--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,676 @@
+
+
+                    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
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+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    {one line to give the program's name and a brief idea of what it does.}
+    Copyright (C) {year}  {name of author}
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    {project}  Copyright (C) {year}  {fullname}
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,34 @@
+#!/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())

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.sh	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,15 @@
+#!/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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_vcf.xml	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,99 @@
+<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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/__init__.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,4 @@
+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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/metadata/__init__.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,16 @@
+"""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.")

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant/GATKVariantCaller.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,133 @@
+'''
+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")
+
+        make_aux = kwargs.get("make_aux", False)
+
+        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 make_aux:
+            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
+
+        if not os.path.exists("%s.dict" % ref_name):
+            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
+        else:
+            logging.debug("PICARD AUX EXISTS.")
+
+        return True

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant/MPileupVariantCaller.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,103 @@
+'''
+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")
+
+        make_aux = kwargs.get("make_aux", False)
+
+        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}
+
+        if make_aux:
+            if not self.create_aux_files(ref):
+                logging.warn("Auxiliary files were not created.")
+                return False
+
+        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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant/__init__.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,291 @@
+"""Classes and methods to work with _variants and such."""
+import abc
+from collections import OrderedDict
+import gzip
+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 __iter__(self):
+        '''Iterator over **all** variants'''
+        return self.variants(only_good=False)
+
+    def variants(self, only_good=False):
+        '''Generator over the variant set.
+        Parameters:
+        -----------
+        only_good: bool, optional
+            Iff True good and bad variants are returned, 
+            otherwise only good are returned (default: False).
+        '''
+        for var in self._variants:
+            if not only_good:
+                yield var
+            elif not var.FILTER :
+                yield var
+
+    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 is 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 = []
+                # 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 not variant.FILTER]
+
+    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
+
+        # Check if the output file ends with .gz, then compress data.
+        open_func = gzip.open if vcf_out.endswith(".gz") else open
+
+        with open_func(vcf_out, "w") as out_vcf:
+            writer = vcf.Writer(out_vcf, self.out_template)
+
+            # Output internal _variants (if exist) otherwise, output data from reader.
+            variants = self._variants if self._variants else self._reader
+
+            for record in variants:
+
+                if only_snps and not record.is_snp:
+                    continue
+
+                if only_good and record.FILTER:
+                    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
+        # Check if the output file ends with .gz, then compress data.
+        open_func = gzip.open if vcf_out.endswith(".gz") else open
+        with open_func(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 _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.
+        make_aux: bool, optional
+            True/False create auxilliary files (default: False).
+
+        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.")

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant/variant_factory.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,92 @@
+'''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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/ADFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,82 @@
+'''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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a float!")
+                raise Exception("Could not create AD filter from parameters: %s" % args)
+
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_record
+
+        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.warn("Could not calculate AD ratio from %s POS: %s", record, 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/DP4Filter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,79 @@
+'''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 DP4 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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a float!")
+                raise Exception("Could not create DP4 filter from parameters: %s" % args)
+
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_record
+
+        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.warn("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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/DepthFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,69 @@
+'''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, ValueError):
+                logging.error("Could not retrieve integer threshold from %s", args.get(self.parameter))
+                raise Exception("Could not create depth filter from parameters: %s" % args)
+
+    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.")
+            logging.warn("This parameter requires to be an integer!")
+
+        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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/GQFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,72 @@
+'''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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be an integer!")
+                raise Exception("Could not create GQ filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_record
+
+        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.warn("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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/GTFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,73 @@
+'''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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a string!")
+                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.warn("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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/MQ0FFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,64 @@
+'''Filter VCF on MQ filter.
+Created on 24 Sep 2015
+
+@author: alex
+'''
+
+import argparse
+import logging
+
+from phe.variant_filters import PHEFilterBase
+
+
+class MQ0FFilter(PHEFilterBase):
+    '''Filter sites by MQ0F (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(MQ0FFilter, 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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a float!")
+                raise Exception("Could not create MQ0F filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/MQ0Filter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,69 @@
+'''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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a float!")
+                raise Exception("Could not create MQ0 filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/MQFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,65 @@
+'''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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be an integer!")
+                raise Exception("Could not create MQ filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/QualFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,65 @@
+'''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, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a float!")
+                raise Exception("Could not create QUAL filter from parameters: %s" % args)
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        good_record = self._check_record(record)
+
+        if good_record is not True:
+            return good_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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/__init__.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,234 @@
+"""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"]): "A",
+               frozenset(["C"]): "C",
+               frozenset(["G"]): "G",
+               frozenset(["T"]): "T",
+               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()
+
+    def _check_record(self, record):
+        if self.is_uncallable(record):
+            return False
+        elif record.is_monomorphic:
+            return None
+        else:
+            return True
+
+    @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
+
+    def is_uncallable(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.warn("Could not retrieve GQ score POS %i", record.POS)
+            record_gt = "./."
+
+        if record_gt == "./.":
+            return True
+        else:
+            return False
+
+    @staticmethod
+    def call_concensus(record):
+        if not record.FILTER:
+            sample_ad = frozenset([str(c).upper() for c in record.ALT])
+            return IUPAC_CODES.get(sample_ad, "N")
+
+        else:
+            sample_ad = frozenset([str(c).upper() for c in record.ALT] + [record.REF])
+
+            return IUPAC_CODES.get(sample_ad, "N")
+
+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.error("Could not find appropriate filter for %s",
+                             custom_filter)
+                raise Exception("Filter %s could not be created. Please check your filter arguments." % custom_filter)
+
+    return filters

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input.vcf	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,1000 @@
+##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	./.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output.vcf	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,1001 @@
+##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	./.