1000 +0,0 @@ -##fileformat=VCFv4.1 -##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:24:36 BST 2014",Epoch=1400747076888,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:10:24 BST 2014",Epoch=1400746224902,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=STRICT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=6 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##reference=file:///phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta -##source=SelectVariants -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> -##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> -##INFO=<ID=BasesToClosestSNP,Number=1,Type=Integer,Description="Number of bases to the closest SNP in the file."> -##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##FILTER=<ID=LowQual,Description="Low quality"> -##FILTER=<ID=mq_score:50,Description="Filter sites by Mapping Quality (MQ) score. (MQ > 50)"> -##FILTER=<ID=gq_score:10,Description="Filter sites by GQ score. (GQ > 10)"> -##FILTER=<ID=uncall_gt:,Description="Filter uncallable genotypes (GT != ./. )"> -##contig=<ID=gi|15829254|ref|NC_002695.1|,length=5498450> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H133840545_1 -gi|15829254|ref|NC_002695.1| 6065 . C T 5384.77 PASS AC=2;AF=1.0;AN=2;DP=161;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.45;BasesToClosestSNP=4136 GT:AD:DP:GQ:PL 1/1:0,161:161:99:5413,427,0 -gi|15829254|ref|NC_002695.1| 10201 . C T 5819.77 PASS AC=2;AF=1.0;AN=2;DP=154;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.21;BasesToClosestSNP=4136 GT:AD:DP:GQ:PL 1/1:0,154:154:99:5848,451,0 -gi|15829254|ref|NC_002695.1| 14114 . A T 6039.77 PASS AC=2;AF=1.0;AN=2;DP=166;Dels=0.0;FS=0.0;HaplotypeScore=1.6229;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.07;BasesToClosestSNP=3913 GT:AD:DP:GQ:PL 1/1:0,166:166:99:6068,469,0 -gi|15829254|ref|NC_002695.1| 15404 . T . 17.31 LowQual AN=2;DP=33;MQ=60.0;MQ0=0 GT:DP 0/0:32 -gi|15829254|ref|NC_002695.1| 18711 . A C 3657.77 PASS AC=2;AF=1.0;AN=2;DP=99;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.28;BasesToClosestSNP=4597 GT:AD:DP:GQ:PL 1/1:0,99:99:99:3686,274,0 -gi|15829254|ref|NC_002695.1| 18968 . G A 6350.77 PASS AC=2;AF=1.0;AN=2;DP=181;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.07;BasesToClosestSNP=257 GT:AD:DP:GQ:PL 1/1:0,181:181:99:6379,470,0 -gi|15829254|ref|NC_002695.1| 47847 . C T 4038.77 PASS AC=2;AF=1.0;AN=2;DP=113;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.05;BasesToClosestSNP=28879 GT:AD:DP:GQ:PL 1/1:0,113:113:99:4067,313,0 -gi|15829254|ref|NC_002695.1| 48272 . A G 3836.77 PASS AC=2;AF=1.0;AN=2;DP=106;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.18;BasesToClosestSNP=99 GT:AD:DP:GQ:PL 1/1:0,106:106:99:3865,298,0 -gi|15829254|ref|NC_002695.1| 48371 . G A 4075.77 PASS AC=2;AF=1.0;AN=2;DP=106;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=25.66;BasesToClosestSNP=99 GT:AD:DP:GQ:PL 1/1:0,106:106:99:4104,310,0 -gi|15829254|ref|NC_002695.1| 51967 . C T 3137.77 PASS AC=2;AF=1.0;AN=2;DP=97;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.35;BasesToClosestSNP=1748 GT:AD:DP:GQ:PL 1/1:0,96:96:99:3166,259,0 -gi|15829254|ref|NC_002695.1| 53715 . C T 3985.77 PASS AC=2;AF=1.0;AN=2;DP=110;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.04;BasesToClosestSNP=1748 GT:AD:DP:GQ:PL 1/1:0,110:110:99:4014,301,0 -gi|15829254|ref|NC_002695.1| 57677 . T C 3587.77 PASS AC=2;AF=1.0;AN=2;DP=106;Dels=0.0;FS=0.0;HaplotypeScore=1.3302;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.85;BasesToClosestSNP=3962 GT:AD:DP:GQ:PL 1/1:0,106:106:99:3616,283,0 -gi|15829254|ref|NC_002695.1| 63127 . T G 4466.77 PASS AC=2;AF=1.0;AN=2;DP=117;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.14;BasesToClosestSNP=5450 GT:AD:DP:GQ:PL 1/1:0,117:117:99:4495,337,0 -gi|15829254|ref|NC_002695.1| 64020 . A C 872.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.689;DP=248;Dels=0.0;FS=36.815;HaplotypeScore=3.9529;MLEAC=1;MLEAF=0.5;MQ=57.45;MQ0=0;MQRankSum=-2.381;QD=3.52;ReadPosRankSum=-10.71;BasesToClosestSNP=47 GT:AD:DP:GQ:PL 0/1:185,63:236:99:901,0,5685 -gi|15829254|ref|NC_002695.1| 64067 . G C 2096.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.146;DP=209;Dels=0.0;FS=153.841;HaplotypeScore=4.9521;MLEAC=1;MLEAF=0.5;MQ=57.15;MQ0=0;MQRankSum=4.711;QD=10.03;ReadPosRankSum=-7.39;BasesToClosestSNP=47 GT:AD:DP:GQ:PL 0/1:137,72:199:99:2125,0,4003 -gi|15829254|ref|NC_002695.1| 70555 . C T 2890.77 PASS AC=2;AF=1.0;AN=2;DP=85;Dels=0.01;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.01;BasesToClosestSNP=6488 GT:AD:DP:GQ:PL 1/1:0,84:84:99:2919,229,0 -gi|15829254|ref|NC_002695.1| 85412 . G A 5899.77 PASS AC=2;AF=1.0;AN=2;DP=160;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.27;BasesToClosestSNP=14857 GT:AD:DP:GQ:PL 1/1:0,160:160:99:5928,445,0 -gi|15829254|ref|NC_002695.1| 88701 . T C 848.77 PASS AC=2;AF=1.0;AN=2;DP=24;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.62;BasesToClosestSNP=3289 GT:AD:DP:GQ:PL 1/1:0,24:24:66:877,66,0 -gi|15829254|ref|NC_002695.1| 93390 . T G 3211.76 PASS AC=2;AF=1.0;AN=2;BaseQRankSum=1.653;DP=87;Dels=0.0;FS=0.0;HaplotypeScore=3.5473;MLEAC=2;MLEAF=1.0;MQ=59.89;MQ0=0;MQRankSum=1.653;QD=34.49;ReadPosRankSum=1.015;BasesToClosestSNP=4689 GT:AD:DP:GQ:PL 1/1:1,86:86:99:3240,247,0 -gi|15829254|ref|NC_002695.1| 120398 . G A 4149.77 PASS AC=2;AF=1.0;AN=2;DP=109;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.29;BasesToClosestSNP=13502 GT:AD:DP:GQ:PL 1/1:0,109:109:99:4178,313,0 -gi|15829254|ref|NC_002695.1| 133900 . A G 4414.77 PASS AC=2;AF=1.0;AN=2;DP=122;Dels=0.0;FS=0.0;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.13;BasesToClosestSNP=13502 GT:AD:DP:GQ:PL 1/1:0,122:122:99:4443,340,0 -gi|15829254|ref|NC_002695.1| 142584 . T C 4353.77 PASS AC=2;AF=1.0;AN=2;DP=116;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.86;BasesToClosestSNP=295 GT:AD:DP:GQ:PL 1/1:0,116:116:99:4382,331,0 -gi|15829254|ref|NC_002695.1| 142879 . C A 4885.77 PASS AC=2;AF=1.0;AN=2;DP=140;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.9;BasesToClosestSNP=295 GT:AD:DP:GQ:PL 1/1:0,140:140:99:4914,376,0 -gi|15829254|ref|NC_002695.1| 157462 . C T 4419.77 PASS AC=2;AF=1.0;AN=2;DP=121;Dels=0.0;FS=0.0;HaplotypeScore=1.6644;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.08;BasesToClosestSNP=3210 GT:AD:DP:GQ:PL 1/1:0,121:121:99:4448,337,0 -gi|15829254|ref|NC_002695.1| 160672 . T C 5929.77 PASS AC=2;AF=1.0;AN=2;DP=159;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.52;BasesToClosestSNP=3210 GT:AD:DP:GQ:PL 1/1:0,159:159:99:5958,448,0 -gi|15829254|ref|NC_002695.1| 165369 . C T 4012.77 PASS AC=2;AF=1.0;AN=2;DP=116;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.59;BasesToClosestSNP=578 GT:AD:DP:GQ:PL 1/1:0,116:116:99:4041,304,0 -gi|15829254|ref|NC_002695.1| 165947 . A C 2779.77 PASS AC=2;AF=1.0;AN=2;DP=85;Dels=0.0;FS=0.0;HaplotypeScore=4.3247;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.7;BasesToClosestSNP=578 GT:AD:DP:GQ:PL 1/1:0,85:85:99:2808,229,0 -gi|15829254|ref|NC_002695.1| 171915 . T C 3539.77 PASS AC=2;AF=1.0;AN=2;DP=96;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.7;BasesToClosestSNP=5968 GT:AD:DP:GQ:PL 1/1:0,96:96:99:3568,277,0 -gi|15829254|ref|NC_002695.1| 180160 . T C 4020.77 PASS AC=2;AF=1.0;AN=2;DP=109;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.54;BasesToClosestSNP=8245 GT:AD:DP:GQ:PL 1/1:0,109:109:99:4049,307,0 -gi|15829254|ref|NC_002695.1| 184717 . T C 5621.77 PASS AC=2;AF=1.0;AN=2;DP=151;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=25.05;BasesToClosestSNP=1393 GT:AD:DP:GQ:PL 1/1:0,151:151:99:5650,421,0 -gi|15829254|ref|NC_002695.1| 186110 . C T 5816.77 PASS AC=2;AF=1.0;AN=2;DP=155;Dels=0.0;FS=0.0;HaplotypeScore=1.6644;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.83;BasesToClosestSNP=1393 GT:AD:DP:GQ:PL 1/1:0,155:155:99:5845,439,0 -gi|15829254|ref|NC_002695.1| 205552 . C T 3913.77 PASS AC=2;AF=1.0;AN=2;DP=112;Dels=0.0;FS=0.0;HaplotypeScore=2.6603;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.94;BasesToClosestSNP=11905 GT:AD:DP:GQ:PL 1/1:0,112:112:99:3942,304,0 -gi|15829254|ref|NC_002695.1| 217457 . A T 3215.74 PASS AC=2;AF=1.0;AN=2;DP=88;Dels=0.0;FS=0.0;HaplotypeScore=1.6229;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.68;BasesToClosestSNP=11905 GT:AD:DP:GQ:PL 1/1:0,88:88:99:3244,247,0 -gi|15829254|ref|NC_002695.1| 218091 . T C 3066.77 PASS AC=2;AF=1.0;AN=2;DP=81;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.01;BasesToClosestSNP=634 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3095,232,0 -gi|15829254|ref|NC_002695.1| 226900 . A . 284.23 mq_score:50 AN=2;DP=106;MQ=49.79;MQ0=17 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226901 . A . 284.23 mq_score:50 AN=2;DP=106;MQ=49.79;MQ0=17 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226902 . G . 278.23 mq_score:50 AN=2;DP=105;MQ=49.34;MQ0=18 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226903 . A . 275.23 mq_score:50 AN=2;DP=104;MQ=49.22;MQ0=18 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226904 . G . 275.23 mq_score:50 AN=2;DP=106;MQ=48.91;MQ0=19 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226905 . G . 275.23 mq_score:50 AN=2;DP=105;MQ=48.79;MQ0=19 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226906 . A . 284.23 mq_score:50 AN=2;DP=107;MQ=48.64;MQ0=19 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226907 . A . 278.23 mq_score:50 AN=2;DP=107;MQ=48.64;MQ0=19 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226908 . A . 284.23 mq_score:50 AN=2;DP=107;MQ=48.64;MQ0=19 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226909 . G . 281.23 mq_score:50 AN=2;DP=109;MQ=48.19;MQ0=21 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226910 . C . 275.23 mq_score:50 AN=2;DP=111;MQ=47.76;MQ0=23 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 226911 . G . 281.23 mq_score:50 AN=2;DP=112;MQ=47.69;MQ0=23 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 226912 . T . 275.23 mq_score:50 AN=2;DP=109;MQ=47.12;MQ0=23 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226913 . A . 269.23 mq_score:50 AN=2;DP=107;MQ=46.84;MQ0=23 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226914 . A . 260.23 mq_score:50 AN=2;DP=115;MQ=44.48;MQ0=33 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 226915 . T . 269.23 mq_score:50 AN=2;DP=115;MQ=44.48;MQ0=33 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 226916 . A . 266.23 mq_score:50 AN=2;DP=118;MQ=43.91;MQ0=36 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 226917 . T . 272.23 mq_score:50 AN=2;DP=120;MQ=43.85;MQ0=36 GT:DP 0/0:120 -gi|15829254|ref|NC_002695.1| 226918 . A . 215.23 mq_score:50 AN=2;DP=102;MQ=40.35;MQ0=36 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 226919 . C . 227.23 mq_score:50 AN=2;DP=103;MQ=40.35;MQ0=36 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 226920 . G . 218.23 mq_score:50 AN=2;DP=101;MQ=39.86;MQ0=36 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226921 . C . 218.23 mq_score:50 AN=2;DP=101;MQ=39.86;MQ0=36 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226922 . C . 209.23 mq_score:50 AN=2;DP=101;MQ=39.61;MQ0=36 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226923 . A . 199.23 mq_score:50 AN=2;DP=98;MQ=38.82;MQ0=36 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226924 . C . 206.23 mq_score:50 AN=2;DP=98;MQ=38.34;MQ0=37 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226925 . C . 203.23 mq_score:50 AN=2;DP=96;MQ=37.76;MQ0=37 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 226926 . T . 197.23 mq_score:50 AN=2;DP=97;MQ=37.57;MQ0=38 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 226927 . C . 206.23 mq_score:50 AN=2;DP=98;MQ=37.59;MQ0=38 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226928 . G . 206.23 mq_score:50 AN=2;DP=98;MQ=37.59;MQ0=38 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226929 . C . 203.23 mq_score:50 AN=2;DP=98;MQ=37.13;MQ0=39 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226930 . G . 200.23 mq_score:50 AN=2;DP=97;MQ=36.86;MQ0=39 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 226931 . A . 197.23 mq_score:50 AN=2;DP=96;MQ=36.55;MQ0=39 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 226932 . C . 197.23 mq_score:50 AN=2;DP=96;MQ=36.55;MQ0=39 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 226933 . A . 184.23 mq_score:50 AN=2;DP=91;MQ=34.96;MQ0=39 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 226934 . G . 184.23 mq_score:50 AN=2;DP=91;MQ=34.96;MQ0=39 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 226935 . T . 178.23 mq_score:50 AN=2;DP=89;MQ=34.26;MQ0=39 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 226936 . G . 178.23 mq_score:50 AN=2;DP=89;MQ=34.26;MQ0=39 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 226937 . A . 172.23 mq_score:50 AN=2;DP=89;MQ=34.26;MQ0=39 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 226938 . G . 178.23 mq_score:50 AN=2;DP=92;MQ=33.96;MQ0=41 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 226939 . C . 181.23 mq_score:50 AN=2;DP=92;MQ=33.96;MQ0=41 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 226940 . T . 187.23 mq_score:50 AN=2;DP=94;MQ=34.28;MQ0=41 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 226941 . G . 187.23 mq_score:50 AN=2;DP=94;MQ=34.01;MQ0=41 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 226942 . A . 188.23 mq_score:50 AN=2;DP=94;MQ=34.01;MQ0=41 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 226943 . A . 181.23 mq_score:50 AN=2;DP=93;MQ=33.66;MQ0=41 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 226944 . A . 181.23 mq_score:50 AN=2;DP=93;MQ=33.66;MQ0=41 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 226945 . G . 175.23 mq_score:50 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226946 . C . 166.23 mq_score:50 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226947 . C . 175.23 mq_score:50 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226948 . G . 175.23 mq_score:50 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226949 . C . 166.23 mq_score:50 AN=2;DP=88;MQ=31.11;MQ0=42 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 226950 . G . 166.23 mq_score:50 AN=2;DP=88;MQ=31.11;MQ0=42 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 226951 . T . 178.23 mq_score:50 AN=2;DP=93;MQ=31.65;MQ0=42 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 226952 . C . 184.23 mq_score:50 AN=2;DP=94;MQ=31.75;MQ0=42 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 226953 . G . 203.23 mq_score:50 AN=2;DP=101;MQ=32.39;MQ0=42 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226954 . C . 203.23 mq_score:50 AN=2;DP=102;MQ=31.72;MQ0=44 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 226955 . A . 200.23 mq_score:50 AN=2;DP=102;MQ=31.72;MQ0=44 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 226956 . A . 206.23 mq_score:50 AN=2;DP=104;MQ=31.9;MQ0=44 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226957 . C . 206.23 mq_score:50 AN=2;DP=104;MQ=31.9;MQ0=44 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226958 . T . 209.23 mq_score:50 AN=2;DP=102;MQ=32.21;MQ0=42 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 226959 . G . 215.23 mq_score:50 AN=2;DP=106;MQ=32.07;MQ0=44 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226960 . C . 206.23 mq_score:50 AN=2;DP=106;MQ=31.06;MQ0=46 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226961 . T . 197.23 mq_score:50 AN=2;DP=104;MQ=30.31;MQ0=46 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226962 . C . 203.23 mq_score:50 AN=2;DP=105;MQ=30.17;MQ0=47 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226963 . T . 191.23 mq_score:50 AN=2;DP=101;MQ=29.49;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226964 . T . 191.23 mq_score:50 AN=2;DP=101;MQ=29.49;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226965 . T . 191.23 mq_score:50 AN=2;DP=101;MQ=29.49;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226966 . A . 191.23 mq_score:50 AN=2;DP=101;MQ=29.63;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226967 . A . 203.23 mq_score:50 AN=2;DP=105;MQ=30.09;MQ0=47 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226968 . C . 206.23 mq_score:50 AN=2;DP=108;MQ=29.92;MQ0=49 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226969 . A . 194.23 mq_score:50 AN=2;DP=104;MQ=29.2;MQ0=49 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226970 . A . 194.23 mq_score:50 AN=2;DP=106;MQ=28.92;MQ0=51 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226971 . T . 188.23 mq_score:50 AN=2;DP=105;MQ=28.42;MQ0=52 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226972 . T . 188.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226973 . T . 187.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226974 . A . 188.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226975 . T . 185.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226976 . C . 188.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226977 . A . 184.23 mq_score:50 AN=2;DP=107;MQ=27.88;MQ0=55 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226978 . G . 184.23 mq_score:50 AN=2;DP=108;MQ=27.76;MQ0=56 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226979 . A . 181.23 mq_score:50 AN=2;DP=107;MQ=27.62;MQ0=56 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226980 . C . 181.23 mq_score:50 AN=2;DP=109;MQ=27.36;MQ0=58 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226981 . A . 172.23 mq_score:50 AN=2;DP=106;MQ=26.92;MQ0=58 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226982 . A . 178.23 mq_score:50 AN=2;DP=108;MQ=27.22;MQ0=58 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226983 . T . 178.23 mq_score:50 AN=2;DP=109;MQ=27.09;MQ0=59 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226984 . C . 178.23 mq_score:50 AN=2;DP=113;MQ=26.61;MQ0=63 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 226985 . T . 175.23 mq_score:50 AN=2;DP=110;MQ=26.7;MQ0=61 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 226986 . G . 175.23 mq_score:50 AN=2;DP=111;MQ=26.58;MQ0=62 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 226987 . T . 172.23 mq_score:50 AN=2;DP=108;MQ=26.67;MQ0=60 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226988 . G . 172.23 mq_score:50 AN=2;DP=108;MQ=26.67;MQ0=60 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226989 . T . 169.23 mq_score:50 AN=2;DP=105;MQ=26.76;MQ0=58 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226990 . G . 166.23 mq_score:50 AN=2;DP=105;MQ=26.76;MQ0=58 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226991 . G . 166.23 mq_score:50 AN=2;DP=105;MQ=26.48;MQ0=59 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226992 . G . 157.23 mq_score:50 AN=2;DP=104;MQ=26.31;MQ0=59 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226993 . C . 160.23 mq_score:50 AN=2;DP=105;MQ=26.19;MQ0=60 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226994 . A . 151.23 mq_score:50 AN=2;DP=104;MQ=26.31;MQ0=59 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226995 . C . 157.23 mq_score:50 AN=2;DP=106;MQ=25.48;MQ0=63 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226996 . T . 154.23 mq_score:50 AN=2;DP=104;MQ=25.42;MQ0=62 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226997 . C . 151.23 mq_score:50 AN=2;DP=106;MQ=25.18;MQ0=64 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226998 . G . 151.23 mq_score:50 AN=2;DP=105;MQ=25.3;MQ0=63 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226999 . A . 154.23 mq_score:50 AN=2;DP=104;MQ=25.42;MQ0=62 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227000 . A . 151.23 mq_score:50 AN=2;DP=103;MQ=25.24;MQ0=62 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227001 . G . 151.23 mq_score:50 AN=2;DP=103;MQ=25.24;MQ0=62 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227002 . A . 151.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227003 . T . 148.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227004 . A . 142.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227005 . C . 148.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227006 . G . 148.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227007 . G . 148.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227008 . A . 151.23 mq_score:50 AN=2;DP=101;MQ=25.49;MQ0=60 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227009 . T . 151.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227010 . T . 151.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227011 . C . 148.23 mq_score:50 AN=2;DP=103;MQ=24.93;MQ0=63 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227012 . T . 145.23 mq_score:50 AN=2;DP=102;MQ=24.73;MQ0=63 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227013 . T . 145.23 mq_score:50 AN=2;DP=102;MQ=24.73;MQ0=63 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227014 . A . 145.23 mq_score:50 AN=2;DP=94;MQ=25.76;MQ0=55 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227015 . A . 145.23 mq_score:50 AN=2;DP=93;MQ=25.9;MQ0=54 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227016 . C . 145.23 mq_score:50 AN=2;DP=92;MQ=26.38;MQ0=52 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227017 . G . 142.23 mq_score:50 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227018 . T . 142.23 mq_score:50 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227019 . C . 142.23 mq_score:50 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227020 . G . 145.23 mq_score:50 AN=2;DP=92;MQ=26.04;MQ0=53 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227021 . C . 148.23 mq_score:50 AN=2;DP=92;MQ=26.38;MQ0=52 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227022 . A . 142.23 mq_score:50 AN=2;DP=91;MQ=26.19;MQ0=52 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227023 . A . 145.23 mq_score:50 AN=2;DP=91;MQ=26.19;MQ0=52 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227024 . G . 145.23 mq_score:50 AN=2;DP=90;MQ=26.33;MQ0=51 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227025 . A . 145.23 mq_score:50 AN=2;DP=90;MQ=26.33;MQ0=51 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227026 . C . 145.23 mq_score:50 AN=2;DP=90;MQ=26.33;MQ0=51 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227027 . G . 142.23 mq_score:50 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227028 . A . 142.23 mq_score:50 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227029 . A . 142.23 mq_score:50 AN=2;DP=89;MQ=26.14;MQ0=51 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227030 . A . 142.23 mq_score:50 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227031 . A . 145.23 mq_score:50 AN=2;DP=94;MQ=25.76;MQ0=55 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227032 . A . 145.23 mq_score:50 AN=2;DP=97;MQ=25.36;MQ0=58 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227033 . T . 145.23 mq_score:50 AN=2;DP=98;MQ=25.23;MQ0=59 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227034 . G . 145.23 mq_score:50 AN=2;DP=98;MQ=25.23;MQ0=59 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227035 . A . 145.23 mq_score:50 AN=2;DP=98;MQ=25.23;MQ0=59 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227036 . A . 148.23 mq_score:50 AN=2;DP=99;MQ=25.43;MQ0=59 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227037 . T . 148.23 mq_score:50 AN=2;DP=100;MQ=25.61;MQ0=59 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227038 . A . 142.23 mq_score:50 AN=2;DP=99;MQ=25.43;MQ0=59 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227039 . C . 148.23 mq_score:50 AN=2;DP=101;MQ=25.49;MQ0=60 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227040 . C . 142.23 mq_score:50 AN=2;DP=98;MQ=24.91;MQ0=60 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227041 . A . 139.23 mq_score:50 AN=2;DP=97;MQ=24.7;MQ0=60 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227042 . A . 139.23 mq_score:50 AN=2;DP=100;MQ=24.33;MQ0=63 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227043 . G . 139.23 mq_score:50 AN=2;DP=105;MQ=23.74;MQ0=68 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227044 . T . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227045 . C . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227046 . T . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227047 . C . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227048 . A . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227049 . A . 136.23 mq_score:50 AN=2;DP=107;MQ=23.2;MQ0=71 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227050 . G . 136.23 mq_score:50 AN=2;DP=107;MQ=23.2;MQ0=71 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227051 . A . 115.23 mq_score:50 AN=2;DP=100;MQ=21.54;MQ0=71 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227052 . G . 115.23 mq_score:50 AN=2;DP=100;MQ=21.54;MQ0=71 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227053 . T . 100.23 mq_score:50 AN=2;DP=92;MQ=20.43;MQ0=68 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227054 . G . 103.23 mq_score:50 AN=2;DP=92;MQ=20.85;MQ0=67 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227055 . A . 106.23 mq_score:50 AN=2;DP=97;MQ=20.71;MQ0=71 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227056 . A . 106.23 mq_score:50 AN=2;DP=102;MQ=19.96;MQ0=76 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227057 . C . 103.23 mq_score:50 AN=2;DP=104;MQ=19.76;MQ0=78 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227058 . A . 100.23 mq_score:50 AN=2;DP=106;MQ=19.19;MQ0=81 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227059 . C . 100.23 mq_score:50 AN=2;DP=105;MQ=18.88;MQ0=81 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227060 . G . 100.23 mq_score:50 AN=2;DP=103;MQ=19.06;MQ0=79 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227061 . T . 97.23 mq_score:50 AN=2;DP=103;MQ=19.06;MQ0=79 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227062 . A . 100.23 mq_score:50 AN=2;DP=102;MQ=19.15;MQ0=78 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227063 . A . 97.23 mq_score:50 AN=2;DP=106;MQ=18.79;MQ0=82 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227064 . T . 97.23 mq_score:50 AN=2;DP=106;MQ=18.79;MQ0=82 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227065 . T . 100.23 mq_score:50 AN=2;DP=108;MQ=18.62;MQ0=84 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227066 . C . 97.23 mq_score:50 AN=2;DP=106;MQ=18.38;MQ0=83 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227067 . A . 79.23 mq_score:50 AN=2;DP=99;MQ=16.76;MQ0=81 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227068 . T . 82.23 mq_score:50 AN=2;DP=98;MQ=16.85;MQ0=80 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227069 . T . 82.23 mq_score:50 AN=2;DP=99;MQ=16.76;MQ0=81 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227070 . A . 82.23 mq_score:50 AN=2;DP=97;MQ=16.94;MQ0=79 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227071 . C . 82.23 mq_score:50 AN=2;DP=95;MQ=17.11;MQ0=77 GT:DP 0/0:95 -gi|15829254|ref|NC_002695.1| 227072 . G . 82.23 mq_score:50 AN=2;DP=93;MQ=17.3;MQ0=75 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227073 . A . 82.23 mq_score:50 AN=2;DP=93;MQ=17.3;MQ0=75 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227074 . A . 82.23 mq_score:50 AN=2;DP=93;MQ=17.3;MQ0=75 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227075 . G . 82.23 mq_score:50 AN=2;DP=97;MQ=16.94;MQ0=79 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227076 . T . 82.23 mq_score:50 AN=2;DP=97;MQ=16.94;MQ0=79 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227077 . T . 85.23 mq_score:50 AN=2;DP=98;MQ=17.33;MQ0=79 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227078 . T . 85.23 mq_score:50 AN=2;DP=97;MQ=17.42;MQ0=78 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227079 . A . 85.23 mq_score:50 AN=2;DP=102;MQ=16.98;MQ0=83 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227080 . A . 85.23 mq_score:50 AN=2;DP=100;MQ=17.15;MQ0=81 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227081 . T . 85.23 mq_score:50 AN=2;DP=99;MQ=17.24;MQ0=80 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227082 . T . 76.23 mq_score:50 AN=2;DP=97;MQ=16.44;MQ0=80 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227083 . C . 79.23 mq_score:50 AN=2;DP=95;MQ=16.61;MQ0=78 GT:DP 0/0:95 -gi|15829254|ref|NC_002695.1| 227084 . T . 79.23 mq_score:50 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227085 . T . 79.23 mq_score:50 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227086 . T . 79.23 mq_score:50 AN=2;DP=94;MQ=16.7;MQ0=77 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227087 . G . 76.23 mq_score:50 AN=2;DP=94;MQ=16.7;MQ0=77 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227088 . A . 79.23 mq_score:50 AN=2;DP=94;MQ=16.7;MQ0=77 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227089 . G . 76.23 mq_score:50 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227090 . C . 79.23 mq_score:50 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227091 . A . 76.23 mq_score:50 AN=2;DP=91;MQ=16.45;MQ0=75 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227092 . T . 76.23 mq_score:50 AN=2;DP=91;MQ=16.45;MQ0=75 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227093 . C . 76.23 mq_score:50 AN=2;DP=89;MQ=16.63;MQ0=73 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227094 . A . 76.23 mq_score:50 AN=2;DP=88;MQ=16.73;MQ0=72 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227095 . A . 73.23 mq_score:50 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227096 . A . 70.23 mq_score:50 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227097 . C . 76.23 mq_score:50 AN=2;DP=86;MQ=16.92;MQ0=70 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227098 . T . 76.23 mq_score:50 AN=2;DP=86;MQ=16.92;MQ0=70 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227099 . T . 73.23 mq_score:50 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227100 . T . 73.23 mq_score:50 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227101 . T . 76.23 mq_score:50 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227102 . A . 79.23 mq_score:50 AN=2;DP=86;MQ=17.46;MQ0=69 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227103 . A . 76.23 mq_score:50 AN=2;DP=85;MQ=17.57;MQ0=68 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227104 . A . 82.23 mq_score:50 AN=2;DP=86;MQ=17.99;MQ0=68 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227105 . T . 79.23 mq_score:50 AN=2;DP=86;MQ=17.99;MQ0=68 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227106 . T . 73.23 mq_score:50 AN=2;DP=84;MQ=17.12;MQ0=68 GT:DP 0/0:84 -gi|15829254|ref|NC_002695.1| 227107 . G . 73.23 mq_score:50 AN=2;DP=84;MQ=17.12;MQ0=68 GT:DP 0/0:84 -gi|15829254|ref|NC_002695.1| 227108 . A . 70.23 mq_score:50 AN=2;DP=83;MQ=16.66;MQ0=68 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227109 . A . 70.23 mq_score:50 AN=2;DP=80;MQ=16.97;MQ0=65 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227110 . G . 73.23 mq_score:50 AN=2;DP=85;MQ=16.46;MQ0=70 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227111 . A . 70.23 mq_score:50 AN=2;DP=83;MQ=16.66;MQ0=68 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227112 . G . 70.23 mq_score:50 AN=2;DP=86;MQ=16.36;MQ0=71 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227113 . T . 70.23 mq_score:50 AN=2;DP=88;MQ=16.18;MQ0=73 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227114 . T . 73.23 mq_score:50 AN=2;DP=88;MQ=16.18;MQ0=73 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227115 . T . 73.23 mq_score:50 AN=2;DP=90;MQ=15.99;MQ0=75 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227116 . G . 70.23 mq_score:50 AN=2;DP=89;MQ=15.52;MQ0=75 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227117 . A . 70.23 mq_score:50 AN=2;DP=89;MQ=15.52;MQ0=75 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227118 . T . 70.23 mq_score:50 AN=2;DP=91;MQ=15.34;MQ0=77 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227119 . C . 67.23 mq_score:50 AN=2;DP=90;MQ=14.84;MQ0=77 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227120 . A . 70.23 mq_score:50 AN=2;DP=92;MQ=15.26;MQ0=78 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227121 . T . 67.23 mq_score:50 AN=2;DP=91;MQ=14.76;MQ0=78 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227122 . G . 76.23 mq_score:50 AN=2;DP=101;MQ=15.3;MQ0=85 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227123 . G . 76.23 mq_score:50 AN=2;DP=101;MQ=15.3;MQ0=85 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227124 . C . 76.23 mq_score:50 AN=2;DP=101;MQ=15.3;MQ0=85 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227125 . T . 82.23 mq_score:50 AN=2;DP=104;MQ=16.07;MQ0=86 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227126 . C . 82.23 mq_score:50 AN=2;DP=106;MQ=15.92;MQ0=88 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227127 . A . 82.23 mq_score:50 AN=2;DP=107;MQ=15.84;MQ0=89 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227128 . G . 82.23 mq_score:50 AN=2;DP=107;MQ=15.84;MQ0=89 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227129 . A . 79.23 mq_score:50 AN=2;DP=106;MQ=15.92;MQ0=88 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227130 . T . 85.23 mq_score:50 AN=2;DP=106;MQ=16.38;MQ0=87 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227131 . T . 85.23 mq_score:50 AN=2;DP=105;MQ=16.46;MQ0=86 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227132 . G . 82.23 mq_score:50 AN=2;DP=105;MQ=16.46;MQ0=86 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227133 . A . 85.23 mq_score:50 AN=2;DP=105;MQ=16.46;MQ0=86 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227134 . A . 85.23 mq_score:50 AN=2;DP=106;MQ=16.38;MQ0=87 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227135 . C . 85.23 mq_score:50 AN=2;DP=106;MQ=16.38;MQ0=87 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227136 . G . 76.23 mq_score:50 AN=2;DP=104;MQ=15.58;MQ0=87 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227137 . C . 73.23 mq_score:50 AN=2;DP=102;MQ=15.23;MQ0=86 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227138 . T . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227139 . G . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227140 . G . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227141 . C . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227142 . G . 76.23 mq_score:50 AN=2;DP=97;MQ=15.61;MQ0=81 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227143 . G . 76.23 mq_score:50 AN=2;DP=93;MQ=15.95;MQ0=77 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227144 . C . 76.23 mq_score:50 AN=2;DP=92;MQ=16.03;MQ0=76 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227145 . A . 76.23 mq_score:50 AN=2;DP=93;MQ=15.95;MQ0=77 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227146 . G . 76.23 mq_score:50 AN=2;DP=97;MQ=15.61;MQ0=81 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227147 . G . 76.23 mq_score:50 AN=2;DP=97;MQ=15.61;MQ0=81 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227148 . C . 73.23 mq_score:50 AN=2;DP=96;MQ=15.7;MQ0=80 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227149 . C . 76.23 mq_score:50 AN=2;DP=96;MQ=15.7;MQ0=80 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227150 . T . 76.23 mq_score:50 AN=2;DP=96;MQ=15.7;MQ0=80 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227151 . A . 76.23 mq_score:50 AN=2;DP=98;MQ=15.53;MQ0=82 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227152 . A . 76.23 mq_score:50 AN=2;DP=98;MQ=15.53;MQ0=82 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227153 . C . 76.23 mq_score:50 AN=2;DP=98;MQ=15.53;MQ0=82 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227154 . A . 73.23 mq_score:50 AN=2;DP=97;MQ=15.08;MQ0=82 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227155 . C . 73.23 mq_score:50 AN=2;DP=96;MQ=15.16;MQ0=81 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227156 . A . 70.23 mq_score:50 AN=2;DP=92;MQ=15.26;MQ0=78 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227157 . T . 67.23 mq_score:50 AN=2;DP=90;MQ=15.43;MQ0=76 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227158 . G . 70.23 mq_score:50 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227159 . C . 70.23 mq_score:50 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227160 . A . 70.23 mq_score:50 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227161 . A . 70.23 mq_score:50 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227162 . G . 70.23 mq_score:50 AN=2;DP=88;MQ=15.6;MQ0=74 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227163 . T . 79.23 mq_score:50 AN=2;DP=90;MQ=17.07;MQ0=73 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227164 . C . 79.23 mq_score:50 AN=2;DP=90;MQ=17.07;MQ0=73 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227165 . G . 79.23 mq_score:50 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227166 . A . 79.23 mq_score:50 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227167 . A . 79.23 mq_score:50 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227168 . C . 79.23 mq_score:50 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227169 . G . 79.23 mq_score:50 AN=2;DP=88;MQ=17.26;MQ0=71 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227170 . G . 79.23 mq_score:50 AN=2;DP=92;MQ=16.88;MQ0=75 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227171 . T . 79.23 mq_score:50 AN=2;DP=92;MQ=16.88;MQ0=75 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227172 . A . 79.23 mq_score:50 AN=2;DP=92;MQ=16.88;MQ0=75 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227173 . A . 85.23 mq_score:50 AN=2;DP=94;MQ=17.69;MQ0=75 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227174 . C . 85.23 mq_score:50 AN=2;DP=94;MQ=17.69;MQ0=75 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227175 . A . 88.23 mq_score:50 AN=2;DP=92;MQ=18.1;MQ0=72 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227176 . G . 88.23 mq_score:50 AN=2;DP=94;MQ=17.91;MQ0=74 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227177 . G . 85.23 mq_score:50 AN=2;DP=98;MQ=17.07;MQ0=79 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227178 . A . 85.23 mq_score:50 AN=2;DP=98;MQ=17.07;MQ0=79 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227179 . A . 85.23 mq_score:50 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227180 . G . 85.23 mq_score:50 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227181 . A . 85.23 mq_score:50 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227182 . A . 85.23 mq_score:50 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227183 . G . 85.23 mq_score:50 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227184 . C . 85.23 mq_score:50 AN=2;DP=91;MQ=17.71;MQ0=72 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227185 . T . 85.23 mq_score:50 AN=2;DP=91;MQ=17.71;MQ0=72 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227186 . T . 85.23 mq_score:50 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227187 . G . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227188 . C . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227189 . T . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227190 . T . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227191 . C . 82.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227192 . T . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227193 . T . 82.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227194 . T . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227195 . G . 85.23 mq_score:50 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227196 . C . 85.23 mq_score:50 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227197 . T . 85.23 mq_score:50 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227198 . G . 85.23 mq_score:50 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227199 . A . 85.23 mq_score:50 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227200 . C . 85.23 mq_score:50 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227201 . G . 85.23 mq_score:50 AN=2;DP=88;MQ=18.01;MQ0=69 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227202 . A . 85.23 mq_score:50 AN=2;DP=88;MQ=18.01;MQ0=69 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227203 . G . 85.23 mq_score:50 AN=2;DP=88;MQ=18.01;MQ0=69 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227204 . T . 82.23 mq_score:50 AN=2;DP=87;MQ=17.6;MQ0=69 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227205 . G . 82.23 mq_score:50 AN=2;DP=87;MQ=17.6;MQ0=69 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227206 . G . 82.23 mq_score:50 AN=2;DP=87;MQ=17.6;MQ0=69 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227207 . C . 82.23 mq_score:50 AN=2;DP=88;MQ=17.5;MQ0=70 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227208 . G . 85.23 mq_score:50 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227209 . G . 85.23 mq_score:50 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227210 . A . 85.23 mq_score:50 AN=2;DP=82;MQ=18.66;MQ0=63 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227211 . C . 85.23 mq_score:50 AN=2;DP=82;MQ=18.66;MQ0=63 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227212 . G . 85.23 mq_score:50 AN=2;DP=80;MQ=18.89;MQ0=61 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227213 . G . 85.23 mq_score:50 AN=2;DP=79;MQ=19.01;MQ0=60 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227214 . G . 85.23 mq_score:50 AN=2;DP=79;MQ=19.01;MQ0=60 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227215 . T . 85.23 mq_score:50 AN=2;DP=74;MQ=19.64;MQ0=55 GT:DP 0/0:74 -gi|15829254|ref|NC_002695.1| 227216 . G . 88.23 mq_score:50 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:76 -gi|15829254|ref|NC_002695.1| 227217 . A . 88.23 mq_score:50 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:76 -gi|15829254|ref|NC_002695.1| 227218 . G . 88.23 mq_score:50 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:76 -gi|15829254|ref|NC_002695.1| 227219 . T . 88.23 mq_score:50 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:75 -gi|15829254|ref|NC_002695.1| 227220 . A . 82.23 mq_score:50 AN=2;DP=73;MQ=19.22;MQ0=55 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227221 . A . 82.23 mq_score:50 AN=2;DP=73;MQ=19.22;MQ0=55 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227222 . T . 73.23 mq_score:50 AN=2;DP=63;MQ=19.16;MQ0=48 GT:DP 0/0:63 -gi|15829254|ref|NC_002695.1| 227223 . G . 73.23 mq_score:50 AN=2;DP=65;MQ=18.86;MQ0=50 GT:DP 0/0:64 -gi|15829254|ref|NC_002695.1| 227224 . T . 70.23 mq_score:50 AN=2;DP=65;MQ=18.86;MQ0=50 GT:DP 0/0:65 -gi|15829254|ref|NC_002695.1| 227225 . C . 67.23 mq_score:50 AN=2;DP=61;MQ=18.07;MQ0=48 GT:DP 0/0:61 -gi|15829254|ref|NC_002695.1| 227226 . T . 67.23 mq_score:50 AN=2;DP=58;MQ=18.54;MQ0=45 GT:DP 0/0:58 -gi|15829254|ref|NC_002695.1| 227227 . G . 67.23 mq_score:50 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227228 . G . 67.23 mq_score:50 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227229 . G . 64.23 mq_score:50 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227230 . A . 64.23 mq_score:50 AN=2;DP=55;MQ=18.26;MQ0=43 GT:DP 0/0:55 -gi|15829254|ref|NC_002695.1| 227231 . A . 58.23 mq_score:50 AN=2;DP=53;MQ=17.77;MQ0=42 GT:DP 0/0:53 -gi|15829254|ref|NC_002695.1| 227232 . A . 61.23 mq_score:50 AN=2;DP=49;MQ=18.48;MQ0=38 GT:DP 0/0:49 -gi|15829254|ref|NC_002695.1| 227233 . C . 61.23 mq_score:50 AN=2;DP=49;MQ=18.48;MQ0=38 GT:DP 0/0:49 -gi|15829254|ref|NC_002695.1| 227234 . T . 61.23 mq_score:50 AN=2;DP=48;MQ=18.67;MQ0=37 GT:DP 0/0:48 -gi|15829254|ref|NC_002695.1| 227235 . G . 61.23 mq_score:50 AN=2;DP=50;MQ=18.29;MQ0=39 GT:DP 0/0:48 -gi|15829254|ref|NC_002695.1| 227236 . C . 61.23 mq_score:50 AN=2;DP=50;MQ=18.29;MQ0=39 GT:DP 0/0:50 -gi|15829254|ref|NC_002695.1| 227237 . C . 64.23 mq_score:50 AN=2;DP=51;MQ=18.96;MQ0=39 GT:DP 0/0:51 -gi|15829254|ref|NC_002695.1| 227238 . T . 64.23 mq_score:50 AN=2;DP=51;MQ=18.96;MQ0=39 GT:DP 0/0:51 -gi|15829254|ref|NC_002695.1| 227239 . G . 64.23 mq_score:50 AN=2;DP=52;MQ=18.77;MQ0=40 GT:DP 0/0:52 -gi|15829254|ref|NC_002695.1| 227240 . A . 64.23 mq_score:50 AN=2;DP=54;MQ=18.42;MQ0=42 GT:DP 0/0:54 -gi|15829254|ref|NC_002695.1| 227241 . T . 61.23 mq_score:50 AN=2;DP=54;MQ=18.42;MQ0=42 GT:DP 0/0:54 -gi|15829254|ref|NC_002695.1| 227242 . G . 64.23 mq_score:50 AN=2;DP=53;MQ=18.6;MQ0=41 GT:DP 0/0:53 -gi|15829254|ref|NC_002695.1| 227243 . G . 64.23 mq_score:50 AN=2;DP=52;MQ=18.77;MQ0=40 GT:DP 0/0:52 -gi|15829254|ref|NC_002695.1| 227244 . A . 64.23 mq_score:50 AN=2;DP=50;MQ=19.15;MQ0=38 GT:DP 0/0:50 -gi|15829254|ref|NC_002695.1| 227245 . G . 67.23 mq_score:50 AN=2;DP=51;MQ=19.77;MQ0=38 GT:DP 0/0:51 -gi|15829254|ref|NC_002695.1| 227246 . A . 67.23 mq_score:50 AN=2;DP=48;MQ=20.38;MQ0=35 GT:DP 0/0:48 -gi|15829254|ref|NC_002695.1| 227247 . G . 67.23 mq_score:50 AN=2;DP=56;MQ=18.86;MQ0=43 GT:DP 0/0:56 -gi|15829254|ref|NC_002695.1| 227248 . G . 67.23 mq_score:50 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227249 . G . 67.23 mq_score:50 AN=2;DP=58;MQ=18.54;MQ0=45 GT:DP 0/0:58 -gi|15829254|ref|NC_002695.1| 227250 . A . 67.23 mq_score:50 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227251 . T . 70.23 mq_score:50 AN=2;DP=62;MQ=18.63;MQ0=48 GT:DP 0/0:62 -gi|15829254|ref|NC_002695.1| 227252 . A . 70.23 mq_score:50 AN=2;DP=63;MQ=18.49;MQ0=49 GT:DP 0/0:63 -gi|15829254|ref|NC_002695.1| 227253 . A . 70.23 mq_score:50 AN=2;DP=63;MQ=18.49;MQ0=49 GT:DP 0/0:63 -gi|15829254|ref|NC_002695.1| 227254 . C . 70.23 mq_score:50 AN=2;DP=64;MQ=18.34;MQ0=50 GT:DP 0/0:64 -gi|15829254|ref|NC_002695.1| 227255 . T . 67.23 mq_score:50 AN=2;DP=60;MQ=18.22;MQ0=47 GT:DP 0/0:60 -gi|15829254|ref|NC_002695.1| 227256 . A . 64.23 mq_score:50 AN=2;DP=61;MQ=17.33;MQ0=49 GT:DP 0/0:61 -gi|15829254|ref|NC_002695.1| 227257 . C . 64.23 mq_score:50 AN=2;DP=66;MQ=16.66;MQ0=54 GT:DP 0/0:66 -gi|15829254|ref|NC_002695.1| 227258 . T . 67.23 mq_score:50 AN=2;DP=67;MQ=17.25;MQ0=54 GT:DP 0/0:67 -gi|15829254|ref|NC_002695.1| 227259 . G . 67.23 mq_score:50 AN=2;DP=68;MQ=17.12;MQ0=55 GT:DP 0/0:68 -gi|15829254|ref|NC_002695.1| 227260 . G . 67.23 mq_score:50 AN=2;DP=70;MQ=16.87;MQ0=57 GT:DP 0/0:70 -gi|15829254|ref|NC_002695.1| 227261 . A . 70.23 mq_score:50 AN=2;DP=73;MQ=17.17;MQ0=59 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227262 . A . 70.23 mq_score:50 AN=2;DP=73;MQ=17.17;MQ0=59 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227263 . A . 61.23 mq_score:50 AN=2;DP=67;MQ=15.8;MQ0=56 GT:DP 0/0:67 -gi|15829254|ref|NC_002695.1| 227264 . C . 61.23 mq_score:50 AN=2;DP=70;MQ=15.46;MQ0=59 GT:DP 0/0:70 -gi|15829254|ref|NC_002695.1| 227265 . G . 61.23 mq_score:50 AN=2;DP=69;MQ=15.57;MQ0=58 GT:DP 0/0:69 -gi|15829254|ref|NC_002695.1| 227266 . G . 61.23 mq_score:50 AN=2;DP=73;MQ=15.14;MQ0=62 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227267 . T . 61.23 mq_score:50 AN=2;DP=73;MQ=15.14;MQ0=62 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227268 . A . 61.23 mq_score:50 AN=2;DP=83;MQ=14.2;MQ0=72 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227269 . G . 61.23 mq_score:50 AN=2;DP=83;MQ=14.2;MQ0=72 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227270 . C . 61.23 mq_score:50 AN=2;DP=82;MQ=14.28;MQ0=71 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227271 . T . 61.23 mq_score:50 AN=2;DP=82;MQ=14.28;MQ0=71 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227272 . A . 61.23 mq_score:50 AN=2;DP=82;MQ=14.28;MQ0=71 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227273 . A . 55.23 mq_score:50 AN=2;DP=81;MQ=12.92;MQ0=72 GT:DP 0/0:81 -gi|15829254|ref|NC_002695.1| 227274 . T . 55.23 mq_score:50 AN=2;DP=83;MQ=12.77;MQ0=74 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227275 . A . 49.23 mq_score:50 AN=2;DP=82;MQ=12.49;MQ0=74 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227276 . C . 52.23 mq_score:50 AN=2;DP=82;MQ=12.49;MQ0=74 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227277 . C . 52.23 mq_score:50 AN=2;DP=77;MQ=12.89;MQ0=69 GT:DP 0/0:77 -gi|15829254|ref|NC_002695.1| 227278 . G . 52.23 mq_score:50 AN=2;DP=79;MQ=12.73;MQ0=71 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227279 . C . 55.23 mq_score:50 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227280 . A . 55.23 mq_score:50 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227281 . T . 55.23 mq_score:50 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227282 . A . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227283 . A . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227284 . C . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227285 . G . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227286 . T . 55.23 mq_score:50 AN=2;DP=79;MQ=13.5;MQ0=70 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227287 . C . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227288 . G . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227289 . C . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:77 -gi|15829254|ref|NC_002695.1| 227290 . A . 55.23 mq_score:50 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227291 . A . 55.23 mq_score:50 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227292 . G . 55.23 mq_score:50 AN=2;DP=87;MQ=12.87;MQ0=78 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227293 . A . 52.23 mq_score:50 AN=2;DP=94;MQ=12.38;MQ0=85 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227294 . C . 55.23 mq_score:50 AN=2;DP=95;MQ=12.31;MQ0=86 GT:DP 0/0:95 -gi|15829254|ref|NC_002695.1| 227295 . C . 55.23 mq_score:50 AN=2;DP=96;MQ=12.25;MQ0=87 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227296 . A . 55.23 mq_score:50 AN=2;DP=96;MQ=12.25;MQ0=87 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227297 . A . 55.23 mq_score:50 AN=2;DP=97;MQ=12.18;MQ0=88 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227298 . A . 55.23 mq_score:50 AN=2;DP=97;MQ=12.18;MQ0=88 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227299 . G . 55.23 mq_score:50 AN=2;DP=101;MQ=11.94;MQ0=92 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227300 . A . 55.23 mq_score:50 AN=2;DP=101;MQ=11.94;MQ0=92 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227301 . G . 55.23 mq_score:50 AN=2;DP=100;MQ=12.0;MQ0=91 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227302 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227303 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227304 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227305 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227306 . A . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227307 . C . 55.23 mq_score:50 AN=2;DP=107;MQ=11.6;MQ0=98 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227308 . C . 52.23 mq_score:50 AN=2;DP=106;MQ=10.99;MQ0=98 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227309 . T . 52.23 mq_score:50 AN=2;DP=109;MQ=10.84;MQ0=101 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227310 . T . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227311 . C . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227312 . G . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227313 . G . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227314 . G . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227315 . C . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227316 . C . 49.23 mq_score:50 AN=2;DP=108;MQ=10.18;MQ0=101 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227317 . T . 49.23 mq_score:50 AN=2;DP=106;MQ=10.28;MQ0=99 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227318 . C . 49.23 mq_score:50 AN=2;DP=107;MQ=10.23;MQ0=100 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227319 . T . 49.23 mq_score:50 AN=2;DP=107;MQ=10.23;MQ0=100 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227320 . T . 49.23 mq_score:50 AN=2;DP=108;MQ=10.18;MQ0=101 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227321 . G . 49.23 mq_score:50 AN=2;DP=108;MQ=10.18;MQ0=101 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227322 . C . 49.23 mq_score:50 AN=2;DP=107;MQ=10.23;MQ0=100 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227323 . C . 49.23 mq_score:50 AN=2;DP=106;MQ=10.28;MQ0=99 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227324 . A . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227325 . T . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227326 . C . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227327 . G . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227328 . G . 49.23 mq_score:50 AN=2;DP=111;MQ=10.04;MQ0=104 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227329 . A . 49.23 mq_score:50 AN=2;DP=112;MQ=10.0;MQ0=105 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227330 . T . 49.23 mq_score:50 AN=2;DP=113;MQ=9.96;MQ0=106 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227331 . G . 49.23 mq_score:50 AN=2;DP=115;MQ=9.87;MQ0=108 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227332 . T . 49.23 mq_score:50 AN=2;DP=115;MQ=9.87;MQ0=108 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227333 . G . 49.23 mq_score:50 AN=2;DP=117;MQ=9.78;MQ0=110 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227334 . C . 49.23 mq_score:50 AN=2;DP=117;MQ=9.78;MQ0=110 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227335 . C . 49.23 mq_score:50 AN=2;DP=116;MQ=9.83;MQ0=109 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227336 . C . 49.23 mq_score:50 AN=2;DP=116;MQ=9.83;MQ0=109 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227337 . A . 46.23 mq_score:50 AN=2;DP=116;MQ=9.1;MQ0=110 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227338 . G . 46.23 mq_score:50 AN=2;DP=117;MQ=9.06;MQ0=111 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227339 . A . 46.23 mq_score:50 AN=2;DP=116;MQ=9.1;MQ0=110 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227340 . T . 46.23 mq_score:50 AN=2;DP=115;MQ=9.14;MQ0=109 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227341 . G . 46.23 mq_score:50 AN=2;DP=116;MQ=9.1;MQ0=110 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227342 . G . 49.23 mq_score:50 AN=2;DP=129;MQ=9.32;MQ0=122 GT:DP 0/0:129 -gi|15829254|ref|NC_002695.1| 227343 . G . 49.23 mq_score:50 AN=2;DP=129;MQ=9.32;MQ0=122 GT:DP 0/0:129 -gi|15829254|ref|NC_002695.1| 227344 . A . 49.23 mq_score:50 AN=2;DP=129;MQ=9.32;MQ0=122 GT:DP 0/0:129 -gi|15829254|ref|NC_002695.1| 227345 . T . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227346 . T . 43.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:127 -gi|15829254|ref|NC_002695.1| 227347 . A . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227348 . G . 46.23 mq_score:50 AN=2;DP=127;MQ=8.69;MQ0=121 GT:DP 0/0:127 -gi|15829254|ref|NC_002695.1| 227349 . C . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227350 . T . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227351 . A . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227352 . G . 43.23 mq_score:50 AN=2;DP=124;MQ=8.03;MQ0=119 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227353 . T . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227354 . A . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227355 . G . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227356 . G . 43.23 mq_score:50 AN=2;DP=123;MQ=8.06;MQ0=118 GT:DP 0/0:123 -gi|15829254|ref|NC_002695.1| 227357 . T . 46.23 mq_score:50 AN=2;DP=119;MQ=8.98;MQ0=113 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227358 . G . 43.23 mq_score:50 AN=2;DP=117;MQ=8.27;MQ0=112 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227359 . G . 43.23 mq_score:50 AN=2;DP=121;MQ=8.13;MQ0=116 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227360 . G . 43.23 mq_score:50 AN=2;DP=119;MQ=8.2;MQ0=114 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227361 . G . 40.23 mq_score:50 AN=2;DP=116;MQ=7.43;MQ0=112 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227362 . T . 40.23 mq_score:50 AN=2;DP=116;MQ=7.43;MQ0=112 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227363 . A . 40.23 mq_score:50 AN=2;DP=115;MQ=7.46;MQ0=111 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227364 . A . 40.23 mq_score:50 AN=2;DP=113;MQ=7.53;MQ0=109 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227365 . C . 40.23 mq_score:50 AN=2;DP=114;MQ=7.49;MQ0=110 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227366 . G . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227367 . G . 40.23 mq_score:50 AN=2;DP=111;MQ=7.59;MQ0=107 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227368 . C . 40.23 mq_score:50 AN=2;DP=105;MQ=7.81;MQ0=101 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227369 . T . 40.23 mq_score:50 AN=2;DP=104;MQ=7.84;MQ0=100 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227370 . C . 40.23 mq_score:50 AN=2;DP=106;MQ=7.77;MQ0=102 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227371 . A . 40.23 mq_score:50 AN=2;DP=106;MQ=7.77;MQ0=102 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227372 . C . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227373 . C . 40.23 mq_score:50 AN=2;DP=109;MQ=7.66;MQ0=105 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227374 . T . 40.23 mq_score:50 AN=2;DP=111;MQ=7.59;MQ0=107 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227375 . A . 40.23 mq_score:50 AN=2;DP=111;MQ=7.59;MQ0=107 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227376 . G . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227377 . G . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227378 . C . 40.23 mq_score:50 AN=2;DP=109;MQ=7.66;MQ0=105 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227379 . G . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227380 . A . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227381 . C . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227382 . G . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227383 . A . 37.23 mq_score:50 AN=2;DP=119;MQ=6.35;MQ0=116 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227384 . T . 37.23 mq_score:50 AN=2;DP=124;MQ=6.22;MQ0=121 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227385 . C . 37.23 mq_score:50 AN=2;DP=124;MQ=6.22;MQ0=121 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227386 . C . 37.23 mq_score:50 AN=2;DP=123;MQ=6.25;MQ0=120 GT:DP 0/0:123 -gi|15829254|ref|NC_002695.1| 227387 . C . 37.23 mq_score:50 AN=2;DP=125;MQ=6.2;MQ0=122 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227388 . T . 37.23 mq_score:50 AN=2;DP=128;MQ=6.12;MQ0=125 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227389 . A . 37.23 mq_score:50 AN=2;DP=128;MQ=6.12;MQ0=125 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227390 . G . 37.23 mq_score:50 AN=2;DP=126;MQ=6.17;MQ0=123 GT:DP 0/0:126 -gi|15829254|ref|NC_002695.1| 227391 . C . 37.23 mq_score:50 AN=2;DP=126;MQ=6.17;MQ0=123 GT:DP 0/0:126 -gi|15829254|ref|NC_002695.1| 227392 . T . 37.23 mq_score:50 AN=2;DP=119;MQ=6.35;MQ0=116 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227393 . G . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227394 . G . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227395 . T . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227396 . C . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227397 . T . 37.23 mq_score:50 AN=2;DP=113;MQ=6.52;MQ0=110 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227398 . G . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227399 . A . 37.23 mq_score:50 AN=2;DP=111;MQ=6.58;MQ0=108 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227400 . G . 37.23 mq_score:50 AN=2;DP=112;MQ=6.55;MQ0=109 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227401 . A . 37.23 mq_score:50 AN=2;DP=112;MQ=6.55;MQ0=109 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227402 . G . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227403 . G . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227404 . A . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227405 . T . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227406 . G . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227407 . A . 34.23 mq_score:50 AN=2;DP=104;MQ=5.55;MQ0=102 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227408 . C . 34.23 mq_score:50 AN=2;DP=104;MQ=5.55;MQ0=102 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227409 . C . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227410 . A . 34.23 mq_score:50 AN=2;DP=100;MQ=5.66;MQ0=98 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227411 . G . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227412 . C . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227413 . C . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227414 . A . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227415 . C . 34.23 mq_score:50 AN=2;DP=112;MQ=5.35;MQ0=110 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227416 . A . 34.23 mq_score:50 AN=2;DP=116;MQ=5.25;MQ0=114 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227417 . C . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227418 . T . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227419 . G . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227420 . G . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227421 . A . 34.23 mq_score:50 AN=2;DP=119;MQ=5.19;MQ0=117 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227422 . A . 34.23 mq_score:50 AN=2;DP=119;MQ=5.19;MQ0=117 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227423 . C . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227424 . T . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227425 . G . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227426 . A . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227427 . G . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227428 . A . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227429 . C . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227430 . A . 34.23 mq_score:50 AN=2;DP=116;MQ=5.25;MQ0=114 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227431 . C . 34.23 mq_score:50 AN=2;DP=114;MQ=5.3;MQ0=112 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227432 . G . 34.23 mq_score:50 AN=2;DP=113;MQ=5.32;MQ0=111 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227433 . G . 34.23 mq_score:50 AN=2;DP=120;MQ=5.16;MQ0=118 GT:DP 0/0:120 -gi|15829254|ref|NC_002695.1| 227434 . T . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227435 . C . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227436 . C . 34.23 mq_score:50 AN=2;DP=122;MQ=5.12;MQ0=120 GT:DP 0/0:122 -gi|15829254|ref|NC_002695.1| 227437 . A . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227438 . G . 34.23 mq_score:50 AN=2;DP=122;MQ=5.12;MQ0=120 GT:DP 0/0:122 -gi|15829254|ref|NC_002695.1| 227439 . A . 34.23 mq_score:50 AN=2;DP=123;MQ=5.1;MQ0=121 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227440 . C . 34.23 mq_score:50 AN=2;DP=126;MQ=5.04;MQ0=124 GT:DP 0/0:126 -gi|15829254|ref|NC_002695.1| 227441 . T . 34.23 mq_score:50 AN=2;DP=124;MQ=5.08;MQ0=122 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227442 . C . 31.24 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227443 . C . 31.24 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227444 . T . 31.23 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227445 . A . 31.23 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227446 . C . 31.23 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227447 . G . 31.23 mq_score:50 AN=2;DP=104;MQ=3.92;MQ0=103 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227448 . G . 31.23 mq_score:50 AN=2;DP=107;MQ=3.87;MQ0=106 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227449 . G . 31.23 mq_score:50 AN=2;DP=105;MQ=3.9;MQ0=104 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227450 . A . 31.23 mq_score:50 AN=2;DP=107;MQ=3.87;MQ0=106 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227451 . G . 31.23 mq_score:50 AN=2;DP=103;MQ=3.94;MQ0=102 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227452 . G . 31.23 mq_score:50 AN=2;DP=102;MQ=3.96;MQ0=101 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227453 . C . 31.23 mq_score:50 AN=2;DP=103;MQ=3.94;MQ0=102 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227454 . A . 31.23 mq_score:50 AN=2;DP=102;MQ=3.96;MQ0=101 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227455 . G . 31.23 mq_score:50 AN=2;DP=104;MQ=3.92;MQ0=103 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227456 . C . 31.23 mq_score:50 AN=2;DP=103;MQ=3.94;MQ0=102 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227457 . A . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227458 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227459 . T . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227460 . G . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227461 . G . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227462 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227463 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227464 . A . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227465 . A . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227466 . T . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227467 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227468 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227469 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227470 . G . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227471 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227472 . A . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227473 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227474 . A . . mq_score:50 DP=119;MQ=0.0;MQ0=119 GT ./. -gi|15829254|ref|NC_002695.1| 227475 . A . . mq_score:50 DP=119;MQ=0.0;MQ0=119 GT ./. -gi|15829254|ref|NC_002695.1| 227476 . T . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227477 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227478 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227479 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227480 . C . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227481 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227482 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227483 . A . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227484 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227485 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227486 . C . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227487 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227488 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227489 . G . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227490 . A . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227491 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227492 . G . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227493 . C . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227494 . A . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227495 . G . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227496 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227497 . C . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227498 . A . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227499 . T . . mq_score:50 DP=127;MQ=0.0;MQ0=127 GT ./. -gi|15829254|ref|NC_002695.1| 227500 . G . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227501 . C . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227502 . C . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227503 . G . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227504 . C . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227505 . G . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227506 . T . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227507 . G . . mq_score:50 DP=132;MQ=0.0;MQ0=132 GT ./. -gi|15829254|ref|NC_002695.1| 227508 . T . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227509 . A . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227510 . T . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227511 . G . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227512 . A . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227513 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227514 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227515 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227516 . A . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227517 . G . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227518 . G . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227519 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227520 . C . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227521 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227522 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227523 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227524 . G . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227525 . G . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227526 . G . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227527 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227528 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227529 . G . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227530 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227531 . A . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227532 . A . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227533 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227534 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227535 . T . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227536 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227537 . C . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227538 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227539 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227540 . T . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227541 . C . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227542 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227543 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227544 . C . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227545 . G . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227546 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227547 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227548 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227549 . A . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227550 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227551 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227552 . A . . mq_score:50 DP=134;MQ=0.0;MQ0=134 GT ./. -gi|15829254|ref|NC_002695.1| 227553 . A . . mq_score:50 DP=135;MQ=0.0;MQ0=135 GT ./. -gi|15829254|ref|NC_002695.1| 227554 . G . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227555 . G . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227556 . G . . mq_score:50 DP=139;MQ=0.0;MQ0=139 GT ./. -gi|15829254|ref|NC_002695.1| 227557 . A . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227558 . G . . mq_score:50 DP=136;MQ=0.0;MQ0=136 GT ./. -gi|15829254|ref|NC_002695.1| 227559 . T . . mq_score:50 DP=136;MQ=0.0;MQ0=136 GT ./. -gi|15829254|ref|NC_002695.1| 227560 . A . . mq_score:50 DP=134;MQ=0.0;MQ0=134 GT ./. -gi|15829254|ref|NC_002695.1| 227561 . A . . mq_score:50 DP=134;MQ=0.0;MQ0=134 GT ./. -gi|15829254|ref|NC_002695.1| 227562 . A . . mq_score:50 DP=135;MQ=0.0;MQ0=135 GT ./. -gi|15829254|ref|NC_002695.1| 227563 . G . . mq_score:50 DP=143;MQ=0.0;MQ0=143 GT ./. -gi|15829254|ref|NC_002695.1| 227564 . T . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227565 . T . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227566 . A . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227567 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227568 . T . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227569 . A . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227570 . C . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227571 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227572 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227573 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227574 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227575 . G . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227576 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227577 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227578 . C . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227579 . A . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227580 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227581 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227582 . G . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227583 . A . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227584 . C . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227585 . G . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227586 . T . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227587 . T . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227588 . A . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227589 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227590 . C . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227591 . C . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227592 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227593 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227594 . A . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227595 . G . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227596 . A . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227597 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227598 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227599 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227600 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227601 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227602 . C . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227603 . A . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227604 . C . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227605 . C . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227606 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227607 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227608 . C . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227609 . T . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227610 . A . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227611 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227612 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227613 . T . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227614 . C . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227615 . C . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227616 . G . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227617 . T . . mq_score:50 DP=98;MQ=0.0;MQ0=98 GT ./. -gi|15829254|ref|NC_002695.1| 227618 . G . . mq_score:50 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227619 . C . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227620 . C . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227621 . A . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227622 . G . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227623 . C . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227624 . A . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227625 . G . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227626 . C . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227627 . C . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227628 . G . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227629 . C . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227630 . G . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227631 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227632 . T . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227633 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227634 . A . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227635 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227636 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227637 . C . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227638 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227639 . G . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227640 . A . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227641 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227642 . G . . mq_score:50 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227643 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227644 . T . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227645 . G . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227646 . C . . mq_score:50 DP=98;MQ=0.0;MQ0=98 GT ./. -gi|15829254|ref|NC_002695.1| 227647 . A . . mq_score:50 DP=98;MQ=0.0;MQ0=98 GT ./. -gi|15829254|ref|NC_002695.1| 227648 . A . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227649 . G . . mq_score:50 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227650 . C . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227651 . G . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227652 . T . . mq_score:50 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227653 . T . . mq_score:50 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227654 . A . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227655 . A . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227656 . T . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227657 . C . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227658 . G . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227659 . G . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227660 . A . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227661 . A . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227662 . T . . mq_score:50 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227663 . T . . mq_score:50 DP=86;MQ=0.0;MQ0=86 GT ./. -gi|15829254|ref|NC_002695.1| 227664 . A . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227665 . C . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227666 . T . . mq_score:50 DP=90;MQ=0.0;MQ0=90 GT ./. -gi|15829254|ref|NC_002695.1| 227667 . G . . mq_score:50 DP=90;MQ=0.0;MQ0=90 GT ./. -gi|15829254|ref|NC_002695.1| 227668 . G . . mq_score:50 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227669 . G . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227670 . C . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227671 . G . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227672 . T . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227673 . A . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227674 . A . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227675 . A . . mq_score:50 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227676 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227677 . C . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227678 . G . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227679 . C . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227680 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227681 . C . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227682 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227683 . C . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227684 . A . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227685 . G . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227686 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227687 . C . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227688 . G . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227689 . G . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227690 . T . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227691 . T . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227692 . T . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227693 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227694 . T . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227695 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227696 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227697 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227698 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227699 . T . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227700 . C . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227701 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227702 . G . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227703 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227704 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227705 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227706 . T . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227707 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227708 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227709 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227710 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227711 . T . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227712 . C . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227713 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227714 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227715 . C . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227716 . G . . mq_score:50 DP=119;MQ=0.0;MQ0=119 GT ./. -gi|15829254|ref|NC_002695.1| 227717 . G . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227718 . G . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227719 . C . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227720 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227721 . C . . mq_score:50 DP=127;MQ=0.0;MQ0=127 GT ./. -gi|15829254|ref|NC_002695.1| 227722 . A . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227723 . A . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227724 . C . . mq_score:50 DP=132;MQ=0.0;MQ0=132 GT ./. -gi|15829254|ref|NC_002695.1| 227725 . C . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227726 . T . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227727 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227728 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227729 . G . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227730 . A . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227731 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227732 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227733 . T . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227734 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227735 . C . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227736 . A . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227737 . T . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227738 . C . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227739 . T . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227740 . G . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227741 . A . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227742 . T . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227743 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227744 . C . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227745 . T . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227746 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227747 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227748 . C . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227749 . A . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227750 . A . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227751 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227752 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227753 . T . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227754 . T . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227755 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227756 . A . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227757 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227758 . T . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227759 . C . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227760 . T . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227761 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227762 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227763 . T . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227764 . A . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227765 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227766 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227767 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227768 . G . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227769 . G . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227770 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227771 . G . . mq_score:50 DP=100;MQ=0.0;MQ0=100 GT ./. -gi|15829254|ref|NC_002695.1| 227772 . G . . mq_score:50 DP=100;MQ=0.0;MQ0=100 GT ./. -gi|15829254|ref|NC_002695.1| 227773 . T . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227774 . A . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227775 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227776 . A . . mq_score:50 DP=100;MQ=0.0;MQ0=100 GT ./. -gi|15829254|ref|NC_002695.1| 227777 . A . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227778 . T . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227779 . T . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227780 . C . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227781 . C . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227782 . A . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227783 . G . . mq_score:50 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227784 . G . . mq_score:50 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227785 . T . . mq_score:50 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227786 . G . . mq_score:50 DP=90;MQ=0.0;MQ0=90 GT ./. -gi|15829254|ref|NC_002695.1| 227787 . T . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227788 . A . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227789 . G . . mq_score:50 DP=88;MQ=0.0;MQ0=88 GT ./. -gi|15829254|ref|NC_002695.1| 227790 . C . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227791 . G . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227792 . G . . mq_score:50 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227793 . T . . mq_score:50 DP=84;MQ=0.0;MQ0=84 GT ./. -gi|15829254|ref|NC_002695.1| 227794 . G . . mq_score:50 DP=84;MQ=0.0;MQ0=84 GT ./. -gi|15829254|ref|NC_002695.1| 227795 . A . . mq_score:50 DP=89;MQ=0.0;MQ0=89 GT ./. -gi|15829254|ref|NC_002695.1| 227796 . A . . mq_score:50 DP=89;MQ=0.0;MQ0=89 GT ./. -gi|15829254|ref|NC_002695.1| 227797 . A . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227798 . T . . mq_score:50 DP=89;MQ=0.0;MQ0=89 GT ./. -gi|15829254|ref|NC_002695.1| 227799 . G . . mq_score:50 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227800 . C . . mq_score:50 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227801 . G . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227802 . T . . mq_score:50 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227803 . A . . mq_score:50 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227804 . G . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227805 . A . . mq_score:50 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227806 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227807 . A . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227808 . T . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227809 . C . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227810 . T . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227811 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227812 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227813 . A . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227814 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227815 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227816 . A . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227817 . A . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227818 . T . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227819 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227820 . C . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227821 . C . . mq_score:50 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227822 . G . . mq_score:50 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227823 . G . . mq_score:50 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227824 . T . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227825 . G . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227826 . G . . mq_score:50 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227827 . C . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227828 . G . . mq_score:50 DP=94;MQ=0.0;MQ0=94 GT ./.
--- a/test-data/test_output.vcf Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1001 +0,0 @@ -##fileformat=VCFv4.1 -##GATKCommandLine=<ID=SelectVariants,Version=2.6-5-gba531bd,Date="Thu May 22 09:24:36 BST 2014",Epoch=1400747076888,CommandLineOptions="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/input_variant.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.6-5-gba531bd,Date="Thu May 22 09:10:24 BST 2014",Epoch=1400746224902,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input_0.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/phengs/galaxy/database/tmp/tmp-gatk-x7S0pF/gatk_input.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=STRICT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=2 num_cpu_threads_per_data_thread=6 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##reference=file:///phengs/galaxy/database/tmp/tmp-gatk-lMh4vi/gatk_input.fasta -##source=SelectVariants -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> -##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> -##INFO=<ID=BasesToClosestSNP,Number=1,Type=Integer,Description="Number of bases to the closest SNP in the file."> -##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##FILTER=<ID=LowQual,Description="Low quality"> -##FILTER=<ID=mq_score:50,Description="Filter sites by Mapping Quality (MQ) score. (MQ > 50)"> -##FILTER=<ID=gq_score:10,Description="Filter sites by GQ score. (GQ > 10)"> -##FILTER=<ID=uncall_gt:,Description="Filter uncallable genotypes (GT != ./. )"> -##FILTER=<ID=min_depth:100,Description="Filter sites by depth. (DP > 100)"> -##contig=<ID=gi|15829254|ref|NC_002695.1|,length=5498450> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H133840545_1 -gi|15829254|ref|NC_002695.1| 6065 . C T 5384.77 PASS AC=2;AF=1.0;AN=2;DP=161;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.45;BasesToClosestSNP=4136 GT:AD:DP:GQ:PL 1/1:0,161:161:99:5413,427,0 -gi|15829254|ref|NC_002695.1| 10201 . C T 5819.77 PASS AC=2;AF=1.0;AN=2;DP=154;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.21;BasesToClosestSNP=4136 GT:AD:DP:GQ:PL 1/1:0,154:154:99:5848,451,0 -gi|15829254|ref|NC_002695.1| 14114 . A T 6039.77 PASS AC=2;AF=1.0;AN=2;DP=166;Dels=0.0;FS=0.0;HaplotypeScore=1.6229;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.07;BasesToClosestSNP=3913 GT:AD:DP:GQ:PL 1/1:0,166:166:99:6068,469,0 -gi|15829254|ref|NC_002695.1| 15404 . T . 17.31 LowQual;min_depth:100 AN=2;DP=33;MQ=60.0;MQ0=0 GT:DP 0/0:32 -gi|15829254|ref|NC_002695.1| 18711 . A C 3657.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=99;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.28;BasesToClosestSNP=4597 GT:AD:DP:GQ:PL 1/1:0,99:99:99:3686,274,0 -gi|15829254|ref|NC_002695.1| 18968 . G A 6350.77 PASS AC=2;AF=1.0;AN=2;DP=181;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.07;BasesToClosestSNP=257 GT:AD:DP:GQ:PL 1/1:0,181:181:99:6379,470,0 -gi|15829254|ref|NC_002695.1| 47847 . C T 4038.77 PASS AC=2;AF=1.0;AN=2;DP=113;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.05;BasesToClosestSNP=28879 GT:AD:DP:GQ:PL 1/1:0,113:113:99:4067,313,0 -gi|15829254|ref|NC_002695.1| 48272 . A G 3836.77 PASS AC=2;AF=1.0;AN=2;DP=106;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.18;BasesToClosestSNP=99 GT:AD:DP:GQ:PL 1/1:0,106:106:99:3865,298,0 -gi|15829254|ref|NC_002695.1| 48371 . G A 4075.77 PASS AC=2;AF=1.0;AN=2;DP=106;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=25.66;BasesToClosestSNP=99 GT:AD:DP:GQ:PL 1/1:0,106:106:99:4104,310,0 -gi|15829254|ref|NC_002695.1| 51967 . C T 3137.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=97;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.35;BasesToClosestSNP=1748 GT:AD:DP:GQ:PL 1/1:0,96:96:99:3166,259,0 -gi|15829254|ref|NC_002695.1| 53715 . C T 3985.77 PASS AC=2;AF=1.0;AN=2;DP=110;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.04;BasesToClosestSNP=1748 GT:AD:DP:GQ:PL 1/1:0,110:110:99:4014,301,0 -gi|15829254|ref|NC_002695.1| 57677 . T C 3587.77 PASS AC=2;AF=1.0;AN=2;DP=106;Dels=0.0;FS=0.0;HaplotypeScore=1.3302;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.85;BasesToClosestSNP=3962 GT:AD:DP:GQ:PL 1/1:0,106:106:99:3616,283,0 -gi|15829254|ref|NC_002695.1| 63127 . T G 4466.77 PASS AC=2;AF=1.0;AN=2;DP=117;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.14;BasesToClosestSNP=5450 GT:AD:DP:GQ:PL 1/1:0,117:117:99:4495,337,0 -gi|15829254|ref|NC_002695.1| 64020 . A C 872.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.689;DP=248;Dels=0.0;FS=36.815;HaplotypeScore=3.9529;MLEAC=1;MLEAF=0.5;MQ=57.45;MQ0=0;MQRankSum=-2.381;QD=3.52;ReadPosRankSum=-10.71;BasesToClosestSNP=47 GT:AD:DP:GQ:PL 0/1:185,63:236:99:901,0,5685 -gi|15829254|ref|NC_002695.1| 64067 . G C 2096.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.146;DP=209;Dels=0.0;FS=153.841;HaplotypeScore=4.9521;MLEAC=1;MLEAF=0.5;MQ=57.15;MQ0=0;MQRankSum=4.711;QD=10.03;ReadPosRankSum=-7.39;BasesToClosestSNP=47 GT:AD:DP:GQ:PL 0/1:137,72:199:99:2125,0,4003 -gi|15829254|ref|NC_002695.1| 70555 . C T 2890.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=85;Dels=0.01;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.01;BasesToClosestSNP=6488 GT:AD:DP:GQ:PL 1/1:0,84:84:99:2919,229,0 -gi|15829254|ref|NC_002695.1| 85412 . G A 5899.77 PASS AC=2;AF=1.0;AN=2;DP=160;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.27;BasesToClosestSNP=14857 GT:AD:DP:GQ:PL 1/1:0,160:160:99:5928,445,0 -gi|15829254|ref|NC_002695.1| 88701 . T C 848.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=24;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.62;BasesToClosestSNP=3289 GT:AD:DP:GQ:PL 1/1:0,24:24:66:877,66,0 -gi|15829254|ref|NC_002695.1| 93390 . T G 3211.76 min_depth:100 AC=2;AF=1.0;AN=2;BaseQRankSum=1.653;DP=87;Dels=0.0;FS=0.0;HaplotypeScore=3.5473;MLEAC=2;MLEAF=1.0;MQ=59.89;MQ0=0;MQRankSum=1.653;QD=34.49;ReadPosRankSum=1.015;BasesToClosestSNP=4689 GT:AD:DP:GQ:PL 1/1:1,86:86:99:3240,247,0 -gi|15829254|ref|NC_002695.1| 120398 . G A 4149.77 PASS AC=2;AF=1.0;AN=2;DP=109;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.29;BasesToClosestSNP=13502 GT:AD:DP:GQ:PL 1/1:0,109:109:99:4178,313,0 -gi|15829254|ref|NC_002695.1| 133900 . A G 4414.77 PASS AC=2;AF=1.0;AN=2;DP=122;Dels=0.0;FS=0.0;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.13;BasesToClosestSNP=13502 GT:AD:DP:GQ:PL 1/1:0,122:122:99:4443,340,0 -gi|15829254|ref|NC_002695.1| 142584 . T C 4353.77 PASS AC=2;AF=1.0;AN=2;DP=116;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.86;BasesToClosestSNP=295 GT:AD:DP:GQ:PL 1/1:0,116:116:99:4382,331,0 -gi|15829254|ref|NC_002695.1| 142879 . C A 4885.77 PASS AC=2;AF=1.0;AN=2;DP=140;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.9;BasesToClosestSNP=295 GT:AD:DP:GQ:PL 1/1:0,140:140:99:4914,376,0 -gi|15829254|ref|NC_002695.1| 157462 . C T 4419.77 PASS AC=2;AF=1.0;AN=2;DP=121;Dels=0.0;FS=0.0;HaplotypeScore=1.6644;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.08;BasesToClosestSNP=3210 GT:AD:DP:GQ:PL 1/1:0,121:121:99:4448,337,0 -gi|15829254|ref|NC_002695.1| 160672 . T C 5929.77 PASS AC=2;AF=1.0;AN=2;DP=159;Dels=0.0;FS=0.0;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.52;BasesToClosestSNP=3210 GT:AD:DP:GQ:PL 1/1:0,159:159:99:5958,448,0 -gi|15829254|ref|NC_002695.1| 165369 . C T 4012.77 PASS AC=2;AF=1.0;AN=2;DP=116;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.59;BasesToClosestSNP=578 GT:AD:DP:GQ:PL 1/1:0,116:116:99:4041,304,0 -gi|15829254|ref|NC_002695.1| 165947 . A C 2779.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=85;Dels=0.0;FS=0.0;HaplotypeScore=4.3247;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.7;BasesToClosestSNP=578 GT:AD:DP:GQ:PL 1/1:0,85:85:99:2808,229,0 -gi|15829254|ref|NC_002695.1| 171915 . T C 3539.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=96;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.7;BasesToClosestSNP=5968 GT:AD:DP:GQ:PL 1/1:0,96:96:99:3568,277,0 -gi|15829254|ref|NC_002695.1| 180160 . T C 4020.77 PASS AC=2;AF=1.0;AN=2;DP=109;Dels=0.0;FS=0.0;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.54;BasesToClosestSNP=8245 GT:AD:DP:GQ:PL 1/1:0,109:109:99:4049,307,0 -gi|15829254|ref|NC_002695.1| 184717 . T C 5621.77 PASS AC=2;AF=1.0;AN=2;DP=151;Dels=0.0;FS=0.0;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=25.05;BasesToClosestSNP=1393 GT:AD:DP:GQ:PL 1/1:0,151:151:99:5650,421,0 -gi|15829254|ref|NC_002695.1| 186110 . C T 5816.77 PASS AC=2;AF=1.0;AN=2;DP=155;Dels=0.0;FS=0.0;HaplotypeScore=1.6644;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.83;BasesToClosestSNP=1393 GT:AD:DP:GQ:PL 1/1:0,155:155:99:5845,439,0 -gi|15829254|ref|NC_002695.1| 205552 . C T 3913.77 PASS AC=2;AF=1.0;AN=2;DP=112;Dels=0.0;FS=0.0;HaplotypeScore=2.6603;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.94;BasesToClosestSNP=11905 GT:AD:DP:GQ:PL 1/1:0,112:112:99:3942,304,0 -gi|15829254|ref|NC_002695.1| 217457 . A T 3215.74 min_depth:100 AC=2;AF=1.0;AN=2;DP=88;Dels=0.0;FS=0.0;HaplotypeScore=1.6229;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.68;BasesToClosestSNP=11905 GT:AD:DP:GQ:PL 1/1:0,88:88:99:3244,247,0 -gi|15829254|ref|NC_002695.1| 218091 . T C 3066.77 min_depth:100 AC=2;AF=1.0;AN=2;DP=81;Dels=0.0;FS=0.0;HaplotypeScore=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.01;BasesToClosestSNP=634 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3095,232,0 -gi|15829254|ref|NC_002695.1| 226900 . A . 284.23 mq_score:50 AN=2;DP=106;MQ=49.79;MQ0=17 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226901 . A . 284.23 mq_score:50 AN=2;DP=106;MQ=49.79;MQ0=17 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226902 . G . 278.23 mq_score:50 AN=2;DP=105;MQ=49.34;MQ0=18 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226903 . A . 275.23 mq_score:50 AN=2;DP=104;MQ=49.22;MQ0=18 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226904 . G . 275.23 mq_score:50 AN=2;DP=106;MQ=48.91;MQ0=19 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226905 . G . 275.23 mq_score:50 AN=2;DP=105;MQ=48.79;MQ0=19 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226906 . A . 284.23 mq_score:50 AN=2;DP=107;MQ=48.64;MQ0=19 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226907 . A . 278.23 mq_score:50 AN=2;DP=107;MQ=48.64;MQ0=19 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226908 . A . 284.23 mq_score:50 AN=2;DP=107;MQ=48.64;MQ0=19 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226909 . G . 281.23 mq_score:50 AN=2;DP=109;MQ=48.19;MQ0=21 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226910 . C . 275.23 mq_score:50 AN=2;DP=111;MQ=47.76;MQ0=23 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 226911 . G . 281.23 mq_score:50 AN=2;DP=112;MQ=47.69;MQ0=23 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 226912 . T . 275.23 mq_score:50 AN=2;DP=109;MQ=47.12;MQ0=23 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226913 . A . 269.23 mq_score:50 AN=2;DP=107;MQ=46.84;MQ0=23 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226914 . A . 260.23 mq_score:50 AN=2;DP=115;MQ=44.48;MQ0=33 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 226915 . T . 269.23 mq_score:50 AN=2;DP=115;MQ=44.48;MQ0=33 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 226916 . A . 266.23 mq_score:50 AN=2;DP=118;MQ=43.91;MQ0=36 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 226917 . T . 272.23 mq_score:50 AN=2;DP=120;MQ=43.85;MQ0=36 GT:DP 0/0:120 -gi|15829254|ref|NC_002695.1| 226918 . A . 215.23 mq_score:50;min_depth:100 AN=2;DP=102;MQ=40.35;MQ0=36 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 226919 . C . 227.23 mq_score:50 AN=2;DP=103;MQ=40.35;MQ0=36 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 226920 . G . 218.23 mq_score:50 AN=2;DP=101;MQ=39.86;MQ0=36 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226921 . C . 218.23 mq_score:50 AN=2;DP=101;MQ=39.86;MQ0=36 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226922 . C . 209.23 mq_score:50 AN=2;DP=101;MQ=39.61;MQ0=36 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226923 . A . 199.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=38.82;MQ0=36 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226924 . C . 206.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=38.34;MQ0=37 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226925 . C . 203.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=37.76;MQ0=37 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 226926 . T . 197.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=37.57;MQ0=38 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 226927 . C . 206.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=37.59;MQ0=38 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226928 . G . 206.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=37.59;MQ0=38 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226929 . C . 203.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=37.13;MQ0=39 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 226930 . G . 200.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=36.86;MQ0=39 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 226931 . A . 197.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=36.55;MQ0=39 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 226932 . C . 197.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=36.55;MQ0=39 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 226933 . A . 184.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=34.96;MQ0=39 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 226934 . G . 184.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=34.96;MQ0=39 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 226935 . T . 178.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=34.26;MQ0=39 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 226936 . G . 178.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=34.26;MQ0=39 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 226937 . A . 172.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=34.26;MQ0=39 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 226938 . G . 178.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=33.96;MQ0=41 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 226939 . C . 181.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=33.96;MQ0=41 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 226940 . T . 187.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=34.28;MQ0=41 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 226941 . G . 187.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=34.01;MQ0=41 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 226942 . A . 188.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=34.01;MQ0=41 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 226943 . A . 181.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=33.66;MQ0=41 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 226944 . A . 181.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=33.66;MQ0=41 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 226945 . G . 175.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226946 . C . 166.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226947 . C . 175.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226948 . G . 175.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=32.54;MQ0=41 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 226949 . C . 166.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=31.11;MQ0=42 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 226950 . G . 166.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=31.11;MQ0=42 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 226951 . T . 178.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=31.65;MQ0=42 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 226952 . C . 184.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=31.75;MQ0=42 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 226953 . G . 203.23 mq_score:50 AN=2;DP=101;MQ=32.39;MQ0=42 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226954 . C . 203.23 mq_score:50 AN=2;DP=102;MQ=31.72;MQ0=44 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 226955 . A . 200.23 mq_score:50 AN=2;DP=102;MQ=31.72;MQ0=44 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 226956 . A . 206.23 mq_score:50 AN=2;DP=104;MQ=31.9;MQ0=44 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226957 . C . 206.23 mq_score:50 AN=2;DP=104;MQ=31.9;MQ0=44 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226958 . T . 209.23 mq_score:50 AN=2;DP=102;MQ=32.21;MQ0=42 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 226959 . G . 215.23 mq_score:50 AN=2;DP=106;MQ=32.07;MQ0=44 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226960 . C . 206.23 mq_score:50 AN=2;DP=106;MQ=31.06;MQ0=46 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226961 . T . 197.23 mq_score:50 AN=2;DP=104;MQ=30.31;MQ0=46 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226962 . C . 203.23 mq_score:50 AN=2;DP=105;MQ=30.17;MQ0=47 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226963 . T . 191.23 mq_score:50 AN=2;DP=101;MQ=29.49;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226964 . T . 191.23 mq_score:50 AN=2;DP=101;MQ=29.49;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226965 . T . 191.23 mq_score:50 AN=2;DP=101;MQ=29.49;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226966 . A . 191.23 mq_score:50 AN=2;DP=101;MQ=29.63;MQ0=47 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226967 . A . 203.23 mq_score:50 AN=2;DP=105;MQ=30.09;MQ0=47 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226968 . C . 206.23 mq_score:50 AN=2;DP=108;MQ=29.92;MQ0=49 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226969 . A . 194.23 mq_score:50 AN=2;DP=104;MQ=29.2;MQ0=49 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226970 . A . 194.23 mq_score:50 AN=2;DP=106;MQ=28.92;MQ0=51 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226971 . T . 188.23 mq_score:50 AN=2;DP=105;MQ=28.42;MQ0=52 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226972 . T . 188.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226973 . T . 187.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226974 . A . 188.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226975 . T . 185.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226976 . C . 188.23 mq_score:50 AN=2;DP=108;MQ=28.02;MQ0=55 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226977 . A . 184.23 mq_score:50 AN=2;DP=107;MQ=27.88;MQ0=55 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226978 . G . 184.23 mq_score:50 AN=2;DP=108;MQ=27.76;MQ0=56 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226979 . A . 181.23 mq_score:50 AN=2;DP=107;MQ=27.62;MQ0=56 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 226980 . C . 181.23 mq_score:50 AN=2;DP=109;MQ=27.36;MQ0=58 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226981 . A . 172.23 mq_score:50 AN=2;DP=106;MQ=26.92;MQ0=58 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226982 . A . 178.23 mq_score:50 AN=2;DP=108;MQ=27.22;MQ0=58 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226983 . T . 178.23 mq_score:50 AN=2;DP=109;MQ=27.09;MQ0=59 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 226984 . C . 178.23 mq_score:50 AN=2;DP=113;MQ=26.61;MQ0=63 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 226985 . T . 175.23 mq_score:50 AN=2;DP=110;MQ=26.7;MQ0=61 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 226986 . G . 175.23 mq_score:50 AN=2;DP=111;MQ=26.58;MQ0=62 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 226987 . T . 172.23 mq_score:50 AN=2;DP=108;MQ=26.67;MQ0=60 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226988 . G . 172.23 mq_score:50 AN=2;DP=108;MQ=26.67;MQ0=60 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 226989 . T . 169.23 mq_score:50 AN=2;DP=105;MQ=26.76;MQ0=58 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226990 . G . 166.23 mq_score:50 AN=2;DP=105;MQ=26.76;MQ0=58 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226991 . G . 166.23 mq_score:50 AN=2;DP=105;MQ=26.48;MQ0=59 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226992 . G . 157.23 mq_score:50 AN=2;DP=104;MQ=26.31;MQ0=59 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226993 . C . 160.23 mq_score:50 AN=2;DP=105;MQ=26.19;MQ0=60 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226994 . A . 151.23 mq_score:50 AN=2;DP=104;MQ=26.31;MQ0=59 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 226995 . C . 157.23 mq_score:50 AN=2;DP=106;MQ=25.48;MQ0=63 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226996 . T . 154.23 mq_score:50 AN=2;DP=104;MQ=25.42;MQ0=62 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 226997 . C . 151.23 mq_score:50 AN=2;DP=106;MQ=25.18;MQ0=64 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 226998 . G . 151.23 mq_score:50 AN=2;DP=105;MQ=25.3;MQ0=63 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 226999 . A . 154.23 mq_score:50 AN=2;DP=104;MQ=25.42;MQ0=62 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227000 . A . 151.23 mq_score:50;min_depth:100 AN=2;DP=103;MQ=25.24;MQ0=62 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227001 . G . 151.23 mq_score:50 AN=2;DP=103;MQ=25.24;MQ0=62 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227002 . A . 151.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227003 . T . 148.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227004 . A . 142.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227005 . C . 148.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227006 . G . 148.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227007 . G . 148.23 mq_score:50 AN=2;DP=100;MQ=25.3;MQ0=60 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227008 . A . 151.23 mq_score:50 AN=2;DP=101;MQ=25.49;MQ0=60 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227009 . T . 151.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227010 . T . 151.23 mq_score:50 AN=2;DP=102;MQ=25.36;MQ0=61 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227011 . C . 148.23 mq_score:50 AN=2;DP=103;MQ=24.93;MQ0=63 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227012 . T . 145.23 mq_score:50 AN=2;DP=102;MQ=24.73;MQ0=63 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227013 . T . 145.23 mq_score:50 AN=2;DP=102;MQ=24.73;MQ0=63 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227014 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=25.76;MQ0=55 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227015 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=25.9;MQ0=54 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227016 . C . 145.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=26.38;MQ0=52 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227017 . G . 142.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227018 . T . 142.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227019 . C . 142.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227020 . G . 145.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=26.04;MQ0=53 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227021 . C . 148.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=26.38;MQ0=52 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227022 . A . 142.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=26.19;MQ0=52 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227023 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=26.19;MQ0=52 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227024 . G . 145.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=26.33;MQ0=51 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227025 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=26.33;MQ0=51 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227026 . C . 145.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=26.33;MQ0=51 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227027 . G . 142.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227028 . A . 142.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227029 . A . 142.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=26.14;MQ0=51 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227030 . A . 142.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=25.99;MQ0=52 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227031 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=25.76;MQ0=55 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227032 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=25.36;MQ0=58 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227033 . T . 145.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=25.23;MQ0=59 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227034 . G . 145.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=25.23;MQ0=59 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227035 . A . 145.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=25.23;MQ0=59 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227036 . A . 148.23 mq_score:50;min_depth:100 AN=2;DP=99;MQ=25.43;MQ0=59 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227037 . T . 148.23 mq_score:50 AN=2;DP=100;MQ=25.61;MQ0=59 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227038 . A . 142.23 mq_score:50;min_depth:100 AN=2;DP=99;MQ=25.43;MQ0=59 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227039 . C . 148.23 mq_score:50 AN=2;DP=101;MQ=25.49;MQ0=60 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227040 . C . 142.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=24.91;MQ0=60 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227041 . A . 139.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=24.7;MQ0=60 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227042 . A . 139.23 mq_score:50 AN=2;DP=100;MQ=24.33;MQ0=63 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227043 . G . 139.23 mq_score:50 AN=2;DP=105;MQ=23.74;MQ0=68 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227044 . T . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227045 . C . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227046 . T . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227047 . C . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227048 . A . 139.23 mq_score:50 AN=2;DP=108;MQ=23.41;MQ0=71 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227049 . A . 136.23 mq_score:50 AN=2;DP=107;MQ=23.2;MQ0=71 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227050 . G . 136.23 mq_score:50 AN=2;DP=107;MQ=23.2;MQ0=71 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227051 . A . 115.23 mq_score:50 AN=2;DP=100;MQ=21.54;MQ0=71 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227052 . G . 115.23 mq_score:50 AN=2;DP=100;MQ=21.54;MQ0=71 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227053 . T . 100.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=20.43;MQ0=68 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227054 . G . 103.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=20.85;MQ0=67 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227055 . A . 106.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=20.71;MQ0=71 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227056 . A . 106.23 mq_score:50 AN=2;DP=102;MQ=19.96;MQ0=76 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227057 . C . 103.23 mq_score:50 AN=2;DP=104;MQ=19.76;MQ0=78 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227058 . A . 100.23 mq_score:50 AN=2;DP=106;MQ=19.19;MQ0=81 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227059 . C . 100.23 mq_score:50 AN=2;DP=105;MQ=18.88;MQ0=81 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227060 . G . 100.23 mq_score:50 AN=2;DP=103;MQ=19.06;MQ0=79 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227061 . T . 97.23 mq_score:50 AN=2;DP=103;MQ=19.06;MQ0=79 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227062 . A . 100.23 mq_score:50 AN=2;DP=102;MQ=19.15;MQ0=78 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227063 . A . 97.23 mq_score:50 AN=2;DP=106;MQ=18.79;MQ0=82 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227064 . T . 97.23 mq_score:50 AN=2;DP=106;MQ=18.79;MQ0=82 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227065 . T . 100.23 mq_score:50 AN=2;DP=108;MQ=18.62;MQ0=84 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227066 . C . 97.23 mq_score:50 AN=2;DP=106;MQ=18.38;MQ0=83 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227067 . A . 79.23 mq_score:50;min_depth:100 AN=2;DP=99;MQ=16.76;MQ0=81 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227068 . T . 82.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=16.85;MQ0=80 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227069 . T . 82.23 mq_score:50;min_depth:100 AN=2;DP=99;MQ=16.76;MQ0=81 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227070 . A . 82.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=16.94;MQ0=79 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227071 . C . 82.23 mq_score:50;min_depth:100 AN=2;DP=95;MQ=17.11;MQ0=77 GT:DP 0/0:95 -gi|15829254|ref|NC_002695.1| 227072 . G . 82.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.3;MQ0=75 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227073 . A . 82.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.3;MQ0=75 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227074 . A . 82.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.3;MQ0=75 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227075 . G . 82.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=16.94;MQ0=79 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227076 . T . 82.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=16.94;MQ0=79 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227077 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=17.33;MQ0=79 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227078 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=17.42;MQ0=78 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227079 . A . 85.23 mq_score:50 AN=2;DP=102;MQ=16.98;MQ0=83 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227080 . A . 85.23 mq_score:50 AN=2;DP=100;MQ=17.15;MQ0=81 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227081 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=99;MQ=17.24;MQ0=80 GT:DP 0/0:99 -gi|15829254|ref|NC_002695.1| 227082 . T . 76.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=16.44;MQ0=80 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227083 . C . 79.23 mq_score:50;min_depth:100 AN=2;DP=95;MQ=16.61;MQ0=78 GT:DP 0/0:95 -gi|15829254|ref|NC_002695.1| 227084 . T . 79.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227085 . T . 79.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227086 . T . 79.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=16.7;MQ0=77 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227087 . G . 76.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=16.7;MQ0=77 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227088 . A . 79.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=16.7;MQ0=77 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227089 . G . 76.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227090 . C . 79.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=16.79;MQ0=76 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227091 . A . 76.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=16.45;MQ0=75 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227092 . T . 76.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=16.45;MQ0=75 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227093 . C . 76.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=16.63;MQ0=73 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227094 . A . 76.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=16.73;MQ0=72 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227095 . A . 73.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227096 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227097 . C . 76.23 mq_score:50;min_depth:100 AN=2;DP=86;MQ=16.92;MQ0=70 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227098 . T . 76.23 mq_score:50;min_depth:100 AN=2;DP=86;MQ=16.92;MQ0=70 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227099 . T . 73.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227100 . T . 73.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227101 . T . 76.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=17.02;MQ0=69 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227102 . A . 79.23 mq_score:50;min_depth:100 AN=2;DP=86;MQ=17.46;MQ0=69 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227103 . A . 76.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=17.57;MQ0=68 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227104 . A . 82.23 mq_score:50;min_depth:100 AN=2;DP=86;MQ=17.99;MQ0=68 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227105 . T . 79.23 mq_score:50;min_depth:100 AN=2;DP=86;MQ=17.99;MQ0=68 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227106 . T . 73.23 mq_score:50;min_depth:100 AN=2;DP=84;MQ=17.12;MQ0=68 GT:DP 0/0:84 -gi|15829254|ref|NC_002695.1| 227107 . G . 73.23 mq_score:50;min_depth:100 AN=2;DP=84;MQ=17.12;MQ0=68 GT:DP 0/0:84 -gi|15829254|ref|NC_002695.1| 227108 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=83;MQ=16.66;MQ0=68 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227109 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=80;MQ=16.97;MQ0=65 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227110 . G . 73.23 mq_score:50;min_depth:100 AN=2;DP=85;MQ=16.46;MQ0=70 GT:DP 0/0:85 -gi|15829254|ref|NC_002695.1| 227111 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=83;MQ=16.66;MQ0=68 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227112 . G . 70.23 mq_score:50;min_depth:100 AN=2;DP=86;MQ=16.36;MQ0=71 GT:DP 0/0:86 -gi|15829254|ref|NC_002695.1| 227113 . T . 70.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=16.18;MQ0=73 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227114 . T . 73.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=16.18;MQ0=73 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227115 . T . 73.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=15.99;MQ0=75 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227116 . G . 70.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=15.52;MQ0=75 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227117 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=15.52;MQ0=75 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227118 . T . 70.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=15.34;MQ0=77 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227119 . C . 67.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=14.84;MQ0=77 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227120 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=15.26;MQ0=78 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227121 . T . 67.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=14.76;MQ0=78 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227122 . G . 76.23 mq_score:50 AN=2;DP=101;MQ=15.3;MQ0=85 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227123 . G . 76.23 mq_score:50 AN=2;DP=101;MQ=15.3;MQ0=85 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227124 . C . 76.23 mq_score:50 AN=2;DP=101;MQ=15.3;MQ0=85 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227125 . T . 82.23 mq_score:50 AN=2;DP=104;MQ=16.07;MQ0=86 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227126 . C . 82.23 mq_score:50 AN=2;DP=106;MQ=15.92;MQ0=88 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227127 . A . 82.23 mq_score:50 AN=2;DP=107;MQ=15.84;MQ0=89 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227128 . G . 82.23 mq_score:50 AN=2;DP=107;MQ=15.84;MQ0=89 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227129 . A . 79.23 mq_score:50 AN=2;DP=106;MQ=15.92;MQ0=88 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227130 . T . 85.23 mq_score:50 AN=2;DP=106;MQ=16.38;MQ0=87 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227131 . T . 85.23 mq_score:50 AN=2;DP=105;MQ=16.46;MQ0=86 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227132 . G . 82.23 mq_score:50 AN=2;DP=105;MQ=16.46;MQ0=86 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227133 . A . 85.23 mq_score:50 AN=2;DP=105;MQ=16.46;MQ0=86 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227134 . A . 85.23 mq_score:50 AN=2;DP=106;MQ=16.38;MQ0=87 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227135 . C . 85.23 mq_score:50 AN=2;DP=106;MQ=16.38;MQ0=87 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227136 . G . 76.23 mq_score:50 AN=2;DP=104;MQ=15.58;MQ0=87 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227137 . C . 73.23 mq_score:50 AN=2;DP=102;MQ=15.23;MQ0=86 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227138 . T . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227139 . G . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227140 . G . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227141 . C . 76.23 mq_score:50 AN=2;DP=100;MQ=15.38;MQ0=84 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227142 . G . 76.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=15.61;MQ0=81 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227143 . G . 76.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=15.95;MQ0=77 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227144 . C . 76.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=16.03;MQ0=76 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227145 . A . 76.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=15.95;MQ0=77 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227146 . G . 76.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=15.61;MQ0=81 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227147 . G . 76.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=15.61;MQ0=81 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227148 . C . 73.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=15.7;MQ0=80 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227149 . C . 76.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=15.7;MQ0=80 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227150 . T . 76.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=15.7;MQ0=80 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227151 . A . 76.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=15.53;MQ0=82 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227152 . A . 76.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=15.53;MQ0=82 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227153 . C . 76.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=15.53;MQ0=82 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227154 . A . 73.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=15.08;MQ0=82 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227155 . C . 73.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=15.16;MQ0=81 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227156 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=15.26;MQ0=78 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227157 . T . 67.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=15.43;MQ0=76 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227158 . G . 70.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227159 . C . 70.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227160 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227161 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=15.69;MQ0=73 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227162 . G . 70.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=15.6;MQ0=74 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227163 . T . 79.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.07;MQ0=73 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227164 . C . 79.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.07;MQ0=73 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227165 . G . 79.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227166 . A . 79.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227167 . A . 79.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227168 . C . 79.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.17;MQ0=72 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227169 . G . 79.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=17.26;MQ0=71 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227170 . G . 79.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=16.88;MQ0=75 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227171 . T . 79.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=16.88;MQ0=75 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227172 . A . 79.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=16.88;MQ0=75 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227173 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=17.69;MQ0=75 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227174 . C . 85.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=17.69;MQ0=75 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227175 . A . 88.23 mq_score:50;min_depth:100 AN=2;DP=92;MQ=18.1;MQ0=72 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227176 . G . 88.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=17.91;MQ0=74 GT:DP 0/0:94 -gi|15829254|ref|NC_002695.1| 227177 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=17.07;MQ0=79 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227178 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=98;MQ=17.07;MQ0=79 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227179 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227180 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227181 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227182 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227183 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=93;MQ=17.52;MQ0=74 GT:DP 0/0:93 -gi|15829254|ref|NC_002695.1| 227184 . C . 85.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=17.71;MQ0=72 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227185 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=91;MQ=17.71;MQ0=72 GT:DP 0/0:91 -gi|15829254|ref|NC_002695.1| 227186 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227187 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227188 . C . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227189 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227190 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227191 . C . 82.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227192 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227193 . T . 82.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227194 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227195 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=90;MQ=17.81;MQ0=71 GT:DP 0/0:90 -gi|15829254|ref|NC_002695.1| 227196 . C . 85.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227197 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227198 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227199 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227200 . C . 85.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=18.12;MQ0=68 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227201 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=18.01;MQ0=69 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227202 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=18.01;MQ0=69 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227203 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=18.01;MQ0=69 GT:DP 0/0:88 -gi|15829254|ref|NC_002695.1| 227204 . T . 82.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=17.6;MQ0=69 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227205 . G . 82.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=17.6;MQ0=69 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227206 . G . 82.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=17.6;MQ0=69 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227207 . C . 82.23 mq_score:50;min_depth:100 AN=2;DP=88;MQ=17.5;MQ0=70 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227208 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227209 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=89;MQ=17.91;MQ0=70 GT:DP 0/0:89 -gi|15829254|ref|NC_002695.1| 227210 . A . 85.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=18.66;MQ0=63 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227211 . C . 85.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=18.66;MQ0=63 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227212 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=80;MQ=18.89;MQ0=61 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227213 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=79;MQ=19.01;MQ0=60 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227214 . G . 85.23 mq_score:50;min_depth:100 AN=2;DP=79;MQ=19.01;MQ0=60 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227215 . T . 85.23 mq_score:50;min_depth:100 AN=2;DP=74;MQ=19.64;MQ0=55 GT:DP 0/0:74 -gi|15829254|ref|NC_002695.1| 227216 . G . 88.23 mq_score:50;min_depth:100 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:76 -gi|15829254|ref|NC_002695.1| 227217 . A . 88.23 mq_score:50;min_depth:100 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:76 -gi|15829254|ref|NC_002695.1| 227218 . G . 88.23 mq_score:50;min_depth:100 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:76 -gi|15829254|ref|NC_002695.1| 227219 . T . 88.23 mq_score:50;min_depth:100 AN=2;DP=76;MQ=19.92;MQ0=56 GT:DP 0/0:75 -gi|15829254|ref|NC_002695.1| 227220 . A . 82.23 mq_score:50;min_depth:100 AN=2;DP=73;MQ=19.22;MQ0=55 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227221 . A . 82.23 mq_score:50;min_depth:100 AN=2;DP=73;MQ=19.22;MQ0=55 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227222 . T . 73.23 mq_score:50;min_depth:100 AN=2;DP=63;MQ=19.16;MQ0=48 GT:DP 0/0:63 -gi|15829254|ref|NC_002695.1| 227223 . G . 73.23 mq_score:50;min_depth:100 AN=2;DP=65;MQ=18.86;MQ0=50 GT:DP 0/0:64 -gi|15829254|ref|NC_002695.1| 227224 . T . 70.23 mq_score:50;min_depth:100 AN=2;DP=65;MQ=18.86;MQ0=50 GT:DP 0/0:65 -gi|15829254|ref|NC_002695.1| 227225 . C . 67.23 mq_score:50;min_depth:100 AN=2;DP=61;MQ=18.07;MQ0=48 GT:DP 0/0:61 -gi|15829254|ref|NC_002695.1| 227226 . T . 67.23 mq_score:50;min_depth:100 AN=2;DP=58;MQ=18.54;MQ0=45 GT:DP 0/0:58 -gi|15829254|ref|NC_002695.1| 227227 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227228 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227229 . G . 64.23 mq_score:50;min_depth:100 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227230 . A . 64.23 mq_score:50;min_depth:100 AN=2;DP=55;MQ=18.26;MQ0=43 GT:DP 0/0:55 -gi|15829254|ref|NC_002695.1| 227231 . A . 58.23 mq_score:50;min_depth:100 AN=2;DP=53;MQ=17.77;MQ0=42 GT:DP 0/0:53 -gi|15829254|ref|NC_002695.1| 227232 . A . 61.23 mq_score:50;min_depth:100 AN=2;DP=49;MQ=18.48;MQ0=38 GT:DP 0/0:49 -gi|15829254|ref|NC_002695.1| 227233 . C . 61.23 mq_score:50;min_depth:100 AN=2;DP=49;MQ=18.48;MQ0=38 GT:DP 0/0:49 -gi|15829254|ref|NC_002695.1| 227234 . T . 61.23 mq_score:50;min_depth:100 AN=2;DP=48;MQ=18.67;MQ0=37 GT:DP 0/0:48 -gi|15829254|ref|NC_002695.1| 227235 . G . 61.23 mq_score:50;min_depth:100 AN=2;DP=50;MQ=18.29;MQ0=39 GT:DP 0/0:48 -gi|15829254|ref|NC_002695.1| 227236 . C . 61.23 mq_score:50;min_depth:100 AN=2;DP=50;MQ=18.29;MQ0=39 GT:DP 0/0:50 -gi|15829254|ref|NC_002695.1| 227237 . C . 64.23 mq_score:50;min_depth:100 AN=2;DP=51;MQ=18.96;MQ0=39 GT:DP 0/0:51 -gi|15829254|ref|NC_002695.1| 227238 . T . 64.23 mq_score:50;min_depth:100 AN=2;DP=51;MQ=18.96;MQ0=39 GT:DP 0/0:51 -gi|15829254|ref|NC_002695.1| 227239 . G . 64.23 mq_score:50;min_depth:100 AN=2;DP=52;MQ=18.77;MQ0=40 GT:DP 0/0:52 -gi|15829254|ref|NC_002695.1| 227240 . A . 64.23 mq_score:50;min_depth:100 AN=2;DP=54;MQ=18.42;MQ0=42 GT:DP 0/0:54 -gi|15829254|ref|NC_002695.1| 227241 . T . 61.23 mq_score:50;min_depth:100 AN=2;DP=54;MQ=18.42;MQ0=42 GT:DP 0/0:54 -gi|15829254|ref|NC_002695.1| 227242 . G . 64.23 mq_score:50;min_depth:100 AN=2;DP=53;MQ=18.6;MQ0=41 GT:DP 0/0:53 -gi|15829254|ref|NC_002695.1| 227243 . G . 64.23 mq_score:50;min_depth:100 AN=2;DP=52;MQ=18.77;MQ0=40 GT:DP 0/0:52 -gi|15829254|ref|NC_002695.1| 227244 . A . 64.23 mq_score:50;min_depth:100 AN=2;DP=50;MQ=19.15;MQ0=38 GT:DP 0/0:50 -gi|15829254|ref|NC_002695.1| 227245 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=51;MQ=19.77;MQ0=38 GT:DP 0/0:51 -gi|15829254|ref|NC_002695.1| 227246 . A . 67.23 mq_score:50;min_depth:100 AN=2;DP=48;MQ=20.38;MQ0=35 GT:DP 0/0:48 -gi|15829254|ref|NC_002695.1| 227247 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=56;MQ=18.86;MQ0=43 GT:DP 0/0:56 -gi|15829254|ref|NC_002695.1| 227248 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227249 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=58;MQ=18.54;MQ0=45 GT:DP 0/0:58 -gi|15829254|ref|NC_002695.1| 227250 . A . 67.23 mq_score:50;min_depth:100 AN=2;DP=57;MQ=18.7;MQ0=44 GT:DP 0/0:57 -gi|15829254|ref|NC_002695.1| 227251 . T . 70.23 mq_score:50;min_depth:100 AN=2;DP=62;MQ=18.63;MQ0=48 GT:DP 0/0:62 -gi|15829254|ref|NC_002695.1| 227252 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=63;MQ=18.49;MQ0=49 GT:DP 0/0:63 -gi|15829254|ref|NC_002695.1| 227253 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=63;MQ=18.49;MQ0=49 GT:DP 0/0:63 -gi|15829254|ref|NC_002695.1| 227254 . C . 70.23 mq_score:50;min_depth:100 AN=2;DP=64;MQ=18.34;MQ0=50 GT:DP 0/0:64 -gi|15829254|ref|NC_002695.1| 227255 . T . 67.23 mq_score:50;min_depth:100 AN=2;DP=60;MQ=18.22;MQ0=47 GT:DP 0/0:60 -gi|15829254|ref|NC_002695.1| 227256 . A . 64.23 mq_score:50;min_depth:100 AN=2;DP=61;MQ=17.33;MQ0=49 GT:DP 0/0:61 -gi|15829254|ref|NC_002695.1| 227257 . C . 64.23 mq_score:50;min_depth:100 AN=2;DP=66;MQ=16.66;MQ0=54 GT:DP 0/0:66 -gi|15829254|ref|NC_002695.1| 227258 . T . 67.23 mq_score:50;min_depth:100 AN=2;DP=67;MQ=17.25;MQ0=54 GT:DP 0/0:67 -gi|15829254|ref|NC_002695.1| 227259 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=68;MQ=17.12;MQ0=55 GT:DP 0/0:68 -gi|15829254|ref|NC_002695.1| 227260 . G . 67.23 mq_score:50;min_depth:100 AN=2;DP=70;MQ=16.87;MQ0=57 GT:DP 0/0:70 -gi|15829254|ref|NC_002695.1| 227261 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=73;MQ=17.17;MQ0=59 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227262 . A . 70.23 mq_score:50;min_depth:100 AN=2;DP=73;MQ=17.17;MQ0=59 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227263 . A . 61.23 mq_score:50;min_depth:100 AN=2;DP=67;MQ=15.8;MQ0=56 GT:DP 0/0:67 -gi|15829254|ref|NC_002695.1| 227264 . C . 61.23 mq_score:50;min_depth:100 AN=2;DP=70;MQ=15.46;MQ0=59 GT:DP 0/0:70 -gi|15829254|ref|NC_002695.1| 227265 . G . 61.23 mq_score:50;min_depth:100 AN=2;DP=69;MQ=15.57;MQ0=58 GT:DP 0/0:69 -gi|15829254|ref|NC_002695.1| 227266 . G . 61.23 mq_score:50;min_depth:100 AN=2;DP=73;MQ=15.14;MQ0=62 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227267 . T . 61.23 mq_score:50;min_depth:100 AN=2;DP=73;MQ=15.14;MQ0=62 GT:DP 0/0:73 -gi|15829254|ref|NC_002695.1| 227268 . A . 61.23 mq_score:50;min_depth:100 AN=2;DP=83;MQ=14.2;MQ0=72 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227269 . G . 61.23 mq_score:50;min_depth:100 AN=2;DP=83;MQ=14.2;MQ0=72 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227270 . C . 61.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=14.28;MQ0=71 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227271 . T . 61.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=14.28;MQ0=71 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227272 . A . 61.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=14.28;MQ0=71 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227273 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=81;MQ=12.92;MQ0=72 GT:DP 0/0:81 -gi|15829254|ref|NC_002695.1| 227274 . T . 55.23 mq_score:50;min_depth:100 AN=2;DP=83;MQ=12.77;MQ0=74 GT:DP 0/0:83 -gi|15829254|ref|NC_002695.1| 227275 . A . 49.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=12.49;MQ0=74 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227276 . C . 52.23 mq_score:50;min_depth:100 AN=2;DP=82;MQ=12.49;MQ0=74 GT:DP 0/0:82 -gi|15829254|ref|NC_002695.1| 227277 . C . 52.23 mq_score:50;min_depth:100 AN=2;DP=77;MQ=12.89;MQ0=69 GT:DP 0/0:77 -gi|15829254|ref|NC_002695.1| 227278 . G . 52.23 mq_score:50;min_depth:100 AN=2;DP=79;MQ=12.73;MQ0=71 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227279 . C . 55.23 mq_score:50;min_depth:100 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227280 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227281 . T . 55.23 mq_score:50;min_depth:100 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227282 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227283 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227284 . C . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227285 . G . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227286 . T . 55.23 mq_score:50;min_depth:100 AN=2;DP=79;MQ=13.5;MQ0=70 GT:DP 0/0:79 -gi|15829254|ref|NC_002695.1| 227287 . C . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227288 . G . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227289 . C . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:77 -gi|15829254|ref|NC_002695.1| 227290 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=78;MQ=13.59;MQ0=69 GT:DP 0/0:78 -gi|15829254|ref|NC_002695.1| 227291 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=80;MQ=13.42;MQ0=71 GT:DP 0/0:80 -gi|15829254|ref|NC_002695.1| 227292 . G . 55.23 mq_score:50;min_depth:100 AN=2;DP=87;MQ=12.87;MQ0=78 GT:DP 0/0:87 -gi|15829254|ref|NC_002695.1| 227293 . A . 52.23 mq_score:50;min_depth:100 AN=2;DP=94;MQ=12.38;MQ0=85 GT:DP 0/0:92 -gi|15829254|ref|NC_002695.1| 227294 . C . 55.23 mq_score:50;min_depth:100 AN=2;DP=95;MQ=12.31;MQ0=86 GT:DP 0/0:95 -gi|15829254|ref|NC_002695.1| 227295 . C . 55.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=12.25;MQ0=87 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227296 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=96;MQ=12.25;MQ0=87 GT:DP 0/0:96 -gi|15829254|ref|NC_002695.1| 227297 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=12.18;MQ0=88 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227298 . A . 55.23 mq_score:50;min_depth:100 AN=2;DP=97;MQ=12.18;MQ0=88 GT:DP 0/0:97 -gi|15829254|ref|NC_002695.1| 227299 . G . 55.23 mq_score:50 AN=2;DP=101;MQ=11.94;MQ0=92 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227300 . A . 55.23 mq_score:50 AN=2;DP=101;MQ=11.94;MQ0=92 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227301 . G . 55.23 mq_score:50 AN=2;DP=100;MQ=12.0;MQ0=91 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227302 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227303 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227304 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227305 . G . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227306 . A . 55.23 mq_score:50 AN=2;DP=103;MQ=11.82;MQ0=94 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227307 . C . 55.23 mq_score:50 AN=2;DP=107;MQ=11.6;MQ0=98 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227308 . C . 52.23 mq_score:50 AN=2;DP=106;MQ=10.99;MQ0=98 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227309 . T . 52.23 mq_score:50 AN=2;DP=109;MQ=10.84;MQ0=101 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227310 . T . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227311 . C . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227312 . G . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227313 . G . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227314 . G . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227315 . C . 52.23 mq_score:50 AN=2;DP=110;MQ=10.79;MQ0=102 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227316 . C . 49.23 mq_score:50 AN=2;DP=108;MQ=10.18;MQ0=101 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227317 . T . 49.23 mq_score:50 AN=2;DP=106;MQ=10.28;MQ0=99 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227318 . C . 49.23 mq_score:50 AN=2;DP=107;MQ=10.23;MQ0=100 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227319 . T . 49.23 mq_score:50 AN=2;DP=107;MQ=10.23;MQ0=100 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227320 . T . 49.23 mq_score:50 AN=2;DP=108;MQ=10.18;MQ0=101 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227321 . G . 49.23 mq_score:50 AN=2;DP=108;MQ=10.18;MQ0=101 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227322 . C . 49.23 mq_score:50 AN=2;DP=107;MQ=10.23;MQ0=100 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227323 . C . 49.23 mq_score:50 AN=2;DP=106;MQ=10.28;MQ0=99 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227324 . A . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227325 . T . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227326 . C . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227327 . G . 49.23 mq_score:50 AN=2;DP=109;MQ=10.14;MQ0=102 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227328 . G . 49.23 mq_score:50 AN=2;DP=111;MQ=10.04;MQ0=104 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227329 . A . 49.23 mq_score:50 AN=2;DP=112;MQ=10.0;MQ0=105 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227330 . T . 49.23 mq_score:50 AN=2;DP=113;MQ=9.96;MQ0=106 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227331 . G . 49.23 mq_score:50 AN=2;DP=115;MQ=9.87;MQ0=108 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227332 . T . 49.23 mq_score:50 AN=2;DP=115;MQ=9.87;MQ0=108 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227333 . G . 49.23 mq_score:50 AN=2;DP=117;MQ=9.78;MQ0=110 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227334 . C . 49.23 mq_score:50 AN=2;DP=117;MQ=9.78;MQ0=110 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227335 . C . 49.23 mq_score:50 AN=2;DP=116;MQ=9.83;MQ0=109 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227336 . C . 49.23 mq_score:50 AN=2;DP=116;MQ=9.83;MQ0=109 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227337 . A . 46.23 mq_score:50 AN=2;DP=116;MQ=9.1;MQ0=110 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227338 . G . 46.23 mq_score:50 AN=2;DP=117;MQ=9.06;MQ0=111 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227339 . A . 46.23 mq_score:50 AN=2;DP=116;MQ=9.1;MQ0=110 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227340 . T . 46.23 mq_score:50 AN=2;DP=115;MQ=9.14;MQ0=109 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227341 . G . 46.23 mq_score:50 AN=2;DP=116;MQ=9.1;MQ0=110 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227342 . G . 49.23 mq_score:50 AN=2;DP=129;MQ=9.32;MQ0=122 GT:DP 0/0:129 -gi|15829254|ref|NC_002695.1| 227343 . G . 49.23 mq_score:50 AN=2;DP=129;MQ=9.32;MQ0=122 GT:DP 0/0:129 -gi|15829254|ref|NC_002695.1| 227344 . A . 49.23 mq_score:50 AN=2;DP=129;MQ=9.32;MQ0=122 GT:DP 0/0:129 -gi|15829254|ref|NC_002695.1| 227345 . T . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227346 . T . 43.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:127 -gi|15829254|ref|NC_002695.1| 227347 . A . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227348 . G . 46.23 mq_score:50 AN=2;DP=127;MQ=8.69;MQ0=121 GT:DP 0/0:127 -gi|15829254|ref|NC_002695.1| 227349 . C . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227350 . T . 46.23 mq_score:50 AN=2;DP=128;MQ=8.66;MQ0=122 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227351 . A . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227352 . G . 43.23 mq_score:50 AN=2;DP=124;MQ=8.03;MQ0=119 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227353 . T . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227354 . A . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227355 . G . 43.23 mq_score:50 AN=2;DP=125;MQ=8.0;MQ0=120 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227356 . G . 43.23 mq_score:50 AN=2;DP=123;MQ=8.06;MQ0=118 GT:DP 0/0:123 -gi|15829254|ref|NC_002695.1| 227357 . T . 46.23 mq_score:50 AN=2;DP=119;MQ=8.98;MQ0=113 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227358 . G . 43.23 mq_score:50 AN=2;DP=117;MQ=8.27;MQ0=112 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227359 . G . 43.23 mq_score:50 AN=2;DP=121;MQ=8.13;MQ0=116 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227360 . G . 43.23 mq_score:50 AN=2;DP=119;MQ=8.2;MQ0=114 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227361 . G . 40.23 mq_score:50 AN=2;DP=116;MQ=7.43;MQ0=112 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227362 . T . 40.23 mq_score:50 AN=2;DP=116;MQ=7.43;MQ0=112 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227363 . A . 40.23 mq_score:50 AN=2;DP=115;MQ=7.46;MQ0=111 GT:DP 0/0:115 -gi|15829254|ref|NC_002695.1| 227364 . A . 40.23 mq_score:50 AN=2;DP=113;MQ=7.53;MQ0=109 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227365 . C . 40.23 mq_score:50 AN=2;DP=114;MQ=7.49;MQ0=110 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227366 . G . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227367 . G . 40.23 mq_score:50 AN=2;DP=111;MQ=7.59;MQ0=107 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227368 . C . 40.23 mq_score:50 AN=2;DP=105;MQ=7.81;MQ0=101 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227369 . T . 40.23 mq_score:50 AN=2;DP=104;MQ=7.84;MQ0=100 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227370 . C . 40.23 mq_score:50 AN=2;DP=106;MQ=7.77;MQ0=102 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227371 . A . 40.23 mq_score:50 AN=2;DP=106;MQ=7.77;MQ0=102 GT:DP 0/0:106 -gi|15829254|ref|NC_002695.1| 227372 . C . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227373 . C . 40.23 mq_score:50 AN=2;DP=109;MQ=7.66;MQ0=105 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227374 . T . 40.23 mq_score:50 AN=2;DP=111;MQ=7.59;MQ0=107 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227375 . A . 40.23 mq_score:50 AN=2;DP=111;MQ=7.59;MQ0=107 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227376 . G . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227377 . G . 40.23 mq_score:50 AN=2;DP=110;MQ=7.63;MQ0=106 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227378 . C . 40.23 mq_score:50 AN=2;DP=109;MQ=7.66;MQ0=105 GT:DP 0/0:109 -gi|15829254|ref|NC_002695.1| 227379 . G . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227380 . A . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227381 . C . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227382 . G . 37.23 mq_score:50 AN=2;DP=108;MQ=6.67;MQ0=105 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227383 . A . 37.23 mq_score:50 AN=2;DP=119;MQ=6.35;MQ0=116 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227384 . T . 37.23 mq_score:50 AN=2;DP=124;MQ=6.22;MQ0=121 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227385 . C . 37.23 mq_score:50 AN=2;DP=124;MQ=6.22;MQ0=121 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227386 . C . 37.23 mq_score:50 AN=2;DP=123;MQ=6.25;MQ0=120 GT:DP 0/0:123 -gi|15829254|ref|NC_002695.1| 227387 . C . 37.23 mq_score:50 AN=2;DP=125;MQ=6.2;MQ0=122 GT:DP 0/0:125 -gi|15829254|ref|NC_002695.1| 227388 . T . 37.23 mq_score:50 AN=2;DP=128;MQ=6.12;MQ0=125 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227389 . A . 37.23 mq_score:50 AN=2;DP=128;MQ=6.12;MQ0=125 GT:DP 0/0:128 -gi|15829254|ref|NC_002695.1| 227390 . G . 37.23 mq_score:50 AN=2;DP=126;MQ=6.17;MQ0=123 GT:DP 0/0:126 -gi|15829254|ref|NC_002695.1| 227391 . C . 37.23 mq_score:50 AN=2;DP=126;MQ=6.17;MQ0=123 GT:DP 0/0:126 -gi|15829254|ref|NC_002695.1| 227392 . T . 37.23 mq_score:50 AN=2;DP=119;MQ=6.35;MQ0=116 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227393 . G . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227394 . G . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227395 . T . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227396 . C . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227397 . T . 37.23 mq_score:50 AN=2;DP=113;MQ=6.52;MQ0=110 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227398 . G . 37.23 mq_score:50 AN=2;DP=114;MQ=6.49;MQ0=111 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227399 . A . 37.23 mq_score:50 AN=2;DP=111;MQ=6.58;MQ0=108 GT:DP 0/0:111 -gi|15829254|ref|NC_002695.1| 227400 . G . 37.23 mq_score:50 AN=2;DP=112;MQ=6.55;MQ0=109 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227401 . A . 37.23 mq_score:50 AN=2;DP=112;MQ=6.55;MQ0=109 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227402 . G . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227403 . G . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227404 . A . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227405 . T . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227406 . G . 34.23 mq_score:50 AN=2;DP=108;MQ=5.44;MQ0=106 GT:DP 0/0:108 -gi|15829254|ref|NC_002695.1| 227407 . A . 34.23 mq_score:50 AN=2;DP=104;MQ=5.55;MQ0=102 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227408 . C . 34.23 mq_score:50 AN=2;DP=104;MQ=5.55;MQ0=102 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227409 . C . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227410 . A . 34.23 mq_score:50 AN=2;DP=100;MQ=5.66;MQ0=98 GT:DP 0/0:100 -gi|15829254|ref|NC_002695.1| 227411 . G . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227412 . C . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227413 . C . 34.23 mq_score:50 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227414 . A . 34.23 mq_score:50;min_depth:100 AN=2;DP=101;MQ=5.63;MQ0=99 GT:DP 0/0:98 -gi|15829254|ref|NC_002695.1| 227415 . C . 34.23 mq_score:50 AN=2;DP=112;MQ=5.35;MQ0=110 GT:DP 0/0:112 -gi|15829254|ref|NC_002695.1| 227416 . A . 34.23 mq_score:50 AN=2;DP=116;MQ=5.25;MQ0=114 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227417 . C . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227418 . T . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227419 . G . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227420 . G . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227421 . A . 34.23 mq_score:50 AN=2;DP=119;MQ=5.19;MQ0=117 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227422 . A . 34.23 mq_score:50 AN=2;DP=119;MQ=5.19;MQ0=117 GT:DP 0/0:119 -gi|15829254|ref|NC_002695.1| 227423 . C . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227424 . T . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227425 . G . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227426 . A . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227427 . G . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227428 . A . 34.23 mq_score:50 AN=2;DP=118;MQ=5.21;MQ0=116 GT:DP 0/0:118 -gi|15829254|ref|NC_002695.1| 227429 . C . 34.23 mq_score:50 AN=2;DP=117;MQ=5.23;MQ0=115 GT:DP 0/0:117 -gi|15829254|ref|NC_002695.1| 227430 . A . 34.23 mq_score:50 AN=2;DP=116;MQ=5.25;MQ0=114 GT:DP 0/0:116 -gi|15829254|ref|NC_002695.1| 227431 . C . 34.23 mq_score:50 AN=2;DP=114;MQ=5.3;MQ0=112 GT:DP 0/0:114 -gi|15829254|ref|NC_002695.1| 227432 . G . 34.23 mq_score:50 AN=2;DP=113;MQ=5.32;MQ0=111 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227433 . G . 34.23 mq_score:50 AN=2;DP=120;MQ=5.16;MQ0=118 GT:DP 0/0:120 -gi|15829254|ref|NC_002695.1| 227434 . T . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227435 . C . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227436 . C . 34.23 mq_score:50 AN=2;DP=122;MQ=5.12;MQ0=120 GT:DP 0/0:122 -gi|15829254|ref|NC_002695.1| 227437 . A . 34.23 mq_score:50 AN=2;DP=121;MQ=5.14;MQ0=119 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227438 . G . 34.23 mq_score:50 AN=2;DP=122;MQ=5.12;MQ0=120 GT:DP 0/0:122 -gi|15829254|ref|NC_002695.1| 227439 . A . 34.23 mq_score:50 AN=2;DP=123;MQ=5.1;MQ0=121 GT:DP 0/0:121 -gi|15829254|ref|NC_002695.1| 227440 . C . 34.23 mq_score:50 AN=2;DP=126;MQ=5.04;MQ0=124 GT:DP 0/0:126 -gi|15829254|ref|NC_002695.1| 227441 . T . 34.23 mq_score:50 AN=2;DP=124;MQ=5.08;MQ0=122 GT:DP 0/0:124 -gi|15829254|ref|NC_002695.1| 227442 . C . 31.24 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227443 . C . 31.24 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227444 . T . 31.23 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227445 . A . 31.23 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:110 -gi|15829254|ref|NC_002695.1| 227446 . C . 31.23 mq_score:50 AN=2;DP=113;MQ=3.76;MQ0=112 GT:DP 0/0:113 -gi|15829254|ref|NC_002695.1| 227447 . G . 31.23 mq_score:50 AN=2;DP=104;MQ=3.92;MQ0=103 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227448 . G . 31.23 mq_score:50 AN=2;DP=107;MQ=3.87;MQ0=106 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227449 . G . 31.23 mq_score:50 AN=2;DP=105;MQ=3.9;MQ0=104 GT:DP 0/0:105 -gi|15829254|ref|NC_002695.1| 227450 . A . 31.23 mq_score:50 AN=2;DP=107;MQ=3.87;MQ0=106 GT:DP 0/0:107 -gi|15829254|ref|NC_002695.1| 227451 . G . 31.23 mq_score:50 AN=2;DP=103;MQ=3.94;MQ0=102 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227452 . G . 31.23 mq_score:50 AN=2;DP=102;MQ=3.96;MQ0=101 GT:DP 0/0:101 -gi|15829254|ref|NC_002695.1| 227453 . C . 31.23 mq_score:50 AN=2;DP=103;MQ=3.94;MQ0=102 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227454 . A . 31.23 mq_score:50 AN=2;DP=102;MQ=3.96;MQ0=101 GT:DP 0/0:102 -gi|15829254|ref|NC_002695.1| 227455 . G . 31.23 mq_score:50 AN=2;DP=104;MQ=3.92;MQ0=103 GT:DP 0/0:104 -gi|15829254|ref|NC_002695.1| 227456 . C . 31.23 mq_score:50 AN=2;DP=103;MQ=3.94;MQ0=102 GT:DP 0/0:103 -gi|15829254|ref|NC_002695.1| 227457 . A . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227458 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227459 . T . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227460 . G . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227461 . G . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227462 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227463 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227464 . A . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227465 . A . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227466 . T . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227467 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227468 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227469 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227470 . G . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227471 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227472 . A . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227473 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227474 . A . . mq_score:50 DP=119;MQ=0.0;MQ0=119 GT ./. -gi|15829254|ref|NC_002695.1| 227475 . A . . mq_score:50 DP=119;MQ=0.0;MQ0=119 GT ./. -gi|15829254|ref|NC_002695.1| 227476 . T . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227477 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227478 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227479 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227480 . C . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227481 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227482 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227483 . A . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227484 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227485 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227486 . C . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227487 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227488 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227489 . G . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227490 . A . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227491 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227492 . G . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227493 . C . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227494 . A . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227495 . G . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227496 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227497 . C . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227498 . A . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227499 . T . . mq_score:50 DP=127;MQ=0.0;MQ0=127 GT ./. -gi|15829254|ref|NC_002695.1| 227500 . G . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227501 . C . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227502 . C . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227503 . G . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227504 . C . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227505 . G . . mq_score:50 DP=126;MQ=0.0;MQ0=126 GT ./. -gi|15829254|ref|NC_002695.1| 227506 . T . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227507 . G . . mq_score:50 DP=132;MQ=0.0;MQ0=132 GT ./. -gi|15829254|ref|NC_002695.1| 227508 . T . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227509 . A . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227510 . T . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227511 . G . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227512 . A . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227513 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227514 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227515 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227516 . A . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227517 . G . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227518 . G . . mq_score:50 DP=125;MQ=0.0;MQ0=125 GT ./. -gi|15829254|ref|NC_002695.1| 227519 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227520 . C . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227521 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227522 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227523 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227524 . G . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227525 . G . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227526 . G . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227527 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227528 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227529 . G . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227530 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227531 . A . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227532 . A . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227533 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227534 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227535 . T . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227536 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227537 . C . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227538 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227539 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227540 . T . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227541 . C . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227542 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227543 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227544 . C . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227545 . G . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227546 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227547 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227548 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227549 . A . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227550 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227551 . G . . mq_score:50 DP=133;MQ=0.0;MQ0=133 GT ./. -gi|15829254|ref|NC_002695.1| 227552 . A . . mq_score:50 DP=134;MQ=0.0;MQ0=134 GT ./. -gi|15829254|ref|NC_002695.1| 227553 . A . . mq_score:50 DP=135;MQ=0.0;MQ0=135 GT ./. -gi|15829254|ref|NC_002695.1| 227554 . G . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227555 . G . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227556 . G . . mq_score:50 DP=139;MQ=0.0;MQ0=139 GT ./. -gi|15829254|ref|NC_002695.1| 227557 . A . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227558 . G . . mq_score:50 DP=136;MQ=0.0;MQ0=136 GT ./. -gi|15829254|ref|NC_002695.1| 227559 . T . . mq_score:50 DP=136;MQ=0.0;MQ0=136 GT ./. -gi|15829254|ref|NC_002695.1| 227560 . A . . mq_score:50 DP=134;MQ=0.0;MQ0=134 GT ./. -gi|15829254|ref|NC_002695.1| 227561 . A . . mq_score:50 DP=134;MQ=0.0;MQ0=134 GT ./. -gi|15829254|ref|NC_002695.1| 227562 . A . . mq_score:50 DP=135;MQ=0.0;MQ0=135 GT ./. -gi|15829254|ref|NC_002695.1| 227563 . G . . mq_score:50 DP=143;MQ=0.0;MQ0=143 GT ./. -gi|15829254|ref|NC_002695.1| 227564 . T . . mq_score:50 DP=137;MQ=0.0;MQ0=137 GT ./. -gi|15829254|ref|NC_002695.1| 227565 . T . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227566 . A . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227567 . A . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227568 . T . . mq_score:50 DP=130;MQ=0.0;MQ0=130 GT ./. -gi|15829254|ref|NC_002695.1| 227569 . A . . mq_score:50 DP=128;MQ=0.0;MQ0=128 GT ./. -gi|15829254|ref|NC_002695.1| 227570 . C . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227571 . C . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227572 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227573 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227574 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227575 . G . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227576 . C . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227577 . T . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227578 . C . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227579 . A . . mq_score:50 DP=121;MQ=0.0;MQ0=121 GT ./. -gi|15829254|ref|NC_002695.1| 227580 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227581 . T . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227582 . G . . mq_score:50 DP=124;MQ=0.0;MQ0=124 GT ./. -gi|15829254|ref|NC_002695.1| 227583 . A . . mq_score:50 DP=123;MQ=0.0;MQ0=123 GT ./. -gi|15829254|ref|NC_002695.1| 227584 . C . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227585 . G . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227586 . T . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227587 . T . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227588 . A . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227589 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227590 . C . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227591 . C . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227592 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227593 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227594 . A . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227595 . G . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227596 . A . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227597 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227598 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227599 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227600 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227601 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227602 . C . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227603 . A . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227604 . C . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227605 . C . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227606 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227607 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227608 . C . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227609 . T . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227610 . A . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227611 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227612 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227613 . T . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227614 . C . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227615 . C . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227616 . G . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227617 . T . . mq_score:50;min_depth:100 DP=98;MQ=0.0;MQ0=98 GT ./. -gi|15829254|ref|NC_002695.1| 227618 . G . . mq_score:50;min_depth:100 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227619 . C . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227620 . C . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227621 . A . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227622 . G . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227623 . C . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227624 . A . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227625 . G . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227626 . C . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227627 . C . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227628 . G . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227629 . C . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227630 . G . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227631 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227632 . T . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227633 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227634 . A . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227635 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227636 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227637 . C . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227638 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227639 . G . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227640 . A . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227641 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227642 . G . . mq_score:50;min_depth:100 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227643 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227644 . T . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227645 . G . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227646 . C . . mq_score:50;min_depth:100 DP=98;MQ=0.0;MQ0=98 GT ./. -gi|15829254|ref|NC_002695.1| 227647 . A . . mq_score:50;min_depth:100 DP=98;MQ=0.0;MQ0=98 GT ./. -gi|15829254|ref|NC_002695.1| 227648 . A . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227649 . G . . mq_score:50;min_depth:100 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227650 . C . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227651 . G . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227652 . T . . mq_score:50;min_depth:100 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227653 . T . . mq_score:50;min_depth:100 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227654 . A . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227655 . A . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227656 . T . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227657 . C . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227658 . G . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227659 . G . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227660 . A . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227661 . A . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227662 . T . . mq_score:50;min_depth:100 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227663 . T . . mq_score:50;min_depth:100 DP=86;MQ=0.0;MQ0=86 GT ./. -gi|15829254|ref|NC_002695.1| 227664 . A . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227665 . C . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227666 . T . . mq_score:50;min_depth:100 DP=90;MQ=0.0;MQ0=90 GT ./. -gi|15829254|ref|NC_002695.1| 227667 . G . . mq_score:50;min_depth:100 DP=90;MQ=0.0;MQ0=90 GT ./. -gi|15829254|ref|NC_002695.1| 227668 . G . . mq_score:50;min_depth:100 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227669 . G . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227670 . C . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227671 . G . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227672 . T . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227673 . A . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227674 . A . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227675 . A . . mq_score:50;min_depth:100 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227676 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227677 . C . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227678 . G . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227679 . C . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227680 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227681 . C . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227682 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227683 . C . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227684 . A . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227685 . G . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227686 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227687 . C . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227688 . G . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227689 . G . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227690 . T . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227691 . T . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227692 . T . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227693 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227694 . T . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227695 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227696 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227697 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227698 . G . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227699 . T . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227700 . C . . mq_score:50 DP=118;MQ=0.0;MQ0=118 GT ./. -gi|15829254|ref|NC_002695.1| 227701 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227702 . G . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227703 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227704 . T . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227705 . G . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227706 . T . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227707 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227708 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227709 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227710 . A . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227711 . T . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227712 . C . . mq_score:50 DP=116;MQ=0.0;MQ0=116 GT ./. -gi|15829254|ref|NC_002695.1| 227713 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227714 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227715 . C . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227716 . G . . mq_score:50 DP=119;MQ=0.0;MQ0=119 GT ./. -gi|15829254|ref|NC_002695.1| 227717 . G . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227718 . G . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227719 . C . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227720 . T . . mq_score:50 DP=120;MQ=0.0;MQ0=120 GT ./. -gi|15829254|ref|NC_002695.1| 227721 . C . . mq_score:50 DP=127;MQ=0.0;MQ0=127 GT ./. -gi|15829254|ref|NC_002695.1| 227722 . A . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227723 . A . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227724 . C . . mq_score:50 DP=132;MQ=0.0;MQ0=132 GT ./. -gi|15829254|ref|NC_002695.1| 227725 . C . . mq_score:50 DP=131;MQ=0.0;MQ0=131 GT ./. -gi|15829254|ref|NC_002695.1| 227726 . T . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227727 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227728 . G . . mq_score:50 DP=129;MQ=0.0;MQ0=129 GT ./. -gi|15829254|ref|NC_002695.1| 227729 . G . . mq_score:50 DP=122;MQ=0.0;MQ0=122 GT ./. -gi|15829254|ref|NC_002695.1| 227730 . A . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227731 . A . . mq_score:50 DP=115;MQ=0.0;MQ0=115 GT ./. -gi|15829254|ref|NC_002695.1| 227732 . C . . mq_score:50 DP=117;MQ=0.0;MQ0=117 GT ./. -gi|15829254|ref|NC_002695.1| 227733 . T . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227734 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227735 . C . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227736 . A . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227737 . T . . mq_score:50 DP=114;MQ=0.0;MQ0=114 GT ./. -gi|15829254|ref|NC_002695.1| 227738 . C . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227739 . T . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227740 . G . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227741 . A . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227742 . T . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227743 . A . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227744 . C . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227745 . T . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227746 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227747 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227748 . C . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227749 . A . . mq_score:50 DP=108;MQ=0.0;MQ0=108 GT ./. -gi|15829254|ref|NC_002695.1| 227750 . A . . mq_score:50 DP=107;MQ=0.0;MQ0=107 GT ./. -gi|15829254|ref|NC_002695.1| 227751 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227752 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227753 . T . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227754 . T . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227755 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227756 . A . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227757 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227758 . T . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227759 . C . . mq_score:50 DP=112;MQ=0.0;MQ0=112 GT ./. -gi|15829254|ref|NC_002695.1| 227760 . T . . mq_score:50 DP=113;MQ=0.0;MQ0=113 GT ./. -gi|15829254|ref|NC_002695.1| 227761 . C . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227762 . G . . mq_score:50 DP=110;MQ=0.0;MQ0=110 GT ./. -gi|15829254|ref|NC_002695.1| 227763 . T . . mq_score:50 DP=111;MQ=0.0;MQ0=111 GT ./. -gi|15829254|ref|NC_002695.1| 227764 . A . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227765 . G . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227766 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227767 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227768 . G . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227769 . G . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227770 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227771 . G . . mq_score:50 DP=100;MQ=0.0;MQ0=100 GT ./. -gi|15829254|ref|NC_002695.1| 227772 . G . . mq_score:50 DP=100;MQ=0.0;MQ0=100 GT ./. -gi|15829254|ref|NC_002695.1| 227773 . T . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227774 . A . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227775 . G . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227776 . A . . mq_score:50 DP=100;MQ=0.0;MQ0=100 GT ./. -gi|15829254|ref|NC_002695.1| 227777 . A . . mq_score:50 DP=101;MQ=0.0;MQ0=101 GT ./. -gi|15829254|ref|NC_002695.1| 227778 . T . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227779 . T . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227780 . C . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227781 . C . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227782 . A . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227783 . G . . mq_score:50;min_depth:100 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227784 . G . . mq_score:50;min_depth:100 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227785 . T . . mq_score:50;min_depth:100 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227786 . G . . mq_score:50;min_depth:100 DP=90;MQ=0.0;MQ0=90 GT ./. -gi|15829254|ref|NC_002695.1| 227787 . T . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227788 . A . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227789 . G . . mq_score:50;min_depth:100 DP=88;MQ=0.0;MQ0=88 GT ./. -gi|15829254|ref|NC_002695.1| 227790 . C . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227791 . G . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227792 . G . . mq_score:50;min_depth:100 DP=87;MQ=0.0;MQ0=87 GT ./. -gi|15829254|ref|NC_002695.1| 227793 . T . . mq_score:50;min_depth:100 DP=84;MQ=0.0;MQ0=84 GT ./. -gi|15829254|ref|NC_002695.1| 227794 . G . . mq_score:50;min_depth:100 DP=84;MQ=0.0;MQ0=84 GT ./. -gi|15829254|ref|NC_002695.1| 227795 . A . . mq_score:50;min_depth:100 DP=89;MQ=0.0;MQ0=89 GT ./. -gi|15829254|ref|NC_002695.1| 227796 . A . . mq_score:50;min_depth:100 DP=89;MQ=0.0;MQ0=89 GT ./. -gi|15829254|ref|NC_002695.1| 227797 . A . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227798 . T . . mq_score:50;min_depth:100 DP=89;MQ=0.0;MQ0=89 GT ./. -gi|15829254|ref|NC_002695.1| 227799 . G . . mq_score:50;min_depth:100 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227800 . C . . mq_score:50;min_depth:100 DP=93;MQ=0.0;MQ0=93 GT ./. -gi|15829254|ref|NC_002695.1| 227801 . G . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227802 . T . . mq_score:50;min_depth:100 DP=91;MQ=0.0;MQ0=91 GT ./. -gi|15829254|ref|NC_002695.1| 227803 . A . . mq_score:50;min_depth:100 DP=92;MQ=0.0;MQ0=92 GT ./. -gi|15829254|ref|NC_002695.1| 227804 . G . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227805 . A . . mq_score:50;min_depth:100 DP=96;MQ=0.0;MQ0=96 GT ./. -gi|15829254|ref|NC_002695.1| 227806 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227807 . A . . mq_score:50 DP=109;MQ=0.0;MQ0=109 GT ./. -gi|15829254|ref|NC_002695.1| 227808 . T . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227809 . C . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227810 . T . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227811 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227812 . G . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227813 . A . . mq_score:50 DP=105;MQ=0.0;MQ0=105 GT ./. -gi|15829254|ref|NC_002695.1| 227814 . G . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227815 . G . . mq_score:50 DP=106;MQ=0.0;MQ0=106 GT ./. -gi|15829254|ref|NC_002695.1| 227816 . A . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227817 . A . . mq_score:50 DP=102;MQ=0.0;MQ0=102 GT ./. -gi|15829254|ref|NC_002695.1| 227818 . T . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227819 . A . . mq_score:50 DP=103;MQ=0.0;MQ0=103 GT ./. -gi|15829254|ref|NC_002695.1| 227820 . C . . mq_score:50 DP=104;MQ=0.0;MQ0=104 GT ./. -gi|15829254|ref|NC_002695.1| 227821 . C . . mq_score:50;min_depth:100 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227822 . G . . mq_score:50;min_depth:100 DP=99;MQ=0.0;MQ0=99 GT ./. -gi|15829254|ref|NC_002695.1| 227823 . G . . mq_score:50;min_depth:100 DP=97;MQ=0.0;MQ0=97 GT ./. -gi|15829254|ref|NC_002695.1| 227824 . T . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227825 . G . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227826 . G . . mq_score:50;min_depth:100 DP=95;MQ=0.0;MQ0=95 GT ./. -gi|15829254|ref|NC_002695.1| 227827 . C . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./. -gi|15829254|ref|NC_002695.1| 227828 . G . . mq_score:50;min_depth:100 DP=94;MQ=0.0;MQ0=94 GT ./.
--- a/tool_dependencies.xml Fri Dec 18 07:30:22 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pyyaml" version="3.11"> - <repository changeset_revision="99267d131c05" name="package_python_2_7_pyyaml_3_11" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pyvcf" version="0.6.8dev"> - <repository changeset_revision="7ef691e979b5" name="package_python_2_7_pyvcf_0_6_8dev" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>