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changeset 0:aa82b2e54055 draft
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamsort.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,97 @@ +<tool id="mimodd_sort" name="MiModD Sort" version="@MIMODD_WRAPPER_VERSION@"> + <description>takes a SAM/BAM dataset and generates a coordinate/name-sorted copy</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + mimodd sort '$input.ifile' + -o '$ofile' --iformat $input.iformat --oformat $oformat $by_name + </command> + + <inputs> + <conditional name="input"> + <param name="iformat" type="select" label="Input data format"> + <option value="bam">bam</option> + <option value="sam">sam</option> + </param> + <when value="bam"> + <param name="ifile" type="data" format="bam" + label="BAM input dataset to sort" /> + </when> + <when value="sam"> + <param name="ifile" type="data" format="sam" + label="SAM input dataset to sort" /> + </when> + </conditional> + <param name="oformat" type="select" label="Output format for the sorted data"> + <option value="bam">bam</option> + <option value="sam">sam</option> + </param> + <param name="by_name" type="boolean" truevalue="-n" falsevalue="" checked="false" + label="Sort by read names instead of coordinates" + help="A less common option, but necessary, e.g., if you want to re-align coordinate sorted paired-end reads with the MiModD Read Alignment Tool or other NGS mapping tools." /> + </inputs> + + <outputs> + <data name="ofile" format="bam" + label="Sorted output from MiModd ${tool.name} on ${on_string}"> + <change_format> + <when input="oformat" value="sam" format="sam" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + <conditional name="input"> + <param name="iformat" value="sam" /> + <param name="ifile" value="header_only.sam" /> + </conditional> + <param name="oformat" value="bam" /> + <assert_command> + <not_has_text text="-n" /> + </assert_command> + <output name="ofile" ftype="bam" file="so_coordinate.bam" /> + </test> + <test> + <conditional name="input"> + <param name="iformat" value="bam" /> + <param name="ifile" value="header_only.bam" /> + </conditional> + <param name="oformat" value="sam" /> + <param name="by_name" value="true" /> + <assert_command> + <has_text text=" -n" /> + </assert_command> + <output name="ofile" ftype="sam" file="so_queryname.sam" /> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool sorts an aligned reads input dataset, typically by the reference +genome coordinates that the reads have been mapped to. + +Coordinate-sorted input files are expected by most downstream MiModD tools, but +note that the *MiModD Read Alignment* produces coordinate-sorted output by +default and it is only necessary to sort files that come from other sources or +from *MiModD Read Alignment* jobs with a custom sort order. + +The option *Sort by read names instead of coordinates* is useful if you want to +re-align coordinate-sorted paired-end data. In *paired-end mode*, the +*MiModD Read Alignment* tool expects the reads in the input file to be arranged +in read pairs, *i.e.*, the forward read information of a pair must be followed +immediately by its reverse mate information, which is typically not the case in +coordinate-sorted data. Resorting such data by read names fixes this problem. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cloudmap.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,591 @@ +<tool id="mimodd_map" name="MiModD NacreousMap" version="@MIMODD_WRAPPER_VERSION@"> + <description>maps phenotypically selected variants by multi-variant linkage analysis</description> + <macros> + <import>macros.xml</import> + <macro name="svd_unconditional"> + <expand macro="hidden_algo_params" /> + <expand macro="seqdict_param" /> + <expand macro="bins" /> + <conditional name="plotopts"> + <param name="plots" type="select" label="graphical output settings"> + <option value="-p">Give me graphics.</option> + <option value="">Do not generate graphs.</option> + </param> + <when value=""> + </when> + <when value="-p"> + <expand macro="scatter_default" /> + <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true" + label="show kde line in histogram plots" + help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." /> + <param name="hylim" type="text" + label="upper limit for the histogram y-axis (leave blank for automatic scaling)" /> + <param name="xlim" type="select" label="x-axis scaling"> + <option value="">preserve relative contig sizes</option> + <option value="--fit-width">scale each contig to fit the plot width</option> + </param> + <expand macro="hist_colors" /> + </when> + </conditional> + </macro> + <macro name="vaf_unconditional"> + <expand macro="bins" /> + <conditional name="plotopts"> + <param name="plots" type="select" label="graphical output settings"> + <option value="-p">Give me everything (scatter plots and histograms)</option> + <option value="--no-scatter -p">Generate only histograms</option> + <option value="--no-hist -p">Generate only scatter plots</option> + <option value="">Do not generate graphs.</option> + </param> + <when value=""> + </when> + <when value="--no-scatter -p"> + <expand macro="scatter_default" /> + <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true" + label="show kde line in histogram plots" + help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." /> + <param name="hylim" type="text" + label="upper limit for the histogram y-axis (leave blank for automatic scaling)" /> + <param name="xlim" type="select" label="x-axis scaling"> + <option value="">preserve relative contig sizes</option> + <option value="--fit-width">scale each contig to fit the plot width</option> + </param> + <expand macro="hist_colors" /> + </when> + <when value="--no-hist -p"> + <expand macro="hist_default" /> + <param name="sylim" type="text" + label="upper limit for the scatter plot y-axis (default: 1)" /> + <param name="xlim" type="select" label="x-axis scaling"> + <option value="">preserve relative contig sizes</option> + <option value="--fit-width">scale each contig to fit the plot width</option> + </param> + <param name="span" type="text" + label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" + help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." /> + <expand macro="scatter_colors" /> + </when> + <when value="-p"> + <expand macro="plot_all" /> + </when> + </conditional> + </macro> + <macro name="vac_unconditional"> + <expand macro="bins" /> + <conditional name="plotopts"> + <param name="plots" type="select" label="graphical output settings"> + <option value="--no-scatter -p">Give me graphical output</option> + <option value="">Do not generate graphs.</option> + </param> + <when value=""> + </when> + <when value="--no-scatter -p"> + <expand macro="scatter_default" /> + <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true" + label="show kde line in histogram plots" + help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." /> + <param name="hylim" type="text" + label="upper limit for the histogram y-axis (leave blank for automatic scaling)" /> + <param name="xlim" type="select" label="x-axis scaling"> + <option value="">preserve relative contig sizes</option> + <option value="--fit-width">scale each contig to fit the plot width</option> + </param> + <expand macro="hist_colors" /> + </when> + </conditional> + </macro> + <macro name="hidden_algo_params"> + <param name="sample" type="hidden" value="" /> + <expand macro="hidden_vaf_algo_params" /> + <param name="contrast_sample" type="hidden" value="" /> + </macro> + <macro name="hidden_vaf_algo_params"> + <param name="related_parent_sample" type="hidden" value="" /> + <param name="unrelated_parent_sample" type="hidden" value="" /> + <param name="infer_missing" type="hidden" value="" /> + </macro> + <macro name="bins"> + <repeat name="bin_sizes" default="0" min="0" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb)" + help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed."> + <param name="bin_size" type="text" /> + </repeat> + </macro> + <macro name="scatter_default"> + <param name="sylim" type="hidden" value="" /> + <param name="span" type="hidden" value="" /> + <param name="pcols" type="hidden" value="" /> + <param name="lcols" type="hidden" value="" /> + </macro> + <macro name="hist_default"> + <param name="show_kde" type="hidden" value="" /> + <param name="hylim" type="hidden" value="" /> + <param name="hcols" type="hidden" value="" /> + </macro> + <macro name="hist_colors"> + <repeat name="hcols" default="0" min="0" title="histogram colors" + help="For each bin size chosen above a histogram will be generated with its color selected from the list provided here (defaults to alternating darkgrey, red)."> + <param name="hcolor" type="color" value="darkgrey"> + <sanitizer><valid><add value="#" /></valid></sanitizer> + </param> + </repeat> + </macro> + <macro name="scatter_colors"> + <repeat name="pcols" default="0" min="0" title="data point colors" + help="Series of data points will be plotted based on the colors selected here."> + <param name="pcol" type="color" value="black"> + <sanitizer><valid><add value="#" /></valid></sanitizer> + </param> + </repeat> + <repeat name="lcols" default="0" min="0" + title="regression line colors" + help="Regression lines through series of data will be plotted in the colors selected here."> + <param name="lcol" type="color" value="red"> + <sanitizer><valid><add value="#" /></valid></sanitizer> + </param> + </repeat> + </macro> + <macro name="plot_all"> + <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true" + label="show kde line in histogram plots" + help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." /> + <param name="hylim" type="text" + label="upper limit for the histogram y-axis (leave blank for automatic scaling)" /> + <param name="sylim" type="text" + label="upper limit for the scatter plot y-axis (default: 1)" /> + <param name="xlim" type="select" label="x-axis scaling"> + <option value="">preserve relative contig sizes</option> + <option value="--fit-width">scale each contig to fit the plot width</option> + </param> + <param name="span" type="text" + label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" + help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." /> + <expand macro="hist_colors" /> + <expand macro="scatter_colors" /> + </macro> + <macro name="seqdict_param"> + <conditional name="seqinfo_external"> + <param name="source" type="select" + label="does this input provide contig name and size information?" + help="ALWAYS select 'yes' here if the input dataset was generated with MiModD. Input generated with third-party tools may or may not provide the information. If in doubt, execute the job with 'yes' selected and see if you are getting a corresponding error message."> + <option value="">Yes</option> + <option value="fasta">No, get the information from a reference genome in my history</option> + <option value="cached">No, get the information from a built-in genome</option> + <option value="seqdict">No, get the information from a CloudMap-style sequence dictionary in my history</option> + </param> + <when value="fasta"> + <param name="seqinfo" type="data" format="fasta" + label="Reference genome to extract contig info from" /> + </when> + <when value="cached"> + <param name="seqinfo" type="select" + label="Reference genome to extract contig info from"> + <options from_data_table="all_fasta" /> + </param> + </when> + <when value="seqdict"> + <param name="seqinfo" type="data" format="tabular" + label="CloudMap-style sequence dictionary to extract contig info from" /> + </when> + <when value=""> + </when> + </conditional> + </macro> + <macro name="test_tabular_out"> + <output name="ofile" ftype="tabular"> + <assert_contents> + <has_text text="chrI" /> + <has_text text="chrII" /> + <has_text text="chrIII" /> + <has_text text="chrIV" /> + <has_text text="chrV" /> + <has_text text="chrX" /> + <has_text text="MtDNA" /> + </assert_contents> + </output> + </macro> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd map ${opt.mode} "${opt.source.ifile}" + #if $str($opt.source.sample): + -m '${opt.source.sample}' + #end if + #if $str($opt.source.related_parent_sample): + -r '${opt.source.related_parent_sample}' + #end if + #if $str($opt.source.unrelated_parent_sample): + -u '${opt.source.unrelated_parent_sample}' + #end if + #if $str($opt.source.contrast_sample): + -c '${opt.source.contrast_sample}' + #end if + $opt.source.infer_missing + -o '$ofile' + #if $str($opt.source.seqinfo_external.source) in ("fasta", "seqdict"): + -s '${opt.source.seqinfo_external.seqinfo}' + #else if $str($opt.source.seqinfo_external.source) == "cached": + -s '${opt.source.seqinfo_external.seqinfo.fields.path}' + #end if + #if $len($opt.source.bin_sizes): + --bin-sizes + #for $size in $opt.source.bin_sizes: + '${size.bin_size}' + #end for + #end if + #if $str($opt.source.tabfile): + $str($opt.source.tabfile) '$tfile' + #end if + #if $str($opt.source.plotopts.plots): + $str($opt.source.plotopts.plots) '$pfile' + $opt.source.plotopts.show_kde + $str($opt.source.plotopts.xlim) + #if $str($opt.source.plotopts.hylim): + --ylim-hist $str($opt.source.plotopts.hylim) + #end if + #if $str($opt.source.plotopts.hcols) and $len($opt.source.plotopts.hcols): + --hist-colors + #for $color in $opt.source.plotopts.hcols: + '${color.hcolor}' + #end for + #end if + #if $str($opt.source.plotopts.sylim): + --ylim-scatter $str($opt.source.plotopts.sylim) + #end if + #if $str($opt.source.plotopts.pcols) and $len($opt.source.plotopts.pcols): + --points-colors + #for $color in $opt.source.plotopts.pcols: + '${color.pcol}' + #end for + #end if + #if $str($opt.source.plotopts.lcols) and $len($opt.source.plotopts.lcols): + --loess-colors + #for $color in $opt.source.plotopts.lcols: + '${color.lcol}' + #end for + #end if + #if $str($opt.source.plotopts.span): + --loess-span $str($opt.source.plotopts.span) + #end if + #end if + ]]></command> + + <inputs> + <conditional name="opt"> + <param name="mode" type="select" label="type of mapping analysis to perform" + help="Select Simple Variant Density (SVD) Mapping to map mutations based on linked inheritance in near isogenic populations, Variant Allele Frequency (VAF) Mapping for bulk segregant analysis. Select Reprocess for rapidly replotting the result of a previous VAF analysis."> + <option value="SVD">Simple Variant Density Mapping</option> + <option value="VAF">Variant Allele Frequency Mapping</option> + <option value="VAC">Variant Allele Contrast Mapping</option> + </param> + <when value="SVD"> + <conditional name="source"> + <param name="inputtype" type="select" label="data source to use"> + <option value="vcf">VCF file of variants (for de-novo mapping)</option> + <option value="rep">per-variant report file (for remapping a previous analysis)</option> + </param> + <when value="vcf"> + <param name="ifile" type="data" format="vcf" + label="input file with variants to analyze" /> + <expand macro="svd_unconditional" /> + <param name="tabfile" type="select" + label="additional per-variant output file" + help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings, or a VCF-like CloudMap-compatibility output that can be used as input for the older CloudMap EMS Variant Density Mapping tool as an alternative plotting tool."> + <option value="">Do not generate per-variant output</option> + <option value="-t">Tabular per-variant report</option> + <option value="--cloudmap -t">CloudMap compatibility output</option> + </param> + </when> + <when value="rep"> + <param name="ifile" type="data" format="tabular,csv" + label="input file with variants to analyze" /> + <param name="tabfile" type="hidden" value="" /> + <expand macro="svd_unconditional" /> + </when> + </conditional> + </when> + <when value="VAF"> + <conditional name="source"> + <param name="inputtype" type="select" label="data source to use"> + <option value="vcf">VCF file of variants (for de-novo mapping)</option> + <option value="rep">per-variant report file (for remapping a previous analysis)</option> + </param> + <when value="vcf"> + <param name="ifile" type="data" format="vcf" + label="input file with variants to analyze" /> + <expand macro="seqdict_param" /> + <param name="sample" type="text" + label="mapping sample name" help="the sample to perform mutation mapping for"> + <validator type="empty_field" /> + </param> + <param name="related_parent_sample" type="text" + label="name of the related parent sample" + help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" /> + <param name="unrelated_parent_sample" type="text" + label="name of the unrelated parent sample" + help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" /> + <param name="infer_missing" type="boolean" truevalue="--infer-missing" falsevalue="" checked="false" + label="Infer alleles for missing parent" + help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. Use with caution on carefully filtered variant lists only!" /> + <param name="contrast_sample" type="hidden" value="" /> + <expand macro="vaf_unconditional" /> + <param name="tabfile" type="select" + label="additional per-variant output file" + help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings, or a VCF-like CloudMap-compatibility output that can be used as input for the older CloudMap Hawaiian Variant Mapping tool as an alternative plotting tool."> + <option value="">Do not generate per-variant output</option> + <option value="-t">Tabular per-variant report</option> + <option value="--cloudmap -t">CloudMap compatibility output</option> + </param> + </when> + <when value="rep"> + <param name="ifile" type="data" format="tabular,csv" + label="input file with variants to analyze" /> + <expand macro="seqdict_param" /> + <param name="tabfile" type="hidden" value="" /> + <expand macro="hidden_algo_params" /> + <expand macro="vaf_unconditional" /> + </when> + </conditional> + </when> + <when value="VAC"> + <conditional name="source"> + <param name="inputtype" type="select" + label="data source to use"> + <option value="vcf">VCF file of variants (for de-novo mapping)</option> + <option value="rep">per-variant report file (for remapping a previous analysis)</option> + </param> + <when value="vcf"> + <param name="ifile" type="data" format="vcf" + label="input file with variants to analyze" /> + <expand macro="seqdict_param" /> + <expand macro="hidden_vaf_algo_params" /> + <param name="sample" type="text" + label="mapping sample name" + help="the sample to perform mutation mapping for"> + <validator type="empty_field" /> + </param> + <param name="contrast_sample" type="text" + label="name of the contrast sample" + help="the sample that provides contrasting allele composition around the causal variant"> + <validator type="empty_field" /> + </param> + <expand macro="vac_unconditional" /> + <param name="tabfile" type="select" + label="additional per-variant output file" + help="You can choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings."> + <option value="">Do not generate per-variant output</option> + <option value="-t">Tabular per-variant report</option> + </param> + </when> + <when value="rep"> + <param name="ifile" type="data" format="tabular,csv" + label="input file with variants to analyze" /> + <expand macro="seqdict_param" /> + <param name="tabfile" type="hidden" value="" /> + <expand macro="hidden_algo_params" /> + <expand macro="vac_unconditional" /> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="ofile" format="tabular" + label="MiModD ${opt.mode} Mapping - binned variant counts for ${on_string}" /> + <data name="tfile" format="tabular" + label="MiModD ${opt.mode} Mapping - per-variant report for ${on_string}"> + <filter>(opt['source']['tabfile'])</filter> + </data> + <data name="pfile" format="pdf" + label="MiModD ${opt.mode} Mapping - linkage plots for ${on_string}"> + <filter>(opt['source']['plotopts']['plots'])</filter> + </data> + </outputs> + + <tests> + <test expect_num_outputs="1"> + <conditional name="opt"> + <param name="mode" value="SVD" /> + <conditional name="source"> + <param name="inputtype" value="vcf" /> + <conditional name="plotopts"> + <param name="plots" value="" /> + </conditional> + <param name="ifile" value="a.vcf" /> + </conditional> + </conditional> + <expand macro="test_tabular_out" /> + </test> + <test expect_num_outputs="2"> + <conditional name="opt"> + <param name="mode" value="VAF" /> + <conditional name="source"> + <param name="inputtype" value="vcf" /> + <conditional name="plotopts"> + <param name="plots" value="-p" /> + </conditional> + <param name="sample" value="ot266" /> + <param name="related_parent_sample" value="N2" /> + <param name="ifile" value="a.vcf" /> + </conditional> + </conditional> + <expand macro="test_tabular_out" /> + <output name="pfile" file="vaf_linkage.pdf" ftype="pdf" + compare="sim_size" delta="100000" /> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +This is the most downstream tool in +`mapping-by-sequencing analysis workflows in MiModD`_. + +It can be used to analyze and visualize the inheritance pattern of variants +detected and selected with other MiModD tools or as an alternative (and more +versatile) plotting engine for data generated with `CloudMap`_. + +------------- + +**Usage Modes:** + +This tool can be run in one of three different modes depending on the type of +mapping analysis that should be performed: + +1) *Simple Variant Density (SVD) Mapping* mode analyzes the density of variants + along the reference genome by dividing each chromosome into regions of + user-defined size (bins) and counting the variants found in each bin. + + All variants listed in the input file are analyzed in this mode, which means + that as input you will typically want to use filtered lists of variants (as + produced by the VCF Filter tool). + + The aim of SVD analysis is to identify clusters of variants in an outcrossed + strain carrying a selectable unknown mutation, which is interpreted as + linkage between the corresponding genomic region and the unknown mutation. + + This mode corresponds roughly to EMS Variant Density Mapping in CloudMap. + +2) *Variant Allele Frequency (VAF) Mapping* mode analyzes the inheritance + pattern in cross-progeny at sites, at which the parents are homozygous for + different alleles. + + The aim of VAF analysis is to identify clusters of variants with (near) + homozygous inheritance in a F2 (or later generation) population obtained + from a cross between a strain carrying a selectable unknown mutation and an + unrelated mapping strain. Such a cluster is interpreted as linkage between + the corresponding genomic region and the unknown mutation selected for in + the F2 generation. + + This mode corresponds roughly to Hawaiian Variant Mapping in CloudMap, but + can simultaneously take into account non-reference alleles found in either + parent strain (CloudMap users may think of this as a combined Hawaiian + Variant and Variant Discovery Mapping analysis). + +3) *Variant Allele Contrast (VAC) Mapping* mode analyzes and visualizes the + divergence between two samples at all sites in the input dataset. It works + independent of any parent strain information and can be used if you have two + samples selected for contrary phenotypes, but also with a selected and a + non-selected sample. + +------------- + +**Input:** + +Valid input for this tool are VCF datasets (any such dataset in SVD mode, a +MiModD-generated multi-sample VCF dataset in VAF and VAC modes) or a tabular +report as generated by the CloudMap Hawaiian Variant Mapping tool. +Alternatively, the tool can generate (in both modes) its own tabular reports, +which can be used as input instead of the original VCF dataset, when rerunning +the tool with different plotting parameters, to reduce analysis time. + +------------- + +**Output:** + +The tool produces up to three output files: + +1) a default tabular report of binned variant counts that can be used to plot + the data with external software such as Excel, + +2) an optional pdf containing linkage plots, and + +3) an optional tabular per-variant report, which can be configured to be either + valid input for the corresponding original CloudMap tool (for users who + really, really want to continue using CloudMap for plotting) or to be + reusable in fast reruns of the tool (which can be useful to experiment with + different plotting parameters). + +------------- + +**Settings:** + +1) Analysis settings + + *bin size to analyze variants in* - determines the width of the regions + along each chromosome, in which variants are counted and analyzed together. + + Several bin sizes can be specified and for each size you will get a + corresponding results section in the binned variant counts report and a + linkage histogram plot. + + *sample names (in VAF and VAC modes only)* - to analyze inheritance + patterns, the VAF and VAC modes need information about the relationship + between the samples defined in the input. While VAC mode simply requires + you to name the two contrasting samples for the analysis, the sample roles + in VAF mode are a bit more complicated to understand. Specifically: + + The *mapping sample name* should be set to the name of the sample for which + the inheritance pattern is to be analyzed (the pooled progeny population). + + The *name of the related sample* should indicate the parent sample that + carried and brought in the unknown mutation to be mapped (or, alternatively, + a closely related ancestor). + + The *name of the unrelated sample* should be that of the other parent strain + used in the cross. + + At least one of the parent samples MUST be specified, but if the input + contains variant information for both parents, they can be analyzed together + for higher mapping accuracy. If you are reanalyzing a tabular report from a + previous tool run or from CloudMap, the association between variants and + samples is already stored in the input dataset and cannot be specified + again. + +2) Graphical output settings + + .. class:: warningmark + + To be able to generate plots, the system running MiModD needs to have the + statistical programming environment R and its Python interface rpy2 + installed. Disable graphical output if this is not the case. + + *y-axes scaling* - if you want to override the defaults + + *x-axis scaling* - choose *preserve relative contig sizes* if you want the + largest chromosome to fit the page width and smaller chromosomes to appear + according to their relative size or choose *scale each contig to fit the + plot width* if all chromosomes should exploit the available space + + *span value to be used in calculating the Loess regression line* - this + value determines the degree of smoothing of the regression line through the + scatterplot data. Information on loess regression and the loess span + parameter can be found at http://en.wikipedia.org/wiki/Local_regression. + + *colors used for plotting* - can be selected freely from the offered + palette. For histogram colors, the list of selected colors will be used to + provide the colors for the different histograms plotted. If less colors than + histograms (determined by the number of bin sizes selected) are specified, + colors from the list will be recycled. + +.. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap +.. _mapping-by-sequencing analysis workflows in MiModD: http://mimodd.readthedocs.io/en/latest/nacreousmap.html +.. _CloudMap-style sequence dictionary: http://mimodd.readthedocs.io/en/latest/fileformats.html#cloudmap-style-sequence-dictionary + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,439 @@ +<tool id="mimodd_convert" name="MiModD Convert" version="@MIMODD_WRAPPER_VERSION@"> + <description>converts sequence data into different formats</description> + <macros> + <import>macros.xml</import> + <macro name="to_format"> + <param name="oformat" type="select" label="to"> + <option value="sam">sam</option> + <option value="bam">bam</option> + <yield /> + </param> + </macro> + <macro name="se_selector" token_format="fastq"> + <conditional name="input"> + <param name="repr" type="select" + label="Single-end input data provided as"> + <option value="individual">Individual datasets</option> + <option value="collection">Collection of datasets</option> + </param> + <when value="individual"> + <repeat name="input_data" title="fastq input datasets" + default="1" min="1"> + <param name="file1" type="data" format="@FORMAT@" + label="single-end read data"/> + </repeat> + </when> + <when value="collection"> + <param name="input_data" type="data_collection" + collection_type="list" format="fastq, fastq.gz" + label="collection of single-end read input datasets" /> + </when> + </conditional> + <param name="header" type="data" format="sam" label="Use Header File" + help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/> + + </macro> + <macro name="pe_selector" token_format="fastq"> + <conditional name="input"> + <param name="repr" type="select" + label="Paired-end input data provided as"> + <option value="individual">Individual datasets</option> + <option value="collection">Paired collection</option> + <option value="list_of_pairs">List of pairs</option> + </param> + <when value="individual"> + <repeat name="input_data" title="fastq input datasets" + default="1" min="1"> + <param name="file1" type="data" format="@FORMAT@" + label="first set of reads of paired-end data"/> + <param name="file2" type="data" format="@FORMAT@" + label="second set of reads of paired-end data"/> + </repeat> + </when> + <when value="collection"> + <param name="input_data" type="data_collection" + collection_type="paired" format="fastq, fastq.gz" + label="paired input dataset collection" /> + </when> + <when value="list_of_pairs"> + <param name="input_data" type="data_collection" + collection_type="list:paired" format="fastq, fastq.gz" + label="nested collection of paired input datasets" /> + </when> + </conditional> + <param name="header" type="data" format="sam" label="Use Header File" + help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/> + + </macro> + <macro name="sam_bam_selector" token_format="sam"> + <param name="input_data" type="data" format="@FORMAT@" + label="input dataset"/> + <param name="header" type="hidden" value="None"/> + </macro> + <macro name="fastq_output_choices"> + <param name="split_on_rgs" type="hidden" value=""/> + <param name="reads_to_report" type="select" display="radio" + label="Types of reads to generate output for" + help="By default, the tool will generate two dataset collections, one for single reads found in the input file, and one for paired reads. If you know, in advance, that the input contains only single or only paired reads, you can prevent the generation of an empty dataset collection by selecting the appropriate option here."> + <option value="default">Single and paired reads</option> + <option value="single">Single reads only</option> + <option value="paired">Paired reads only</option> + </param> + <param name="multisegment_report" type="boolean" checked="false" + label="Generate additional output for multi-segment reads" + help="Multi-segment reads, as opposed to single- and two-segment/paired reads, are not present in typical NGS data, but allowed in SAM/BAM files. If you expect multi-segment reads in the input file, enable this option." /> + </macro> + <macro name="bam_output_choices"> + <param name="split_on_rgs" type="boolean" truevalue="--split-on-rgs" falsevalue="" checked="false" + label="Split output based on read group IDs" + help="If the input file contains reads from different read groups, write them to separate output files; implied automatically for conversions to fastq and gzipped fastq format"/> + </macro> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + ## Currently Galaxy does not autoconvert collections of fastq.gz files. + ## This tool wrapper fixes that by allowing fastq and fastq.gz as input + ## collection formats. + ## gz_input is then used as flag to indicate a fastq.gz input file + #set gz_input = False + #if $str($mode.output.split_on_rgs) or $str($mode.output.oformat) == "fastq" or $str($mode.output.oformat) == "gz": + mkdir converted_data && + #end if + + mimodd convert + #if $str($mode.iformat) in ("sam", "bam"): + '${mode.output.input_data}' + #else if $str($mode.iformat) == "fastq_pe": + #if $str($mode.output.input.repr) == "collection": + '$mode.output.input.input_data.forward' '$mode.output.input.input_data.reverse' + ## A paired collection - if the forward dataset is gzipped we assume + ## the reverse dataset is too. + #if $mode.output.input.input_data.forward.is_of_type('fastq.gz'): + #set gz_input = True + #end if + #else + #for $i in $mode.output.input.input_data + #if $str($mode.output.input.repr) == "individual": + '${i.file1}' '${i.file2}' + #else + '$i.forward' '$i.reverse' + ## A list:paired collection - let the last forward dataset + ## indicate whether input is gzipped + #if $i.forward.is_of_type('fastq.gz'): + #set gz_input = True + #end if + #end if + #end for + #end if + #else + #for $i in $mode.output.input.input_data + #if $str($mode.output.input.repr) == "collection": + '$i' + ## A simple collection of files - the last one determines + ## whether we assume gzipped input + #if $i.is_of_type('fastq.gz'): + #set gz_input = True + #end if + #else + '${i.file1}' + #end if + #end for + #end if + #if $str($mode.output.header) != "None": + --header '$(mode.output.header)' + #end if + #if $str($outputname) == "None": + --ofile converted_data/read_group + #else + --ofile '$outputname' + #end if + #if $gz_input: + ## a gzipped input dataset was found so lets set --iformat accordingly + #if $str($mode.iformat) == "fastq_pe": + --iformat gz_pe + #else + --iformat gz + #end if + #else + --iformat $(mode.iformat) + #end if + --oformat $(mode.output.oformat) + ${mode.output.split_on_rgs} + + #if $str($mode.output.oformat) == "fastq" or $str($mode.output.oformat) == "gz": + && + cd converted_data && + for f in *2segments_r1.fastq.gz; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r1.fastq.gz`_forward.fastq.gz"; done && + for f in *2segments_r2.fastq.gz; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r2.fastq.gz`_reverse.fastq.gz"; done && + for f in *2segments_r1.fastq; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r1.fastq`_forward.fastq"; done && + for f in *2segments_r2.fastq; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r2.fastq`_reverse.fastq"; done + #end if + + ]]></command> + + <inputs> + <conditional name="mode"> + <param name="iformat" type="select" label="Convert from" + help="Your choice will update the interface to display further choices appropriate for your type of input data."> + <option value="fastq">fastq: single-end (one file)</option> + <option value="fastq_pe">fastq: paired-end (two files)</option> + <option value="sam">sam</option> + <option value="bam">bam</option> + </param> + <when value="fastq"> + <conditional name="output"> + <expand macro="to_format" /> + <when value="sam"> + <expand macro="se_selector" format="fastq" /> + <param name="split_on_rgs" type="hidden" value=""/> + </when> + <when value="bam"> + <expand macro="se_selector" format="fastq" /> + <param name="split_on_rgs" type="hidden" value=""/> + </when> + </conditional> + </when> + <when value="fastq_pe"> + <conditional name="output"> + <expand macro="to_format" /> + <when value="sam"> + <expand macro="pe_selector" format="fastq" /> + <param name="split_on_rgs" type="hidden" value=""/> + </when> + <when value="bam"> + <expand macro="pe_selector" format="fastq" /> + <param name="split_on_rgs" type="hidden" value=""/> + </when> + </conditional> + </when> + <when value="sam"> + <conditional name="output"> + <expand macro="to_format"> + <option value="fastq">fastq</option> + <option value="gz">gzipped fastq</option> + </expand> + <when value="fastq"> + <expand macro="sam_bam_selector" format="sam" /> + <expand macro="fastq_output_choices" /> + </when> + <when value="gz"> + <expand macro="sam_bam_selector" format="sam" /> + <expand macro="fastq_output_choices" /> + </when> + <when value="bam"> + <expand macro="sam_bam_selector" format="sam" /> + <expand macro="bam_output_choices" /> + </when> + <when value="sam"> + <expand macro="sam_bam_selector" format="sam" /> + <expand macro="bam_output_choices" /> + </when> + </conditional> + </when> + <when value="bam"> + <conditional name="output"> + <expand macro="to_format"> + <option value="fastq">fastq</option> + <option value="gz">gzipped fastq</option> + </expand> + <when value="fastq"> + <expand macro="sam_bam_selector" format="bam" /> + <expand macro="fastq_output_choices" /> + </when> + <when value="gz"> + <expand macro="sam_bam_selector" format="bam" /> + <expand macro="fastq_output_choices" /> + </when> + <when value="bam"> + <expand macro="sam_bam_selector" format="bam" /> + <expand macro="bam_output_choices" /> + </when> + <when value="sam"> + <expand macro="sam_bam_selector" format="bam" /> + <expand macro="bam_output_choices" /> + </when> + </conditional> + </when> + </conditional> + </inputs> + + <outputs> + <data name="outputname" format="bam" + label="Reads converted to ${mode.output.oformat} by ${tool.name} on ${on_string}"> + <change_format> + <when input="mode.output.oformat" value="sam" format="sam" /> + </change_format> + <filter> + (mode['output']['oformat'] in ("bam", "sam") and not mode['output']['split_on_rgs']) + </filter> + </data> + <collection name="bam_split_on_read_groups" type="list" + label="Reads converted to ${mode.output.oformat} by ${tool.name} on ${on_string}"> + <discover_datasets pattern="__designation_and_ext__" + directory="converted_data" /> + <filter> + (mode['output']['oformat'] in ('bam', 'sam') and mode['output']['split_on_rgs']) + </filter> + </collection> + <collection name="fastq_SE_output_split_on_read_groups" type="list" + label="Single reads converted to fastq by ${tool.name} on ${on_string}"> + <discover_datasets + pattern="(?P<designation>.+)_1segments_r1\.(?P<ext>fastq(\.gz)*)" + directory="converted_data" /> + <filter> + (mode['output']['oformat'] in ('fastq', 'gz') and mode['output']['reads_to_report'] in ('default', 'single')) + </filter> + </collection> + <collection name="fastq_PE_reads_split_on_read_groups" type="list:paired" + label="Read pairs converted to fastq by ${tool.name} on ${on_string}"> + <discover_datasets + pattern="(?P<identifier_0>read_group_.+)_2segments_(?P<identifier_1>(forward|reverse))\.(?P<ext>fastq(\.gz)*)" + directory="converted_data" /> + <filter> + (mode['output']['oformat'] in ('fastq', 'gz') and mode['output']['reads_to_report'] in ('default', 'paired')) + </filter> + </collection> + <collection name="fastq_multi-segment_reads_split_on_read_groups" type="list:list" + label="Multi-segment reads converted to fastq by ${tool.name} on ${on_string}"> + <discover_datasets + pattern="(?P<identifier_0>read_group_.+)_(?P<identifier_1>[3-9]|[1-9][0-9]+)segments_r[0-9]+\.(?P<ext>fastq(\.gz)*)" + directory="converted_data" /> + <filter> + (mode['output']['oformat'] in ('fastq', 'gz') and mode['output']['multisegment_report']) + </filter> + </collection> + </outputs> + + <tests> + <test expect_num_outputs="1"> + <conditional name="mode"> + <param name="iformat" value="fastq" /> + <conditional name="output"> + <param name="oformat" value="bam" /> + <conditional name="input"> + <param name="repr" value="individual" /> + <repeat name="input_data"> + <param name="file1" + value="split_pair_reads_1.fastqsanger" /> + </repeat> + </conditional> + <param name="header" value="header_only.sam" /> + </conditional> + </conditional> + <output name="outputname" file="reads_1_w_header.bam" + ftype="bam" /> + </test> + <test expect_num_outputs="1"> + <conditional name="mode"> + <param name="iformat" value="fastq_pe" /> + <conditional name="output"> + <param name="oformat" value="bam" /> + <conditional name="input"> + <param name="repr" value="individual" /> + <repeat name="input_data"> + <param name="file1" + value="split_pair_reads_1.fastqsanger" /> + <param name="file2" + value="split_pair_reads_2.fastqsanger" /> + </repeat> + </conditional> + <param name="header" value="header_only.sam" /> + </conditional> + </conditional> + <output name="outputname" file="reads_1and2_w_header.bam" + ftype="bam" /> + </test> + <test expect_num_outputs="1"> + <conditional name="mode"> + <param name="iformat" value="fastq_pe" /> + <conditional name="output"> + <param name="oformat" value="bam" /> + <conditional name="input"> + <param name="repr" value="collection" /> + <param name="input_data"> + <collection type="paired"> + <element name="forward" + value="split_pair_reads_1.fastqsanger" /> + <element name="reverse" + value="split_pair_reads_2.fastqsanger" /> + </collection> + </param> + </conditional> + <param name="header" value="header_only.sam" /> + </conditional> + </conditional> + <output name="outputname" file="reads_1and2_w_header.bam" ftype="bam" /> + </test> + <test expect_num_outputs="1"> + <conditional name="mode"> + <param name="iformat" value="bam" /> + <conditional name="output"> + <param name="oformat" value="sam" /> + <param name="input_data" value="a.bam" /> + </conditional> + </conditional> + <output name="outputname" file="a.sam" ftype="sam" /> + </test> + <test> + <conditional name="mode"> + <param name="iformat" value="sam" /> + <conditional name="output"> + <param name="oformat" value="bam" /> + <param name="input_data" value="a.sam" /> + <param name="split_on_rgs" value="true" /> + </conditional> + </conditional> + <output_collection name="bam_split_on_read_groups" type="list" count="2"> + <element name="read_group_000" file="a_part1.bam" ftype="bam" /> + </output_collection> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool converts between different file formats used for storing +next-generation sequencing data. + +As input file types it can handle fastq, SAM or BAM format, which it can +convert to SAM or BAM format. + +**Notes:** + +1) The tool can convert fastq files representing data from paired-end +sequencing runs to appropriate SAM/BAM format provided that the mate +information is split over two fastq files in corresponding order. + + **TIP:** If your paired-end data is arranged differently, you may look into + the *fastq splitter* and *fastq de-interlacer* tools for Galaxy from the + `Fastq Manipulation category`_ of the Galaxy Tool Shed to see if they can + convert your files to the expected format. + +2) Merging partial fastq (or gzipped fastq) files into a single SAM/BAM file is +supported both for single-end and paired-end data. Simply add additional input +datasets and select the appropriate files (pairs of files in case of paired-end +data). + + Concatenation of SAM/BAM file during conversion is currently not supported. + +3) For input in fastq format a SAM header file providing run metadata +**has to be specified**. The information in this file will be used as the +header data of the new SAM/BAM file. You can use the *NGS Run Annotation* tool +to generate a new header file for your data. + + For input in SAM/BAM format the tool will simply copy the existing header + data to the new file. To modify the header of an existing SAM/BAM file, use + the *Reheader BAM file* tool instead. + +.. _Fastq Manipulation category: https://toolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=310ff67d4caf6531 +.. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy +.. _MiModD user guide: http://mimodd.readthedocs.org/en/latest + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/covstats.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,57 @@ +<tool id="mimodd_covstats" name="MiModD Coverage Statistics" +version="@MIMODD_WRAPPER_VERSION@"> + <description> + calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd covstats '$ifile' --ofile '$ofile' + ]]></command> + + <inputs> + <param name="ifile" type="data" format="bcf" label="BCF input file" + help="Use the Variant Calling tool to generate input for this tool."/> + </inputs> + <outputs> + <data name="ofile" format="tabular" + label="Coverage Statistics for ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="ifile" value="a.bcf" /> + <output name="ofile" ftype="tabular"> + <assert_contents> + <has_n_columns n="3" /> + <has_line_matching expression="^chrI	.+" /> + <has_line_matching expression="^chrII	.+" /> + <has_line_matching expression="^chrIII	.+" /> + <has_line_matching expression="^chrIV	.+" /> + <has_line_matching expression="^chrV	.+" /> + <has_line_matching expression="^chrX	.+" /> + <has_line_matching expression="^MtDNA	.+" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it. + +.. class:: warningmark + + The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deletion_predictor.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,117 @@ +<tool id="mimodd_delcall" name="MiModD Deletion Calling (for PE data)" +version="@MIMODD_WRAPPER_VERSION@"> + <description> + predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd delcall + #for $bam_file in $list_input + '$bam_file' + #end for + '$covfile' -o '$ofile' + --index-files + #for $bam_file in $list_input + '${bam_file.metadata.bam_index}' + #end for + --max-cov $max_cov --min-size $min_size + $include_uncovered + $group_by_id + --verbose + ]]></command> + + <inputs> + <param name="list_input" type="data" multiple="true" format="bam" + label="Aligned reads input dataset(s)" /> + <param name="covfile" type="data" format="bcf" + label="BCF variant call dataset to extract coverage from" + help="Use the MiModD Variant Calling Tool to generate this file."/> + <param name="group_by_id" type="boolean" truevalue="-i" falsevalue="" checked="false" + label="group reads based on read group id only" + help="If selected, reads from different read groups will be treated strictly separate. If turned off, read groups with identical sample names are used together for identifying uncovered regions, but are still treated separately for the prediction of deletions." /> + <param name="include_uncovered" type="boolean" truevalue="-u" falsevalue="" checked="false" + label="include low-coverage regions" + help="If selected, regions that fulfill the coverage criteria below, but are not statistically significant deletions, will be included in the output." /> + <param name="max_cov" type="integer" value="0" + label="maximal coverage allowed inside a low-coverage region (default: 0)" + help="The maximal coverage at a site allowed to consider it as part of a low-coverage region" /> + <param name="min_size" type="integer" value="100" + label="minimal deletion size (default: 100)" + help="A low-coverage region must consist of at least this number of consecutive bases below the maximal coverage to consider it in further analyses."/> + </inputs> + + <outputs> + <data name="ofile" format="gff" /> + </outputs> + + <tests> + <test> + <param name="list_input" value="a.bam" /> + <param name="covfile" value="a.bcf" /> + <param name="include_uncovered" value="true" /> + <assert_command> + <has_text text=" -u " /> + <not_has_text text=" -i " /> + </assert_command> + <output name="ofile" ftype="gff"> + <assert_contents> + <has_n_columns n="9" /> + <has_line_matching + expression="^chrI	MiModD	Uncovered_Region.+" /> + <has_line_matching + expression="^chrII	MiModD	Uncovered_Region.+" /> + <has_line_matching + expression="^chrIII	MiModD	Uncovered_Region.+" /> + <has_line_matching + expression="^chrIV	MiModD	Uncovered_Region.+" /> + <has_line_matching + expression="^chrV	MiModD	Uncovered_Region.+" /> + <has_line_matching + expression="^chrX	MiModD	Uncovered_Region.+" /> + <has_line_matching + expression="^MtDNA	MiModD	Uncovered_Region.+" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool predicts deletions from paired-end data in a two-step process: + +1) It finds regions of low-coverage, i.e., candidate regions for deletions, by scanning a BCF file produced by the *Variant Calling* tool. + + The *maximal coverage allowed inside a low-coverage region* and the *minimal deletion size* parameters are used at this step to define what is considered a low-coverage region. + + .. class:: warningmark + + The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites. + +2) It assesses every low-coverage region statistically for evidence of it being a real deletion. **This step requires paired-end data** since it relies on shifts in the distribution of read pair insert sizes around real deletions. + +By default, the tool only reports Deletions, i.e., the subset of low-coverage regions that pass the statistical test. +If *include low-coverage regions* is selected, regions that failed the test will also be reported. + +With *group reads based on read group id only* selected, as it is by default, grouping of reads into samples is done strictly based on their read group IDs. +With the option deselected, grouping is done based on sample names in the first step of the analysis, i.e. the reads of all samples with a shared sample name are used to identify low-coverage regions. +In the second step, however, reads will be regrouped by their read group IDs again, i.e. the statistical assessment for real deletions is always done on a per read group basis. + +**TIP:** +Deselecting *group reads based on read group id only* can be useful, for example, if you have both paired-end and single-end sequencing data for the same sample. + +In this case, the two sets of reads will usually share a common sample name, but differ in their read groups. +With grouping based on sample names, the single-end data can be used together with the paired-end data to identify low-coverage regions, thus increasing overall coverage and reliability of this step. +Still, the assessment of deletions will use only the paired-end data (auto-detecting that the single-end reads do not provide insert size information). + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fileinfo.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,102 @@ +<tool id="mimodd_info" name="MiModD File Information" version="@MIMODD_WRAPPER_VERSION@"> + <description>provides summary reports for supported sequence data formats.</description> + <macros> + <import>macros.xml</import> + <xml name="test_with_formats" token_ifile="a.sam" token_oformat="text" + token_expectformat="txt"> + <test> + <conditional name="input_selection"> + <param name="source" value="history" /> + <param name="ifile" value="@IFILE@" /> + </conditional> + <param name="oformat" value="@OFORMAT@" /> + <output name="ofile" ftype="@EXPECTFORMAT@"> + <assert_contents> + <has_text text="chrI" /> + <has_text text="chrII" /> + <has_text text="chrIII" /> + <has_text text="chrIV" /> + <has_text text="chrV" /> + <has_text text="chrX" /> + </assert_contents> + </output> + </test> + </xml> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd info -o '$ofile' --verbose --oformat $oformat + #if str($input_selection.source) == "history": + '$input_selection.ifile' + #else: + '$input_selection.ifile.fields.path' + #end if + ]]></command> + + <inputs> + <conditional name="input_selection"> + <param name="source" type="select" label="Input is a"> + <option value="history">Dataset in history</option> + <option value="cached">Genome on server</option> + </param> + <when value="history"> + <param name="ifile" type="data" format="bam,sam,vcf,bcf,fasta" + label="input dataset" /> + </when> + <when value="cached"> + <param name="ifile" type="select" label="installed genome"> + <options from_data_table="all_fasta" /> + </param> + </when> + </conditional> + <param name="oformat" type="select" display="radio" + label="output format"> + <option value="txt">text</option> + <option value="html">html</option> + </param> + </inputs> + + <outputs> + <data name="ofile" format="txt" label="Sample Info on ${on_string}"> + <change_format> + <when input="oformat" value="html" format="html"/> + </change_format> + <actions> + <conditional name="input_selection.source"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" ref="input_selection.ifile" column="0" /> + </option> + </action> + </when> + </conditional> + </actions> + </data> + </outputs> + + <tests> + <expand macro="test_with_formats" ifile="a.bam" /> + <expand macro="test_with_formats" ifile="a.sam" /> + <expand macro="test_with_formats" ifile="a.bcf" /> + <expand macro="test_with_formats" ifile="a.vcf" /> + <expand macro="test_with_formats" ifile="a.fa" /> + <expand macro="test_with_formats" ifile="a.bam" oformat="html" + expectformat="html" /> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool inspects the input datasets and generates a report summarizing its contents. + +It autodetects and works with most file formats produced by MiModD, i.e., **SAM / BAM, vcf / bcf and fasta**, and produces a standardized report for all of them. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,46 @@ +<macros> + <token name="@MIMODD_VERSION_REQUIRED@">0.1.8</token> + <token name="@MIMODD_REAL_VERSION@">0.1.8</token> + <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_0</token> + <token name="@HELP_FOOTER@"><![CDATA[ +---- + +.. class:: infomark + + For **additional help** see these resources: + +- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/v0.1.8/usage_toc.html>`__ + +- The `MiModD help forum <https://groups.google.com/forum/#!forum/mimodd>`__ reachable also via `email <mailto:mimodd@googlegroups.com>`__ + + ]]></token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@MIMODD_VERSION_REQUIRED@">MiModD</requirement> + <yield /> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + <xml name="version_command"> + <version_command><![CDATA[mimodd version -q]]></version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{ +maier_mimodd_2014, +title = {{MiModD} - {Mutation} {Identification} in {Model} {Organism} {Genomes}}, +shorttitle = {{MiModD}}, +url = {https://sourceforge.net/projects/mimodd/}, +author = {Maier, Wolfgang and Moos, Katharina and Seifert, Mark and Baumeister, Ralf}, +year = {2014}, publisher={SourceForge.net} } + </citation> + </citations> + </xml> +</macros> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rebase.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,75 @@ +<tool id="mimodd_rebase" name="MiModD Rebase Sites" +version="@MIMODD_WRAPPER_VERSION@"> + <description>from a VCF file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd rebase '$ifile' + '$chainfile' + $reverse + --ofile '$output_vcf' + --filter $filter + --verbose + ]]></command> + + <inputs> + <param name="ifile" type="data" format="vcf" label="VCF input file" + help="the VCF file to rebase"/> + <param name="chainfile" type="data" format="tabular" label="Input chainfile" + help="the UCSC chain file to calculate new coordinates from"/> + <param name="reverse" type="boolean" truevalue="-r" falsevalue="" checked="false" + label="reverse the target and query sites of the initial chainfile" + help="swap the genome versions specified in the chain file, i.e., assume the coordinates in the input file are based on the chain file target genome version and should be mapped to the source genome version" /> + <param name="filter" type="select" display="radio" + label="Ambiguously mapping variants" + help="How to treat variants that map to more than one position in the target coordinate system" > + <option value="unique">Ignore</option> + <option value="best">Report only the mapping with the highest score</option> + <option value="all">Report all possible mappings</option> + </param> + </inputs> + <outputs> + <data name="output_vcf" format="vcf" + label="Variants rebased with MiModd from ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="ifile" value="a.vcf" /> + <param name="chainfile" value="ce11ToCe10.over.chain" /> + <assert_command> + <not_has_text text=" -r" /> + </assert_command> + <output name="output_vcf" file="rebased.vcf" ftype="vcf" + lines_diff="0" /> + </test> + <test> + <param name="ifile" value="rebased.vcf" /> + <param name="chainfile" value="ce11ToCe10.over.chain" /> + <param name="reverse" value="true" /> + <assert_command> + <has_text text=" -r" /> + </assert_command> + <output name="output_vcf" file="a.vcf" ftype="vcf" + lines_diff="20" /> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool takes as input a VCF file like the ones produced by the +**Extract Variant** tool and a Genome Browser chain format, and maps the +variant positions found in the VCF file to a different reference genome +coordinate system according to the mapping defined in a UCSC chain file. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reheader.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,270 @@ +<tool id="mimodd_reheader" name="MiModD Reheader" version="@MIMODD_WRAPPER_VERSION@"> + <description> + takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file + </description> + <macros> + <import>macros.xml</import> + <macro name="getreadgroupinfo"> + <conditional name="rginfo"> + <param name="source" type="select" + label="source of new read-group information"> + <option value="from_file">existing SAM file</option> + <option value="from_form">input form</option> + </param> + <when value="from_file"> + <param name="data" type="data" format="sam" + label="read-group template file in SAM format" + help="use the read group information found in this file" /> + <repeat name="rg" title="custom read-group mapping" default="0" min="0" + help="read-group information found in the input file, by default, gets updated / replaced with information from template file read-groups with matching IDs. Alternatively, you may specify explicit read-group mappings below."> + <param name="source_id" type="text" + label="modify input file information for read-group ID (will create the read-group if it does not exist)" /> + <param name="rg_id" type="text" + label="with template file information for read-group ID" /> + </repeat> + </when> + <when value="from_form"> + <repeat name="rg" title="new read-group info" default="1" min="1"> + <param name="source_id" type="text" + label="read-group ID (will create the read-group if it does not exist)" + help="required field"> + <validator type="empty_field" /> + </param> + <param name="rg_id" type="hidden" value="" /> + <param name="rg_sm" type="text" label="sample name" + help="required field"> + <validator type="empty_field" /> + </param> + <param name="rg_ds" type="text" label="description" /> + <param name="rg_date" type="text" + label="date (YY-MM-DD format) the run was produced" /> + <param name="rg_cn" type="text" + label="name of sequencing center" /> + <param name="rg_lb" type="text" label="read-group library" /> + <param name="rg_pl" type="text" + label="platform/technology used to produce the reads" /> + <param name="rg_pi" type="text" + label="predicted median insert size" /> + <param name="rg_pu" type="text" + label="platform unit; unique identifier" /> + </repeat> + </when> + </conditional> + </macro> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore": + mimodd header + #if $str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form": + #for $rginfo in $rg.rginfo.rg + #if $str($rginfo.source_id): + --rg-id '${rginfo.source_id}' + #end if + #if $str($rginfo.rg_sm): + --rg-sm '${rginfo.rg_sm}' + #end if + #if $str($rginfo.rg_cn): + --rg-cn '${rginfo.rg_cn}' + #else: + --rg-cn "" + #end if + #if $str($rginfo.rg_ds): + --rg-ds '${rginfo.rg_ds}' + #else: + --rg-ds "" + #end if + #if $str($rginfo.rg_date): + --rg-dt '${rginfo.rg_date}' + #else: + --rg-dt "" + #end if + #if $str($rginfo.rg_lb): + --rg-lb '${rginfo.rg_lb}' + #else: + --rg-lb "" + #end if + #if $str($rginfo.rg_pl): + --rg-pl '${rginfo.rg_pl}' + #else: + --rg-pl "" + #end if + #if $str($rginfo.rg_pi): + --rg-pi '${rginfo.rg_pi}' + #else: + --rg-pi "" + #end if + #if $str($rginfo.rg_pu): + --rg-pu '${rginfo.rg_pu}' + #else: + --rg-pu "" + #end if + #end for + #end if + #if $str($co.treat_co) != "ignore": + --co + #for $comment in $co.coinfo + #if $str($comment.line): + '${comment.line}' + #end if + #end for + #end if + | + #end if + mimodd reheader '$inputfile' --sq ignore --rg ${rg.treat_rg} + #if $str($rg.treat_rg) != "ignore": + #if $str($rg.rginfo.source) == "from_file": + '${rg.rginfo.data}' + #else: + - + #end if + #for $rgmapping in $rg.rginfo.rg + #if $str($rgmapping.source_id) and $str($rgmapping.rg_id): + '$str($rgmapping.source_id)' : '$str($rgmapping.rg_id)' + #end if + #end for + #end if + + --co ${co.treat_co} + #if $str($co.treat_co) != "ignore": + - + #end if + + #set $restr = "" + #for $rename in $rg_renaming + #set $restr = $restr + ($str($rename.from) and $str($rename.to) and "'" + $str($rename.from) + "' : '" + $str($rename.to) + "' ") + #end for + #if $restr + --rgm $restr + #end if + + #set $restr = "" + #for $rename in $sq_renaming + #set $restr = $restr + ($str($rename.from) and $str($rename.to) and "'" + $str($rename.from) + "' : '" + $str($rename.to) + "' ") + #end for + #if $restr + --sqm $restr + #end if + + -o '$output' + ]]></command> + + <inputs> + <param name="inputfile" type="data" format="bam" + label="input dataset in BAM format" help="the file to reheader." /> + <conditional name="rg"> + <param name="treat_rg" type="select" + label="modify read-group information?" + help="Replace mode will ignore ALL existing read group information in the input file and use ONLY template information, Update mode will COPY existing input file information and UPDATE it with template information; choose No, ... to leave read-group information alone."> + <option value="ignore">No, do not change read-groups.</option> + <option value="update">Yes, update existing information</option> + <option value="replace">Yes, replace existing information</option> + </param> + <when value="update"> + <expand macro="getreadgroupinfo" /> + </when> + <when value="replace"> + <expand macro="getreadgroupinfo" /> + </when> + <when value="ignore"> + </when> + </conditional> + <conditional name="co"> + <param name="treat_co" type="select" + label="modify comments in the input file?"> + <option value="ignore">No, do not change comments.</option> + <option value="update">Yes, append new comments to existing ones</option> + <option value="replace">Yes, replace all existing comments</option> + </param> + <when value="update"> + <repeat name="coinfo" title="comment line" default="0" min="0"> + <param name="line" type="text" size="80" /> + </repeat> + </when> + <when value="replace"> + <repeat name="coinfo" title="comment line" default="0" min="0"> + <param name="line" type="text" size="80" /> + </repeat> + </when> + <when value="ignore"> + </when> + </conditional> + <repeat name="rg_renaming" title="rename read-group" default="0" min="0" + help="Warning: changing read-group IDs may increase job runtime substantially."> + <param name="from" type="text" size="30" label="old name" + help="as it appears in the current input file header"/> + <param name="to" type="text" size="30" label="new name" /> + </repeat> + <repeat name="sq_renaming" title="rename sequence" default="0" min="0" + help="Warning: changing sequence names may increase job runtime substantially."> + <param name="from" type="text" size="30" label="old name" + help="as it appears in the current input file header"/> + <param name="to" type="text" size="30" label="new name" /> + </repeat> + </inputs> + + <outputs> + <data name="output" format="bam" + label="(Re)headered bam file from MiModd ${tool.name} on ${on_string}" /> + </outputs> + + <tests> + <test> + <param name="inputfile" value="a.bam" /> + <conditional name="co"> + <param name="treat_co" value="update" /> + <repeat name="coinfo"> + <param name="line" value="ceterum censeo ..." /> + </repeat> + </conditional> + <output name="output" file="a.bam" ftype="bam" lines_diff="1" /> + </test> + <test> + <param name="inputfile" value="header_only.bam" /> + <conditional name="rg"> + <param name="treat_rg" value="update" /> + <conditional name="rginfo"> + <param name="source" value="from_form" /> + <repeat name="rg"> + <param name="source_id" value="000" /> + <param name="rg_sm" value="Bristol" /> + </repeat> + </conditional> + </conditional> + <output name="output" file="header_only.bam" ftype="bam" lines_diff="2" /> + </test> + <test> + <param name="inputfile" value="header_only.bam" /> + <conditional name="rg"> + <param name="treat_rg" value="update" /> + <conditional name="rginfo"> + <param name="source" value="from_form" /> + <repeat name="rg"> + <param name="source_id" value="001" /> + <param name="rg_sm" value="Hawaiian" /> + </repeat> + </conditional> + </conditional> + <output name="output" file="header_only.bam" ftype="bam" lines_diff="1" /> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool generates a copy of the BAM input file with a modified header (i.e., metadata). + +It can update or replace read-group information (i.e., information about the samples in the file), add or replace comment lines, and rename reference sequences declared in the header. + +The tool ensures that the resulting BAM file is valid and can be further processed by other MiModD tools and standard software like samtools. It aborts with an error message if a valid BAM file cannot be generated with the user-specified settings. + +The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_header.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,169 @@ +<tool id="mimodd_header" name="MiModD Run Annotation" version="@MIMODD_WRAPPER_VERSION@"> + <description> + writes run metadata in SAM format for attaching it to sequenced reads data + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd header + --rg-id '$rg_id' + --rg-sm '$rg_sm' + #if $str($rg_cn): + --rg-cn '$rg_cn' + #end if + #if $str($rg_ds): + --rg-ds '$rg_ds' + #end if + #if $str($rg_date): + --rg-dt '$rg_date' + #end if + #if $str($rg_lb): + --rg-lb '$rg_lb' + #end if + #if $str($rg_pl): + --rg-pl '$rg_pl' + #end if + #if $str($rg_pi): + --rg-pi '$rg_pi' + #end if + #if $str($rg_pu): + --rg-pu '$rg_pu' + #end if + --ofile '$ofile' + + ]]></command> + + <inputs> + <param name="rg_id" type="text" size="80" + label="read-group ID (required)"> + <validator type="empty_field" /> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + <param name="rg_sm" type="text" size="80" + label="sample name (required)"> + <validator type="empty_field" /> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + <param name="rg_ds" type="text" size="80" label="description"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + <param name="rg_date" type="text" + label="date (YYYY-MM-DD) the run was produced"> + <validator type="expression" message="YYYY-MM-DD date format required">not value or (len(value.split('-')) == 3 and all(part.isdigit() and len(part)==expect_len for part, expect_len in zip(value.split('-'), [4,2,2])))</validator> + </param> + <param name="rg_cn" type="text" size="80" + label="name of sequencing center"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + <param name="rg_lb" type="text" size="80" label="read-group library"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + <param name="rg_pl" type="text" + label="platform/technology used to produce the reads"> + <option value="ILLUMINA">ILLUMINA</option> + <option value="PACBIO">PACBIO</option> + <option value="IONTORRENT">IONTORRENT</option> + <option value="ONT">ONT</option> + <option value="LS454">LS454</option> + <option value="SOLID">SOLID</option> + <option value="HELICOS">HELICOS</option> + <option value="CAPILLARY">CAPILLARY</option> + </param> + <param name="rg_pi" type="text" label="predicted median insert size" /> + <param name="rg_pu" type="text" size="80" + label="platform unit; unique identifier"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value=""" /> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + </inputs> + + <outputs> + <data name="ofile" format="sam" + label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="rg_id" value="000" /> + <param name="rg_sm" value="N2" /> + <param name="rg_ds" value="C. elegans wt" /> + <param name="rg_date" value="2017-06-27" /> + <param name="rg_cn" value="ABC" /> + <param name="rg_lb" value="XYZ" /> + <param name="rg_pl" value="ILLUMINA" /> + <param name="rg_pi" value="400" /> + <param name="rg_pu" value="SEQ123" /> + <output name="ofile" ftype="sam" file="header_only.sam" /> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +This tool takes user-provided information about a next-generation sequencing +run and constructs a valid SAM format header from it. + +The resulting dataset can be used by the *MiModD Convert*, *MiModD Reheader* +and the *MiModD Read Alignment* tool to add run metadata to sequenced reads +input datasets (or to overwrite pre-existing information). + +**Note:** + +**MiModD requires run metadata for every input file at the Alignment step !** + +**Tip:** + +While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, we **recommend** you to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming, this practice protects against information loss and ensures that the input datasets will remain useful for others in the future. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snp_caller_caller.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,191 @@ +<tool id="mimodd_varcall" name="MiModD Variant Calling" +version="@MIMODD_WRAPPER_VERSION@"> + <description> + generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it + </description> + <macros> + <import>macros.xml</import> + <macro name="test_mentions_samples"> + <assert_stdout> + <has_text_matching expression="000.+N2" /> + <has_text_matching expression="266-1.+ot266" /> + </assert_stdout> + </macro> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd varcall + #if str($reference.source) == "cached": + '$reference.genome.fields.path' + #else: + '$reference.genome' + #end if + #for $input_file in $list_input + '$input_file' + #end for + --index-files + #for $input_file in $list_input + '${input_file.metadata.bam_index}' + #end for + --ofile '$ofile' + $group_by_id + $adv_settings.md5_check + --max-depth $adv_settings.max_depth + --verbose + --quiet + ]]></command> + + <inputs> + <conditional name="reference"> + <param name="source" type="select" + label="Will you select a reference genome from your history or use a built-in genome?"> + <option value="cached">Use a built-in genome</option> + <option value="history">Use a genome from my history</option> + </param> + <when value="cached"> + <param name="genome" type="select" + label="reference genome" + help="The fasta reference genome that variants should be called against."> + <options from_data_table="all_fasta" /> + </param> + </when> + <when value="history"> + <param name="genome" type="data" format="fasta" + label="reference genome" + help="The fasta reference genome that variants should be called against."/> + </when> + </conditional> + <param name="list_input" type="data" multiple="true" format="bam" + label="Aligned reads input dataset(s)" + help="Select at least one dataset to call variants on. If you select several datasets or a dataset collection, this tool will perform joint variant calling on all of them and produce a single, possibly multisample, output dataset." /> + <param name="group_by_id" type="boolean" truevalue="-i" falsevalue="" checked="false" + label="group reads based on read group id only" + help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." /> + <section name="adv_settings" title="More options" expanded="False"> + <param name="md5_check" type="boolean" truevalue="" falsevalue="-x" checked="true" + label="md5 sum verification of contigs/chromosomes" + help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." /> + <param name="max_depth" type="integer" value="250" min="0" + label="average sample depth cap limit (default: 250)" + help="only relevant for very large sample numbers and/or very high sample coverage; increase to use more of the data, decrease to save memory"/> + </section> + </inputs> + + <outputs> + <data name="ofile" format="bcf" + label="Variant Calls from MiModd Variant Calling on ${on_string}"> + <actions> + <conditional name="reference.source"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" ref="reference.genome" column="0" /> + </option> + </action> + </when> + </conditional> + </actions> + </data> + </outputs> + + <tests> + <test> + <conditional name="reference"> + <param name="source" value="history" /> + <param name="genome" value="a.fa" /> + </conditional> + <param name="list_input" value="a.bam" /> + <expand macro="test_mentions_samples" /> + </test> + <test> + <conditional name="reference"> + <param name="source" value="history" /> + <param name="genome" value="a.fa" /> + </conditional> + <param name="list_input" value="a_part1.bam,a_part2.bam" /> + <expand macro="test_mentions_samples" /> + </test> + <test> + <conditional name="reference"> + <param name="source" value="history" /> + <param name="genome" value="a.fa" /> + </conditional> + <param name="list_input" value="a.bam" /> + <param name="group_by_id" value="true" /> + <section name="adv_settings"> + <param name="md5_check" value="false" /> + <param name="max_depth" value="1000" /> + </section> + <assert_command> + <has_text text="-i" /> + <has_text text="-x" /> + <has_text text="--max-depth 1000" /> + </assert_command> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool transforms the read-centered information in the aligned reads input +datasets into position-centered information including variant call statistics +(using samtools mpileup and bcftools internally). + +**It produces a BCF file that serves as the basis for all further variant +analyses with MiModD**. + +----- + +**Notes on Advanced Settings:** + +**MD5 checksums** + +By default, the tool will check whether the input BAM dataset(s) provide(s) MD5 +checksums for the reference genome contig/chromosome sequences used during read +alignment (e.g., the *MiModD Read Alignment* tool stores these in the BAM file +header). If it finds MD5 sums for all sequences, it will compare them to the +checksums of the reference genome sequences used in the current tool run and +abort with an error message if there is a discrepancy between them. If it finds +contigs/chromosomes with matching checksum, but different names in the aligned +reads dataset(s) and the reference genome dataset, it will use the name from +the reference genome in its output. + +This behavior has two benefits: + +1) It protects from accidental variant calling against a wrong reference genome +(*i.e.*, a different one than that used during the alignment step), which would +result in wrong calls. This is the primary reason why we recommend to leave the +check activated. + +2) It provides an opportunity to change sequence names between aligned reads +files and variant call files by providing a reference genome file with altered +sequence names (but identical sequence data). + +Since there may be rare cases where you *really* want to align against a +reference genome with different checksums (e.g., you may have edited the +reference sequence based on the alignment results), the check can be turned +off, but only do this if you know *exactly* why. + + +**Average sample depth cap limit** + +For each of a total of ``M`` BAM input datasets, the tool will only pile up a +maximum number of reads ``N`` per position to avoid excessive memory usage with +very large numbers of samples sequenced at high coverage. +N will be calculated as the maximum of ``8000/M`` and ``DEPTH*S``, where ``S`` +is the maximum number of samples found in a single input dataset and ``DEPTH`` +is the *average sample depth cap limit* specified in the tool form. + +This parameter, thus sets the average depth of the pile-up per sample that is +guaranteed to be used even when there is a very large number of samples. As can +be seen from the formula above, however, it will rarely become relevant for any +regular-size analysis. + + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
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+aatcttcttaacatcccaagacttttcttatacgtagatttttttggccc +tctagtatttttatttataataatttttttatcttttttaattttaaaaa +tattatttaaggagttaatatacaagtttttagttgattatttggctaaa +aatagtatttataaaataaagaatttaaaatttatagatttatttttaaa +taatattaattctaaggggtacaccttatttttaagcagtggtatattta +aaaattactatttaaaaaggttaaattttaatagtgtagtagttttaatt +tttattttttttataatttgttaagggattttagtttaataaaaatatat +gttttgcatacataagataataattctagatagttttacacgcgcgtata +cgcgcgttataaatatatatatatatatatatatatatatatatatataa +taataatattatatttatattataaatataatatttattataaattatat +attatatttatattataaatataatatttattataaattatatattatat +ttatattataaatataatatttattataaattatatattatatttatatt +ataaatataatatttattataaattatatattatatttatattataaata +taatatttattatatattatatatattatatttatattataaatataata +tttattattaataattcatcatatttatattataaatatgatgaagtact +aaaaaaaagatgaatattctataatatatttagatatattatagagtatt +tatcttattatttatagatatatactttgtatatatctatatta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.sam Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,824 @@ +@HD VN:1.5 SO:coordinate +@RG ID:000 SM:N2 +@RG ID:266-1 SM:ot266 DS:mutant strain carrying the vab-3 allele ot266 CN:Columbia University PL:Illumina +@SQ SN:chrI LN:25050 M5:7d9f340160ce45568f9bf48d8e16dcf4 +@SQ SN:chrII LN:25050 M5:ba5a89bf12f55a4bd88ddf14e6d27bd6 +@SQ SN:chrIII LN:25050 M5:ba78739f84b6c850448bec286bdd8798 +@SQ SN:chrIV LN:25050 M5:0807d4df5c3593363a5b015f19ef81c2 +@SQ SN:chrV LN:25050 M5:cf942c1556ef72fd9ba352e4a7d9cf9e +@SQ SN:chrX LN:25050 M5:5ce1b12d74140cfc288b493c16fe280b +@SQ SN:MtDNA LN:13794 M5:199e147d502d88e45047413dc83c039c +@PG ID:SNAP PN:MiModD snap VN:0.1.8.0 CL:paired /var/tmp/batch_dataset_548966_dataset_35_20_0.3 /var/tmp/batch_dataset_54896612531.sam -d 8 -S 200 -n 25 -a 7 -F s -o /var/tmp/batch_dataset_54896615435.tmp -h 250 -c 2 -C++ -M -s 100 10000 -t 2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:19049:65217 99 chrI 556 60 100M = 702 246 CCTATATGCTCCTGTGTTTAGGCCTAATACTAAGCCTAAGCCTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAG CCCFFFFDHHHHHJJJJJJJIJJJJJJIIIIIJIJJJJJGIIJIIHIJIJJHIJIJJHIJJIIJJJIIIIGGGIJHHHHHFFEFFFEECEEDDCACDDC? PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:56:17087:17617/1 0 chrI 575 60 101M * 0 0 AGGCCTAATACTAAGCCTAAGCCTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCC GGFGGGDGFGEFBGFGFGGGGGGFGGEGGGGGGGGGGGGGGGGGEGGFFEFGGFFGEAFGFDEGGGGGGGEEFDDEEEEEGFGGEGEDBEEAEDEECFEBC PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:19049:65217 147 chrI 702 60 100M = 556 -246 AGCCTAAGACTAAGCCTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGAC CCC>AA>;(CCC;C@3HEEEGCIGED=EGGGJHGJIGGCIJIIDFGGIGDIHJIHEGIHJIIEGGIIGJJJIGIGJIJJJIGDIHGIHHFHGFFFFFCB@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:81:6795:13435/1 16 chrI 842 60 101M * 0 0 TTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAGTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATA A:@EEEEEBEEEEEEEEEGEEEEGEEEEEEEED=BFEEEGEEGEGFGGGEEGGGGGGGGFGGGFDDAGG=GGEGGGFFFEFEECBFDGGEGDGDGGGFGEG PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:1:46:9721:15037/1 16 chrI 842 60 101M * 0 0 TTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATA AEEBEBBEEEAAEFEFFFE?FCCCBC?DDBD5DD=D:DDC:CC?C>6EB@CEEEDDEECEEEEE8BFFEEFEEADDCCC@CBCCEEFDFFAEFGFDFGGGD PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:77:15674:6412/1 0 chrI 844 60 101M * 0 0 GAAATGAATATCGTAGCTACAGAAACGGCAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAACATA GFFGGGCGDFGEGDFEEFEGGFEGFEEEACC?BCCDDCDECBECDEFEECEEDEEEEEEEEBEEEEEEAEEEEE=AC:=CBBCCCC@::?CACC@BBBABE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:88:10221:3318/1 16 chrI 845 60 101M * 0 0 AAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCATATATAG AEBABBEEBGEGEBGGGEEEEGEEGGEEGGCEEEFEFEEBGGFDEGAEFGGEDFF=EEGEGGGGGG?DBDFGGFGGDFECCFDDCGEEEE:AG?GFFGDGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:87:4119:14575/1 16 chrI 845 60 101M * 0 0 AAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAA GEEGEDEEGEGGEAEFEB?DEEDBGGBGGFGEFBGFGGBGGGGGFGGEGFGGGGGGGGGGGGFEFAGGGGEGGDGGGGDFGGBFGGGGDFDGGDGGGGGEG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:95:9634:15406/1 16 chrI 845 60 101M * 0 0 AAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAA FEEE?GEFEBE:ECE=BEGGGEGEGBFFFEFAFDFFGEBBGGGFGDGEGGGEEEEE5FFFFCFGAEGGEGGGGGGGFGDGGGFGGGGGGGFGDFFFGGGFD PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:2113:3662:39793 73 chrI 846 60 100M = 846 0 AATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAA CCCFFFFFHHHHHJJJJIIIIJIJJJFGIGIIJJIGIJIJJGEHIHJHEHHHJIIJJJJJIJJIGIJIHHHHHHEFFFFECEEDBDDCCDDDDD?CDDDC PG:Z:SNAP RG:Z:000 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:2113:3662:39793 133 chrI 846 0 * = 846 0 GTGTACTACCGTTTCTGGAGCTACGATTTATTTTTCAAAACACGCAAAAAGTGTTTTTCACTATGTACAAAATCATCTCAAAATCGGAAATATTTTTTGT <<<@@@@@@@@@@???#################################################################################### PG:Z:SNAP RG:Z:000 +EAGLE:2:45:11395:10768/1 0 chrI 846 60 40M3I58M * 0 0 AATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCTAAATAT G?FEGGBGGEFDFDDEDEBEEDFFEC@D=AFFFCFFFFFEAFEDFFEF=FFFFFFFD>DF?FFAFFFFFECCAFE=BEAEEFBDEEFEEEEEEEEBEFDDA PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:47:11205:5807/1 16 chrI 846 60 101M * 0 0 AATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAGTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAG FEEDBBFEAEFDEFEE?EDFEEACFEDAFDDFEFFFFFFFFFFFFEEBFFEFEFFFFFFFEEFFFFEEFFFFFFFEEACAFDGGFGGGGGGGGGGGGDGEG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:69:6499:16127/1 0 chrI 847 60 101M * 0 0 ATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGC GGGGGGGGGEGGGGGGGGGGGFGGGDGGEGGGGGGGGGGGFGGGGGGDFGGDGEGGFGG=EFFFFAG;CGGEBGEEFEFGGGGF?CEBCFFEBFEEEEF?F PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:24:6173:14843/1 0 chrI 847 60 101M * 0 0 ATGAGTATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGC FDGFGGDEGEEG?GGAEEEEBEE?::AB;AADB=CEFFFD=EDFF?EBEEEC@@EFDEEDADEDFE;EAFD::D:BCB<BEEDB8=DB??BBB5:=@:@@: PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:52:5204:4050/1 0 chrI 847 60 101M * 0 0 ATGAGTATCATAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGC FFFFEFFFFAEAEAEGGGGDEGGGGBFEDEFFFFFGGGGF=FDFFGGGGGGGAEGGGGGFFFGFGGGAGEEGFG?GFDEEGFFGBEEEEEFEDGFDG5FFB PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:88:14674:10686/1 16 chrI 847 60 101M * 0 0 ATGAGTATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGC EEEEAEBBEDAEEEEEFDFDDEGEGGEDFBEBFEFEBGCEGCEE?8DEFDEFGGGEEEEC>?FEGGFEGGGCEEBE:CCEEEDFGG=EFBGGEBFGGGDDG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:29:17996:20445/1 16 chrI 847 60 101M * 0 0 ATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGC EE5?EEBBBB?E=DEDFEFEBADCEECBAAE=E=EBDF?EGEE=GCDFFEDBDFGGDGGGGEF=GGGGGBDGGGDGBGGFGGGGGGGFEGGGEEGEEGGFG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:112:10138:4083/1 16 chrI 847 60 101M * 0 0 ATGAGTATCATAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGC EC?@BEACB:C@=EE?CAECC@CCCE>=A<55CCD?BEE?E?FFA;GGGGGEGEGEEDBGGGGEGBGGEGGBFGDGCCCGEG?GDGDFFGGFFFFFE?EDE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:54:15434:16430/1 16 chrI 847 60 101M * 0 0 ATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGC EEEE@EEEEEEDGEEEGEGDEEGGGGEG?DFEGFGGFFGGGFGGEEFGGGGGGGGGGGGGGGGEGGGGGGGFGGFGBGDGGGEGGGEGGGEGGGFDDGGGF PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:58:7649:14576/1 0 chrI 848 60 101M * 0 0 TGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAGTTGCAATTTTTATAGCTAAGACACTTTTTGTCTGCCCAAATATAAGCA GGGGGGGGGGGGGGGGGGFGGGGGEFFEDFEGGGGGGGGFGGGGGGCFFGGGGEFEGGFGGGGGFGGGGGFFFGGGGEGGGGEEEGGGGGFEGEF?FBBFG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:76:11197:2138/1 0 chrI 848 60 101M * 0 0 TGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCA EEDFFFEFBDADEEEFFBFFFEFFE=C@?CFFFFFFFDF?EEEDEFBDFFFFFFFFFFAEAEDEBC;FFEFEFFDDABFFFFE;CFEFEEBEFBDBDDDEB PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:59:14370:7837/1 0 chrI 849 60 101M * 0 0 GAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAAAACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCATATATAGGCAA FGFGEGGEBGFGFGGDGFFGEED=EA@=DDFFE?FEFFFFFFFFFEEEEEFEEADFAFFFFFFFEEFEEBEEBEFEDEEEFEEEEBEEBE:EBBBB@BBAD PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:79:15239:5534/1 16 chrI 849 60 101M * 0 0 GAATATCGTAGCTACAGAAACGATAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGGCACTTTTTGTCTGCACAAATATAGGCAA BFDGDDFFEDEGGDGFEEFBEFFFFEECECEGAEEGGGGFGGGEEGGGEGGBFGGGGGFGGFGGGFGGDEGGGGEGGFGGGGGEFGEGFGDFGFGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:83:6103:1248/1 16 chrI 849 60 101M * 0 0 GAGTATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAA @>B:9?BBBBDBB?DBEBEEEBDDDDD?FAEEEEEEEEEEEEEEFFEFFFEDFEFEECCDAFFFFFFFFFFEBE?@EDFFEFFEFFFFFFFFF?DFEFFDD PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:60:3721:11022/1 0 chrI 851 60 35M3I63M * 0 0 ATATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCA DGBGGGFGFFE=EEEDEFFFEBEEEED=EDFDFDFFFFE:FEFEDFDFFFEFFFFFFEDFFFFEFCAFFBBEEBEFFEEEFEAEEEEEEFEFFEEEEBEEF PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:56:9356:7127/1 0 chrI 851 60 101M * 0 0 GTATCATAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACC GFGGGGGGDGGFGCFDBFFFGDGGDGEFFGGDFEEFGDGGEGGGFGGEEEG?GFGEEEFEED;@EGEBEEEEE?BDDDECEEEEEGEE?EA?AC@CCA5?? PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:26:13486:6669/1 16 chrI 851 60 101M * 0 0 ATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACC GE:EEEDDDDAEGEBEEEFEGEEDABFCDEEEEEGGGEGGEEGGFGEDEEFAGDGEGBGFFGGGEGEGGGDFACCFFFGGDGGGEEBGGGEEEEEEEE?EE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:90:7286:17726/1 0 chrI 852 60 101M * 0 0 TATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCA GGGGFGGGGGGGGGFEGFFGFDDBGGFGGGEFGGGDAGEGGGFDGGDGGGGGGGE?GGGGGGEGGGGDFGGGGEEFBCEEDGFFBGGDGDGGEDBEEGDEB PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:60:11520:19697/1 0 chrI 852 60 101M * 0 0 TATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCA DEDEEFFFFFEGGGFFFFFFBEE?EEEEEEFBFFFFFFF?FFFFFCFFCFFDFFAEFFFFEEADFDDF?EFFFEFFFBEEEEFEFFEFF@FDED:BEEBEE PG:Z:SNAP RG:Z:266-1 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1102:21095:33794 73 chrI 853 60 100M = 853 0 ATCGTAGCTACAGAAACGGTAATACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGGCACTTTTTGTCTGCCCAAATATAGGCAACCA @@@FDFFFHHFHHJJJIJJIJJJJJJJIIJGGIIGGIIII4?GIJJIIJIJJJJGIJJGGIIJJJJJDEHGEFCDCEDEEEEDCDDBDDDFEDCDDDDDB PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1102:21095:33794 133 chrI 853 0 * = 853 0 GCTTCACAGTATATTTTACTTTCTGTGGCTTCACAGTATATTTTACTCTCTGTGGCTTCACAGTATATTTTACTCTCTGTGGCTTCACAGTATATTTTAC A>;6;6(CA;;@B?3DB=AA7EGGIJIIGGIGEIJJJJJHEGGCBFGGFBBFG@IGDJIIJJIIJJIJJIGHIGHGJGHGIHCJJJIHHHHHFFFFFCCB PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1304:18505:45478 73 chrI 853 60 33M3I64M = 853 0 ATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAA @CCFFFFFHHHHHIIIIJJHDHCHIIHIIJIJGIEGGHEDFFGEGIIJIJJJJGIJGGGIJIGEGGGJIHDHEH;?CDFFDECECAA?>BBDDDE>:CCC PG:Z:SNAP RG:Z:000 NM:i:6 +BS-DSFCONTROL03:121:D0M8KACXX:5:1304:18505:45478 133 chrI 853 0 * = 853 0 GGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTC ?;;5::>CDED@DEFDDDDFFFFFFHHHHHJIIIEJJIJJJJJJJJIIHFIGGIIGJJIGJIJJJJJIJJJIJJIJJJJIJJIIIIIHFFAHFFFFFCCB PG:Z:SNAP RG:Z:000 +EAGLE:2:96:9394:5489/1 16 chrI 854 60 101M * 0 0 TCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAA EGEBEEEEEFEGEBEGEEE:E?DFCFFFGEGGFGGGFGEFGGGFGEEEGGGGEGGGGFGGGGGDGGGGEEGGGGGFGGGGGGFGGGGGGDGGGGG?GGGGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:110:3453:13829/1 16 chrI 855 60 101M * 0 0 CGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAA EAEAE?5EEEEC5=EBDFFDFDGEGEGGDBEFGGBFAEEGGGGGGEEEEDEE8FFFGGGGFGEGGGFFEEEDG?GGGDGGGGGGGFGAGDEGGGAFGEGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:34:16346:19478/1 16 chrI 856 60 101M * 0 0 GTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAA DDD?BB@B=BBB>DDC@@B?:A?:AAEEDEABCCB6EEEEEBEEDDED:DC>EEEEBDDCBD5CEBED=CEEBEEEEEEDEAEEAEEFGGFBEBEAEEDEE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:75:1484:17855/1 0 chrI 857 60 101M * 0 0 TAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAGTTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAAT DD@CADEEEEEEFFDBDDCDEEDEEAFDEFAFFFFDFFFFFFD=FDFFFFFFFEF;CCEEDDDFDBEAAFFFFF8EBDEDDDFFAFDFFBFFFEF5FFEF= PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:110:6822:2912/1 16 chrI 857 60 43M1I44M1I2M1D10M * 0 0 TAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAAATTGCAATTTTGATAGCTAGGACACTTTTTGTCTGCACAAATATGAGCAACCAAAAA DBFBDCECFEDEFGFGEGFEGEGGGGEFFGGEGF=BGGGGGGGGGFGGGGGGFGFGGGGGGGGGGEGCGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:12858:84933 83 chrI 858 60 100M = 876 118 AGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAGTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAAT CCCEEDDDDBDBCDEDDEDCDDDDDDDCEEEEEEEDFHHHHHJIJIJJIHJJJJJJJJJJJJIGGBJJJIJJJJJJIIJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:4 +EAGLE:2:91:13868:11992/1 0 chrI 859 60 41M1I59M * 0 0 GCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAAATTGCAATTTTCATAGCTAGGACACTTTTTGTCTGCACAAATATAGGCAACCAAAAATA GGGEGGGBEDGGECEEDFFFGGGGGGGGFGGGEGGGGFFGGGGAG=FFBDFFGGGEAFGBGEGBGGAEGEGFEEEEDEEEDFF=ECBCCC?AECCCDDECE PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:119:12921:6612/1 16 chrI 859 60 27M3I71M * 0 0 GCTACAGAAACGGTAGTACACTCTTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAA BBEEGEE=FBEEFDFGFAGBGGGFEGEFGDGEEGGAEGGGDGGGGDDFGDGGEEGEGGGEGEEEEBEBCCEFDGFFGDGGEFFGGFEEEEEFFBFFGGFGF PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:111:6913:8666/1 0 chrI 860 60 101M * 0 0 CTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAAT GGGGGGFFFGFF@EEAEEEEBGGGFGGEGGGGEGGGDGEDCFA5F?EEEEGGG>GGBFEEFFEGGEFFAFF>EDEC?FEDABBBBD=A:D=B=EB@E@?;> PG:Z:SNAP RG:Z:266-1 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:2216:18829:62698 83 chrI 860 60 100M = 871 111 CTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAA CEDDDC?BBBCDEEEECC@EDEEECEFFFFEFHHHJJJJJIJIJIJJJJJJJJJIJJJJJIGGGJJJJJJJJJJJJJIIJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:3 +EAGLE:1:67:7435:14824/1 16 chrI 861 60 101M * 0 0 TACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCATATATAGGCAACCAAAAATAATT ::GEEGEEGDGGGEGEGDDBGG?GGGGFGGG@FFAFEGGFFEFGDGEFGGGFFGGGFFFFFGBFGGFGDGGGGGGGGGEFGGBGGGGFFGGGFGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:2 +EAGLE:2:11:15002:3991/1 16 chrI 862 60 101M * 0 0 ACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTT DEEFEDBEFEFDFBDF?EEFFDG?GEFEFC=EGAFGEGDFDFGGEEG=?GGGDDDFCEEBE6@@>A=GFFGGCFGGEEEEE:E?EEAEDEECEEE?5EEEE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:96:4105:9079/1 0 chrI 863 60 101M * 0 0 CAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTC GGGGDGGGGEGGEGGDGGGGGGGDGGGGGFGGGEGGFEBGDGGEGEG?GEFEEGEEEEEGDDEDEFEBEECC=DFDDDCCEAEBGEECGE@DEF???;?BE PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:1204:8976:92778 73 chrI 864 60 100M = 864 0 AGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTC BCCFFFFFHHGHHJJJJJJJJJJJJJHHGHHJJJJJJJJJJIIJJJJJJJIIJJJIJJJJGIJJJJJHHHHHHFFFFFEEEEDEDDDDDDDBBDDDEDEC PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:1204:8976:92778 133 chrI 864 0 * = 864 0 AGAGTGTACTACCGTTTCTGTAGCTATGATACTCATTTCAAAAAACCCGAAAAATGATTTTTTCAATATGCAACAAATCATCAAAAACTTGGAAATTATT BCCFDFDFHHHHHJHJIIJJJJJJJJJJJFJJJJJJJJJJJJJIJJJJJJJJJJJIJJJJIJHFFFFFFECDCEEBDDDDDDDDDDDDDDDDDDDDDDED PG:Z:SNAP RG:Z:000 +EAGLE:2:89:4630:12148/1 0 chrI 865 60 101M * 0 0 GAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCA GFEGGFFFFFB=DDCGGGGGEEFFFDFFFFGGDGGDGG=EDCGGGGGEG>GGFGFBFFFBGEGGGDCC=FEEEEEEE=E:EBEEEFGF?GGCAA8;EEBE: PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:71:6779:3992/1 0 chrI 866 60 20M3I78M * 0 0 AAACGGTAGTACACTCTTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTC GGGGEFGGFFEGGFEGGGGGBGFEGFGGFEGGFGEACCFFDGEBFGGGGFGEGGADBFEFGGEE5EEE=ABBFEGGGGBFEE=EEEDGGBEEE=E@B;CAE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:90:8794:13563/1 0 chrI 867 60 101M * 0 0 AACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAG FFFFFEDFFFGFFFGGGGFFEGGGFFGGGGFGDGEFFGGAGGDGFGGGGFFCGGDGGGBGDF:F;ACEEEFF:AEDEEAEEDECGEGFGGE8C;DD=BD?B PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:12542:49797 73 chrI 869 60 100M = 869 0 CAGTAGTACACTCTTCTCAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGT BCCDFFFFHHGHFJJGGJJJJJHJIJIJJJIIJIJGIJJJJJJJJJIIIJJJIGHHGGGIGEHGIGEHEGHFGGHCCFBDFFEDDDDDDDDEFEDEDCCD PG:Z:SNAP RG:Z:000 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:12542:49797 133 chrI 869 0 * = 869 0 GTGTCCTAGCTATAAAAATTGCAAATTTTTTGTATTTTCAGAAGAGTGTACTACCGTTTCTGTAGCTACGATATTCATTTCAAAAAACCCGAAAAATGTT CB@DFFFFHHGHHJJJJIGGIJJIJIGIIJJJHIIIJIIJJHHIIIGHHIIJJJJJJJJJJJIJJJJJJJIHHGHFFFFFFFEEEDDDDDDDDDDDDDBD PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2216:18829:62698 163 chrI 871 60 100M = 860 -111 GTAGTACACTCTTCTCAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTT CBCFDFFFHHHHHJJJJJJIJJIIJJJJJJJJJJJJJJJJJJJJJJIJJIDHGHIIJJJJJJJIJJJEIIEEHHHHGFFFFDDDDDDDDDE<@DC5@@>> PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2306:15570:52084 73 chrI 871 60 100M = 871 0 GTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTT @@CFDDFFHHHHHJJJJJJJIJIJJIIJIJJJJJJJJJJJJJJJJJJJJJIIJGIJJJJHHFHHHFFFFEEEFEDCCCDBDDDDDDDDDEEEDEECDDDC PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2306:15570:52084 133 chrI 871 0 * = 871 0 TTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTT BBDDDDDDDBBCECEEEEFFFFFFHHHJJJJJJJJJJJJIIIJJJIIIGJJJJJGJJJJJJIHFJJJIGJJJJJJJJJJJIJJJJJJHHHFHFDDFFCCB PG:Z:SNAP RG:Z:000 +EAGLE:2:85:11800:16523/1 16 chrI 871 60 101M * 0 0 GTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTT GEGGEEFEGEGEEGEGGFGGE@GGGGGGGEGGGFGEGEGEGGGGGGGFGGEGEGEGGFGGGGFGGGAGGGGGGGGGGGGGGGGGGGGGGFGGGEGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:50:15754:14085/1 0 chrI 872 60 101M * 0 0 TAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTT FFFFFFFFDFFAFFFFBDFFFFFFFFFFFFFFFFBFFFFFFFEFFFFFFFFFFEFFFFFEEFFFFFFFFFEFFBFEFFEFFF?FFDEEEEFFEEEF@DFEA PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:51:4256:7814/1 0 chrI 873 60 101M * 0 0 AGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATTATTTCCAAGTTTTTG EFFDGGGGGEGGGFAFFGGGGGGFFGGGGFGGF?DGFGGGGGFGGFFAFGDGEDEGGGEGEFGGGEGGGDDFGGFGGEGBGGEFBGFEEEEEEBEEEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:83:2757:15592/1 0 chrI 874 60 101M * 0 0 GTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGA FEFFFFDFFEGBGGGGFDGGGEFFEDGGDGFBEAFFFFEACDGDEEDGGDEGEGGGGEEDEEEDDAE?EDBEEEBEEEBBGEEE@@@@BDD@?B@@BBB@; PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:74:11870:7997/1 0 chrI 874 60 101M * 0 0 GTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGA GGEGGGGGGGGGDFGGGGFGGGGGGFDFFGGGGDFGGGFGGGGFGGGFGGGFEGGDB@GEGEGGGBGEFGEEGEEGEGEEBFEDCEEEE?EC@FACFDFDC PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:12858:84933 163 chrI 876 60 100M = 858 -118 ACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGAT CCCFFFFFHHHHHJIHJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJHHHHHDFFFDDEEEEEEDEEDDDDEDDDBC PG:Z:SNAP RG:Z:000 NM:i:4 +EAGLE:1:89:11320:10564/1 16 chrI 876 60 101M * 0 0 ACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATG @EEFEGFEGFEG=GDFEGGEGGEGEGFBGGGEGFGFGGGGGGGGFDFEGGGGGDGAFGGFFGFGGGGFGGGDGGGBFGGGGGFGGGGGGGGGGGDGDGGFG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:87:16027:10849/1 16 chrI 880 60 101M * 0 0 TCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAATTTTTGATGATTT ?BBBB@BBBB?;<BBB?BBBBBBDAB88?:?=BBBBBAADA?B;<<BC?BBBDDDABBADCA=B=?@@=5>@A:C?BC??DBEABDE=EEDDDD??DDDBD PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:98:7014:9919/1 16 chrI 880 60 101M * 0 0 TCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTGAGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTT =BGECGFEEGG>?EFEAFEFAEGGABG@DBEFDGDGGFEEGEDCCGGFGDGDEEEDEFGFGDGGGDGGGFGGEGGGGFGGFDGGFGGGGGGEDGGGGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:53:7732:11243/1 16 chrI 882 60 101M * 0 0 TTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGT E@D=DF@BB:8EFDEEBB==B?FEEEAABBAEFFFDECEEEBB@EDCE?CAE:EAE?AE=EEEE?ED=D<>EDAF?DDFBFAE?EE??BFAEEDEEFEDF? PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:65:9151:20950/1 0 chrI 884 60 101M * 0 0 CTGAAAATACAAAAAATTTGCAATTTTTATAGCTGAGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTG GFGGGFGGFGGGEGEGGGGGGFEGGGEGGDGGFGG?GGGGGGGGGFGEGGGGGGGGGFGFGFGGFGFGGEFGGGEE@EDFEBBE?EEEEEBBEBDEEEEE? PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:96:16607:9367/1 16 chrI 884 60 101M * 0 0 CTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTG GEEGEGFCCFAGD:GEEAGFBGGGFGE=DDE:BFFFDCE5@AAFBDAEFBCCGFFFAFFFEFDDFDDBB@ABF?FDEGAGEFFFFAGGGDGEFAF?DEFFF PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:99:9928:13510/1 16 chrI 884 60 101M * 0 0 CTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTG GEFEEGEEEGG?GGGGEBEGEFEEEBEGFGGEGFGFFCFCEEFFFFGFGBGFGEGFGGGGFGGEGGGGDGGFEGGGGGBGGGGGGGGGGGGEGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:88:16505:15331/1 16 chrI 885 60 101M * 0 0 TGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGC BEFGEDEEGGEEDEEDDEEEDEEGEEGBGGEEEEEEDF?CCGGGGGGFGGFFGDDGGGGGFGGGGGGFFFGGEFDGDEFFDGFFGGGGGGGGGFFGGGDGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:78:3200:13969/1 16 chrI 886 60 101M * 0 0 GAAAATACAAAAAGTTCGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCA @B:BA88EEEE?=BBB=CEB8>DE?EEFCBFCBCCBE@B@C;DEFFFEFFFBFFDFFFFFFFFFFEEEBFFDEE5EBEEEEEAEE?EEE?DD;DEEFEF=D PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:87:17306:17581/1 16 chrI 886 60 101M * 0 0 GAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCA AABE=8;AAA<?AA?:=EDBC@DFFFACCC=BADEEDB@;AFEFFFFDFDFEDAEEBEDEEEDEEEBCEEADFDFFEEE=AFFFFFEEFBBBEFFDEAAD? PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:48:14507:16490/1 0 chrI 887 60 101M * 0 0 AAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCAT FFFFAGGGDGGGAGGFDFFFADEDEDAEDDFFB:FEAEEAEABBA::@C@BE?EECE?BB?CDACBAABEE?C=ABBB@B>==A=AAAAAEEEEEBD?BB: PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:54:4351:16632/1 16 chrI 887 60 101M * 0 0 AAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCATATATAGGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCAT EGEGAEGGGGGEGGEGGGGEGGGGGGGGFFGGGGGGEGGFFGGGDGFGFGGGFGFGGGGGGGGGGGDDFFF:EGGEGGGEGFFGFGGGGGGGGGGGGGDGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:115:17415:17791/1 0 chrI 888 60 101M * 0 0 AAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATA DD@D7EEEEE>CCEFFFFDFFFFFF8EFFFEFFFFFFBFFBFF:DDFFFFFFDFDFF?E@DEBAEFDFF;C@C?EE=DADEEEE;D:DD@EEE?BE>E=ED PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:9:16465:5809/1 16 chrI 888 60 101M * 0 0 AAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATA D?FDGDGGGGFDGGGBB=DGEFEGGGFFDFFEEEECD=GEGGFGGDGGGGG?FGFGGFGGG?GGGGGGGEGGEGFGGGGGFGGDBGFEGGGFFF:FGGGBG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:98:3753:20118/1 16 chrI 889 60 101M * 0 0 AATACAAAGAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCATATATAGGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATAT BGBDFGFFFBF=BDFGGEFFGGG?GE?FDEFECEBB>FF=FEDGFDF=EFBGFGGGEEDADE>AAEFDGAGDBGFGDFFFE?FDEEGEEDDFEDFFDADG= PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:33:4809:11289/1 16 chrI 890 60 101M * 0 0 ATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATT =EEFEGFFF=BDBBGG=EGGBEDGGG:DBEF?GCFGGDGFGEGEFGGEGGEGGDGGGDFDGCGGGGFFGGGGGGGGGGDFGFFGFGGFGGGGDGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:71:4682:12647/1 0 chrI 891 60 101M * 0 0 TACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTG GGGGGEGGGGGDGGGGGGGDGGGGGGGGGGDGGGFGGGEGAGGFGGGFGGFGGFGGGGGGGGFGGGGGGGGGDGFAEA:CEEECEE9CCECABCBDDDCDD PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:75:5406:10078/1 0 chrI 891 60 101M * 0 0 TACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGGGGGGGGGGGGEGFGGDGGGFGGGGGGGGFGGGBGCGFGGEEGGFEGGEEGCFFGFFE? PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:39:9088:2610/1 0 chrI 891 60 101M * 0 0 TACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTG ECE??D>A<>EEE:EDEEEEDEBBCE=EEEEE?DEEEEED@B=EADDEEEA;EEEDEEEE=EDD=EECCADDED?BAACDDB6?@?5DDBBEAE=EE=EAA PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:66:8142:4981/1 16 chrI 891 60 81M1D20M * 0 0 TACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAGGCAACCAAAAATAATTTCCAAGTTTTAATGATTTGTTGCATATTGA >@DFGGE=EA:FEDFCABBE?DBEE?EEEEEFBCCFADFEGDFF?CEEEEBE?EEEDCAA>GFDEGEADEDFDFDAFBADFGFAEFFFEDEDDDEEFDFFE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:77:9937:16848/1 16 chrI 895 60 101M * 0 0 AAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAA BEEEEEEEEEEEEEEEEEDEGEEDFEAE<CCGFDEEFFGGFGEGGGGDGFGGGGDFFGGGFGGGGGGEGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:20:3429:5322/1 16 chrI 895 60 101M * 0 0 AAAAATTTGCAATTGTTTTAGCTAGGACACTTTTGGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAA ABGEGFEEAEECEFDFDEAFGFGGGGCEDEEEEE:DEFGGFF?FGFFFFFFFFD=FFGGGGGGGFGFGEEDGGEEGFFFFEGGEEEGEEEEECE??CEBEE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:106:10002:5503/1 16 chrI 896 60 101M * 0 0 AAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAA BBEEECEBGFGDGDGFGGAEGEDAB?EBB8DFD=EADDGGGDGEG?GFFGDFFFFCAFGFGGFFGGDDF:DADGGDFGGGGFFFBFGBFDGFFDDDEBGFD PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:51:12803:14933/1 0 chrI 897 60 101M * 0 0 AAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAA GFFGFGGFGFGGDGGGGGGGGGGGGGGGGGGGGDEGGGGGGGGGGGGGGGGGGGGFGGGGEAACEEGGEEFAEEEGEEEDEEEEABDDGDDECDDCDDEDG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:51:2990:9988/1 16 chrI 897 60 101M * 0 0 AAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAA GGGEFGGFEGEFGFGFEFGGGGGGEGEGGGFGGGGGFGBGGGGGGGFGGGEGFGGGGGGGFGGGFFGGGGGGGGFGGGFGGFDGGEGGDFGGGEGGFGFGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:50:10205:11996/1 16 chrI 897 60 101M * 0 0 AAATTTGCAATTTTTATAGCTGAGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAA GFGEEEEFEEEEEEEGEGAGGGEEFEEGEFEEBGEGGFFEEGGGEGGGGGDGEDGGFGGGGGGGGFGEGGGGFGGGGGGGGGGGGGGGGGFFEGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:99:12968:10523/1 16 chrI 898 60 101M * 0 0 AATTTGCAATTTTTATAGCTGAGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAT GFBGGEGGEGFGGFGGEEDEE?B>B5>5DCCFE:AFGG:GGGG?FGFDGGGEGGGGGGGGGGGGFFGGFGGEGGGGDDGGFGGGGGGGGGGGGGGGGGGFF PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:108:8721:8141/1 16 chrI 898 60 101M * 0 0 AATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAA D5:B=AFC?CF?FFFFE=FFFAFFDDDF=DFFFDFEFF=BFFFCFFFFFFFFFCFAFFFDFFFFFFABAFFADAEDFFFDFED?FFFFBBEDFEEDGFEGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:41:18519:16779/1 16 chrI 900 60 101M * 0 0 TTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACA BEEFFFE=BEEEBEEFEEAEEBD=>>EFBAF:FBFF:FFFFDDFDFFFFEEFFFFFFFEFFFEFEFFFFFEFFFAFFFFDFFFFFEDFFFEAEEEBEDEDE PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1112:7827:74939 165 chrI 901 0 * = 901 0 CATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTGAGACACTT CCCFFFFFHHHDFIJJJJJJIIJJJJIJJJIIIJJJIJIIJJJJJCGIAGFHIIJJJJIHHHHHHFFFFFDCDDDDDDEDDDCDDDDECCD@3?@:<CCC PG:Z:SNAP RG:Z:000 +EAGLE:2:43:17839:20176/1 0 chrI 901 60 101M * 0 0 TTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACAT ADEFAFEFFFFFEDFEDFDDFEEFFFFEDFFFFFDFFFFDFBFDEAFBFDFDFFDF=FFFFFFFABEBEEFF?DFFADFFACCD5@B?B=C:@B@AE;?:E PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1112:7827:74939 89 chrI 901 60 100M = 901 0 TTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACA DDDDDBDDEDEDEDDDDDDCCCCBBDEEDCFFFFHHHHJIJIJJJJIGHJJJJJJIJJJJJJJJJJJIJJJJIIJJJJIGIJJJJJJHHHHHFFFFF@CC PG:Z:SNAP RG:Z:000 NM:i:5 +EAGLE:2:119:2085:12525/1 16 chrI 901 60 101M * 0 0 TTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACAT ?B?BBC@FFF=GGEFGACDD?ECACEFGEFGD=GEGEGGE?GGDGGGGGFGGGGGFGBGFGGFGDEFFDE?GEGGEFEGGGGGFGDGFGFGCCCEEDD<B= PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:37:2279:9702/1 0 chrI 902 60 101M * 0 0 TGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATT B><=??CCCAFDEFF=F?FFDF=D?AE?E@CFFABFEFFFEEE=C5@CA@FFFFFFFEE??BEDADA=DBEE?EBBEBEEDF>DBEEDEEEED:DEC@@5E PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:41:11602:1908/1 16 chrI 904 60 101M * 0 0 CAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTT EEEEEGDDEDBFEDBEDAE@CEEGEEEEGEFGGGGBGGFGGGGDGEGGGGGGGGFFGGFGGFGGGGGFFGGGGGGGGGGGGFGGGGGGFGGFFGGFGGFGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:51:19603:11640/1 16 chrI 904 60 101M * 0 0 CAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAAAAATTT EEEEEED=DBBAEBBFE?E<?EEFGEEE?EEGFDGGGEGGGGEGDDGDDGGEGFGGGGFGGFGGGGGGGFGGEFGGGFGGGFGFFFGFGFFGGGGGGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:22:13011:15244/1 0 chrI 905 60 101M * 0 0 AATTTTTATAGCTAAGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTT FGGGDGGGEGGGGGFGGGGGFFGGFGEGGFGGGFGEGGGGDGGGGGGGEGGGGDEED=GGE=ECEGEFDBGFGEGE?DEDGEEFBEGEBDEEDEEEEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:11:4741:6849/1 0 chrI 906 60 101M * 0 0 ATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTC GGFGEGGEEFFGDGFFEFDGGGGGGDCFDFGEGGGFGGGGEGGFGGFEGEGGGDGFFFGDEEBEEDEEEEGFFGGFFGGD5EECEFGAFF?FECCCFGGF= PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:17:12718:17138/1 0 chrI 906 60 92M1D8M1I * 0 0 ATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAACTTTTTTCA GGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGDGFGGFGGGGGDFFGGGGFFGFFGGGGFGFFGFGGGFGGDGFGDFGGGGACA PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:84:4848:6681/1 0 chrI 906 60 101M * 0 0 ATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTC GGGGGFGEGGGEGG?GFGGFFFFFFCCFDCFFDEFDECEECFFFFGGFFBGFG?CEACED5C@AAEEBAEEABEEEBBDDEEEEEEEEDEFEEEE@BBBDE PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:70:5828:17291/1 0 chrI 906 60 101M * 0 0 ATTTTTATAGCTAGGACACTTTTTGTCTGCCCATATATAGGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTC FGGGDGGGGGGDGFGGBGD?FFFBFEGGGGGGFGFFFDFBFFEFFGGGGGGFGGAGGGG==EBCBDFFEEGFEEEGEBEFAEEBAEEGEGFGEGA@EDBED PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:88:11351:17404/1 16 chrI 906 60 101M * 0 0 ATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTC E?BBEBABBFEEEEEBGBCCEFEFF?AGGFEDEEFGGFGDGGGEGGGGFFGFFFEBGGGFFGGFBGGGGBGEGEFGGGGGGGGGGGBEEFEFEFFFDGGGF PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:21:9227:5397/1 0 chrI 907 60 101M * 0 0 TTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCG GEFEGFGGGGBGGDFGFFGGGGGGEGFFGGGGGGGGEDFGFF=BFBBDEEDFGCFBFEF?D@CEEECCEEB=EEEAEFFFC?BB:BFEFDC<6>8DDEDDF PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:96:7398:5258/1 0 chrI 907 60 101M * 0 0 TTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCG EGGGFGGFGGGGGFGGGGGGGGGGEGGGGGGGGDGFGGGGGGGGGDEGDFGG=GGGGGFEGDGGGGGEFGEGGGGAGDFFGFEECGEDEGGEEEEFGFDDG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:59:12995:3551/1 16 chrI 909 60 101M * 0 0 TTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGG GFGFEFDFEEEEDDCCCEEE?GDFEFDDBGEEGBGGGGGGGFGGGGFEGGEGGGGGGGGGGGGFGGGGGGGGGEGGFGGEGGGGGGGGFGFEGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:80:3409:18738/1 16 chrI 912 60 101M * 0 0 ATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTT EEEEFEDEBAFA@@DEEEEEGEFFGEGGFEGGGGGGEEDGGGGGFGEGGGEGFFGEGFGGGGGGGFGGFGGGGGBGGGGGGGGGGFEFFFEDFGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:77:1620:5914/1 16 chrI 913 60 101M * 0 0 TAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTT ??@@??<A=?<??CCCEEEEEE@C=EEEEEAFEGGGEGGEEFGBGGFGGGGEGFGGGFGGGGGGGGGGGGGGDFGFGGGGGEGGGBFFFFFF:GGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:72:16563:11844/1 16 chrI 915 60 101M * 0 0 GCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTT AECCB=DDA=CED?DFEEAE:C??A?5EBEEBFFFF>FFEFE?EDE@>ACCAEFFFEEEEE=FFFFE:EEDDFEEFEEEEDDDDDB?:>>?ACC>C?DE?= PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:103:12336:20768/1 0 chrI 917 60 101M * 0 0 TAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGA FGGGGGGDFGGGGGGGDGFGGGGGGGGGGGGGGGFFGGGGGGCE=DGGDGGEGGDFA?EFGGBEDEGGGFEG?@GEE?FFBGGGDGFBGGBFF?A:A>;@E PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:33:12668:17941/1 0 chrI 918 60 101M * 0 0 AGGACACTTTTTGTCTGCCCATATATAGGCAACCAAAAATTATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAA FGGGGGGGGGGGGEGEGFEGDGFFDDBA?FFGDFGGGECDGFDFFFGE=G@EEDEE=BEE=EEECE?A:F=DEDD:E?EEC;@;DDEEADBE5@BEEB:5F PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:70:1514:14146/1 0 chrI 919 60 101M * 0 0 AGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAA DFAAFFDFFEEEC>E=DDDDDEEEDDEDEE?DEEEE?EEE@6CBBEABEB=AAAADBEEBEEDEDEE:EED@BE=AB?B8C?=EEEEEEEA<:@B?????: PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:41:3640:5327/1 16 chrI 919 60 101M * 0 0 AGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAA 5FFF?CFFFFDEEDCE5=DE=EEEEDEEEEB?>@@DAEEDDBFAFFDDDD?DEFFDFFF>FEEDBEDEBFFDDDDD=C:A?FFDEFDEEDBEDEEDBBECE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:70:16168:12341/1 0 chrI 920 60 101M * 0 0 GACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAAT GGGGGGGGGGGGFGGGGGGEGGGGGGEGBGGGGGGGEFGFGGGGGFGGEFGGGF=FFDBFFGCEGDEGFEEDBEGEBEE=@EGGEEBEFE==BBEDB:DAD PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:6:3780:20120/1 16 chrI 920 60 101M * 0 0 GACACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAAT C=B<??FEEBDG5DEGABCFGEB?FFFG?BGGGGFGFDFEFEEDD?FGGGGGGAGGFBGGGFGGFFFGFGGEGDGBGGFGGGFEGGGGGGGDGGGGGGGDE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:38:5564:3174/1 16 chrI 921 60 80M1I20M * 0 0 ACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAAAAATTTTTCGGGTTTTTTGAAAT AEAA?DGEDDEGCEGDFGGGEGDGGDGGEFGGGGGGGGFGFGGGFG?FFFBGEGGDGEFFBGGGGGFFFEEGGGGGGGGFGGGGGGGGEGEGDEF?GGGGD PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:44:6557:3548/1 0 chrI 922 60 101M * 0 0 CACTTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGA GGGEGGGDGE=FFFEGEDFFCFEECGBDEGGGGG=GEEGGGDGEEE?EEEGGEGGEEFGGEFBEEC?A5CEDA=BEEE8EBEDADEEBAEBBBCC5@@ABD PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:23:12527:20440/1 0 chrI 922 60 101M * 0 0 CACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGA GFEGGGEGFGGGFGGEE:DDEE=EEGEGGDAFFA?GEGEGGGGDGGBGEGGG?GGEGGGGEGFGGFCGGDDBGBFF>BD@EGEGEFDFC=DDDEBD5?DBE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:98:18353:7963/1 0 chrI 922 60 101M * 0 0 CACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAACAATCATTTTTCGGGTTTTTTGAAATGA @@C@>ACC:9>D:BDC:DD:DA?ABD?DDDD?BDDCC@>A?DDC5A<5A?BB?BBA=ACA@BBBBCC???@@??@A?AABBBBB@:=?8ABBBBB@@BB?? PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:84:5126:1325/1 0 chrI 922 60 76M1D25M * 0 0 CACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAACAACTTTTTTCAGGTTTTTTGAAATGAA GGGGGGGGGGGGFGGGGGGGGGGGGFGGFGGGGGGGGGGGGGGGFGEEGGGGEEGFEGFGEGGFEEGEGG@BAEEEEEEEEEFEECD@9CCDDD=EEEE?? PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:12:11478:10672/1 0 chrI 922 60 76M1D25M * 0 0 CACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAACAACTTTTTTCAGGTTTTTTGAAATGAA CAC?=:BBD;EFDFEFFDDFADFFEFFFFEFEFFDFCC=EFFD?EEBA?DDFCA;AEEB:DBFDEFEEBADBBDEEDF5=BEE?E?B=@B@BCC@B=ACB? PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:95:5316:12215/1 0 chrI 922 60 101M * 0 0 CACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGA GGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGFBGDGGGFGDGGGGGEGGGGGEGGFEGGGEGGGEGFEGEEFBEEEC=;CEEGEEEDFA@CCCE=C=AEED PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:113:5213:14267/1 16 chrI 923 60 75M1D26M * 0 0 ACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATATTTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCGGGTTTTTTGAAATGAAT =:;AABB??EB?B=DDA:EEEDDDEBB?EEEDEGGGEFEEGFEDC@@EFEFGGEEGCDB?ABA?5ADDGGGEF?AFGFGGFDFABFBDDGGF?GGGFGG5F PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:118:8721:7001/1 0 chrI 924 60 101M * 0 0 CTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAAT GGFDGGGCGGFGGFGGGDGGGGDGGGGFGBGGGGGADFFGGGGGEGFDFGEEGBACECBEBADFFEEBGEBBDBAC@CGGDBBDGB>EEEDFDDF@E:D@8 PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:79:1079:9916/1 16 chrI 924 60 74M1D27M * 0 0 CTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAACAATTTTTTTCAGGTTTTTTGAAATGAATA ;@EAEEEEGEEEEBEGGEGEGGAFEE@:@:;FEEFDEDEDGEGGFGBEBGGBGFGGGEDBGGEFGGGGGDGGGEFGEGGGGGGFGGGGDFFGGGFFGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:85:1256:19207/1 16 chrI 924 60 74M1D27M * 0 0 CTTTTTGTCTGCCCAAACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAACAACTTTTTTCGGGTTTTTTAAAATGAATA ECEEC=FEFGDEGFEDCGFDFGFBGEGEEEGEFBGEEGDGFEEGGGGGBGGAGGGGGGBDGFGGGGGGGEFGGDGGGGGGGFGGGGGGGGGGFGGFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:48:19056:2032/1 16 chrI 924 60 101M * 0 0 CTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAAT C;BAAAB:EDDEGEEEDAE@EDGGGBG:GDEGGEFEEFAGEAGGBGGFCEEGFDGGFFGFGGFGEFEECCAEDE@EGBFDGGDGGGGGEAEGGGFEGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:76:11456:6131/1 16 chrI 924 60 74M1D27M * 0 0 CTTTTTGAATGCCCAAACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCGGGTTTTTTGAAATGAATA EEEEEEGGEEGDGGEEDGGEFFGGEEGEGEGGGEEGEGGGGGGEGEFGGGGFGGGFGGGGGG?GGGDGGGGFFDFFGGGGGGGGGEGGGGGGGGGGGFGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:61:3268:15848/1 16 chrI 924 60 74M1D27M * 0 0 CTTTCTGAATGCCCAAACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCGGGTTTTTTGAAATGAATA FEEDFAGDGEFEEEEAEGDEGGEGGGGGFGGEB=EACEEEBDGGGGEGGFFEEEE?DGBBFGGGDGGGGGGDDCD;DFFF?GGGGGDGGEGDGGGFDFFGG PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:1:86:4115:1680/1 16 chrI 925 60 101M * 0 0 TTTATGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAGTA ?AA9BACFCCFGEEGFCFDFEEGDEGEGGGGDDGEEEDGGGFGGGFGDGGGGGGGFGGFGFGGGGFGGGGGGGGFGGFFGFGGGGFGGGFGGGGFGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:2:10237:11117/1 16 chrI 925 60 101M * 0 0 TTTTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTTAAATGAATA @:FFFFFDE?FFAFFFFFDDDDFEFFDADEEBFEFDBD?FFFFE?FFFDFFDDFBFEFFFFEAADEC<CCBEE:DEFFEBFFFEDDA?FFFBDDDDD=DCB PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:85:13088:19333/1 16 chrI 925 60 101M * 0 0 TTTTTGTCTGCCCAAATATAAGCAACCAAAAATATTTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATA :?GDBEEGBEEEDGEEEEEEEFEEEFGGGFFFEDFEGDGGGFGGBFGGGGGGGEFGGGGGBFFFEAGGEGGECEEBEAGGFDGGGGGEGEGGGGFGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:79:18345:10394/1 16 chrI 926 60 101M * 0 0 TTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAGTAT EBBBCBEEBBBEGBGEFEFDGBEBD>DGGGGBEFAGEFFE?GGEFGEGGEGFGFGGFFFFBFGDGGGGGGGE=EDEEEGAGGGFGGDFBBFGGDGGGGGFF PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:11:6740:20191/1 16 chrI 927 60 101M * 0 0 TTTGTCTGCCCAAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATC AA?@?BAAB=A?::::??B?AB>E>??@EAA@:@?<@>>==@@:CA=D?DBDBB@EEGGEBGEEEE?AEBAADDBBGDBGGGEFGGBGEGGEEEEE5DABD PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:39:17435:10955/1 16 chrI 927 60 101M * 0 0 TTTGTCTGCCCAAATATAAGCAACCAAAAATATTTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGATTTTTTGAAATGAATATC E=D@DFEE=:?GDEBFEEEE?E=ECCBEGDBGGDFBGGGGEFGDGFEEBEAFGEGGGGGGGDGFGAGGGFFEGGGDFGGDGEEEE:GFBGGGDEGFGEGGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:83:18991:16122/1 16 chrI 927 60 74M1I26M * 0 0 TTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAAAAATTTTTCGGGTTTTTTGAAATGAATAT EABA5?DEFFEEC5@BDDFEFDFECCFFFFFACA:?=EFFFEBDEAFBFBBEE=DEAAF=FBDDA>F>BFFEEEED?DD5?GGGGF=EBGG?BGFFFEFFB PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:23:6768:7044/1 16 chrI 929 60 101M * 0 0 TGCCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAGTATCAT FBB??E?CB@??C=B=C?=?:E=CCD@AA?:5E5EDF=FFFDFFFBBEBEEEC:EEEBCBAFFEFDDFDDFADEEFFBFDFFEFFDFBBEFGDGGDAFFDF PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:47:19241:12210/1 16 chrI 929 60 101M * 0 0 TGAATGCCCAAACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCAT GGGEGGEEGFEEGGGFGGGEEFGGEGGGGGFGGGGGFGGFGGGGGGGGGGDFGFGGGGGGGFGGGGGGFEFGGGGGGGGGGFGDEEGGGGGGGGGGGFGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:79:9772:3464/1 16 chrI 931 60 101M * 0 0 TCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAG =ECCBB=?FGFG?GGGGGBGGFEGDCBFFF=EFBFGGFGGGDFGFFGGGGGEFGGGGGBDGCCCEEFEFFEFFEFDGGGGEEGGDGGGGEGDFGGE?GFGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:29:4194:2200/1 16 chrI 932 60 101M * 0 0 CTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGC @:AE5DDEEBE>@@=5BBB8G@DFDFGGEEBEE=BB=GGGEEEEDEFEFFFADGBGEGGGGFBFGAGFGGGGGGDGDEDFGGGGGGGGGGGGGGEFG?GGF PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:32:7810:14929/1 0 chrI 933 60 101M * 0 0 TGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCT GGGGGGGGGGGGGFFGEGGGGGGGGGDFGGGGGGGFGGFGDFFDEGEGGEGGGGGGGFGGGBEGGGECGFGGGFGGGB5GFFFFA:CEE:B5?B?FDEAFE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:38:7229:15314/1 16 chrI 933 60 1I65M1D35M * 0 0 ATGCCCAAACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCT G?EFEDFE=FFFDGFGGBFGGCFDBAGG=FEEGDGFGGGGGFGGGG?G?GBEFEAEGGGGGEEEAAGGGDGGGGGGEGGEDGGGGGFGGFGGGGEGGGEGE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:45:5717:2359/1 0 chrI 935 60 101M * 0 0 CCCAAACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTAC GGGGGGGGFDFFFGDGGGGGGGGGGGGGGGGGGFGGGGBEGGGGGGGFGGEGGFEDGEDEFGGEEFFGEFGGBBGEEEEBEE:CD:AAAADEEEEE?CCC? PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:67:2263:13075/1 0 chrI 935 60 101M * 0 0 CCCAAATATAAGCAACCAAAAATATTTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTAC EDBEEEEEE?E?EEDDEEEEDDEECEDEEA>6C<@>BB>9?ACAAEECEE?CCEE?C:=B5AB??AEEEEB@DDD:>>@@C:?@??@:?@BCAC@@?A@?< PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:94:5592:18698/1 16 chrI 935 60 101M * 0 0 CCCATATATCGGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTAC ECECBEABA9AAEE@C;EDGGFEFGGGDFGFGEEEFFFFGBGGGGGFEAGCDGGFGGGGGGFGEFGGGGGEGGGEDGFGGGGGGGGGGDGFGFGDFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:59:10637:1223/1 16 chrI 936 60 101M * 0 0 CCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACA CAEBDCA?EECEDDF@@GGGEGEEEEDEGEEFGGGFGEGFEEGGGGEDDE:FFFDACECDFEGFCGGFGFGGGFGAGGGFGGGBGGFGGDGGGGGGFGFGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:70:4295:15837/1 16 chrI 937 60 101M * 0 0 CAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAG FCCBCB=CECBEEFEEGEGGEGEEEEGGGGEGEBEEEGGFDGGGGGFDDGBGGFFGGGGGFBGGGGGGGGGGGGDFGGDFFGGGGGGGG?FEEEEDBEEEE PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:64:5817:4431/1 0 chrI 938 60 101M * 0 0 AAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGA GGEGBGDEEGGGGGDGGGDGGGGDGFFDFFGFGGGGGEGGEFEFDGGGGGDAFG?BEEBBFGFGGGGGGGGECGFGEFAEGGGF?FEF:A@?@C:?:@@@E PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:8:6755:19986/1 16 chrI 938 60 101M * 0 0 AAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAGTATCGTAGCTACAGA BBEA==FEBAFFEFFFDADEE=D=CEE=D=;FFFDDFFFDEEEFFA=FB=FEFFFFEFAFFDDDFEFFDFDFFFF?DDFFFEDFFDFDFEFCDDECD:DAD PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:105:14800:10824/1 16 chrI 938 60 101M * 0 0 AAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTGGCTACAGA :GF=EEGGECDEFFGGFGGGGFFBEDDEF@EDGEEGCECEEE5EEEEFEF=FFGGDCGGEEGGDGGEGGGGGGGGGGDFGFGGFGFEB?EEE:EEDFFFFF PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:71:6398:5629/1 16 chrI 938 60 101M * 0 0 AAATTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGA BCCAC:DFD?FF?>ECDDF?DEF?=FF?F?FFF?BFDFD?FDEEA=B??EE?E:B>@ACC5EEEEEDDBDFBDEBDEEDEDEEEE?ED:BECABECBBDA: PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:84:15268:14389/1 16 chrI 938 60 101M * 0 0 AAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGA D:A@A?5:BCA?FCCCABDEEA@@5BFBAADEEDFFEBBBCEBEEED=5DEDDCCAFFFEDDADBD=5FFFDED=AEFDFFFDFFFF=FDDFAFFFEE:EE PG:Z:SNAP RG:Z:266-1 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:1422:86454 99 chrI 939 60 100M = 952 113 AATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGA CCCFFFFFHHFHHJJJJJJJJJJJIJJJJIGJJJJIJJIJJJJJJJJJJJJJJJJJIIJJJJJHHHHHFFFBDCD@BDDDDDDDDEEECBDDDBDEDDDD PG:Z:SNAP RG:Z:000 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1308:20909:7788 73 chrI 939 60 100M = 939 0 AATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGA @@@DFFFFFHHHFFHIIFGIHIIGJJJIGFGHGIGDGG9DGIJBHIJJIIHGHGHCG?A@BGDAECHFFDB;?CDDDD@CCDDC:CAD:?CB<<CD>AAA PG:Z:SNAP RG:Z:000 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1308:20909:7788 133 chrI 939 0 * = 939 0 TGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATT CDDDDC>D@@<>@ADCDEDEECCDBFFFHHHIIHHGBIIIGEHAIJJJHFJJJJJIHFFAJJIHCEIJIIGJJIIIIIHGHEBIIJJHFHHHFFFFF@@C PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2304:7438:34489 99 chrI 939 60 100M = 951 111 AATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAGTATCGTAGCTACAGA CCCFFFFFHHGHHJJIJJJJIJIGJIJJJHIJJJIJJIJJJJJJJJJJIIJIIJJJJIJJJIJGHHGHFDFADDDBDDDDDDDDDCDDEDCDDDDEACDD PG:Z:SNAP RG:Z:000 NM:i:4 +EAGLE:1:25:14090:18624/1 0 chrI 939 60 101M * 0 0 TATATAGGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAA FCFFFGGEGGFGGGGGGGGGGGGGGGGFGEGGGDBEGGGGGGDEGGGGGGGGGGGGEFFEEEEFE?EEDEEC:EBECEEEEFGEDDFE?FBEE@DDDDD=F PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:33:5876:3688/1 0 chrI 940 60 101M * 0 0 ACATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACAGAAA GDBGEFFGGDGGDGGGDFBG@GGFGGFEGFFGGEDGGFDEGGFEFBFFFBC?E=CB?ECAGGG=DGGFFFEFGFGGG??GE::55BCAEDED?EC5D5CC9 PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:55:14770:18631/1 16 chrI 940 60 101M * 0 0 ATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAA FEGBEEEGEEFG@GFGGFGGFGEGGEFGGEFGBGEGGDGGGGFFGGEGGDGGGGGGGEEGGGEGEGGGGGGGFGGFGGGEGGGGBGGGGGGGFDGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:93:9444:3777/1 16 chrI 940 60 101M * 0 0 ACATAGGCAACCAAAAATATTTTCCAAGTTTTTTTTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACAGAAA FFGADEGFFEGGEGGBGGFGGGGBGEEGGGGGGGGGFGGGGGGBGGGGDBFFDGGGGAEGGFGGGFGGGGGEGGGFGFGGGFFF=FDGGDGGGAGGGGFGF PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:50:5922:5719/1 16 chrI 940 60 101M * 0 0 ATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAACATCGTAGCTACAGAAA :???:???5:==8@EECCC5CA?5ECACCCEFEEEEEEFGGGGDEEEGEEEGEEEEEEEGGFGGEEFGGGGEGEGEGGGGFBAAD:GGGGGGGGFFGGFGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:21:17413:6903/1 0 chrI 941 60 101M * 0 0 TTTAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAAC EEBAD:E?DAFFF:FDDEBEGGGDGDGFEFGFGFGGFDDGEEGGGFFGGGGGDG?CDGGGFDFFGEEEEACEC=EEFGGFBG?G?FDGF=?A=D=FFF5F5 PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:120:7503:14055/1 16 chrI 941 60 101M * 0 0 CATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACAGAAAT EEDEB5GFEEGFGGGG:=GGFDDFFFAA7EEG:BBGGDFEGGADG=GGGBGGGGGGGEGGFGGGFGGFFFEGEGDGGGGFGEGGEGGFGGGGGFGGGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:91:17352:13444/1 16 chrI 942 60 56M1D45M * 0 0 ATAGGCAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACATAAATGG @CCBCDE?EEEEEEAEEEEEEGBEE>EEDEEGDGEBFEEEGGE?EGFFGEGFFFECFBEFGDFGGGGGGGGGGGGGFGGGGGDFGGFGGGGGGGGEGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:97:3188:16851/1 16 chrI 943 60 101M * 0 0 TAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGG :B??BB5=8CCEEEEADABDECB:EA@=?BB5C>C;:DAA::A=?D:ECCECEEEEC??C???=D?C??=?DB==?D?BDD:E=AEEEEAEDC?C?DDDDA PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:85:10558:18446/1 0 chrI 946 60 101M * 0 0 GCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAG FGGGGGGFGGGGGGGGGGGGGGEGGGGGGFGFFGGGEFEGFGGEGGDGEFGGGEGDGGGCGGGFADEFFFFEBFEFBEFFEEGEGDBEEEDGEEEDDE?=A PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:35:15009:8527/1 0 chrI 946 60 101M * 0 0 GCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAG GGGBGGGGABGG@EGGGGGGGGEGFGGGEGEFGGCGEGGGFEGGEGEFD?FGC=CEEGGEEDFE?DDFEFAACE=ECCCC?GDEEEEBBCEE@EECCB?CB PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:62:14360:14144/1 0 chrI 946 60 101M * 0 0 GCAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAG GGGGGGGEGGFGGGDGGGGGEGFGGGFGGFFFGDGFEEFFGGGFEFGEGGGGEGEDGGDEFFFFADEFDEEEEED?EEEEEEGEEDEEEEEEEEEABB7AA PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:81:13994:10137/1 0 chrI 947 60 51M1D49M1I * 0 0 CAACCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCAGGTTTTTTGAAATGAATATCATAGCTACAGAAATGGTTGTA EEEEEB?EEDBFFFFFFFFFFBFFFFFCCCABCC5?DDD?FEEDFEFEFDBFEEFFFFFDFFEEEEFFEEBEEEEDDEBEEEEEEEEEEEEEEEE@?@D?@ PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:69:16589:8289/1 16 chrI 947 60 101M * 0 0 CAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGT @A???;>BA@DB:DA=BBB@@AEEDEADEEEEFBEFDFDDEBFEEEAAEBB?FEDFFFEFFFDFFDE:FFFEF?FFFDBFFF?EFDEEEEEE=?DEFDFFF PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:46:11875:10933/1 16 chrI 947 60 101M * 0 0 CAACCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGT =EBDDGEGEGDFGBEEGBEGGGGDFDGAGGGDGGGEEGBGGGGGGGCE?EEAD=D?GGGFGGGFFDGGGGGGFFGGFGEFGGDGGGDFGGFFGDGFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:70:7204:17965/1 0 chrI 950 60 101M * 0 0 CCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACA GGGGGGGGGGGEGGGFBFDFGGGFFDFAGGGBEGGGEFDFEGEEGEGEEE@EFFFFGGGEEGGEEDBDEEEEEEDEEGGEEAB=AEEE@EDD?D@?B9@B= PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:47:16300:14806/1 0 chrI 950 60 48M1D53M * 0 0 CCAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACAGAAATGGTTGTACAC GGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGFGGGGGGGGFGGFGGFGGGEEGGFGGGGGFFDFEGGEGFGDGEGGGGGGGEBFAECC?EEA PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:72:3307:18932/1 0 chrI 950 60 51M1I49M * 0 0 CCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAAAAATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTAC EEDEDDFFEEBGGGFGGFGGGDFGGFGEGGGEDGGEEGEGDFFGGEEGGEGEEFGGGAGFFADFFCEB?CEEDEDDCBCEBDBCCCECEACCACE;??;:: PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:55:6957:9011/1 16 chrI 950 60 101M * 0 0 CCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAGTATCGTAGCTACAGAAACGGTAGTACA :A??BB?AAB=?=BBBBCCDC?BDDDBCDBBCDB?DB?:DDADDDDDD@?=DADD?DDDADDDDDDCDD:DDBD?:DD?DD?DDDDADDD?ACA>ADDD?: PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:41:5354:20962/1 0 chrI 951 60 101M * 0 0 CAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACAC GGGGGGGGGGGGGGGFGEGGGGGGGGGGGGGEGGGGGGGGGGGFGGGGFGGGGGGGFGGBEEGEFB=EEEEBED=BBCABEBEBEEEEEEAAC<=A<:@AA PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2304:7438:34489 147 chrI 951 60 1S99M = 939 -111 CCAAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTAC #DDEEEDCADC@CDDDDDDDDDCDDDDDDDDDDEDEDEEEDEDFJJIHD@IIJJJIJJJJJIIGJJIJJIFGJGIIIJJJJJJIHGJHHHHHFFFFFCB@ PG:Z:SNAP RG:Z:000 NM:i:4 +EAGLE:2:48:13688:1594/1 16 chrI 951 60 101M * 0 0 CAAAAATAATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTGCAGAAATGGTTGTACAC @EEEEE?BEEEADBAC:EEEEEEEEEECEBEECEEEBEEDEEEEEE>>A@=BFDEFGGEEFGEEFEFGGFEFFGGFGGGGGDGGFGEFFFFAFFBFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:14609:5903 165 chrI 952 0 * = 952 0 CTTCTGAAAATACAAAAAAGTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTT CCCFFFFFHHHHHJJJJJJJHHJIJJJJJJJJJJJJJJJJJJJIJIJJJJJJJJJJJHHHHHFFFFFFEEEDDDDDDDDEEEDEEDDACDDDDBDDEEEA PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2106:7309:94230 165 chrI 952 0 * = 952 0 CTTCTTAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAATAATTTCCAAGTTTTTGATGATTT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHHFFFFFEEDDDDDDDDEEEDEEDDCDEDDDDDDEEEE PG:Z:SNAP RG:Z:000 +EAGLE:2:94:15425:16067/1 0 chrI 952 60 101M * 0 0 AAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACT FEGFGGGGFFFGGDGGGFGGFGFFFEGDFFEGGGDEEDDGGFDFGGEEGGDEGFGGGGBDEFFFFEBEEGBEEEEEGEEEEEEFEGDEEEBE;EE?BCCCC PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:14609:5903 89 chrI 952 60 100M = 952 0 AAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACAC DEEEEDDDDDDDDDDDDDCDDDDCCDDDDEEEEDEEFFFFFHHJJJIJJJJGJJJIJJJJJJIGHJJIHGJJJIJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:1422:86454 147 chrI 952 60 100M = 939 -113 AAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACAC CEEEEDDDCCCDCCCBDCADDDDDCDDDDCDDCEDDDDCCDFHIHHCHJJJJJJJJJJJJJJJIIJJIGIJJJIHIJJJIJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2106:7309:94230 89 chrI 952 60 100M = 952 0 AAAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACAC CEEEEDDDDCCDDDDDDDCCCDDDDDDDDDDEDEDEEDEEDFHJJIEIJJJJJIJJJJJJJJJIIJJJJIJJJJJJJIJJJJHJJJJHHHHHFFFFFCBC PG:Z:SNAP RG:Z:000 NM:i:4 +EAGLE:1:48:14890:12005/1 16 chrI 953 60 101M * 0 0 AAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTC CEDF@C@EE=EEDEGEEBGEEEEDEBEFB?BEAEE?FDCC>CFFDDG=GEGFCGGGGGFEGDBGGGGAFGBFGAGEGEGFDFGGGGGGGGFFEGGFGGGGE PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:67:18282:4840/1 16 chrI 953 60 4M1I15M1D42M1D38M1I * 0 0 AAAAATAATTTCCAAGTTTTAATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCT >A9EBCDAD@@EFDEFBDFGFGEGGFEEE?EGFFGGEECCC@?:BAFBFDFGGGFGGGGGFADFGGDGDGGF?FFFDFFDFEEEDDBEEEBFFBFFGEGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:50:13587:7527/1 16 chrI 953 60 101M * 0 0 AAAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTC GEFEEEEGEEFEEBDGEDGDFGGGEEGFGGGGBEGGFGGGGGGGGGGGEGFGBFGGGGEGGGBGGFFGFGGFGGFGFGFGGGFGGGFDGGGFFFFFEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2204:13467:2490 165 chrI 954 0 * = 954 0 TTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAGTATCATAGCTACAGAAACGGTAGTACACTCTTCTGAAAATGCAA CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJIJGIJJJJJIJJBFIIJJJIHHHHHH@DFFFFFFEEEEDEDDDDDD@BDCDDDDDDDDCDCDCC@>::>C PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2210:13891:35020 165 chrI 954 0 * = 954 0 TGGAAATTATTTTTGGTTGCTTATATTTGGGCAGACAAAAAGTGTCCTAGCTAAAAAAATTGCAACTTTTTTGTATTTTCAGAAGAAGAGTGTACTACCG EEDEDDDDBDBDDDDDCCDDEEEDCBCCCEEFFEDFHHHGHIIJIJJJIIGJJJJJJJIGGGGGFIIEJIGDGJIIIIHEFJJJJIIHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 +EAGLE:2:71:10251:4806/1 0 chrI 954 60 101M * 0 0 AAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCT GGGGGGFGGGGGFGEGGGGGGGGGGGGGGBGGFGGEEFDECEGGGEEEGGFGGGDGCCFEFGEDDEEGEEEEEEEEEDEE@GEEECDCDD?CC>CCAACCE PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:2204:13467:2490 89 chrI 954 60 100M = 954 0 AAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAGTATCATAGCTACAGAAACGGTAGTACAATC ::>C@CA>:CCCDDDDDDDDDDDDDDEEEDCFFFFFFFHJJJIHCJJJJHJJJJJJJJJJIIIJJJJJJJJJIJIIJJJGHJIIJIHHHHHFB=24=+B= PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2210:13891:35020 89 chrI 954 60 100M = 954 0 AAATAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTC CCDC@A@@DDDDCDDDCDDCDCDDDDDDDEEEEDEEFFFHHHJJJJIJIGJHGJIIJJJIJIIJJJJJJJIJJJJJIIJIJIJJJJJHHGGHFFFFDCC@ PG:Z:SNAP RG:Z:000 NM:i:5 +EAGLE:2:50:6355:12073/1 16 chrI 957 60 101M * 0 0 TAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCT ?C=@CA=EDCDBEGEEGEEAEDEBEFDFBCEGEEGGGGGGEEFFEEGGFGGGGGGGGGGGGGGDGGGGFDGGGGGGGDGFGGGGGFEEEEEFGFFGGEGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:65:16283:15152/1 16 chrI 957 60 101M * 0 0 TAATTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCT EEEGEEEEBBDGGEGGECEE:BFGGGFFGEGFGEGDC?EEDCEEEAGEAGGGFGGGGGFGGGGGGGGADGGGFGGGGFFGGGGGGGGGGGEGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:79:12640:7363/1 0 chrI 958 60 101M * 0 0 ATTTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACAGAAACGGTTGTACACTTTTCTG FFFEADDDDD?=DD;A:::C=ADDBB?DCDEDFFD?EDEEAAEEAFDFDD=C?:CD?DBAEBEEEF=FAAEEDEE=CB=BBEBBBDBDD?ED@B@D@ED@: PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:65:16789:19099/1 0 chrI 959 60 101M * 0 0 ATTTCCAAGTTTTTATTGATTTGTTGCATATTGAAAAAAACTTTTTTCGGGTTTTTTGAAATGAATATCATAGCTACAGAAATGGTTGTACACTTTTCTGA EEDDDCB?DBACCCCCC>EEEEEAEBBDDBEAEBCDEEDACEEEEEEEEEE@EEEEEBBEE?EAEEEEEBEEEEEEEEEBDEDEE@BDBB@B@@BBD@<DB PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:42:12059:15505/1 0 chrI 960 60 101M * 0 0 TTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAA GGGGGFBFFFFBDFEGGF?GGDGEDFGEDFFFFDFGFGGDACEFEFFFFFAFEFFFEFGGEFG:DB=ECBBEEBBEEEDFEEEA>>=8>=A@@@AE@==BA PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:56:5751:3283/1 16 chrI 960 60 101M * 0 0 TTTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCT AA@ABA5AFFFFBEEGDDE=FEF?AF?EEDA>>@>EEFAFCCCCC=DEG?FGEBFAGGFBGDDC5C5DFFD=GDGGEEEDGGGGBGGGGFFGGGDFGGAEA PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:7:4422:19468/1 16 chrI 961 60 101M * 0 0 TTCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAGTATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAA GBEEE?DBFFFGG:GGEGFCGGDECBFBFFD@@>D5ECEEAGEFGGGGGGAFG:GGEEEEEAFFFDGGGGGEE=EDGGGGGGGFGGFFFBFGGEGGCCGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:24:3469:6979/1 16 chrI 962 60 101M * 0 0 TCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAGTATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAA EBB=BDGFFGFEFAF:GGGEGFAFEBDDEGGGGGFG=DDDGGGGGGGEFGCFFFGFGBGGGGAAFGGDGFGEGFGGFGGGGDFGFFFBFFAGGGGGGFGGD PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:107:10805:16122/1 16 chrI 962 60 101M * 0 0 TCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAA DA?C=EFABFGEC=DBEFFCFCCBBCE=ECCCCEFE:FAFGGGEEEEBDDEGG:EEFGEFG?AFFFFFFEF=FGGGGGGEGGGGGGFAGGGDGGGGGGBGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:103:2608:5570/1 16 chrI 962 60 101M * 0 0 TCCAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAA GEFDEBGFGGGDEFFCDEDEAGGFBG=GGGGCCFDEDFCBFGGGGGGGDGGGGGGGGGGGGGEGDGGGGGGGFGGGGGGFGGGGGDGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:103:8177:14669/1 16 chrI 963 60 101M * 0 0 CCAAGTTTTTGATGATTTGTTGCATATTGAAAAAATCATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAAT EGBFCEEFAFEEEEEGGFEFGEEEEEGFEGGGGEEGGEEGGGGGEFEEFGGFGGGGGGGGGGEGGEGFGGGEFFFFGEGGGGGGGFGGGDGFDGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:77:9271:19697/1 0 chrI 964 60 101M * 0 0 CAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATA GDGFDFGGGEFGFGGGGFGGGGGGGGGGGGGGGGGGFGGGFDGGFFCFGFGGGFGGFFGGGGEGGEGGGEDGFEEEEFFDAEFCDGEGBEEGEEFEEEGEG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:88:12652:14437/1 0 chrI 964 60 101M * 0 0 CAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATA EEDEBEDEDEF=FFBFCFEAFFBFFFBFDF?DFFCE@=FDBBFEEC?BEAFEBEBFEEEEDEEFEBBEF@BE?ABAEDDB5==6=<@?@@@@=@B@A:AAE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:66:2841:12985/1 16 chrI 964 60 101M * 0 0 CAAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATA EBEEGGG=DFEGGEFDGGGGGFEGGFDFGGCFFE?FFGAGGGGGGGGGGGGFGGGGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:47:10826:17209/1 16 chrI 965 60 101M * 0 0 AAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATAC EDDDDBEEGEEEEGEFEGEG?EEFFFEEEGGFECGDGBEGEGGGGGFGGGFGGGFGGGGFEGEFFGGGGEEGGFGGDGGFGFFEFE5GGGGGFGGAEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:42:13795:17461/1 16 chrI 965 60 93M3I5M * 0 0 AAGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCTGAAAA C?CFDFBGEEFE<GGGDDECDAGBFE@CCCFE=EGEFEGGBGGFFGGGGEGGGGGGGGFGFFDGDGGFGBGGGGGEGGGGGGFGGFGGGGDGGGGGGFGGG PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:1:64:12381:18587/1 16 chrI 966 60 92M3I6M * 0 0 AGTTTTTGATGATTTGTTGCATATTGAAAAAAACATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTTCTGAAAAT EBBEEEGGDGGAEFEGGGGEEEGGFECCCFEC=EBE=GGGGGGGGEGGGFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGFGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1316:21338:23882 165 chrI 1001 0 * = 1001 0 TAGCTACAGAAACAATAGAACACTCTTCTCAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATATAAGCAACCAAAAA >==AA>>AB4=AABCBAB+<3<ABCCB7?+A@A<ABABBBAAABBB>BB7AAABAAB78)9)3=BAABABBAAAA9;?9;;.;>@?B=;=??>:=199=9 PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1316:21338:23882 89 chrI 1001 60 46S53M1S = 1001 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTCGNGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCN ##############################################@;C<-0(#??)<????HGD<CFFCE?CACE9B<HGICHEHGFFDHFDDBB:11# PG:Z:SNAP RG:Z:000 NM:i:3 +EAGLE:2:100:13144:11902/1 16 chrI 1359 60 101M * 0 0 TTACGTAATAGCTTCTTTGACATCAATAAGTATTTGCCTATATGACTTTAGACCTAAAATTGACTATTAATGCCAATTTCATGATATCTAGCCACTTTAGT EAAB?@=AB:BBDDDDA@?==@ABE=B:EBB?DE=BFBDBDFDEBFEBGEEDGFAFFAFFBDDFE=GFGGGBE=EAFE?GGDGDFFEFBBGGGDFGGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:48:18830:9303/1 16 chrI 2070 60 101M * 0 0 TTTGTGGGGAAATATATGTTTCTGACTCTAATTTTGCCCCTGATGCCGAATATCGATGTGAAAAAATTCAAAAAAATTTCCCTGATTTTATATTAATTTTT CCDD=FEEBEEEEEEEEEFEEEEFBDEEEGEEEEEGGBDGFGEDGGGGCGGEFGGGGGDGGGGAEGFFFGGGGGFGBGGFGGFGGGGFGFGDGFGFGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:2 +EAGLE:2:28:7318:20945/1 16 chrI 2075 60 101M * 0 0 GGGGAAATATATGTTTCTGACTCTAATTTTGCCCCTGATACCGAATATCGATGTGAAAAAATTTAAAAAAATTTCCCTGATTTTATATTAATTTTTAAAAT CEEEEEDDBDCADB?DGEEEEFBGGDGEBGGDGFGFGGGFEGFGGGGGGGGGFFGGGGGGGGGGGGFGGGFGGFDGGGGGGGGGGGFDGGGGGGGGGFGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:74:12831:9830/1 16 chrI 2094 60 101M * 0 0 ACTCTAATTTTGCCCCTGATACCGAATATCGATGTGAAAAAATTTAAAAAAATTTCCCTGATTTTATATTAATTTTTAAAATACGAAAATCCATTGGATGC =CC=E=GGGEGFFBEDDFFFAFFF?FDFGFGGGGGGEFDGDEDGGGGGGGGFGGGDFGFGGEFDGEGFGGG?GF?GCCCCCD8DDDGFEEGEEEFGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:2:26:9616:12584/1 16 chrI 2512 60 101M * 0 0 TATCATTAATAATATTTATCAATTTTCTTCTGAGAGTCTCATTGAGACTCTTATTTACGCCAAGAAATAAATTTAACATTAAAATTGTTCATTTTTGAAAA =FBEEEEGEEEE?EDEDFEDEEA?EEFGEGFEGEDEDFGFEFDGGGEGDEEGGFGEDGGGFGFGGGGGGFGGGGGGGGGGGFGFGGGDDGGAGGEEGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1305:10647:87203 73 chrI 2547 60 71M1I28M = 2547 0 GTCTCATTGAGACTCTTATTTACGCCAAGAAATAAATTTAACATTAAAATTGTTCATTTTTGAAAAAAAAAATAATAAAAAAAACACATTTTTTGGAAAA CCCFFFFFHHHHHJJJJJJJJIJGIJJJJJJJJIJJJJJJJJJJJJJJJIJJIJJJJJJIJJJJJJJJFDDD?CD;ACDDDDDD<B8<>CDECDBBDDDD PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1305:10647:87203 133 chrI 2547 0 * = 2547 0 AAAAACACATTTTTTGGAAAAAAAATTGTCCTCGAGGATCCTCCGGAGCGCGTCGAATCAATGTTTCCGGAACTCTGAAAATTAAATGTTTGTATTATTG @DCC@C@DDBDDCDEDDDDDDDDDDBDDDDDDDDDDDDDDDFFHHHIJIIJJJJIJJJJJJJJJIIJJIIIFJIJJJJJJJJIJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 +EAGLE:1:84:3615:2746/1 0 chrI 2728 60 101M * 0 0 TTAAATTATTGTAGAACCCTTTCGTTATTGAGATTTGATAACTTTTAAGTAATAAAATTTTCGCAGTAAGACATTAAAACATTTCACAATTAAGCTGGTTC GGGGGFGGEGGGGGEGGGGGGGFGFGEGGFGFGGGGGBGGGGGGGGFGGEEFAGDGEEGGGFEGGGEGGEGFGGEEGFEEEEEEGEGGEEEBFDD?@68?; PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2110:10822:7981 73 chrI 2900 60 100M = 2900 0 TCCCAATATAAACGATGTCAGTTCTGCGACATGCTACAGTCATCCACTAAAGTAACCCGAATACCGACAAAAGAAGAGGAACGCCAACTTTGGATAGACG CCCFFFFFHHGHHJIJJGIIJIJJJJJJJJJJJJJJJGIIIJJJJFHJJJGIIHIJJJJJJJJGHHHFCAEDDDDCCDDDDBDDDDDDDDCCDCCDDDDD PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:2110:10822:7981 133 chrI 2900 0 * = 2900 0 GGCAAATATTATTTAAAATCAATCAAAATATAAAAAATAGTTCGTTCGCTGAAAATTTAAGCGTTTTCCGACCAAAATCAGCCCCTAGAGCGTCTATCCA CCCFFFFFHHHHHJJJJJJJJJJGIEHIJJIJJJIJJIJIHJIJIIJJJJJJHIHIJJJIJJIHIHHHHFECDBD?BDDDDDDDDDBDDDDB<@BDEDCC PG:Z:SNAP RG:Z:000 +EAGLE:2:60:6530:16775/1 0 chrI 2909 60 101M * 0 0 AAACGATGTCAATTCTGCGACATGCTACAGTCATCCACGAAAGTAACCCGAATACCGACAAAAGAAGAGGAACGCCAACTTTGGATAGACGCTCTAGGGGC GGGGFEGGGGGFGGGFFGGFGGGGGGGGEGEGGGGFGGGEGFFEDGGFGGGGFGGGCGGGEEFGEEGGGDBEGEGGEEEEEEBG?EGGBEFEEDDEEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1204:4496:9204 99 chrI 3991 60 100M = 4394 476 GTGCGCCGCGACTCCGCCCACCGGTGGTAACTTTTTGTGGGGGCATCTTTGTTTTTGGTCATTTTTCAGCGCTTTTCAGCGATTATTGACCAATTTTGAA ?=??;=@DDA1:?DBD:D::?@0;-;;-==7=C>>C8?A;>@8'3<5>AAAA????82?3>>3:>A>AA>3085<:>:>>5-28<>B>AAA<2>AAA>04 PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1204:4496:9204 147 chrI 4394 60 27S73M = 3991 -476 TGAATTTTTTTAAAACATTTTTAGTAAAAAATTGTTTTCGTGCAAATTGTCTTCGATATTATCCAAACGTGACGTTTTGCGATTTTCGCGCTAAAATTAC ###########################C>@A?2?;?B@@C>(>C@7;;@@;>?C;@@C;=73@;8FF:=D80)8F:@B;819IHFBD<F8C=,;AA1B?@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:70:7573:20273/1 16 chrI 4573 60 101M * 0 0 TTTTCATAGTTTTTCTCTTTAAATAAATCACTTTTCAACAAAAAACTATGAGACAATAGTTTGAAATTACAGTATTCTTTAAAGGTGCACGCCTGCTCGAA CAA>C@EE:EEB?=DCBCC;DED=EDDCEAEECAA?GEAGGGGEEGBEEEGGEGGEGGEGGGEEGGEGGGFFFGGEFGDFGGFGEGGGEGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2315:14704:45455 99 chrI 5186 60 100M = 5287 201 AACCAGCACCTCTGTTCTCGACCAACTATGATCATCATCGTCGAATAACCGTTTCTCGTGATTTGTCACATTATACTTGAGCACAATACATCCACCAGGT 5;5(@3.@############################################################################################ PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:2315:14704:45455 147 chrI 5287 60 100M = 5186 -201 TCAGTCCTTTCTGAAAATGAAAATTAATTTTAAAAAAATTGAATTATTTTAAATGAAACAGTTTTCAGAGATTTCTCAACTTTTGAGTCCCCCACCAGGC >8?A@BA:4(>AA>;5;:(:5A>>A@;>>;==6C==?=4HE@.@;FB@=4ECGGFB8=>B9*/910<@>B@>B?39DDCAGEHGC8?<C<)A?:?AD;?= PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:1:81:1948:19465/1 0 chrI 5499 60 101M * 0 0 TTGAAAATTAGGGAAATGACCGGACATAAGTTTAGAAACCCGATTTTTTCAATAAAAAGGAAAATTGAAAATTTAATAAAACAGGTTGTAAATCAAGGAGA FFFGGGGGGFGFEEFGGGGGGGFGGGGGGGADDD:EEEECGGGGFGGGFFEGGFGFEGGGEGFGGFGEGFFEGFDGGFGFE@DGGCFG?EBEBDB?EECEA PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:110:7845:14613/1 16 chrI 5562 60 57M1D44M * 0 0 ATTGAAAATTTAATAAAACAGGTTGTAAATCAAGGAGATCGTATTGATTGAAAAAAATCCGAATGTTCCGGATTTTTCAGTGGTTTTTTTTGAAAGAAAAT GFEEFFEFDGEGGFBGGFGFGEGGDBGFFGEGGEEGFFEBFDGGEEFDGEGGGGGGG:GGGEGGGDFEFEF=FGGGGGGDGGGGGGGFGDGGGGEGGEGFG PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:110:4320:17819/1 0 chrI 7437 60 101M * 0 0 AATTTCAGTTCAGACCTCATTAAATTTGGGTATATTTCTAGGATCCGAGTTTTTACACCAGATTTACAAACTTTTAGCCTTTCACCGCCTTTTTATGCGCA GADGGGGFEEGGGGGGDGGGGEGFGGFGFGEGGGFFFFDFGFFEGFFFFDBFFF?BAFFFA5@CCFGADFGGGFBBBFEFGGEEGFFEFEBGGFECAFDD= PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1105:7234:86502 99 chrI 7663 60 100M = 7927 364 TGGCGTGCGTTGGCAAACAACAAGAAAGAATCATTCTCTGAAAACAAAAAGCGTTTTGGGTGCCAAAGTAATATTGAAAATCTGCCGTGTTTTCTCATTT @<@FFADDHDHHGIIIIIIIIIIIIIIGIIIGIIIIIIGIIIIIIIIIIIIIGEIEHFHF?DCEDCEC;@ADFEFDACDD@CCDDDDD@8<?AC@CDEEE PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1105:7234:86502 147 chrI 7927 60 100M = 7663 -364 CAGCTGGTATTATTTCAGACATGGTGCATCGAAAATTCGAAAATTACAGAAATTAACATTTTGGAGCATCTGCCAGAAAATTGAGATTACAGTACCCCAC CDDDDCDDECCCECCCFEFFFDFHGGHJIIJJJJJIHABHFJJJIIIIGFIJIHF@GIGIHGIGGGFHFJIJIDHIJJJJJIIIHIHF?HHHDDFFF@BB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:4421:72371 99 chrI 8558 60 100M = 8629 171 GCTCATCAGCCGTAATCAGGTGACCTCATTAGGCCTACCCAAACACAGATTTGTCATTATTTTTCAGACAAAAAACACGAAAAAAATCTTCACGCATGGG CCCFFFFFHHHHHJJJJJJIHIGHIJJGIJJIJJJJJIJJIJJJJJIIJJIJIJJJJJIJJJJJJIJJJJEHHHFCCDDDDDDDDDDCCDEEDDDDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:4421:72371 147 chrI 8629 60 100M = 8558 -171 AAAACACGAAAAAAATCTTCACGCATGGGGTGATAACCTGATTTTAAATCTTACTGTGCCGGCTGGCGCGGCGAGCTTCGATCACTGAGCCGAAAGATTA ?DB?DDBCDBDDDDCDDDDBBDCCCDDDCDEDDDDCDDDDEDDEDDDDCDDDCEEDDFHHJIIGIIJIJIJIIJIIJJIJJJIIJJJHHHGHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:79:1727:12868/1 16 chrI 11973 60 101M * 0 0 ACGGACCTCTGGGAGTCTGGAAATTCTTGTCTGAAATTATGCTTTTGAATGCTCGAAAGTGGTAAGAATTTAGAATTTATTACAGAAAAACGTTTAATTAA ABCC>CEEEEEEEEEEEEEEECCDEFFGEEEEEEGEEGGGGGGEEFGFEGGGGFGGEGEFGGFGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1315:14029:3494 73 chrI 12099 60 39M1D61M = 12099 0 AGTATTGTATGCACTGTATCAAAACACATTTTCATCTTTCTAGGTATTCAACTTCACGTTTTTCTGTAATAAATTCTAAATTCTTACCACTTTCGAGCAT CCBFFFFDHHHHHJIIGIIEIIJJJJ?BFHJJIEIIIJJJJHJJ?DFGHIGGIJJJIIBHIIIIGIJIGHGGHIJJIIGHEIIEGHHHGGHFFEBCCDDD PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1315:14029:3494 133 chrI 12099 0 * = 12099 0 AAGTTTTTTTTTCCTTTTTTTTTTGGGACGAAAAAATTTGCAAAAAAATTTTCCCGTGGTGGAGAGTTGAACTCAGACAAAGCCTAAGCCTAGGCTTAAT CCCDDFFFHHHHGGHIJJFIJJIJBEH=@>AC@DDD<CDACCDDDDDBBCDDDDDBABBABD?ACBAC>CCCDDD@CC<?CCC8>CCCCCCCCCCC<CDA PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1209:6644:84389 73 chrI 12375 60 100M = 12375 0 GTACTTTTTAAAGGCACATTGTTTTTTTGGGTCAAGCAAAAATTTGTCGTGTCGAGACCGGCTACGGTATTTTGGCGAAAAATACCAAATTCTTGCGGAT #################################################################################################### PG:Z:SNAP RG:Z:000 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:1209:6644:84389 133 chrI 12375 0 * = 12375 0 CCATATGATATCCAAATGAAAAAAATTTTGACTTTACCCCTTATCCTGTTCTACTCGGCCATATAGAGGAAGAAGTATAGCAAAGAAGAAAAACTGGACA :+=BD,=:C2A4C,++A+3+3++1:CGDB####################################################################### PG:Z:SNAP RG:Z:000 +EAGLE:1:37:10171:16610/1 0 chrI 12538 60 101M * 0 0 TTTGAAATCCAAATTTTTTGGATTGCGAAAAAAACCTGTGTCCGGTTGTTTCATTAGGCCAACAAAGTTCCTGGAACACTGATGAAAACCATGATAGAGGC GGGDGGFGGGGGAEGGGGGFFFFFBDFAFFEDFEFFFEFDFFFFFEEE?AAECCCFFFFFDFFFFDC@CCFEF:EFD=D?AEEEBEEDFEFBFEFBEDFE5 PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:14:9791:11230/1 16 chrI 12732 60 101M * 0 0 TATGGATATCATATGGATATCAAAATTTTTCTCATATGGATATGGAGAAAATTTTTCTCATATGGACTTTGAAAGTTGAATCACTTGACATCTGGGAAATT :CDDC=DD?FDGBGEEE=EEEEEEE@GGGBDGDGEFEGFGGGEFGGGGGFECDD?FGFFGGFFFF?FFFFFDDGGFGFGFDGEGGGGEGDGGGGGGEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2305:19351:44996 99 chrI 13367 60 100M = 13462 195 GCATAGAAATGATCATTTGGAAATCACGTTTAATTAGGTTACGGCGAAAATTTGCAAAAAAGAGCAGGAAACTTGGCTCAAATCCTTCGAAATATAACAA CCCFFFFFHHHGHJJJJJIJJJIHIJJJBGICHIIJIJGEHIEIIJJJJJEGIJJJHHHHFBDEEDDBDDDDDACCCDDDDDCCDDDD?B?BDDADECC@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2305:19351:44996 147 chrI 13462 60 100M = 13367 -195 AACAACTAGGACTTCCATGTAGGCGTTAAAGCGCCCTGTCTCTCACCCCAATCCGTACCTTAAGCTGAAACAAACGTGAACTTTTTTCATTTCTTAAAGG <>A>:CC@CCACDDDCCDDB?@DDDDCB@@BDDDCFFFDHHHEA;JJIGFHGJIHF?JJJJIIJJIJJHFJGHFJJJJIIJIJIIJJFFHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2203:20505:85498 73 chrI 13826 60 100M = 13826 0 AAATAATTACATTCAAATTAATATTTTGTTTACGGCTATGGCCTAGAAATCGCGTGGTGGCCTAGGATTCATTTGCGCGCGAAATTCAAATTCAGCCACT CCCFFFFFHHHHHJJJIJJJIJJJJJJJJJJJJJJJJGJJJBHJJIJJJJJJJJJJJJJJJJHHHHHHFFFFFFEEDDDDDDDDDDCDEDDDDDDDCBDC PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2203:20505:85498 133 chrI 13826 0 * = 13826 0 ATCTTAAAGAAGGAGTATCGTCAATGGGGAAGTTGTTTTAAAATGCAGTATTTGTACTCAAACTTTCAATTATTGCAAAAGAAAAAACGAAAAAAATCCG CCCFFFFFHHHHHJJHIJJJIJIIIJJJJHGIGHIHIIJJJJJGHIJJIJGGIJJJJJJJJIHIJIJJIJJJJIHFHHEEFFDDDBDDDDB@@BBBDD@9 PG:Z:SNAP RG:Z:000 +EAGLE:2:66:16575:12892/1 0 chrI 13844 60 101M * 0 0 CAATATTCTGTTAACGAATATGGCCTAGAAGTTGCGTGGTGGCCTAGGATTCATTTGAGCGCGAAATTCAAATTCAGCCACTTTCGTCGATTTCAACGGCA GFDGGEBGFGAEGBEGGGGGGGGGGGEGDGGFDGGGGFGBFFDFEGGDD?FGBDFGAGFGGGGEEGGGGGFBDGGCGEGEEEBGDGAB??BBBBB@ADADD PG:Z:SNAP RG:Z:266-1 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2109:19111:33831 73 chrI 13924 60 100M = 13924 0 CTTTCGTCGATTTCAACGGCTAAATGCGGAATGTTAACGGATTTTTTCCGTTTTTCTTTTGCAATAATTGGAAGTTTGAGTACAAATACTACATTTTAAA CCCFFFFFHHHHHIJJJJIIIJJJIJIJJGIGIIIIJIJJHJJIJJHHHHHFFFFEEEEEDDEDDDDEED=CDDCDEDDDA@CDDDDDDDDDDDDDEDDA PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2109:19111:33831 133 chrI 13924 0 * = 13924 0 AAAGTATAGCACGGCCATGTGTCGATTTACGCAGTTCGTGTACTCCTCGAGGAAAAACTTGGATTTATTTTTAAAAAGGTTATTACAGCTTTAGGTGAAA @CCFDDFFHHHHHJJJJJJIIHHIGIJJIJGIIJFIJJIJGIJJJJJJJJJJJJHGHHFFFFFFEEEEEEEDDCDCCDDCDDDDEDCDDDDDDDDCCCCC PG:Z:SNAP RG:Z:000 +EAGLE:1:88:5129:6620/1 0 chrI 13927 60 101M * 0 0 TCGTCGATTTCAACGGCAAAATGCTTAATGTTAACGGATTTTTTACGTTTTTCTTTTGCAATAATTGGAAGTTTGAGTACAAATACTACATTTTAAAACAA FFFBDEAEEEGGFGFDFEFFGDGGGGDBGGGADEEEE:DEEECE:EEBEEBFFACDD@FBEFDEBBD=:EEAEEDDD@DBEEEEFDBBDDED?EBDEEGEE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:5:16715:13757/1 16 chrI 14162 60 101M * 0 0 ATGTATTTTAACACAGTTGTGACGTCATAAATGTATTTTAATACATTTTGCAACATTACTTGAATAACCCCATTAAAAATCAACTCAAGCATCAAAAAAAT :BB?EEEEEBEEEEAE=EEEEDEDEEBAEEEEEEEEEEEEEDBEBEEEE5EEEBE?E=EDEEEDEBADDDAEE?EDEEEEEEEEEEE=EEBEEEEEE?EED PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:28:17761:20206/1 16 chrI 14335 60 101M * 0 0 CAATTTTTTGTTTTTTGGTCCAACATTTTTTTTTGGTCTCAGCTCTGCTGCCTACCCTAGAAGAACTAATAGCGCTTCAAAAACTGATGAAAACGTTCAAA C:E?EEC?C9DDFGAEAEEFGEEEEGGCE?FBGGFF=GEFGCEDEE5DCAEFEEFGGGFGGGGGGGEGGGGGGGGGGGGGGGFEFGFGFFGGGGGGGFFFD PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2316:19241:55169 165 chrI 15544 0 * = 15544 0 GGCTTAGACATAGGCTCAGATTTAGGAATCTTCAAAAAATTGAATTCTAGATCTACATTATATTAAGCTGTCTAATTCTCTTCGAAAATTGTCGATTTTT CCCFFFFFHHHHHJJJIJJJJJIJJJJJJJJJJJJJJJIJJJIJJIJJJJIEIIJJJJJJJIIJJJIGGIJJJIGEHIHHHHHHFFFDEEEEDDBDDDDD PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2116:4460:94851 165 chrI 15544 0 * = 15544 0 TTTGTACTGTACCGCTACAGTAATCCGTTAGTATCCTAACATCTCTATACTTGAAGTTGAGATGAGTTGTATCTTCACAGACTACAAACTATGAACACAT @CCFFFFFHHHHHJJJJJJJHHGIJJJIJIJGIIJJJJJJJJJJJJIJJJIIJIJJHIJIJIIJJJHIJIIJJJJHHHHHHFCDFFD>BEEDDDEDDDD: PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2316:19241:55169 89 chrI 15544 60 100M = 15544 0 AAACTGCGTGGCGTGTACTGCAGAAAACCTCATATTTAGGCCCCGCCTTTTTCTCGACCACTCACGGTGAAAAGGCAAAAATTCGGGGACCAACCAATAT ADBBBBDBDBBBDDDCADDCDDDBA?9DDEEEDCCDDBDDDDDDFHEIIEIJJJIHFHDBHGGHJJIJJJJJJJJJIJIIIHGIIIJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2116:4460:94851 89 chrI 15544 60 100M = 15544 0 AAACTGCGTGGCGTGTACTGCAGAAAACCTCATATTTAGGCCCCGCCTTTTTCTCGTCCACTCACGGAGAAAAGGCAAAAATTTGGGGACCAACCAATAT DD@DDDDDDDDDDDDDDDDDDDDBCB?DDEEEEDDDDDDDDDDHHJJJJJJJJJJJJIHFIIIHIJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2101:3253:53534 165 chrI 15545 0 * = 15545 0 GTTGAATGTTGATAGCTCTTCCGAGCGAGTTTTTTTAAATTAAGCTTCATAGCTGTAACATTTAATATGAAGAGTTACACTCAAAATAAAAAAACTGCGT ?@@DDFDDFHDHGGEEFFIHHIGGIIEGBDEHJJIICBFHIDEC;CGDEEDA@EGAEECH;CEEDDEFBC@CCA3>CCDD@CDCDDC>ACDDB####### PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2101:3253:53534 89 chrI 15545 60 100M = 15545 0 AACTGCGTGGCGTGTACTGCAGAAAACCTCAAATTTAGGCCCCGCCTTTTTCTCGTCCACTCACGGAGAAAAGGCAAAAATCCGGGGACCAACCAATATC A8DDB@9-?@?:CCCCDCDDDCB@89?DDCAACCC?@DBDDDDFEDEHHBGEIJJIIHEFDIIIIIGIIJJJGFGGGJJHGFJIIJIHHHGHDFFDD@@B PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2302:10568:99340 73 chrI 15561 60 98M1I1M = 15561 0 CTGCAGAAAAACTCATATTCAGGCCCCGCCTTTTTCTCGTCCACTCACGGAGAAAAGGCAAAAATTTGGGGACCAACCAATATCAGGTCGCCGACATCTC =B@FFFFFHH+0AEEEHHAHHHCGHEIDIJGIGIIGGEG=F?HGFHIGIB@AEEHHGFBFDDAC2;>C(9;8;?BB?<<A>@CDA>@4:<50&0>>@@>: PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2302:10568:99340 133 chrI 15561 0 * = 15561 0 AGAAAAGGCAAAAATTTGGGGACCAACCAATATCAGGTCGCCGACCTCTCACGGGTTCCGCGCGCCGCTATGTTTAACTCGCAGCGGGCGGAGACAGCTC A>AAAA@:B@>:BA8298<4(8@??:BEDB>43?5;00B@@;3+8(9?20&<:855'?@>DFIFIIIIFGFB?GFB)D0IFEIEFEEA?FDF?D;DD@@@ PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2205:19343:78160 165 chrI 15566 0 * = 15566 0 TTCTCAACGGTGGTAGAATTTTCACAGAACCGTGCCATGATTCAGATTTTGCAACCCGCGCACAGGTCATGTTTGAACAAATGTTGTCAATCCCTATAAT CA@??829BCCC@::DDCDDEDCDCC@??BBDDDDEEEECDFDFECHHECHGE@HGGGGGGCCIGGF>IGGJIHGIJGHGHEEIIJIFHHHHFFDDF@CB PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2205:19343:78160 89 chrI 15566 60 64M2D3M1I32M = 15566 0 GAAAACCTAATATTTAGGCCCCGCCTTTTTCTCGTCCACTCACGGAGAAAAGGCAAAAATTTTGACCCAACCAATATCAGGCCGCCGACATCTCACAGGT DB@:3DEEDCCDDCD@DDDDB>??5?3C;;@>@CCBC>?BBADCCECEECCFFDEFEHHHHHHGEGIGGBGGIIIIIHGGJIIFJJHDGHGHFFDFFCB@ PG:Z:SNAP RG:Z:000 NM:i:8 +EAGLE:2:5:10071:18909/1 0 chrI 15576 60 101M * 0 0 TATTTAGGCCCCGCCTTTTTCTCGTCCACTCACGGAGAAAAGGCAAAAATTTGGGGACCAACCAATATCAGGCCGCCGACATCCTACGGGTTCCGCGCGCC ECEEEFFFFFGGGGGGGGGGGGGGGGGGGFGGGGGEG?GGGFGGGGFGDBFFGGDGBGFGGGFG:EFDDFGGGGG=BF=FB@:D=BABACBEEGBBEC:E? PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1214:9682:34070 73 chrI 15598 60 61M1I1M37S = 15598 0 CGTCCACTCACGGAGAAAAGGCAAAAATTTTTACCCCAACCAATATCTGGCCACCGACATCTCACGGGCTCCGCGAGCCGCTGCGTTAAACTCGCTGTGG @@@FFFFFHHHDHIJJJIJCHGGF@FFGGHIJI<@D=FGGEHGGIIHI>FEFC-@;':B8CDE##################################### PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1214:9682:34070 133 chrI 15598 0 * = 15598 0 AGTTTTTTTTTATTTTGAGTGTACTCCACGAGGATAATTTTTATAATTCTCCTCCTCTTTTCCTCGAGGAGTACACAAACTCCGTGAATCCACACATGAC ##DDDDDDDDDDDDDDCDDDCC@B@BDDDFFFFFFFHHHHHJJJIJIJJJJJJJJJIJJIJJJJJJJIHGIIHCHIJJIJIJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2101:5512:59159 165 chrI 15648 0 * = 15648 0 GCGTGTACTGCAGAAAACCTAATATTTAGGCCCCGCCTTTTTATCGTCCACTCACGGGGAAAATGCAAAATTCGGGGACCAACCAATATCAGGCCGCCGA :?BD=0=AFHHGHIIJJJJIJIJJJJJIEHGJJJIIIIIJJJIJJJJJJIHGIIJIJHHFCDEEEDDDDDDDDDDDD@BDDDDDDDDDDEEECDBB@DD# PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2101:5512:59159 89 chrI 15648 60 9S91M = 15648 0 AATATCAGGCCGCCGACATCCTACGGGTTCCGCGCGCCGCTATGATTAACTCGTTGTGGGCGCGGCAAGCTGTCTCCGCCCGCTGCGAGTTAAACATAGC #########B>5BDCAC>:B?599>B@93BBBDDDDDDCDDDDDEDC@?DDDDDDDDDDBDDDEDFFFDDEEBIGIIJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1216:7173:80911 99 chrI 15656 60 96M4S = 15842 286 ATCCTACGGGTTCCGCGCGCCGCTATGTTTAACTCGCTGTGGGTGTGGCGAGCTGTCTCCGCCCGCTGCGAGTTAAACATAGCGGCGCGCGGAACCCGTG B@CFFFFFHF@DFHIII1C6DDFHBHGHJHEHIHHCBEFAEFF9AACBBBDB@=A>A>@C<5@B-5>BB9095@>CCC@AC4@B-0559><B3@9@#### PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:17151:68349 73 chrI 15710 60 68M1I24M7S = 15710 0 GTCTCCGCCCGCTGCGAGTTAAACATAGCGGCGCGCGGAACACGTAGGATGTCGGCGGCCTGATATTGGTTGGTCCCCGGATTTTTGCCTTTTTTCCGTG @@?DDFADGHHHDGHIEDCFEEH<DHGGGIBAGHEB??8;@2?:88(23(>@CBB8BB-77?9::>C:(+22;++:?A99-09CC@<@@C:>A####### PG:Z:SNAP RG:Z:000 NM:i:6 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:17151:68349 133 chrI 15710 0 * = 15710 0 ACACCGCTTGTTTCAGGGCTGTCGTTTTTTCGTTTATTCGGGTTTTTTTTTCGGTTTTTAGAACCAAAAAAACAACAAAAAAGTTTGGTCTGTGTGAAGT ######CDC>>C?<C??<3<99553B;BBBBCDDB?<;BB?;8?8;@AB>EHIGGGGGCHF=8A<7<D?BACGF?G<GHACC?;HGBHFFBA4BFDD<@@ PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1216:7173:80911 147 chrI 15842 60 100M = 15656 -286 GGTTTTCTGCAGTACACGCCACGCAGTTTTTTTATTTTGAGTGTATAGGTCTCGATTCTCGAAAGTATGACAGTTATTTAAATGATGAACTCGTGATGAC BDCDDDDDDCDDC>B;DDBBBDDDEDDFHJJJIJGJJJIJJJJIJJIJJJJJJJJIJJJJJJJJJJJJJIJJJJJJIJJJJJJJJJJHHHFHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:82:8204:15172/1 16 chrI 22312 60 101M * 0 0 GGGGGTACATGGACGAGAATTCTCTACCGTATTCCAATTTGGCTGACTGCGTGCTCAACGTTGAATACTCAGTGTAAACTTTCGTACACCGTTGCGTACTG E@EE@B@5BBB@@EE?BEB5BEDEEA?CEEE?DBEDEDEDEEE?EE?EEEEEEEEDEBEEBAEEEEBEEBEEEDDEDEDDE?EEEEDCDDDDAD=DC@CCC PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:2:88:6414:9094/1 0 chrI 23853 60 91M1I9M * 0 0 AAATCGAAAAAAATAATTGCAAAATCCGTCAGCTGAACATTCAAAACTTATCAATTTGAAATCAGCATATTTCAGTGTATAATTAAAAAAGGTTTCAAAAA GGFEFGEEDDDDEECFFFFFDFDDFFFFFFFEFFFFFFFEFFDFAAEEEEFFFBBDFFFFFF:FDCFF?FBFFEDEFEFFFFFFF?FFFFEA?BEFFFFEB PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:88:12428:19742/1 16 chrI 23928 60 1D15M1I85M * 0 0 GTATAATTAAAAAAGGTTTCAAAAATTCTGAGACCAATTTTTATTGAGAAAAATAATTTTTCGCTCGAATTATTGAATTTTCACTAAATGCAAAAAACAGT GBD?CGDEEEEFGFEFFD?FFFDFFDDEEAEE=EEEACCFE?GBFFDGDCGFFFBEDGFDAGGA=GFGFBGFFFGGEG?GDGA?DGEDEGEEEFFDEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:2 +EAGLE:2:39:4472:4563/1 16 chrI 23983 60 101M * 0 0 ATTTTTCGCTCGAATTATTGAATTTTCACTAAATGCAAAAAACAGTAAACTTGGGCCCATGCTACAAGCCTGAATCTTTCAAATTAAGAACCAGCATGATT 6=CCDDGEEEEEEEGEEFGEEDEE?DEEGDGDBGEEGGGEGDGGGEFFCFEAGGFGGGGEGFGGFGFGGGGGFFDGDFDEGFFFDEGFGGGGGFGEFGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:48:8251:3932/1 16 chrI 23995 60 101M * 0 0 AATTATTGAATTTTCACTAAATGCAAAAAACAGTAAACTTGGGCCCGTGCTACAAGCCTGAATCTTTCAAATTAAAAACCAGCATGATTTTTTCAATATTC @DDBD????@==>@>8::FEEEGE@EFGEEGEECACBBCEGEGFGDFFFFBGFEBGFGGGGGFGGGGDBEGEEE5EGEGGGGGGGFGGGFGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:2 +EAGLE:2:96:5841:4603/1 16 chrI 24002 60 101M * 0 0 GAATTTTCACTAAATGCAAAAAACAGTAAACTTGGGCCCATGCTACAAGCCTGAATCTTTCAAATTAAGAACCAGCATGATTTTTTCAATGTTCTAGGACG EDBE=EBE?BBEFAED<<<CA??DC???A;ABCBCE5FFEACEC=EEDE=DFGG=GDFFDGEDEDEDDDD5DDDD?:?FFGGFGEFFDFF?FFBEFEFF?E PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:51:3584:15408/1 0 chrI 24181 60 101M * 0 0 AAAAAAATAGTCAAGTTGGGCCCATGCTGTACACCTAAATCATTAAAATTCAGAACCGCCATGTATTTTTTCTTACCAAAGGCTCTTTAAAAAAAATCTGG =EDEED>AAAEA?BB:DDDADDED?DDDD=DDADDEDEE?EBDEEEEEDDEE5C:EBEE?E=EBBEBE>CEEEAE=?DEDEEBEBDEEE=?BEEACCEEEB PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1209:7257:71539 73 chrII 202 60 100M = 202 0 TAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGGCCGTTCACCAAATTTAGTGACTCTGCCCGTTCACCAAAAATAGTGACTCTGACCGTTCACTA @CCDFFFFHHHGHJJIIIIJJJJJJJIJJFAGGIJJJJJJIIJJJJJJJGIJJJICHIIEIIJJJJGHHFFFFFAA??ACC;ADDDDDCCDCBDDDCDDC PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1209:7257:71539 133 chrII 202 0 * = 202 0 CACTAAATTTGGTGAACGGTCATAGTCACTAAATTTAGTGAACGGTCAGAGTCACTATTTTTGGTGAACGGGCAGAGTCACTAAATTTGGTGAACGGCCA CCCFFFFFHHGHHHIJIGIFGHHIIHIIJJIJGIJJJJFHIJJJIHIIIHFFGHJIJJJJJJIJHIGIIHHGFDDDDACDDDCDDDEDDDDDDDDBDBB> PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2316:19021:74938 165 chrII 231 0 * = 231 0 CTAAAAATAGTGACTATGACCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGGCCG CCCFFFFFHHFHHJJJIJJJJIHJJJJJJJJJIJJJBBCFHEHDFBHEHGHHIJIACFAHGIFFHI@GDGAEABBDFECEEDD??BDDCDCACCAC5:A< PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2316:19021:74938 89 chrII 231 60 100M = 231 0 TGACTCTGGCCGTTCACCAAAAATAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCCGGCCGTTCACTAAAAATAGTGACTATGACCGTTCACCAAAT CA>DB?BDDBBCCC@<DDCEDEDDDDCC>BAB?BBABCDDB?HHIGGHGHGGHC;GJGGHHIJJGHECAJJJJJIIJJJIHJJJJHFHHHHHFDFFFCCC PG:Z:SNAP RG:Z:000 NM:i:6 +BS-DSFCONTROL03:121:D0M8KACXX:5:1313:5017:58480 73 chrII 234 60 100M = 234 0 CTCTGCCCGTTCACCAAAAATAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGGCCGTTTACCAAAAATAGTGACTCTGACCGTTCACCAAATTTA CCCFFFFFHHHHHJJJJJJJGIJHIJJJJJJJJJJIJJJJJJJJIIJJJHIJIGJIJIJJJGEEHHDFFFFDEBCEDDCCDCDDDDD@DDDDDDD@CDC@ PG:Z:SNAP RG:Z:000 NM:i:6 +BS-DSFCONTROL03:121:D0M8KACXX:5:1313:5017:58480 133 chrII 234 0 * = 234 0 CGGCCAGAGTCACTAAATTTGGTGAACGGTCATAGTCACTAAATTTGGTGAACGGCCAGAGTCACTATTTTTGGTAAACGGCCAGAGTCACTATTTTTGG @BCFFFFFHHHHHJJJIJJJIJ@FHIJJJEGIGIIGHIJJJCHJJJJIIIFHIJJJJJJJJDHHHHFHGFFFFCDECEDDDBBBDBA:ACDC>A@CDC<9 PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2113:7908:63038 73 chrII 234 60 100M = 234 0 CTCTGACCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTA CCCFFFFFHFHHFJIIIJIEHIGEEHGIIIJIJJJJFJIIIBGHIIJIJDDIGJJJJJJJJIIHHFGHHBDDEEEBDEEEDCA@C?@BDDDDDDAACDCC PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2113:7908:63038 133 chrII 234 0 * = 234 0 GTCAGAGTCACTATTTTTGGTGAACGGCCAGAGTCACTAAATTTGGTGAACGGCCAGAGTCACTAAATTTGGTGAACGGCCAGAGTCACTAAATTTGGTG BBBFFDFDFFHHHJJJJIJJHIJJJGIIJJIIIFGGHIJJJJIJJJDGIIHJIIGIIHHHHHDDDFDDEECC=ACCCBB8;BDDDACDDCCDDDACACBB PG:Z:SNAP RG:Z:000 +EAGLE:1:59:19240:17867/1 16 chrII 234 60 101M * 0 0 CTCTGGCCGTTCACCAAAAATAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCCGGCCGTTCACCAAAAATAGTGACTATGACCGTTCACCAAATTTAG =?CCCC:5@?:CA56;7???:EEDFAGEGEGGECFEAFDF=GFGBFGGGEGBGGGGEGGGGG=GGGFEGGGGGGGGGGGGGCCCCC7DDDDFGGGGGGFGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:1203:6884:43459 73 chrII 238 60 100M = 238 0 GACCGTTCACCAAATATAGTGACTCTGACCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTAGTGA @CCFFFFFHHHHHJIIJIIAHHIIJJ@HHGIGHIJJJJGIGIJDHIJIJIGGIJJJIIIJEIJIEHIGHHGHFDEEFFACCEDDDCDDDD@DDCD@>@CC PG:Z:SNAP RG:Z:000 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1203:6884:43459 133 chrII 238 0 * = 238 0 GTCAGAGTCACTATATTTGGTGAACGGCCAGAGTCACTAAATTTGGTGAACGGCCAGAGTCACTAAATTTGGTGAACGGCCAGAGTCACTAAATTTGGTG ?@BDBABAFFHHHJJJJJJJEDHIJJGIJJHGICGHIJJJJGIIJJIGIJJIJJJJGIJHHEEHEE@@CFEF=AC>CDDDDD??B:@ACAACDAAAAC?? PG:Z:SNAP RG:Z:000 +EAGLE:1:50:4361:1823/1 0 chrII 240 60 101M * 0 0 CCGTTCACCAAAAGTAGTGACTCTGACCGTTCACCAAAAAGAGTGACTCTGACCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTAGTGACTC GGEGGGGGGGGGGGGGGGGGDAFFFDFFFFGGCGFEGEGGFC@ABFEEFEGEGEFCFGAEEEDE:DD@>CC5@ACAC:CCC:C==?A?@=:;;;=@CA?@5 PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:85:17281:13087/1 16 chrII 240 60 101M * 0 0 CCGTTCACCAAAAATAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAATTTAGTGACTC ==<76>CF@CAGEDEFEEC?EED?CDBCB:=EDEGGGGCDEFFEE?FFFDFDGGFFFGEFFGFEDFFGGDGGGGEGGGGEGDDGGGGGGFDGEGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:78:10927:5210/1 16 chrII 240 60 101M * 0 0 CCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTAGTGACTC F@?@:B;EEEE:D?EEDEEAFEFEEEFFDCEGEDAEFAFDFEDFFDFFFFGGFGGBGGGDGGGGGGGGGGGEGFFGGGGGGGGGGBGDGGFGGGGDGGEGG PG:Z:SNAP RG:Z:266-1 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1116:20571:27060 165 chrII 241 0 * = 241 0 AATTTAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTCAGTGACTCTGGCCGTTCACCAAATTTAGTTACTCTGGTCGTTC @@BFFFFDHHDHGIJJJIIJJJJJJJJJJGHGIHGIJJJIIIJAHIJJJJJIJJJJIGGHIDAHIAHIIHFDDFFEEEBCCDCDDDCDCCCDCDCC==<A PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1116:20571:27060 89 chrII 241 60 100M = 241 0 CGTTCACCAAATTTAGTGACTCTGACCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGATCGTTCACCAAATTTAGTGACTC 8CDDBBDDCD@5:DCA@@;;CCDBAADED@?EHCEFGHJJIGHEFJJIGHIJIFDIHGIHJIIEGIIIHGFJJJIGIGIHEHGGJIJHHHHHFFFFF@@C PG:Z:SNAP RG:Z:000 NM:i:8 +EAGLE:2:77:9514:17665/1 16 chrII 241 60 101M * 0 0 CGTTCACCAAAATTAGTGACTCTGGCCGTTCACCAAATGTAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGGCCGTTCACCAAATATAGTGACTCT EBB@B?DDDDDBBE=EBB5??B?EEDEEBBEBBEBACC?ACDDD@DEEEDEEDEDCEDEEEEEEEEEEEEBDADDDDDDDBDEE:EDFDFFEEDDECEDBE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:97:16219:20975/1 0 chrII 244 60 101M * 0 0 TCACCAAAAATAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAATTTAGTGACTCTGGC CC=CC?DBDB=@@?D:?AA?CD:BBABA?DBE?BEEB>???@>>>@?:EBB?:B:B@EEBBEA?B@?@>8@@>@@;?<??@@?<?8???<=?7?@=<<>>? PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:55:11493:15098/1 0 chrII 245 60 101M * 0 0 CACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGGCCGTTCACCAAATATAGTGACTCTGGCC 5FFFFFFFD?ADBDDFFFAE=?DDBFEFFFAD?F;DDDADEEEEEFABC=B?EEEFDBFE??DAA:?@=B?C=@B>5=@@;8;87>>=>>B?5BAB6@::9 PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:61:8991:6659/1 0 chrII 246 60 101M * 0 0 ACCAAATATAGTGACTCTGACCGTTCACCAAGTATAGTGACTCTGGCCGTTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGGCCG FGFGGGGAGGEDGGGGGGEGGGGGFFAFFFFF:FAD=@CDEEE=EFFED=AAAABFBG:BBBEAEEAEFE=?EEE=>=>>GDDEDDB@D@=A@@?A:BBB9 PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:73:10783:17479/1 0 chrII 249 60 101M * 0 0 AAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGGCCGTTCACCAAATATAGTGACTCTGGCCGTTC GEGGEGDGGGAFFFFGDGGFEGGGGGGGGGFFGFEFFGGGFFGGGDBGGGGGGEFDGBGEBEBFDFCD?ECECDCBDFDEEED?EC<BCCAC?CCACAA=C PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:47:10664:4304/1 0 chrII 249 60 101M * 0 0 AAAAATAGTGACTCTGGCCATTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGGCCGTTC FGGGGGFGBGDGGGGGGGGFGGGGGGGEGGGGGGEGGGGGGGDGGGEGGFGEGGGGGGDGEGDEGGFGEGGGCEEGEGEEEEEEEEEEDEEEEEEEEE?EC PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:84:13989:21133/1 0 chrII 251 60 101M * 0 0 AAATAGTGACTCTGGCCATTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGACCGTTCACCAAATATAGTGACTCTGACCGTTCAC GGGAGGGGBGBFFFFGGGGGGGGGGFGFFGFGEGDGFGGEGGGGEEGEGGFGFEGEDEEEDGEEEEEEGEEEEAEEEEEEBA?A@CACACEB?EEA?AC?C PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:46:5068:2631/1 16 chrII 254 60 101M * 0 0 AAGTGACTCTGACCGTTCACCAAAATTAGTGACTCTGGCCGTTCACCAAAATTAGTGACTCTGGCCGTTTACCAAATAAAGTGACTCTGACCGTTCACCAA CCCBC?C?C?@:CC=?::BDCDFD?EDFF=EFFFFDGEGGEG?GDGDFFF?B?FFFEDGDGGGFGGEEDBBFEEFFFGGGGDFFFFGFFGGFFAFFDCEEE PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:14:17135:3972/1 16 chrII 259 60 101M * 0 0 ACTCTGGCCGTTCACCAAATTCAGTGACTCTGGCCGTTCACCAAAAATAGTGACTCTGATCGTTCACCAAATTTAGTGACTCTGACCGTTCACCAAAAATT 5A?BA=@CCBA5ECEEABCC=DFFBE?GFGFEFFGGDFGEDGGGG?FGEGBGDGGGFGGDGGGGGGGFGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:50:3266:18098/1 16 chrII 264 60 101M * 0 0 GGCCGTTCACCAAATTTAGTGACTCTGACCGTTCACCAAAAATAGTGACTCTGACCGTTCACCAAATTTAGTGACTCTGGCCGTTCACCAAAAATTGTGAC B;????BC@C?B:@?B@EB@E?EBEEE@DEEEEC:E78A@5D?CECE@EBECD;?DBEBD?EEEEEFBEFFAFEFDFFFEEEEAAE?EEE=BEEEADDDDB PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:51:8846:13213/1 0 chrII 675 60 101M * 0 0 TTACCGCCACCGATGTGCCCGACGCGACTTACTGTTAGCCCTTGTTTTGCACAAATCTGTTGGCTTCCATATTTAAAAGTTAATTAATGACCCAATGTTCT A<6?;@>@BBEEEEEEEEEEEEAEEE?E?AEEEEEBDEA?C@>@=EB<8BEEBDDBDBC???CC5@B??@?EBEBEDEE@A:@?B:?=@=@:B@B@???BB PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1316:6280:52543 99 chrII 1371 60 100M = 1443 172 GCTCAGGACACCTCATACAACTCCAGAGAAAATGTGTCTCATTATTCTTGTCTTTTTTCAAGATCTAATCAATTTTCTACATTAACGACGTTTTTGTCGT CCCFFDDDHHHGFGHGGJIJGGGGGIHIGHIJIIJI?FHJIJIJJJIIEIGEGGEHIIJAFC@CHHG>EHH@CEFHHHCDE@C@3;A59;8<CBB@B@0< PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1316:6280:52543 147 chrII 1443 60 100M = 1371 -172 TTTTCTACATTAACGACGTTTTTGTCGTTCTGCTTCTTTTTTTCGTTCGTTTGTCTCGTCCATCAGCTGTCCACTCATTTCTCTCCCACTCACTAGGCAG 9CAC@@:CA?DB@@<?BDBDCBB@B>DDC?>:>9DBBBEFEDFEGIIFJJIHA:IJJJIIGF>GIIGIGIHFC@FFGFJIHDGH?GHFHHFFFDDFFCC@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1302:4189:8113 99 chrII 2989 60 100M = 3262 369 AGTATGGACAATTGTGAACGGAGAGGTTCAATGGAAGACTCCACCGCGGTAAGTGTGTTTCTTTAAAAATTACTTCCTTTTTTCAATTGTTTGAAATTAA CC@FFEFFGHHGHJEIGIJJJFHAHICGFGIIGIGHGGGHHFHIIJJIJ4@EGEDAEECHHFFFEBDFEEEEEDDDDDDDC@BCCDEDDDDC?CCCCDA@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1113:11974:31213 99 chrII 3014 60 100M = 3127 213 GTTCAATGGAAGACTCCACCGCGGTAAGTGTGTTTCTTTAAAAATTACTTCCTTTTTTCAATTGTTTGAAATTAACAAGAAACCTGTTGGAGCGTATTTC CCCFFFFFHHHHHJJJJJJJJIJJEHIJBGGHHIIIIJJEHIIFIJIJIIJJJJJJJJHHFHHHHFFFFFEEEEEECDDDDDDDDDDDDDDDDD9BDDED PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1113:11974:31213 147 chrII 3127 60 100M = 3014 -213 CGAAAATATCATTTGCAAAAAAACTTGAAAATTGAGAAACTTTTTTAAAAGTGGAGTAGCGTCTGCGGGTTTTTTTGCCCTAAATGACAGAATACATACC BEEEEEDCDDCDDDCDDDBDDA>DDDEDDEDDEDDEEDDDDFFFFFFHFHHFJJIJJJJJJJJJJJJJJJJJIJJIFJJIIIJJJJJHHHHHFFFFD@CB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1302:4189:8113 147 chrII 3262 60 4S96M = 2989 -369 TGCGATTTTTATTTTTATTTTTCATGAATGTTAGGGGCAAAAAACCCACATGCGCTACTCCGCCTTAAGAAGAATCAGCTGTGAGCACTATCCACTATAC ####?CCC@C?:@DCDBBCC@>CCDDCC@A<<?DC>A;?BBB;5EEECIHBA@9ED?@0FDBGFIEHIIJIGJHGJJIJJJJIJIHHDHGHHFFFFF@BB PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:87:12598:13225/1 16 chrII 4380 60 101M * 0 0 AAATTCATGAAAACTTTACTGAAAAACGAAGACCCATTCGATCATGCAAACAAAATATAAGTTTCTATGAAATGGACGGGGATATAGAAGAATTTGAAGTG DAAA?CCDACC?=?CAB<A@ACCC=C=@B@?:CCEEE5FGFFFGGGGGEGDGGGGFGGGGGGGGGEGFGGGFFGGGGGGGGGGGGGGGGGGGGFGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:82:12769:6412/1 16 chrII 5968 60 101M * 0 0 TAAAATATCAGTACACTCCTGGTAGAACAAATATTTTATTTCAATGTTTATGTATGAGTAGAAAAGTTAAACAGAACTATTATTTGGCATCAATTTCTGTT GEGEGEEDFEGGEGEGEFGGGGGFGEEGGBGFGGEEGFGGFGFGFGGGGGFGGGFGGGGGGFGGGGGGGGGGGGGGGFGGGF?GGGGGGBGGGGDGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2303:1316:84598 99 chrII 7139 60 100M = 7167 128 CATCTACCGTATATTCTTTACTAGTGCTGCAGGCAGCACTAATTTCTAGGCCCTTTTTTAATGCAGTACTATTAGAGACTGCAGTACTACTGGAGATGCA @C@FFFFFHFFHHJIGIJJIJIJI4BFIEHCGHFGGDHGIGGGIGGIIBGGDHIDHIIIGIIDHIIJFEHHHHECC@DFBEDDD>CCEACD@C?<CCC3: PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2303:1316:84598 147 chrII 7167 60 100M = 7139 -128 GCAGGCAGCACTAATTTCTAGGCCCTTTTTTAATGCAGTACTATTAGAGACTGCAGTACTACTGGAGATGCAGCGCTAATAGAGAATATACGGTATGTAG DCC<CA>3CDCDCACC@;EC?=<FEGIGGGGIGIGIHG@JGGIHFCIHIGHGIHGDFIHEDHGJJIJIJJJIIIEEJIIJFAHDGEIFFDHFFFDDB@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:25:17975:18268/1 0 chrII 7306 60 101M * 0 0 CTTAGAAAGGCTAATATTATTTTTAAAATCAAGATTTAAGTTAATTAACACGACCTCGTATTCTATATTTCAGATATGTCAGTTATGCATGTGTCATGTTT GGGEFGGDGGGGGFEGGGFBFGGGGGGGEGFGGGFFGFDEEGGGE=FFFFEEAAECE?CCEEGEEE@DADEEEGB?:CACFEACECEFBCDBEBECDEC:? PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:15150:63415 99 chrII 7998 60 100M = 8021 123 GTCTATGGAACAAGAAGGAAGACGAGAAAGCGTGTAAGACCATGAAATGTTTTTTGTGTGCGCAACGTAGTGCGAAAAGTTAGTTATTTGGAGAGGAAGT C@@FFFFFFHHHGGGGGIJJIJIJJIJJJIIIIJIJIIGIJJJJJIJJJJFGHIJJHHEEFFDACBDBBB@CCDB=@BC:@D@@CDDDEDC>ACDDDDBD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:15150:63415 147 chrII 8021 60 100M = 7998 -123 GAGAAAGCGTGTAAGACCATGAAATGTTTTTTGTGTGCGCAACGTAGTGCGAAAAGTTAGTTATTTGGAGAGGAAGTTATTTGAAAAGAATCTTTAGAAG CCCBBDD@DDDEDCDCDDEEEDACBDDDDFFFHHHGIIGIHDIIJJIGIIGHJJHIIIJJJJJJIIJIGHFJIHEIJIJJJJJJJIHBHHGHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2314:19499:38834 99 chrII 8057 60 100M = 8275 318 GCGCAACGTAGTGCGAAAAGTTAGTTATTTGGAGAGGAAGTTATTTGAAAAGAATCTTTAGAAGATATTGATATTTTATATTCTGTATGTAGGCGCTGTG 7BBFFFDFHDFDHEHGGIAHGHIJDHIIJJJJBGFHI;DHBGIJJJGHIJIIJIIJJJJII)=EHFHHFFFFFFFFEFDEEEEDEDDCDCDCAA?@BDBC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2314:19499:38834 147 chrII 8275 60 100M = 8057 -318 GTTCGTATTCTCTCAACTCATGGCACTACTCTCGATGTGCATTGCCTTTTATGGTTGCTACGTTATGGTTCCTCTTGGAAGAGAAAAGCATGCTCCATAC BDDDDDDDDDDDDDDCCEEEEECCFEB;FHHHHGDGJIJJIJHGIIJJJJIHCJIHGHHFJIJJIJIJIIFIIIJJJJJJIIHJIJJHHFHGFFFFF@BB PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:79:2735:13063/1 0 chrII 9267 60 101M * 0 0 TACACTATTCTTAACTTTTTGACATGAATTAAATCTTTTTAAACTGAGTCTAAGCGTATTATTGTATCGTATTTTCCCCTTCTGATGTATTCATTTACTTG ADEBED=ADC=C6=CD=DD6C5BA>A?DDDEBE=AACCA<@B:EEEAEB?ED=EEA<AABCCA@:BB?B@5ACCCEBDEDEBBE:5??:?=@:?@E?BCBC PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:17065:72325 99 chrII 9394 60 100M = 9559 265 CAACTACCCAATTTTCCTGTGCCATGTTTCTTGAAACAAATCAAATGTGATAAATAGTTTGAATGCCTTTATGTATAATAAAATCAATTTTTCAAGCCGG CCCFFFFFHHFHHJJJJBIFGHJJJJIJJJIJJJJIJJJJJJJGGIIFIIHIJJJJJGIIIJIJJJJJJJIJJIJIJIJJJJFIHHHHHHFDFFBECCC> PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:17065:72325 147 chrII 9559 60 100M = 9394 -265 ATGAAAAGCCTGTTCTTTGGTGTTTAAAGGTAGCACACAAACCAAAATTTGTTAGCGCAAATTTAAATTTCTATTTCAGTTACCATGAGTTAGTCTAACA @DDDDDB?@DDDBDDDDDDDFFFFFFHHHHHJJIHGGJJJHJJJJJIGIHJIIJJJJJJJJJJIJJJJJIEIJIJIJIJJHFJIIIJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:91:5280:21105/1 16 chrII 10935 60 101M * 0 0 CAATGCCAATACAAAATAAGTCCGAACAGCCAGGTTAACAACTTGAGTATAAACCAGAGGAATCGGCACCATATCGAAAATGACCAGATTTAGAATTTTTG 8==?=AAA??589??A8A5A?BAA?>D?ADAABABADAEE?EBDDBEBEGEBBFFD=:?;5ABEBEGEFFEGEBDGFEFFGGBGGEGGFFEGGFFFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2209:12690:32871 99 chrII 11660 60 100M = 11873 313 TTGTTAAGCAATATTCTATAAATCACTGATAAAATAGAATAACACAAAAGCCAAATTAGTAACTCTGACCATATTGATTTCCAAACCGATCCTTTCCATC CC@FFFFFGHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIIHHHJIJJJJHGIIIJIIIIJJJJJIHGIJJJGGHHH=BFDDDDDDDDDD@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2209:12690:32871 147 chrII 11873 60 100M = 11660 -313 TTGTATCAGTCGGTGGGTGAGCGATTAGTATCAAGTAGCACAAACGCTTCCGTTTCAGATTTGCATATTTTATTGTTATAGGGGTTATTCAGGCATAGGT DDDDDDDDDDDDDDDDDDCEDFFFFFFHHHHHHIIIJJJJJJIJIIHG@JJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:118:13551:9082/1 16 chrII 13278 60 101M * 0 0 TGATACTTATTCCAATTTCATTCCAATTACATTCATGCTTGGATTTTATGTCTCTGCTGTTTTCACACGATGGTGGCAGATTTTCGACAACATAGGGTGGA EBCDADACBC:EFDEBDFEBEDEBEF=EBFEEBFDEEFEF?FFDFFAAFEFEDGFDGFGGFEEE?EEGEGGGEGGGGGGFGGGBBGFGDGEGGGGGGFGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2107:16551:14335 99 chrII 13632 60 100M = 13690 158 TTTAGTTACTGCTGGCTTGATGACAGAAAAAGAAATGGCCGAGTTCGAGTCTATCCCTAGTCCACACGCAAAATATTGGCAGCCAATGCATTGGTTGTTT CCCFFFFFHHHHHJJJJJJJJIIJJJIJJJJGGIJGIJIJJGIFHIJJJGHIJJIJJIJJHIJHHHHFFDDDDCDDDDDDDDBDBCCDCCDDCDCDD9BA PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2107:16551:14335 147 chrII 13690 60 100M = 13632 -158 AGTCCACACGCAAAATATTGGCAGCCAATGCATTGGTTGTTTTCGATGATCACTTTAGCGCGAGACGAAGGAATGATTTCAAGTGATATCATATATGTAG CCCDDBB?DDDEEFDDCDDDDDEEEEEFFFFFHHHHJJJJJJJJJJJIIGHFJIJJJJJJJJJJIJJJJJJJIJJJJJJJJJJIJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:47:2491:18712/1 16 chrII 14238 60 101M * 0 0 GAAAAATTTGATTATTTAATTCAATTTTAAGTTAGAAAAATATCCTACACATTTTCTGAAGAAGTGTCGTAAATGGGGAAACTTTTTAAACATGTACGTTC EEEBCEAGEGEGBFEFFEDEDDEFGDEGDGGGGEGEGDFFCEFFFFDFDFFEBEEFBFGFGGGGGGGGGGGGGGGGGGDGEGEGGGEEGGGGDGFAEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:57:14985:11088/1 0 chrII 15505 60 101M * 0 0 ACTTTAACTCTCCTGTCAAATACAACACTGATGGGATGAAAGACCGAGAGCTTCAAAATCCAACACCAATCACTGATCACATTGATTTGCCTTTGCATGTG FFFFFFADFFDAA?DEEBEEDFFFFFDFFFFFFFF?EEEEFFFFFF=F?BFBEDDBBCBBFEFEDFD?=E@@E@B:=??CDD:EDDBB5>>=5=>B??B?C PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:21:7517:15303/1 16 chrII 15804 60 101M * 0 0 TTCAGGTAGTGATCTAGGCAAGTCTGGAAAGCGGGAGAGAAAGAAGAGCGAGTGATTTTTGAACAGTATGATAAAATATTTTTTGTTTCTCTTTTCACTCT E5AFEBAFDEDEFFCEAEC?ED?DAEFFCF?FFFFFFBFFFFDDFEDDDD?FADFFF=DFFFFFFEEF=FFFFFFFFFEFFC>FFFAEGFEFDBDFBDDEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1212:2979:94901 99 chrII 16035 60 100M = 16399 464 GTTCTATAGGACCCCCCCTAATTTGAAGGTTTGAGGAACTTCCGAAAATTTTTTTGAAAAACTGCTAATGCCATTCGTTTTTAAATTGAAAAAAACCTAT CCCFFFFFHHHHHJJJJJJJJJJJJJIJJHIJJHIJIIJJJJJJJJJHHHHHHDBDDDDDDDDCDDDDDDDDDDDCDCCDBDDDDEECCDDCBDDDD?C@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:11814:52578 99 chrII 16055 60 100M = 16433 478 ATTTGAAGGTTTGAGGAACTTCCGAAAATTTTTTTGAAAAACTGCTAATGCCATTCGTTTTTAAATTGAAAAAAACCTATATACATTTTTTTCCAGAAGT 1=BD=2=ADCFHHGJJJJJJJJJJJJJJJIJIJJJIJJJIIIJJJIJIJJHIJJJHHGHHFFFFFDEEDEDCBBDD@CCDDDEDEEEEDDDDDDECCCDC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:74:13479:19610/1 16 chrII 16067 60 101M * 0 0 GAGGAACTTCCGAAAATTTTTTTGAAAAACTGCTAATGCCATTCGTTTTTAAATTGAAAAAAACCTATATACATTTTTTTCCAGAAGTTTATCTCAAAAAC EEEFBEECBDDEEEEEEEEFEEEEEEEEEGEGGGFEEGFEFBEFGFGEFGGGGGGGGGGGEECEE?GGGGEGGFEGCCDADD:DDDGGGGGFGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:60:16490:10079/1 0 chrII 16083 60 101M * 0 0 TTTTTTTGAAAAACTGCTAATGCCATTCGTTTTTAAATTGAAAAAAACCTATATACATTTTTTTCCAGAAGTTTATCTCAAAAACTGAGGTCGCGCTGGAA GGGGGGGGGGGEGGGGGGGGFGGGGGGGGBGGFGFFGGGFGGGGGGGGGGGFDFGGFGFGGGG8GGGEEGGC?FGDGDGGGEGGGEGEGGBDEGEBAECCG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1313:14692:64885 99 chrII 16208 60 100M = 16423 315 CTTCTATAGGACCCCCCGTTTTTTTTCACGATTTTTACTAAAATCAACAGATTTTGGAATTTTTGACAAAGCTCAAATCAAGTTTGAGTTAGAAATGAGT CCCFFFFFHHHHHJJJJIIJIJJJJJHJJJIJJJJJIJIHHHHHHFFFFFCEEEEEBDDDDDDCB@DCCCDDDDDDDDDDDDDDEDDDDEDDDDCDD>CD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1212:2979:94901 147 chrII 16399 60 100M = 16035 -464 AGTCTGTTTCAAGCTTCCTGGTGCTCTCGGTAATGCCAAAACTTGATAAACTCTCTTTAACAAGTTCCTACTAAAATTCCTAGCACACACACCATAAACA ABDDDDDCBCDCDDDDDDEDCFFFGGHGIJJIIEIGGCJHDB@IIGIHEGIGIIIIJIJIIGGHCIHCIHJJJJJJIJJIGIGGEIHHFFCHFFEFDB@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:79:2445:14024/1 16 chrII 16410 60 101M * 0 0 AGCTTCCTGGTGCTCTCGGTAATGCCAAAACTTGATAAACTCTCTTTAACAAGTTCCTACTAAAATTCCTAGCACACACACCATAAACATTTTTACGCCAT CACAACF=CCDEG@GEFDEAEE:EEFG5EEGEFEFEGFEGEGEFFEGGGGGGF=EGGEEGEDGGFFEFFBFFFFFFEEEAEGGBGDEGGGGGFAGGGFFEF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1313:14692:64885 147 chrII 16423 60 100M = 16208 -315 TCTCGGTAATGCCAAAACTTGATAAACTCTCTTTAACAAGTTCCTACTAAAATTCCTAGCACACACACCATAAACATTTTTACGCCATCCCCAAGAAACC >DDDCDDDDDDDDDEDEEEEEEECB?B>FHHEHGHGIJJIHGJJIHIGJJIIIIJJJIHHDIIIHHGJIGEJJIIJJIJJJIJJJJJHHHHHFFFFDBCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:11814:52578 147 chrII 16433 60 100M = 16055 -478 GCCAAAACTTGATAAACTCTCTTTAACAAGTTCCTACTAAAATTCCTAGCACACACACCATAAACATTTTTACGCCATCCCCAAGAAACCAGTCAGAAAC CDDDCDC@:@DCDAA>DCEDCDED@CBCEHCBHHE@EBIJHFAGHGHEEC;ECGFFDJIJIJIIIEIGGHHEIGIHGEJJJJJJJIHFHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:84:7059:2112/1 0 chrII 16465 60 101M * 0 0 CCTACTAAAATTCCTAGCACACACACCATAAACATTTTTACGCCATCCCCAAGAAACCAGTCAGAAACAGCGTATTAACAAGTTGCAGTTATTTTTGATCA GGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGFGGGGGEGCGGGFGGGGFDGEGGEGGEEGGGEEEEEEDFCD@EEADDEEEEBECE>C@BCC<E=EBEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:23:16149:11703/1 0 chrII 16484 60 101M * 0 0 CACACACCATAAACATTTTTACGCCATCCCCAAGAAACCAGTCAGAAACAGCGTATTAACAAGTTGCAGTTATTTTTGATCAACAACAGAACATTCATATA EEEEE:E?D??DDCADBEEEBEBDBBDBED:DDD5;A?A5C?CC@BEEEEBACBB?5BCEBE=BEEEBC=:@:8<:?5B?E=BB?:BBBBADAA5BE?B=D PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:90:13478:14626/1 16 chrII 16489 60 101M * 0 0 ACCATAAACATTTTTACGCCATCCCCAAGAAACCAGTCAGAAACAGCGTATTAACAAGTTGCAGTTATTTTTGATCAACAACAGAACATTCATATACTAAA :CDD@CEAEEEDC@BCFDEBC=FBFDEGEEEEEGFFEGEGFGEGGGGGGGGGGEGGGFGGGGGGEGFGGGGGGGGGGGGGGGEGGGFGGGFGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:111:13020:19687/1 16 chrII 16513 60 101M * 0 0 CCAAGAAACCAGTCAGAAACAGCGTATTAACAAGTTGCAGTTATTTTTGATCAACAACAGAACATTCATATACTAAAATCAAGAAAGGATCAATAGTTAAT EEC?=ECCBGEBEAFEBEEGGEGEEF=EE5EGEEGGEGGE?EGEGGC=GGEFEFAGGGGGGEGGDDFGGFFBBFGGGGFGGGGGGDGFGFGFFFFFEE=EE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:6052:32630 99 chrII 16537 60 100M = 16752 315 TATTAACAAGTTGCAGTTATTTTTGATCAACAACAGAACATTCATATACTAAAATCAAGAAAGGATCAATAGTTAATCGGGTTTCCTTGTGTGCGGATGA @BCFFFFFHHHHHJJJJJJJJJJJJJIJJJJJJJJJJJJJJIJJIJJJJJJIIJJJJJJIJJJJIJIJJJJJGIIIJHHHFBDDCEEEEDDDDCDDDBDC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:21126:70246 99 chrII 16655 60 76M24S = 16691 101 CCATTGATCTGACCAAACTTTTCAGCTGGTTGTCCGGAATAGACTTCCAAGCGTCGAGAATTCCTTGCTTCAACGATGCAACTGTTGGGTAAGTCTTGTT +=?DDF;?CCFFF<EEF@FI>FDCFEHIIBDEI99:C06DB<4?BBBB<@?67B=AAHG/AAC:?DFDDF(66>>@######################## PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:21126:70246 147 chrII 16691 60 35S65M = 16655 -101 CATTGATCTGACCAAACTTTTCAGCTGGTTGTCCGGAATAGACTTCCAAGCGTCGAGAATTCCTTGCTTCAACGATGCAACTGTTGGGTAAGTCTTGTTC ###################################?C=)?7).):;@CAA@<D?DDBB90)6?BDC9C8;EE:<EAD@FF::?EC3ED:<+:D:D:;?=? PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:6052:32630 147 chrII 16752 60 100M = 16537 -315 GTTCTGAGCATACACGATACGGACAAGAATCCCCCACAAATTTTCGATTGGATTGAGATCAGGACTTCGAGCTGGCCAATCAAGAAGGTTGATCTTCTTG DCDDCDEDEDDDDDDBDDDDDDDDDDDDDDDFHGGDJIJJJIIJJJJIJJJJJJJJJJJJJJJIJJJJJJJJIJJJJJJJJJJJJIIHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2309:5944:13872 99 chrII 16838 60 100M = 16910 172 GGTTGATCTTCTTGAGCTTGAAATAGTCGCGGGTTGAGTTGCTCACATGGATTGTCGCATTATCCTGCTGAAATCTAAAGTTTTTTCTGGAGTAGTGACG BCBDDDEFHHHHHJIJJJJJJJJIIIIGGIJJJDGGGGCGGGIIIJJJJJHHHHHGFFFDDDDEDEDDDDCDDDDCCDDDDDEDDDCDDCCDACDDDEDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1312:16439:9749 99 chrII 16889 60 100M = 17198 409 TTGTCGCATTATCCTGCTGAAATCTAAAGTCTTTTCTGGAGTAGTGACGAAGATATTTGGAGAGCTCCAGTTCCAAGACGTTCTGATAGTCAGTGCTGTT CC@DFFFFHHHHHJJJJIJGJGIIIJJJJDCHIJJJJJJGIHGGHHJJIJHIJJJJIIIIJJIJJIJJJHHHGHHHFFFFDDEDDEEDDCDEDDDDEDC@ PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2309:5944:13872 147 chrII 16910 60 100M = 16838 -172 ATCTAAAGTTTTTTCTGGAGTAGTGACGAAGATATTTGGAGAGCTCCAGTTCCAAGACGTTCTGATAGTCAGTGCTGTTCATCTTGCTACTGACGAACTG CCDDDDDBBDDDDDDEEEEEEFFFFHHHHHHJJJJJJJJJJJJJIJJJJHJJJJJIHJJJJIJJJJJJJJJJJIJJIJIJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:10135:61245 99 chrII 16930 60 100M = 17321 491 TAGTGACGAAGATATTTGGAGAGCTCCAGTTCCAAGACGTTCTGATAGTCAGTGCTGTTCATCTTGCTACTGACGAACTGTATCTCAAGCTTCTTCTTCT @@@FDFDFFFHHDBFHIBFG@@BGEGHGIGHEHICHGIGIJEGHGIIJGGFHIDEGHFEHIJHI;F>EHIJCEHBHFFBC3;ACCECCCCC@CDACACD> PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:75:15288:18925/1 16 chrII 16992 60 101M * 0 0 CTTGCTACTGACGAACTGTATCTCAAGCTTCTTCTTCTCCGTGAACGCTCCCCAAACCATCACCGTTCCTCCTCCAAAATTACGTCTCGAAAAAACCATTG CC@CDD?DDDAEEEEEEDDBEFDEAEEGBEGEEGEEFDGGEGFGEGFGFFFFFFFAEEEEECGFGGEGGGGDFGGFGFGGGGGGBGDGGGGFGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:48:9783:12656/1 16 chrII 16993 60 101M * 0 0 TTGCTACTGACGAACTGTATCTCAAGCTTCTTCTTCTCCGTGAACGCTCCCCAAACCATCACCGTTCCTCCTCCAAAATTACGTCTCGAAAAAACCATTGG =???=7A???A5==>:A??=A5BA?@BBB?B:BAAA5?A>:BA=BBBABBD?B?BACBCDBDCDCBDDBCDBDDDDD?DDBDD?DC>>B==DD=ADDD:DD PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1312:16439:9749 147 chrII 17198 60 100M = 16889 -409 CACTCTTGCTTTTTTAAATTCTCACTTTACTCCAATTCGTTCCCATATTGTTCTTAGCAAATTCCAATCGCTTGAGTTTATGGTCTGCAGAGAGTAACGG 4@DDDDDDDDCDDEDCEEDCCD@;@CDDEHHFHFIIIJIGIJIJJJJJIJIHIJJIJJIJJJIJJIIGJIJJJJJJJJIIJJJJIJJHHHHHFFFFDCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:10135:61245 147 chrII 17321 60 100M = 16930 -491 CGATTACACCAGATCGTTTGATGACATTGAGGATGGTCCTTTTTGAAGCAGACAATTGAAGCTCATTGCGAATATCTCTTGCCGTCTTACAGGAGTTGGA 0:@@@AA:CCB@DB@DDCCDDEDCCCEEFFFFDHHHHEBIJIHJIIGIGEGAGEJJIIJJIHGCHBGHGIGIIIJIIIIJIGJIJGGFHHHHFFFDF@B@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1301:10889:93999 99 chrII 17346 60 99M1S = 17605 341 ATTGAGGATGGTCCTTTTTGAAGCAGACAATTGAAACTCATTGCGAATATCTCTTGCCGTCTTACAGGAGTTGGAGGCAGCACGAATCACATTTCGTTCG @?@DDDDABFHCFEFHIIII=HHCFGHGABBE3<DGHG>@FFH<FFDF=H>=CBCFEGGAAGIGHHEE>5@@B@C@CA?B=?AB;;?B<:@:A>3+8??# PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1116:3353:52872 99 chrII 17407 60 99M1S = 17466 159 TTACAGGAGTTGGAGGCAGCACGAATCACATTTCGTTCGTCACGCACGGAGAGAGCTTTGCGACGAGGAGCTCTTTTAGATGTACCGTAGCTCACCGGAT CCCFFFFFHHHHHIJJIJJJJJJJJJJIJIJJJJJJJJJJJJJJJGIJJJHHHFFFEEDEED@BDDDBBDDDDDDCCDDDDDDDDDDDDBDDDDDDDBD# PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2211:10693:67001 99 chrII 17455 60 100M = 17585 230 GAGAGAGCTTTGCGACGAGGAGCTCTTTTAGATGTACCGTAGCTCACCGGATCCTTCAGATACTCGCGAATACAGTGTCGAGAACGGGAAATTTTCCTAC @@@DDDDFFHHGHJJJGIGJIGGIEGHIJIGGGDDBGHIDHIIGIIGCAEEHFFFFBCCECCCCDDDDDDDDDDCAADEBBBDDDDBDD<BCCDDDDCDA PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1116:3353:52872 147 chrII 17466 60 100M = 17407 -159 GCGACGAGGAGCTCTTTTAGATGTACCGTAGCTCACCGGATCCTTCAGATACACGCGAATACAGTGTCGAGAACGGGAAATTTTCCTACTCATTTCATGC >DDBDDDDCCCCDCCA:CDDDDBBCDDEEDEEDFDHHHIIGGIJJJIHGFGIGJJJJJJIGJJJJJJJJIJJJJJJJJJJIJJJJIHHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1307:19886:52946 99 chrII 17486 60 96M4S = 17520 134 ATGTACCGTAGCTCACCGGATCCTTCAGATACTCGCGAATACAGTGTCGAGAACGGGAAATTTTCCTACTCATTTCATGCAGGGACACATTGAGCAATTT <@@FFDDDCCFGHIIIIGFH6EFGGCH>@H<D9B?F:FA4@FCH)).746=??B98/3953(;;>(5>:>:>@A>;5;>(:48&8@?BC>3>C>CC#### PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1307:19886:52946 147 chrII 17520 60 100M = 17486 -134 GCGAATACAGTGTCGAGAACGGGAAATTTTCCTACTCATTTCATGCAGGGACACATTGAGCAATTTCATAACATCCAGCTGAGCGCGTTCAGTGTCCGAA ><CD>C@4:<BB>@C@<?D?A>CC;@9C;CB?DCDCEEAHEHHA@CCC88;GHCIIGGG<DHBHFBFDCGFGDJGJIHGBJJJIF@<8DAHHFFDDD@@? PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1105:2590:61441 99 chrII 17529 60 100M = 17793 364 GTGTCGAGAACGGGAAATTTTCCTACTCATTTCATGCAGGGACACATTGAGCAATTTCATAACATCCAGCTGAGCGCGTTCAGTGTCCGAAAGGGCAGAT CBCFFFFFHHHGHJIJJJJIJJJJIJJJIIIIIIJJJJJJJJJJJJJJJJHIJJJJJJJIJJJJJHHHFHFFFFFDDDBBDDDFDEEDDBDDDDDBBDB3 PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:108:5608:15871/1 16 chrII 17573 60 101M * 0 0 CATTGAGCAATTTCATAACATCCAGCTGAGCGCGTTCAGTGTCCGAAAGGGCAGATCCTCGAGGCATTGCAAGTTAGACTGCTTTCGAAGTAAGCTTTCCA ;5D???C=FDEEEAEB=?@??CC::@:CBBC?BBEBD5CCC:GAGFDGEGG?FGDEGAEGBGFGGEEEGGGGFDFGGGDFFGDGEGEGGGEGGEFFGBGDE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2211:10693:67001 147 chrII 17585 60 100M = 17455 -230 TCATAACATCCAGCTGAGCGCGTTCAGTGTCCGAAAGGGCAGATCCTCGAGGCATTGCAAGTTAGACTGCTTTCGAAGTAAGCTTTCCAGCCTCTATATG :>A>@4C@AC>CCAB>5B=3,(@>@@CDCFFGHHECIHGECCIDGF@:DEG@BFGHGDGAGGDFD4FBCEGHGB@EGGHGGEFGIGIHHHHHDAFFFC@@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1301:10889:93999 147 chrII 17605 60 18S82M = 17346 -341 ATAACATCCAGCTGAGCGCGTTCAGTGCCCGAAAGGGCAGATCCTCGAGGCATTGCAAGTTAGACTGCTTTCGAAGTAAGCTTTCCAGCCTCTATATGTG ##################?CCC?A;9''<?>ECA?7=DC=)';7''**8/9<GD?09?*G@?9C9:*)FE?++HBBHC3@CGAHHEFA3:DFDDDBD?:; PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:1:56:7956:12354/1 16 chrII 17709 60 101M * 0 0 CCACATTTAATAATTCACGCAAAAAATAGTAAATAACATCTGTGAGGGACAATTTAACTTGAAATATTGGTCCCATGGAACCTTGTAATCAAAGAAAAACG AEBEEEBBDEBDEBBFBFB=CEEFEEEEGGEDEDAABAB:AEEEEEDFADFFFBEDEGCEGFDFCFFAGDEGFGFGGGGDGDDFGFFDEFGGGGGGGEEGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1202:3232:33845 99 chrII 17750 60 100M = 17828 178 GTGAGGGACAATTTAACTTGAAATATTGGTCCCATGGAACCTTGTAATCAAAGAAAAACGATTTGATTCCTGATAAGCCTTCCATTGTTTCCTGCTGCAT @B@FFFFFGGHHHJIJJJJIJJJGHGIIJHHIJIJJJJGJJJJIJJIIJJHGIJJJJIJJJJJJJJJJJIHHHHHHFCFFFFEEDEDDEDDDDDDDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1105:2590:61441 147 chrII 17793 60 100M = 17529 -364 GTAATCAAAGAAAAACGATTTGATTCCTGATAAGCCTTCCATTGTTTCCTGCTGCATATTTTGCCAAATCAGCTTGACTACACAGTCGAAACATCTAAAG CCCDDDDDDCDDBAADEEFFFFFHHHHHHIIGFJJIIIGJIGGIIJJJJJJJJJJJJIJIJIJIGIJJIJJJJIIJDIIHIIJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1202:3232:33845 147 chrII 17828 60 100M = 17750 -178 CTTCCATTGTTTCCTGCTGCATATTTTGCCAAATCAGCTTGACTACACAGTCGAAACATCTAAAGTGCGTGCTAGGAATTTTAGTAGGAACTTGTTAAAG DDDDDDDCDDDDDEEEEEFFFFFFEHHHHHJJJJJJJJIIJIJIGIHJJIJJJJJIJJJJJJJIJJJJJJJIJJJJJJJJJJJJJJJHHFHHFFFFFCCB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2316:7586:92994 99 chrII 18220 60 100M = 18302 182 AGATAAACTTCTGGAAAAAAATGTATATAGGTTTTTTTCAATTTAAAAACGAACGGCATTAGCAGTTTTTCGAAAAAATTTTCGGAAGTTCCTCAAACCT CCCFFFFFHHHHHJJJJJJJJIJIJIIJJIIGHIIIJJJJJJJJJJJJJJGFIHGFFCDDDDDDCCCDCDDDDDDDD@DDDDDDD<@BCDEDDDDDDDBA PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2316:7586:92994 147 chrII 18302 60 100M = 18220 -182 CGGAAGTTCCTCAAACCTTCAAATTAGGGGGGGTCCTATAGAACTTTCCCACACTGTATATTGCAAATACATGACATAAATTTAGATGCAGGGCAAAAAC DDDCDDDCCDCDDCCDDDEDEEDDDDDFIJJJJJIJJIJJIGDJIGIIHEFIFIJJIJJJJJJJJIIHCJJJJJJJJJJJJJIIGIIHHHHHFFFFFCBC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:17571:72038 99 chrII 19694 60 100M = 19888 294 CCTCCATTTCCTACAGAACCTGCGGTTCAAACAATTAAACTTCCCAAATATATGGAGGTAACCATACACTTTTCATATATGTGTAACATGGGGCGGAAAT C@@FFFFAHFDFFIIIIGHGGIIIJIGIIG<FGHIJGIJJIIJJIJIJGHIIIIIJJIJGIJGHGIGGEEFHHHDBDEEDDDCCCDCEDD?@B>@BDB9@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:17571:72038 147 chrII 19888 60 100M = 19694 -294 CAAATTGTTATTTATTTCCGATTCATCTTTATAACTTCAATAATTTATTTGAGAATTCTATTCAATGCTATAAAAGTCAAAAATTTGCGAAACGTGGTTT ADCCDCCDDECC>AACDBFEHEFGHCD:EGGDHHFA>@IHGIJJJGGGGGGHEHFAEHIIGGJIIFF@GGD@IIJIGGIIIGHGIJJHHHFDFDFFFCB@ PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2302:11666:55394 99 chrII 21802 60 100M = 21978 276 CTTCTGAGAAACTCGAACTCATGATCAGAAACGCGCTCTGATCGAACATTCATACTCTAACACATTCCTCTTCACATCTCCAGATGATTATTCATGTCCA CCCFFFFFHGHHHJIJJJJIJJJJJGGGIIIGGIJIJJJJJJGIGHIJJDIGIJJJJJGDEEHHHDEFDFFEECEDCEACCDCDDCCDCCCDDD;3;A;5 PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:89:11611:13275/1 0 chrII 21896 60 101M * 0 0 TGTCCATCATTTTATCATTAAATATCTCATTCTATACTCTCTTCTCGCTTTATTGTTTCTCGCTCACTCCCTACCCACCATTACATAACATCTCTGAAATT EEEEEDEEDEEEEBEFFFBFEFFEEFFFEEGGGGGDGGEGGGDGGGGGFGGGGGGFGEGGGFEGGFGGGGGEEGGGEGE?ABBEEEEGEEEEEEEBEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2302:11666:55394 147 chrII 21978 60 100M = 21802 -276 ACATAACATCTCTGAAATTTCAAAGTTTTGACATTCTTGGCTGTGCCTTTTCCTCTCAATGATATTTTCCAAATTCCATTATTTTTCCCCCGCCTTTGAT 3CDDDEDCCA>3@DDDDDCCACDDDCCCDCDDDDDDDDDDDDBA??CCA<ABDBDDDEEEEEDCDCDCDDDCDCCCCCEEFFFFFHIHGHHGFFFFFC@C PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:109:12018:8736/1 0 chrII 22087 60 101M * 0 0 TGGTTACTTGTTTATTGGTATACTTCTCGGTATTCTTTTTAATGTTCTGCATGTTTCATATGGTATAAATTGCATATTACGTTAGACACAAATTACTGCAA :CC=ADDDDCFFFFFFFFFEFFFFFFFFFFDFFFFDFFEFF:FFFFDDFFEBEEFBBDEDEEB=DFFD5DBDEEEFFFAEEF?F:D:EBCFBBFFFDFFDF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:83:14451:5491/1 16 chrII 24168 60 101M * 0 0 GAGATGCTGGAAGACCAGGACCAGTTGGAGAGCAAGGACCACAAGGACCAGAGGTATATTTATTTTTATTCGATATATTCAAGGCTTTACATTTATTAATT FBBBAB=@DAEAB5EEEEFBF=EDEEFFEEEFFEBFBBCBBFFEFE@CEEE=FFFFFEFFFFEEFFEFEBFEFFFFFFFDFBFFFFDEC:EFDFFFBFFDF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2203:12843:33593 73 chrII 24481 60 56M44S = 24481 0 GTACAGAGAGTGTAGATAGTTAGAGAGGGACATACATCCGGGACCCAGTGGGGCGGGGGGGGGGGGGGGGGGGCGGGGGGCGGGGGTGGAGGAGGGGGGG @?@DFFDEDFADCGEGBEBAEHHCCEA+@@;?CFDD<?F:FB6@FH<D=F@=B8>@############################################ PG:Z:SNAP RG:Z:000 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:2203:12843:33593 133 chrII 24481 0 * = 24481 0 TCGAACTTTCTCGTGCAAAATCTCTGGCCTTTTCTGTATACTTTAGAATTTGAATTTTCATACGCATGGTTTTCTACACCAAATGAACACATCTGAGAAA @DEDCDDDBBDDEEDFFFFFFHHHHJIIGG>JHIGGIIHGJJJJJJJJIIJJJJJJJIJIGCJIJJJJJIIIIHGFGCJJJJJIHEGHFHHHFFFFFCCC PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2102:18771:39670 99 chrIII 1739 60 100M = 1876 237 CACCACAATTCAATACTTTTCAACTCTTGAGAATCGAAATAGGGCAGCGTAGATATAATATCATTGGGTGACACAAAAATAATCGATAATTCCTTCACAT CCCFFFFFHHHHGJJJJJJJJJGJJJJJJJJJJJJJIJJIJIIIJIJJJHFHIJJJJJJJJIIJJJJIEEHHHFFFFDDECEC@BDBDDDFACCDCCDDC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2102:18771:39670 147 chrIII 1876 60 100M = 1739 -237 TGTGGTAACGTTAAGGTCTTGTTGAGTTTGTACAACAAATTCGAATTTCCTGACACGTCCCAGTAATATTCTCAAATCGTTGAAAGCTAGTTGCATGAAG BDCCBDCCDDCDDDDDDEDDEFFDDFHHHHHHHJIJIIJIIIIJJJJIJJJIIIGJJIIJJJJJJJJJJJIHJIJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:51:14937:4579/1 16 chrIII 4052 60 101M * 0 0 CTCAAAAAAAATTCCAACGAACAAAATGTGTAGAACTTTACAAACTTTTTAATAAAGATTTCCAAATTTTTATACAGATTCACTAAATTTCCAGAGTTTTC EB7<<?BBAB=E?BEDBFC8DADBEDBEBBECD?@A@AC=CE=?ECDFFFAEEBEED?B5BB:EBEAFFAEE?BDECAC=CBADDEDEA?GGFGGGF:EFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:59:9937:9794/1 0 chrIII 7949 60 64M1D37M * 0 0 CATACAAATTCGAAGCGGTATTGTACGATCAAGCTGTTATTCACATTTTTTCATCCCAATTTTTCCAATTTTTGATGGAATTTTTGCTCAGCGAGCCTAAT GGGEGEGGGFGGDDGGGGCGGGGBGGFBDGGGFGGBDDEFEEFEEFEFFGFEEEEGEEDEEEGFEEEEEGEEFE:CEEBCEEDEEBDDBCCDC?CEEEEE5 PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:1:120:8762:5690/1 16 chrIII 9639 60 101M * 0 0 CGCCGCGTAAACTTTGAAGCTTTTTATCTTTCTAGGAAGAAGAGTTATGAAAAAGTTGTCATCTAAGAAATTGTGTAGAATTTTCAGCTCTATAATATAAT 5D=AB=FFEDBFFDEFBEDCCCFEBFDDEEFFFFEFBF?FFFFFFEDAFDBDE?EBDFAEEFEFFFBDDBAFAFFFDDFFEED?EFBEEEA=EBEDDB=AD PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:44:18899:7734/1 16 chrIII 11923 60 101M * 0 0 AACGAGTTTGAGTTGTAATAAATTATTAATTTTTTAAACTTTTTTTCCCAACATTTTTCAATTTTTTTGGGTCCCAGGGGGAAAATTGATGGGTATGCTGT DAEE@EE@C@?GEEEGEAEEEEC=ECABC9EDDGDDCAA?CCCC::EAFECF:GGGGGGGCCFFF=B=AA?F?AFFGGGGFGGGEGGFDGGGGGFDGEGGD PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2307:3105:84335 99 chrIII 15487 60 100M = 15624 237 GGCTACACGTTTCTACATGTGATCATTCTATAAAGAATGGAGTGGTTGAAACTTTTGATTTTTTTGCTAAAAATTTGAATTTTTTTAATTGATTTTTTGT CCCFFFFFHHHHHJJJJJJHHIIJIJJJJIJJJJJJJJJIJIGFHCGIGIGHIJJJJJJJJJJJJHHHHFFFFFFEEEEEEDEDDDDDDEDCDCDDDB<A PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2307:3105:84335 147 chrIII 15624 60 100M = 15487 -237 TTTTATGCTAAAACTAAAATTTTCACGCCGAAACTCAAAAATTTCACATTTTCACCTTTTTTCTTGCCATTTCAACACTTTTTCCTGTAATTCTCTATGC DDCCEDDDDDEDDCFDCA<DDB@DDBDFFEHEEHHJJJJJIJJJJIJJJIJIHDJJJIJJJJJJJIJIHIIJIIGECJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:114:2367:17023/1 0 chrIII 15792 60 101M * 0 0 TTTTTTTCCAACAGTTTCAGATTCATGATTCCGTCTACTTCAACAGATTTGCCAATTCCTGATCATATTACTGTGAGTTACAAAAAAATTTTGGAAAAAAT GDGEDEGGGGGGDGGGGGGGFFAFFFFFFFFFFFFFFFFFFFFFF?FFF?EEEEDEFEFDEFEFFFBFFFFEDDE:FEFDFFFAFAC>CCFFBF=FFABEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2312:17962:78103 99 chrIII 19688 60 100M = 19760 172 CTGTAGAGACCCAGGCAGGCGAAACGGGTTTGGCAGAAGCCGCTTCGTTACGCGACAGAACCATCCCCCACCCGCTTGTAAATATATACGCAATCAAGAT @CCFFFFFFHHHHJJJJJJDGHIJIIIJ@GIGHHHICGC;FABEGEEHFFDDDDBDDDCCCDDDDABDDBBBDBB@@DBCDDDDEEEE@BBBBDDDDDAC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2312:17962:78103 147 chrIII 19760 60 100M = 19688 -172 CGCTTGTAAATATATACGCAATCAAGATTACGCAACGCAGCTGAACGAAAAAAAAAAAGAGAATGGGGGAATCTTTGAGGGGAGATAATTGAGAGGAAGG @DDDC@CEEDDCCDDBBCCDCCDCAADBBDBDBBBDDCDCADDDDCEDHIJJJJJJIJJIIIIHJJJJJJJJJJJJJIJJJJJJJJJHHHHHFFFFF@@? PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2109:9506:74934 99 chrIII 21761 60 100M = 22497 836 CAAGGATCTATGCATGATTTGTGGTAGATGTGCCTGGAAAAGGGGGATTTTTGAGTTGTTTTCTAGGTGTGACCAGGTTTTTGATATGATTTTTGAGAAG CC@FDDFFFHGGGGGGGIJIHFHIIE>B4<<?FGHIIDFIGEHGIJAEHBCC@AE@GHEHHFEEDFF);7;>AAC>@AC@BB?<C>>@>CDCCD>8<<>< PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2109:9506:74934 147 chrIII 22497 60 100M = 21761 -836 TCAACAAAAAAAAATCGAATTTGAAAACTTATAAAATTTATCCAATAAATGGGCGGAGCTTAGCCAGCTTTCTCAACAACTCACTTGCAAGGTAATAATC CACB<@<B:CDDC@@B;DFD>;?EEA>EA@74JJIFCC;GHF:GIGIFBDGG@EGB<HEIHF?ECBHHB9E>DCA@>CAEHHGIJJJHHFFGFFFFD@<@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:41:8435:11353/1 0 chrIII 24117 60 101M * 0 0 AAATTTTGGTGAAAGTGGGCGGAGCCTAAGTAAAGGATATATTTTTTAAAAATTATCAAAAAATGTTGCAAACTTTAAAAAAAATTTTAAGTTTTTTTTCA GADGGFFFEEEEEEEEGGGGGGEGGGGFEG?BBCEFFFFFDGGFGEGGGCFGGFGGFGGEEEDEGEGGGFEEDEGGEEEGED@=6DD?EBGADBDDB=C?E PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:95:11679:7360/1 0 chrIV 621 60 101M * 0 0 ATTTCCCCTCAATTTTCTTGCAGATCGACGTGGATATTGACGACCTAGATGACGATTTTCTCTCCACAAACGGAATGGAACGACACGGTTCAGAATTACAA EF@@@EEEEEBBABBBECEEEEEBEBEFBDFDEAFEGD5DGGDEFGGGGDFGFG:DFFFFFGBGGGGGFGF?F:FEADBEEBEEEEBEBEEEE==:EAAEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:58:15136:13881/1 16 chrIV 723 60 101M * 0 0 GAGAAGTGGTTTTCACTACGACGAGTACTGCGAATAACAATGTGAAACGAGCCGTCGAATATTTCGAAGATGATAATCAAGATGATGCACTAACATCCACT @A9A9AAA??A?:?:??;@?:>>??=5A?A?@:C=CCADBCDDCFBAGEEEEFFGEFDEFFDG?GGFGGGFGDDGD?FFDGAEE=?EECDAFEEE?EEEFE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:25:10330:11791/1 0 chrIV 1025 60 101M * 0 0 TTTATTGAGGAATACTCTATTGAGTTGGACACCTCTGGGAAGTATGTGTTGGGAAAAAAAATCCGAAAATTGATTGAAAAATTCGAAAAAAAATCCAAAAA GGGGGGF=GGEGFFGGGFGGGGEGEFBFDFGGGDGGGFGFEFBFFEBEBEFFFEFFAFGGGEFGGEE=GDEDEBEGEDEDEFEEF@DEEEEG>CBBDDEBF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:29:6386:17433/1 16 chrIV 1252 60 101M * 0 0 AATTGATGGATAAAAATTCCAAAAAAGTTCCAGAAACAACATTTCCTCCGCAGCTTCACCTGGTCCCAAGTCTCCATTTGACGATGATTTTACTGATACAG E?===FBDGGFDEE=FE@GGFEEBFACAAD=FFFDEFEDGGFFEDFBAFGGFDFFF=BGGFFFDF=GDAGGG=GGEGFDGGGGEDGFFDFDEEEEDEEEDE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1214:19701:60229 99 chrIV 1474 60 100M = 1594 220 GTCCGGTAGAGACCCATTTGATGAAGATGTACGTTTTTCGTAAAGTTCGGAATTTTTAGGGTATAAATTGAAAAACAAATGGAGAAAATATGAATACCTA BBBFFFDDHHHHHJJJJJJJJBHIJJJJIGIIIFHIJIJJIJJIJIIJJJJIJJJJJJIJJDHHHHHHHFFFFFEACDDDDDDDDDDDDDEDDEEDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1112:16947:43819 99 chrIV 1479 60 100M = 2024 627 GTAGAGACCCATTTGATGAAGATGTACGTTTTTCGTAAAGTTCGGAATTTTTAGGGTATAAATTGAAAAACAAATGGAGAAAATATGAATACCTAGATTT <@@DFFFDHHFHHIIIIIIIHI>FAFHIHGHEDHGCFHIG?F?DFHIIFIGHHGGG.=FEGFH>CDHGBHH2?@C??>>;AC@5@B3;5;>::>>>(:@@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1214:19701:60229 147 chrIV 1594 60 100M = 1474 -220 CCCAACCCTAATATCCACAATTTTTTTTCAGTCTGGAAACTCTAACGAAAACCAGCTCCGCGAGAAGAAGCTCCACAAAAAAGAGCAACTAGCTCACCGG BDBBCDCCDCCCDCBC@DDDDDDDDDDDDDDDDEDDCA;DDDDDBDFFB?=HHHIJIJJJIJJJJJJJJJJJJHFJJJJIJJJJJJHFHHHHFFDDFCCB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1112:16947:43819 147 chrIV 2024 60 18S82M = 1479 -627 ATTAGAAGAGAAGAGGAGGAAGAAGTGGTGGAAGAAGATCCAGCAGTGGTAGTTCCAGTTCTACGGAAGGATCTGGAAGTTGAGGAGGCTCCGAAATCGG ##################CAA>;A;(>D?;>?HEA=74E:C=>@@;=8=89FBFDCGFD;69D:?AD?9?1*9<:9E??AA+;FGFGD<:8A;BA=+1=: PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2204:2799:95211 99 chrIV 2692 60 100M = 2824 232 TTTCAGACGTCTGTATCCGCCGATCCAAAATCTCACACGCCGATTTTGATGGCCGACGAGTACAAAGAACCACAGAAGCAAGGTGAGTTTAGTTCGAAAA CCCFFFFFHGHHHJJJJJJJJJJJJJJJJJJJJJJJJJIIJJJJJHHHHHFFFFDDDDDD8ACDDDDDDDDBDDDDDDDDACB:CCD>@CEDDDDDBDDB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2204:2799:95211 147 chrIV 2824 60 100M = 2692 -232 CATTGTTAGAAAATTTGAAAAAAAAACCAAAAACCGTCGTAAAACTACACTTTTTCTATTGAAAATAGAACAAACAAATCAAATATCCTACATGTAAAAT :@4(DDDDDDDDDDCDDDDDDDDECDFFHHHHBJJJJJJJJJIGIIGHGJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJHJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2203:18040:19562 99 chrIV 2921 60 100M = 3122 301 AATTTAAATCGAGTGGAATTAAATTCTTCAAACAAAAAGAAATCTGCATTTAATATCGATTTCTCATTCAATTGTTATGAATCATAAAACATGATTTTTT CCCFFFFFHHHHHEHIJHIJJJJJJIJJJEHJJJJIIJJIJJJJJJJJJIJJIJJJJJGIJJJJJIJJJJJIIIHDHHHHHHHFFFFFFEDEEEEFEDD@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2203:18040:19562 147 chrIV 3122 60 100M = 2921 -301 ACAATTGGGATTAATTTTCAACTGAACTAGACTGTTTCTGAACGCTCAAAACCTTCAAAATCAATGCTTCTTCAAAACGAAAAAATTGCACACTATAAAC CDDCCCCCDEDDDDDDCCECACEEEFFFFFFFGHHHDJJJIIIIJIHIHFHJIJIIJJJJIJJJJIJJJJIHIJJJIJJJJJJJJJIHHDHHFFFFFCB@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:51:5632:6609/1 16 chrIV 3456 60 101M * 0 0 GATACTGCATTTTTCCGGAAAAGGACAAAGTCGGCTAATTGCCGTTTTTTATAATTTTTGCTCATTAAGCTTATTCCATTAAAAATACAATTCTTGTTTAA ACA;C@CDBCCEEEEEEEEEEEEEEEEEBEEGEEFGEBGEEGGEEEBEEDGEGFEFGGGGGFEGGGGFGGGGGGGGGGFGGEGGGGEGBEDGGEFGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:41:11958:20308/1 0 chrIV 3987 60 83M1I2M1I8M2I4M * 0 0 CTTTGAAAAATAGGGAATTAAATTTAAATAAAATTTTCAACTGAACTAGACTGTTTCTGAACGCTCAAAACCTTCAAAATCAAATGAAATATTCAGGAAAA GGGGEGGGGG?CCFFGGGGFEGGGGGFDGGGFEGGGGGFGGGGDGFFGGGGEGEE?FDFCGEEEEGGEEEEGEEEEEEE@CDDCCEBDDBEAEEEDBEEEA PG:Z:SNAP RG:Z:266-1 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2216:15913:7063 99 chrIV 4720 60 100M = 4891 271 TTCAAGAGCCTAAGTTTTTTTTTTCGAAATGAGTTTTTTAAAATTGATCGAAATGTTTTTAAATACTGAATATTTGGGATTCTAGATTTTTACTACAATA CCCFFFFFGHHHFIHJJJIJJJJJIJJJJIIJIFHIJJJHHHHHHFFFFFDEDDDFEEDDDDCDEDDEDDDEEEEDDDDDDDDEDDDEDDDDDDEDDDD> PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2216:15913:7063 147 chrIV 4891 60 100M = 4720 -271 TCTAAAAAATTTTTTTAGTGCCTGCACCAGTTGTCGTTGCTCAGGAGTCGCCGATCTTAAAACGAAGAAACTCTCTAGTACCATCAAGGATCAGTGGAAG CCDDCDDDDDBDDCDDDDDDDDDDDDDDDDDDDFFFFHHHHHJJJJJIHFJIGIJJIIJJIHIJJJJIGHJHHDJIJIHHJJIIJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:49:18520:10880/1 0 chrIV 6174 60 101M * 0 0 GATTTTGGATTAAAAAATTCCGAATAAAAATCAACTTTAATTTAACGAAATTAATTTTCTATACCTAATTCTCTAATTTTTGCAGAACAGACGTAACGATG EEEBEEDAA?DDB?ADEEEEEEEEEEEBEE>EEEDE?EB=EEEDBEE=EEEEDE5?ADBDEEEEEEEAEEEAEBE:DDBCDEE?EBDEDEEEEB:EEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1103:16672:84478 73 chrIV 6412 60 56M44S = 6412 0 TTTCGATATTCAACACTACCTGCCCAAGAAGTATAGCTCATTTGAAGATCAGTCACGGCTGAAGAACATTCTCGCCGAGCTGCACGGGCATTACGCGGGC 1==A1AA+<4,2>A3A3A7A@=?AABC?9AA:=<*7?*=*:7*0***9?79<A?AB############################################ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1103:16672:84478 133 chrIV 6412 0 * = 6412 0 AAACGGAAATGCTCCGGAACCTGATGTTGGCCTCGTTGCGGACACACGATCCACATGCGCTCCCAAATCTCGGTGTCGCTGACAGATTTGAATGCATTTG +:8;?2=:CDB4B4+@#################################################################################### PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2305:20092:23229 99 chrIV 7114 60 80M20S = 7551 528 GCCGTATCCTCTTTATTTGAAGTGCATGTAAATTTAAAAGAAGATACTTTTCGCTTTTTCGAGTGACCTTTTTTCAGAGAAAATATGTGCTTTTCTTGAA =??DDDBD?DDDD?,C?BFDC@,<EAFE+AEF<FFD9B4?CDDEAF<9*:9B?0?8?D>=ADA8677)7A7AED7;3??@#################### PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2305:20092:23229 147 chrIV 7551 60 9S91M = 7114 -528 CAGTACTCCTGTATTAATCCTACAGTAATCCTAGAGTGCCCCTACAGTACCCCAATAGTATTTCTACTGTACTCATTTACTCCTACACCTAGAGTACCCT #########C>>3@>>;)@@BDCA=)>?77@@CGEG@;F;94?/AD@?0BBDHHFHFB9BBB@FDF<CCHAE?GCHA?AC+HEBDGAHHBF??D?AD@?B PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:25:14196:18951/1 16 chrIV 8235 60 101M * 0 0 TTGTTTTAATTAATAAAATACGTACACTAATTCAAAATATATGTTTTATCGATTTTAAAACCTCAAAAAAATTGTAAAAAAATTGAAAATTAACTGAAAAT CEEEEDAFD=CEEEBEBEEBEGFFGFEDGGGAGEEGGDGEGFGFEDGEDDEGFEEGGGGFGGGGGGGFGGFFFFCFFDFDFEEEEEE:FFBFFF:FEGGF? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:115:8880:13347/1 0 chrIV 8542 60 101M * 0 0 GAAAGCGGTAAGAATTCGAAATTTCAGTCAATATCCCTTTTCCTCGGGGTGTACACTAGAGTTGTGTAAATCTACACATAACGTTTTTTCGATTATCTCTG GDGGFGEDBGFFDFFEGGGGEFGGGGGEEG:EEBEGGF?DEGFBDEAAE<A?CCBEEDEBE?AB=:CCCCCF?EBFD:DFBDDCCCBCACE@EEECEA:55 PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:25:8054:8779/1 16 chrIV 8985 60 101M * 0 0 GGATAGATTTCCATGTGGGCCAGGCATTTTGCTAGCTGAAATTTTGGGATTTTTACTTACAACTGGTTTAGAATAATTTAGAAATTACAAAATCGAGGTTT 5B5EBEBB?C=E5:=EEFEFDEBAEE?:D=ECE::DFFAFFFD:=FEBDDE?B:ADBBBAECEBDBDBCFBEEDDADED=?ED5?DE=:DEFDDDD?EEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2213:7767:73428 99 chrIV 9395 60 100M = 9538 243 ATTGTAGGCCTTGATAAGATATATGATGACCCGTCGTTGAAACCACGTGGCTGGAGATTAATTCTATCAGTTAGTCAAAATTTACTGACAATCACTCAGA CCCFFFFFHGHHHIIJJJIJIIJJJJIJIJJJJIIIJIIIJHIJJIGIGGIGFHGHIJJJJIJHHHHHHHFFFFEEEEECE@CC@@CCCDDDCDDCCDD: PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2108:20580:46115 99 chrIV 9443 60 100M = 9624 281 GGCTGGAAATTAATTCTATCAGTTAGTCAAAATTTACTGACAATCACTCAGACGCTCAATATTGCGATTTTGCTTCAAAACTACTGTACCCGGTCTTGAC @@;DDA+B<FDHFC?EHGGGCIHICF3AFHFCFFCGEGGCFHIHDDD>FHGIHGIII6B8=B8@=<;=DHHECCEACCB@@@:>CCCCC@CBBBBBC<5@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2213:7767:73428 147 chrIV 9538 60 100M = 9395 -243 TTGACATTTTTTTTGGGAAACATGAAAAAAATGAGCATGATTTTTTTTCTATTTTCGATAGACCTGAATATATTTCCGAAAAATTCAACCCATCCATCGC EEDCCDDDDDDDDDDCCEEEDEDDBDDEFEDDDDDDDEEDDHJJJIIJJJIGFIJJIIGGHFJJIJJJIIGIIJJJJIIJJJJJJIHFHHHHFFFDDCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2108:20580:46115 147 chrIV 9624 60 100M = 9443 -281 AACCCATCCATCGCTCACTTACTGTGAAAAAGTTCCACTGCAGCCCGAGATAGTGATGTTTTGTGGGCGAATAGTTGTCGAGAAGCGTTCGCATGTTATG 89<2AC?5BBB>A>@C@DDD@@:CCCCC@A@>A;>>;;?1DCBB?=;CC=4C7.)ADF@BDB;0>F?F?B@HDAHBD?CEHGGGFC@87HHD?ADFD@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:45:8531:9371/1 16 chrIV 10605 60 101M * 0 0 TTTAAATTCAAAAATTTACATAATTTTTTAGTTTCTAGTGCCCTACGTTATTTCTCCTTCCGATAGAAATAACACTAAATCGACAAAACATTTTGCTCAGA :CAEFEDCEGFEDDEEDEEDEGEFEG?FEFDEF?FDCGEGFFGEFGGGBGEG?GGGGFDGGGFFGGEGGGEGFFGGGGEFGGGFGFGGGGGDGFGGGGFGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:45:5297:17573/1 16 chrIV 10799 60 101M * 0 0 AGAAACAACACAAAAACCGGTAATCATTATGGAAGTTCGTTGTGTCAAATTTGCACGATTAGTGAAAACGCTGATCTTCGATGCTTAAAGACTTCATCGGA EBBECBBDC@EDFDCCFBAEEEEBGFGGGGEEFFGFEAFDBGEFGGAGGGEGFGDGFGGBGDBGGEEGGGFGGGDDFBGFFEGFGGFFFFBFFA?F?GFGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:90:8728:2691/1 0 chrIV 11034 60 101M * 0 0 AGATCTGTGATAGAAAGACGAGGAGGAGACTGATCATTTTTTGGAAAAAATAGATTTAGTTAATTAATTAATTAATTTAAAAATAAGTATAAAAGTCGTCG GGGGGFGGGGGGGFDGGGGGEFFGGFEFGGGGFGGG:AGFGGEGEGFFGGEGEDGGBFGEFGEGGGGEGEDEEGEEEGBEEEEEEACAEDDDBDEADB?BD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:58:9805:10604/1 0 chrIV 11061 60 101M * 0 0 GACTGATCATTTTTTGGAAAAAATAGATTTAGTTAATTAATTAATTAATTTAAAAATAAGTATAAAAGTCGTCGTCTCTTCTGCCTCTTTTCGATTTTAAA GGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGEGGGGGEDGGFFGGFGGGGGGGGGGGGEGGGGFFFCFFDFFCGDGEDGFEGGFGEEEDGE=DEDDDCE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2102:2939:36410 99 chrIV 12069 60 100M = 12243 274 GAATTGATTAGTCAAAACCTTACAACTTGTGACTCAGAATTTTGAAAGTCTACCGAAAAAATAACGTTCTTCAACAATTACGATTCTTCAATTCTAATAG CCCFFFFFHHHHHJJJJJJJJJJJJIJJIEHGIGGGGIIJJJJIIJJGGIGHIIIJJIJGH2BEGH?EEFF>DEECDEDEC@B?ACCDCD:;ACDACCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:23:5518:6512/1 16 chrIV 12134 60 101M * 0 0 GTTCTTCAACAATTACGATTCTTCAATTCTAATAGGTTTTTTTTCCGAAACTTTGAGTTTTGCTACCTCTAAAATATGTGATTACAAATTATGGAAACGTA ?CBAC=CA@:AEBBBD=FCEEE?=EECBA?CBFDFC>:EE=:C:EEEEBEE5FAEF=EEEEDEEBEFBFFDFFFFFFBFEEFFBDFFADFF?DDDD5ACC= PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:9:17295:4977/1 0 chrIV 12165 60 101M * 0 0 ATAGGTTTTTTTTCCGAAACTTTGAGTTTTGCTACCTCTAAAATATGTGATTACAAATTATGGAAACGTATTAACAAATTACAACAGTACACTTGGTGTCA AEECDEEEEEDGGGGGFGGGFGGGFGGGFFDEEEEGGGGGGFG?GGAFGGGFGGGFFGGFGGG=GEEEE?E=EEEFFGDDGG?AGABAD?=CEBEEADBEB PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2102:2939:36410 147 chrIV 12243 60 100M = 12069 -274 TTACAACAGTACACTTGGTGTCAGAGTGTCTTATTTCGGCTACAAAAAATGCGGGTAAAGAAACGCAGAGTTCTCAATTAATTTCGCATGGTTAAGAACG ACCCDDCDDDAC>DDDDDDDDDDCCCDDDDDCDBBAFFEFFHHHJJHJIIIJIJJJJIIIHFDHJJJJJJJIJIIJJIJJJIJJJJJHHHHHFFFFF@CC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1211:1649:59300 99 chrIV 12490 60 100M = 12628 238 CTGCCGGCCGTAAAAAGTCATTCACCTCATCATCCGGCGATCTTCTCAATGCTCCAAACCGCACTAATGGACAATCCCGAACACCACCTGCTCCACGAAA CCCDFFFFHHHHHJJJJHIIIJIJJJJJJJJJJIJJJJIIHHHHHHFFFFFFEEEEEEDDDDDDDDDDDDDDDDDCCDDDDDDDDDD@BCDDDD@CB9@@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1211:1649:59300 147 chrIV 12628 60 100M = 12490 -238 GAGCAATCGGAGATGCTCTGCCGACTCTTGACGGCGATAATCTCATCAATATCAAGGCGATCTCGGGGCTTCATTTGGATGAATCTGATGAGGAAAAGGG DDDDDDDDDDDDDCAB?DBDDBC@BDDDDDFFHHIGJJJIJJJJJJJJJIIGJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:57:18691:3342/1 16 chrIV 13429 60 101M * 0 0 ATTCAATTTTCGGCAAAAAATAAATTTATGATGAACAAGTTGAGATTAAAATATAACTTTTCCTCTGATGAAATTTTTTTATTTTATCAAAAAATCGGAAA BBB=FDFFF?FAE;C?EGGGGGGFDGDGGDFFEGBGDEGGGGGF=GEGGFGFGGGDGGGEGDEGDGEEECDDDGGGCCBEAEFFDDDDDE=FFAFFGGFGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2304:10466:54597 99 chrIV 13926 60 95M5S = 14386 560 GTTCAAAGGCCCCCTCCGGCATACTCGGATCAGCATCATGCGAGTTCGACATCTGCTTCGGCTCCGCTGATATCGGTTATGCTTCTGAAGAAGCCGATGG C@@FFFFFGHGHHJJJIJJJJFAFGGGIGIIIJIJJEIJJJJFIADHGEHBDFEFFFEDDDDBDDDDDBDCCACDD?3<CCD@AACACDDDDCCB##### PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1103:15940:55697 99 chrIV 14066 60 100M = 14107 141 GGGCTGTGCGGCTACCGAGTTGCCAAAAGTTGGGGTTCGGCAACTTCGGCAATTGCCGGTTGCCGAAAATTTTGGAGTTCGGCAACTTAGGCAACTGCCG CCCFFFEFHHHHHJJJJJJIJJJJJJJJJGIIJJJGIJJJHJJHHHHHFFDDEDDDDDD=BDDDDDDDDDDDDCDCC>CDDDDDDDCD@CDDDDDDDDDB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1103:15940:55697 147 chrIV 14107 60 100M = 14066 -141 AACTTCGGCAATTGCCGGTTGCCGAAAATTTTGGAGTTCGGCAACTTAGGCAACTGCCGATATCAATGTCAAACATTTTGTAACCCATAAAAAAACATTC @<BBBDDDCDDBBDDDDABBD@?CDDDDDDDDEEDDFFGHGHJIIJJIHFJIGJJJIIJJJIJJJJJJIIJIIJJJJJIJJIHJJJJHHHHHFFDFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2304:10466:54597 147 chrIV 14386 60 100M = 13926 -560 GGTCGTCTAGCCTATCTGAGATTGCCTACGCTCACCTTCATGTTGGCCGAGCCTAAACTCTTACCTACGCCTACTTTGTACCTACTGAGCAATCTAGCCT BBB<>><>(@>@C>3>ACDCA=;5BB=9=3?7;7CHHHHG?GIHGGGHDBJJJIJIGIHGEB?JHF?IIHHCFJJIGHHEJHEIJIGHGHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:45:7639:19200/1 16 chrIV 15054 60 101M * 0 0 CGTGTCAATACCGTTGCCTTATTCTCTTCAAATTTCTAATTTGTAACAATTTTCACACACACACTTATACAAAAATTACGGAAAACTCTCTTGAAACAACG C?BBBBBA@>EFEBDDBB=EABBFAED:FF=EEBBBAE;BE=E?EAEBDBBEBDBEBEBEBEAEBBFC=FFFFECDFDFFFBGGEFFGFGGFFFFEEECEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:32:13629:16208/1 16 chrIV 15294 60 101M * 0 0 ATACAATATTACTGTGATAGAAGCACTGAAAATTCTCTTTCATAAAAAAATTATGTAATGCGTTGTTGTTTGCGACAGACTTTTATTTATATATGACATTA DBDGGBGEFFEFFGGEDGAGGFGGEGAFAF?DGDBGGFGDGFGGGDGFG=GDGFGGEGEGGFGGGGGGFGFGGGGGGGEFGDGGGGGGGGGGGGGGGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:18903:53675 99 chrIV 16174 60 100M = 16449 375 AGTATAGGTTGAGTGTCATATTCGAAAGTGGCCTCCACTCCTCCAAATATTAGGTTATGGATTTATCTGTGCTGTTTCACAAGAAATGCCCAAGCTTCTT @@?DBDDFFHHDDHIBGIIEHJJJEGIG<FHBEHIJIIGGIBFEGGGIJIJIIGFFGIJIIIEHGIIGCFHGDHIGIHHGHFHFFFFFFEEC=ABDDDCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:86:18150:16897/1 0 chrIV 16311 60 101M * 0 0 TAACTCTAGAGCCGTTTGACTGAATTTTATAATATTTGACAGCTTACTAGAAATATTTCACCCCACGGGGGAGCAAAAAACTGCACAAAGTTTGGAGCAAA =EFGGDGBGDGDGGGGGGDGFEF=EFFFAFAFEFDFFEFBF?FBFFFFFDFFFDFFFFFFFFFFEF>FBFB=>9B5??>=F@DFDEB=?B?B@?B@:@@=B PG:Z:SNAP RG:Z:266-1 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1201:4433:4114 73 chrIV 16371 60 100M = 16371 0 CCCCACGGGGGAGCAAAAAACTGCACAAAGTTTGGAGCAAAACTGAGCTCAGGACGGCTTTCCCCAGTTTGAAAAAAAATTTTGTTGCTCTTTTTACCCC @@@FFDFD8CFFHGGGIIJB@HGJFIIJFE.@?ECHGFFD@CEEDECDC;5?CABB@B;5?>@ACC@ACC@:ACCDD9BB@>AAA98:>CC@CCC?>>38 PG:Z:SNAP RG:Z:000 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1201:4433:4114 133 chrIV 16371 0 * = 16371 0 AAAATTAGTTTTTCGTCTTTATCTCAAGTTCTTCTTCATCTTTTTCGATACTTTTTTTTTCTACCCCACGTAAAAAAGTACGCTGAACACGATTTTCAAC :@:4(:4<@9<B<3CCC@:>@8>::>:?>>99(@>>>:?@?BBCB?;>5(BCEFIGHGB=67(HED;?BBEIIGDEF@<3<@<?9GF?AA=<DDDDD@?@ PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1302:19827:42088 73 chrIV 16422 60 100M = 16422 0 GGGCGGCTTTCCCCAGTTTGAAAAAATTTTTTGTTGCTCTTTTTACCCCCAAAAAACCATGTTTTAATTGAATTAAAATTCGGGTTTTGCTCGGTTTTGT BCCFFFFFHHHHGJGHGHGEHIJJJJGGJJJJJIJJIJHHHFHHFFFFFDC@DDDDDDDCD>CDCDDCDCDDDECDDDDDCBBDABDDDCACBD?>@DBA PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1302:19827:42088 133 chrIV 16422 0 * = 16422 0 GCCTTTTGTTTTATCACAACTTTTTTCCATTTGCACTTATGAACTCAATCTTTCTTTCAAAAAATCAGTCTCTCTGAGTAGTATCTTGCACAGAAATTTG CCCFFFFFFFHHGIIIJIJJJJJJJIJJEIIJGIGHGHIJJJJJIJIJJJJJJIGIGIJIEHIIHIIGGHHHHGHEFFBBDBDEEEEEDDDD?CDACCDD PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1216:8211:57172 165 chrIV 16449 0 * = 16449 0 ACATGAAATAATGCGAAATGGATTTTCTAATTTGTAGAAATTATAAGATAGCTCCGAATTCTGCCAAGCAGCCTCTAATAAATGCCGAGTGTACAGACTC ?BBFA=ADHHGHHJJJJJJIJIJJJIHIJIIJJJIIJJJJJJJJIJIJJJJIJJIJJJJJJIJJIJIJEIIHHHHFFFFFFFEEDDDDDBDCDEEECBDC PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:18903:53675 147 chrIV 16449 60 100M = 16174 -375 TTTTTGTTGCTCTTTTTATCCCCAAAAAACCATGTTTTAATTGAATTAAAATTCGGGTTTTGCTCGGTTTTGTTCCAAATTTATGTGCAAGATACTACTC 8DDBBDDCC<?5>A:><:@BBB@>;;@>?>FHFFHGHIIHGHBGGGIIGFHGHGGB;GEH@0EGE7IGGHGCEF@BHJI<HGBGA9HBFFFC=:BDD@?? PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1216:8211:57172 89 chrIV 16449 60 100M = 16449 0 TTTTTGTTGCTCTTTTTACCCCCAAAAAAGCATGTTTTAATTGAATTAAAATTCGGGTTTTGCTCGGTTTTGTTCCAAATTTTTGTGCAAGGTACTACTC 8BBB?DDCDDBBCDDDDBDDDDDDEEEEEFFFDFHGHHFHHJJJJIJIIHIJJIIJJJJJJIIIJJJJJJJIJJJJJJJIJJJJIJJGGHHHFDFDFCB@ PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2211:12400:9160 99 chrIV 16457 60 100M = 16639 282 GCTCTTTTTACCCCCAAAAAAGCATGTTTTAATTGAATTAAAATTCGGGTTTTGCTCGGTTTTGTTCCAAATTTATGTGCAAGATACTACTCAGAGAGGT CCCFFFFFHHGHHJJJJJIJJJIJJJIJJJJJIJJIJJJJJJIJJJJJJGCGIJJJJJHHGFFFFEEEEEEDDDDEDFEDEDDDDDCC@CDDDDCCDDD3 PG:Z:SNAP RG:Z:000 NM:i:2 +EAGLE:1:46:17265:14051/1 16 chrIV 16476 60 62M3D39M * 0 0 AACCATGTTTTAATTGAATTAAAGTTCGGGTTTTGCTCGGTTTTGTTCCAAATTTATGTGCATACTACTCAGAGAGGTGGATTTTTTGAAAGAAAGTTTGA D<>A7?@C==EADFFGFFBE?B?D@=CFFFEFAGGGGFGGGEDEBBBA?BFFFFEDC?DDB?C>C?CA=:=EDDBDGFFGGGGFDGAEEFDF5FFFGDGFB PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:94:17078:10619/1 0 chrIV 16610 60 33M1D38M1D30M * 0 0 ATAAAACAAAAGGCCAAAAAATGACATTTTGCCAAAAAAATTTTTTTTCCGAAAAAGTAGTTTTTCGTCATATCTCAAGTTCTACTTCATCTTTTTAGATA GEGGFGGGDGFFGGGGGGGFGGGFGBGDEDGGGGGGGGGGGGGGGGEEGDGGGFEEFCDECADEBFG@EDAEEBEEC?ABDEDDFEEEEEA?DDBC?BDC@ PG:Z:SNAP RG:Z:266-1 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2211:12400:9160 147 chrIV 16639 60 1M1I18M1D80M = 16457 -282 TTGCCAAAAAAAAATTTTTTCCGAAAAAGTAGTTTTTCGTCTTTATCTCAAGTTCTACTTCATCTTTTTTCATACTTTTTTTGTTTACCCCACGTAAAAA DCDBDDDDDDDDDDDDDDDDDDDDCEDDDDDDDDDDDDEEFFFFFFHHHHHHIIEECIIJJJJJJJIJJHHHFDGJJJJJJJJJIHEHHFFHFFFFFCCB PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2201:10133:75100 165 chrIV 16645 0 * = 16645 0 AATTCACACGGTTCAGGAGTTGGAAATAAAAACGTGGTGTGACATTTTTTCGCAAGCCAAAAAAAACGCGAAAAAACGCGAAAAAGGGGCGGAGTCTGTA #####################################################B@A;/DDFHIGG@GIEIIJIIHFIIJJIJJJJJJHHGHHFFFFFCB@ PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2201:10133:75100 89 chrIV 16645 60 76M1D24M = 16645 0 AAAAAAATTTTTTTCCGAAAAAGTAGTTTTTCGTCTTTATCTCAAGTTCTACTTCATCTTTTTCGATACTTTTTTTTCTACCCCACGTAAAAAAGTACGC >BCDCA8@@BCB?<50+CDDCC@C@BDDDB@@CDCDCADBCCDDDDEC@;9EEEDFFFHHIIHHEEF=GJJJJJGGGGD?IIGHDIGGHHHHFFDDD@C@ PG:Z:SNAP RG:Z:000 NM:i:5 +EAGLE:2:31:3792:4681/1 0 chrIV 16705 60 101M * 0 0 TTTTGAGATTTTTTTTGTTTACCCTACGTAAAAAAGTACGCTGAACACGATTTTCAACTCAGAATTGAGAAAAGTTCTATGAGTCGGCCGAGCAAGACGAA FBFFF?GGGGDGEGFEGGGEGGGGDGGGGGGFFGGDEGGGDFGFGGFGGGDDFDGGGGGGEEDEGGGGGFGGDEBDFEFFGF?DGEFGGGEGBBEFEEEAE PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:48:7607:3697/1 0 chrIV 16768 60 101M * 0 0 ATTGAGAAAAGTTCTATGAGTCGGCCGAGCAAGACGAATAAGTGCCAAATTTTGCCCACTTTCCCGTTTTCGCGAATCTACTTTTTCCATCATAACTCGGT GGGDDGFFGGGGFGGGFDEGEFDFFFF?DFFEFEDFFFFDBDADCFFFFFFG?GGGGFEFGGGGGFBD:BEEEBA@EEBED@?DDDDEDADBD:DB=ABB8 PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:2304:5957:30377 73 chrIV 16778 60 100M = 16778 0 GTTTTATGAGTCGGCCGAGCAAGACGAATAAGTGCCACATTTTGCACACTTTTCTATTTTCGTGAATCTACTTTTTCAATCATAACTCGGTCAGTTTTCA BCCFFFFAHFHHHIFIIIJJJIIIJJIJIJJG>FFHIIJIIIIIIGIJIJGCGIHEHHHHHFFFEAECEACCCDDDDCCDDDD@CCDDBB@B@C:>@CCD PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2304:5957:30377 133 chrIV 16778 0 * = 16778 0 ATGAAGTTTCGTCGCATTAGAAATACTCTGCCAAGAAATATTATTTTTATTAATTTTCAGGCCAAAACTTGTTTTTTTCTACAAATCGACCGGTTTACGA CCA@>DDDDDB?BACCDDDCDDC@@DDDDDDDEEEEFEEDFFFFEHHHHHGHJJJJJJIHFGGJJIGJJJIJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 +EAGLE:2:84:15670:14903/1 16 chrIV 16791 60 101M * 0 0 GCCGAGCAAGACGAATCAGTGCCGAATTTTGCACACTTCCCCTATTTCGCGAATCTACTTTTTCAATCATAACTCGGTCAGTTTTCAATTTTTCTTAGTTT BCADAEB?CCBDFDCDBEEBGEGEEEEECECFCD@FEDFGGEFFEDDFFFFBGEGGDFFFFFGGGGGFGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:1106:14433:6441 165 chrIV 16828 0 * = 16828 0 ACCGTCGGCTGAATTTATAAAAATAGACCATGAGAGGAATTTTTTAAGTCAAACCAAAAAAAACGCGAAAAAACGCGAAAAAGGGGCGGAGTCACCACAC ######################################################################GB:0))*?C9;GE@+C<?HD?=++=DD;=8 PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1106:14433:6441 89 chrIV 16828 60 5S95M = 16828 0 ACACTTTCTCATCTTTGCGAATCTTCTTTTTCAATCATAACTCGGTCAGTTTTCAAGTTTTCTTAGTTTTCTAAAAATTGACGTGTAGGTCTTATCAAGA #####CCCCCCC>?=385;(@>6.(46;@C=:ACAEHHE;@6FCEDBIGCHD<GFD:9HCFF@HGIHFFBF=IHHFFCAACFBEA@BAFHDHD;A1D=:8 PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1306:16001:53612 99 chrIV 16842 60 100M = 16921 179 AATCTACTTTTTCAATCATAACTCGGTCAGTTTTCAAGTTTTCTTAGTTTTCCAAAAATTGACGTGTAGGTCTCATCAAGACGCATCGAGACATATAAAA CCCFFFFFHHHHHIJJJJJJJJJJJJFHJJIJJJJGIJGIJJJJJIJHIJJJJJJJJJJJJJJJHIJJIJJJIJJHFHHHHFFFDDDDDDBDCDDEECDC PG:Z:SNAP RG:Z:000 NM:i:4 +EAGLE:2:76:14252:18422/1 0 chrIV 16876 60 101M * 0 0 CAAGTTTTCTTAGTTTTCCAAAAATTGACGTGTAGGTCTCATCAAGACGCATCGAGACATATAAAATTTGTAAAAAGTTCAGTGGGAAAATTTTTCAAGAA DDDADBFFFFGGEGBGGGGFDDGBGGGFGDCFFDFFDFFFAEEEEGGGEGGGGDGGDGGGGGDGGEDGEGGGDFGGGBDGFFBFFGEGGBDBBFFG=DG?F PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1306:16001:53612 147 chrIV 16921 60 100M = 16842 -179 GACGCATCGAGACATATAAAATTTGTAAAAAGTTCAGTGGGAAAATTTTTCAAGAAAAAAATAATTCAAAAATTTAGTACTGGGGGGAGTGGTTTCCTGC 0BDDEDDDDEEEEEEDEDDDCDCDDDDDDDDDDEEDEEEFFFFFFHHHHHJJJIJJJJJJIFIGIHGJJJJIJJIIHHFJHJJJJJJHHHHFFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:3 +BS-DSFCONTROL03:121:D0M8KACXX:5:1307:16910:75714 165 chrIV 16922 0 * = 16922 0 GGTCAGTTTTCAATTTTTCTTAGTTTTCCAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGCTTATCAAAAACAAACAGAACGAAAAAAATTTTTAAAAAAT @C?DFFDFHHHHGJJJJJJJJJJIJJJJJJJJJJJJJJJJJHFDDDDDDDB################################################# PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1307:16910:75714 89 chrIV 16922 60 100M = 16922 0 ACGCATCGAGACGTATAAAATTTGTAAAAAGTTCAGTGGGAAAATTTTTCAAGAAAAAAATTATTCAAAAATTTAGAACTGGGGGGAGTGGTTTCCTGGG <DDEDDDDDDDDDDDEDDDDDCDDBDDDDDDDDEEEEEDFFFFFHHHHFGJJJJIEJJJJJIIJIIJIJJIJJJIGJHJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:6 +EAGLE:1:116:7753:12206/1 0 chrIV 16940 60 101M * 0 0 AATTTGTAAAAAGTTCAGTGGGAAAATTTTTCAAGAAAAAAATAATTCAAAAATTTAGTACTGGGGGGAGTGGTTTCCTGGGTCCCCTGAACATTTTATCC EBE=EAEEEEFBFDEFFFFFFF;EFAFFDFFFFFDFFF@ECCCCACDFFFEFFFFFFFAFFEF=FEFFBC<FF@BCACBAEE=EBEE?CBEDD?EEA=B7C PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:78:11145:14387/1 0 chrIV 16952 60 101M * 0 0 GTTCAGTGGGAAAATTTTTCAAGAAAAAAATTATTCAAAAATTTAGTACTGGGGGGAGTGGTTTCCTGGGTCTCCTGAGCATTTTTTCCACTAAAGTTTTG GGGGGGFDDGGEGGGGGGGGFGGDFG@GFGDFGGGGDGGGFGFGEGEGFDGGFEGGCEE:@>>>CDDDED:CDCDDC?DEEEEEEEEBEEBBCCCEEEEE? PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:43:19134:12725/1 0 chrIV 16956 60 101M * 0 0 AGTGGGAAAATTTTTCAAGAAAAAAATAATTCAAAAATTTAGTACTGGGGGGAGTGGTTTCCTGGGTCTCCTGAACATTTTTTCCACTAAAGTTTTGCGGA FFFFFGEGGGFGGAGGGFGGGGGGGGGGGGGGGGGGDGGGDFEFFGGGGGGGAD@FFCDFGGEFGFEGFGGFGEEEEEGEGGGEGBGGEEBE@DBEBECEE PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:1:57:3806:20180/1 0 chrIV 16957 60 101M * 0 0 GTGGGAAAATTTTTCAAGAAAAAAATAATTCAAAAATTTAGTACTGGGGGGAGTGGTTTCCTGGGTCTCCTGAACATTTTTTCCACTAAAGTTTTGCGGAA CCC:;DD?BDEEDDEEDE=DECECCEDEEEEAE?EEDEE=ACACCBA=ADDA@;DEBCEEEEEEBBE:EEEEEEEBEDEDEEBEEEB?A@C5@@CC?BD?5 PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:28:11193:2776/1 0 chrIV 16966 60 41M1D59M1I * 0 0 TTTTTCAAGAAAAAAATAATTCAAAAATTTAGTACTGGGGGAGTGGTTTCCTGAGTCCCCTGAACATTTTATCCACTAAAGTTTTGCGGAATGTATTTTTA GGGGGGGGEGGDFGGGGGGGGGGGGGGGGGDGGDFGGGGGGGG?GFCFFFGGGEGEGGGGGGEGFEGGGGEEEGFEEEEEGEEFGECEEA?CECCDEEECE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:63:18448:7383/1 0 chrIV 16991 60 101M * 0 0 AATTTAGTACTGGGGGGAGTGGTTTCCTGGGTCTCCTGAACATTTTATCCACTAAAGTTTTGCGGAATGTATTTTTAATTCATAGTTTTTGATTTTATCTA FDGEGGEGGGGGGFDGGGCGGGEGGGGFGGEAEEEFFDFFFDGGDGGFGGGGGGGGFEGFFFFFFE?FEBBEEEEACEFDFFFAFEGFGGGBFBGDDDGCC PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1213:7683:14705 73 chrIV 16997 60 100M = 16997 0 GTACGGGGTGGAGTAGTTTCCTGGGTCTCCTGAACATTTTTTCCACTAAAGTTTTGCGGAATGTATTTTTGTTTCATAGGTTTTGATTTTATCTAATGGA BBBFDDFF@DHHHDHIHIIJJIJJJCGHJJIHJJIIIJJIJJJIJJJJJJCEHIJIHHFEDDECDDFEEDBACDDDEEDDCCDDDBCDEDEDCDECDDCD PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1213:7683:14705 133 chrIV 16997 0 * = 16997 0 GTTGAGGGCTATATCTTGTAAACTGGTTTATTTATAGAAACAAACAAGTTTTGGTCTGAAAATTTTGAAAAAATAATATCTCTTGGCAGAGCATTGCTAA CCCFFFFFHHHHHJJJJJJIJJJJJJIIJJJJJJJJIJJJJJJJJJJJGIJJJJJJJJJJJIIJJGHIJJJJHFFCDFFFFEEEEDCDBBDDDDDCDDEC PG:Z:SNAP RG:Z:000 +EAGLE:1:53:14974:4822/1 0 chrIV 17018 60 101M * 0 0 TGGGTTTCCTGAACATTTTTTCCACTAAAGTTTTGCAGAATGTATTTTTGATTCATAGTTTTTGATTTTATCTAATGGAAGATGAAGTTTCGTAACATTAA AABA:=DDDDGF?GGGGGGEEFGGFEDE?E?DDDAE=EBEDEEDEEDEB@?DEDBEBECEEE=EAGDGD:FFCB?FDADEGAFGBFDAEFEEA?E?BAA?A PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:79:7894:12928/1 16 chrIV 17065 60 101M * 0 0 TTGATTCATAGTTTTTGATTTTATCTAATGGAAGATGAAGTTTCGTGTCATTAACCATGCTCTGCCAAGAGATATTATTTTTTTAATTTTCAGGCCAAAAC ECCCDCBAE=DEEEEEEEEEEEDDEE=EEGGEEGGGGEEGDFGGFGFEEAFCGBGGGEGGEGGGDGGEGGGGGGGGGGGGGGGGGFGFFAGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:3180:43522 73 chrIV 17244 60 100M = 17244 0 GAGTACAATCCTGTAATAAAATTTTCAAAAATTCGTTTTCCCGCTGACTAATCAGTGATAAACGGTTTTCAAACATATTTTCTCAAATTGTCATTATTGA BCCBDEFFHHHHHBGGGHIJJJIJJJJIGFFA<AGFGHIJIJJJJJJJEIHIJJJHIJIIIIJIJDEFHHHFHFFFFFFDEEEEDECDCC@CDECDDDCC PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:3180:43522 133 chrIV 17244 0 * = 17244 0 TTATTATATAATCCTTAACCGTTCACATTTTTGTCTCATGGGAAGTAAAACAGTTCACTGGTTGTTACTACAACATTTATTCTCAGCTTCTCTCTACAGA CEEDEDEDDDCCCEEDDDFHHGHAHIGIJIGFJIJJIEJJJJJIJIIIJIJJJJIIIIJIGJJIIIIJIHIJJJIJJJJJJJJJIJJGHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1304:3598:47398 165 chrIV 17460 0 * = 17460 0 GGCTTATACAAGGACTGAAGTTATATTTTGAAATTTTTCAGCTGATATAAGTGAAAAAAGGAAGCATAAATTGTTTTCGCAATGTGCCCTTTATGCTCGA CCCFDFFFHHHHHJJJJGIIHGIJJJIJJDIJJJJJJJEHIHJJIIIJJJIHIJIIIIIIIIJJJJEGJJBHEEEAEHE9AACCACDDDDDCDBACDDD? PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1304:3598:47398 89 chrIV 17460 60 35M1D28M2I35M = 17460 0 GTTGGCTCGATTCCCCCAACTGACAAATTTTTTTTGGGTAATTGGGATTCGAATAGAAATGCTCGATTTTAAGCAAAATATGAGTGGGTCTCCTCTCCTC BDDDDDDDDB@5B@DCCDCDEDCCCCDBDEHEHEJJIHGGIGHGHEHGEBIGEDGGIJJJIGIHIGJJIDJJIIJJJHBHEGGGIIJHGHGHFFDDDCB@ PG:Z:SNAP RG:Z:000 NM:i:5 +EAGLE:1:76:16063:11662/1 0 chrIV 18079 60 101M * 0 0 AATATACAAGAAAGAGCTCTCTGATGAAAAAATTGACCCTGAAATAAAAAAAATAGTAATTTGGTACTTTGCAAGGAAGACCTACTTGATATACTGACATG GGGGGGGGGGGGGGGGGDGFGGGGGGGGGGFGGFGEGGGGGGGGGGGGGEEEEDEGEGGGBFFFCGGEEGGGEEEGEDGEEEEEGEEEEEEEEEEEEEEED PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:58:12937:19702/1 0 chrIV 18223 60 101M * 0 0 AACATTAAAACTGTCTTTATCTGAAACATTAAAAGATTGGAGTAATAAAGAACAATGTGACGGATATATTCAGTCATGATTTGATTACCGACTGAGCTGCT EGGEGEGGGGGGGFGGEGGGGGGGGDGEGGGGDDGCGGGGGGEGFGGFGFGGGGGGGEFFGDGFEFGGGGGFGEGGGGEEEGGFEGGGFGEEGGEF=AGBD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:42:10933:8029/1 0 chrIV 18242 60 101M * 0 0 TCTGAAACATTAAAAGATTGGAGTAATAAAGAACAATGTGACGGATATATTCAGTCATGATTTGATTACCGACTGAGCTGCTATTACCGACTGAGCTACTT FGGGDGGGGGGEGAGGFGGGGGGEFDGDGGFEGGGGGGEGGGGGGGGFEGGGGGEGGGGEFGGD=DCDFFGFGEFEGFEGFGEGBGDFGEBGEDEDEEEEG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:57:16376:15904/1 16 chrIV 19300 60 101M * 0 0 ATCTCTTTTCTCGTAACTGCTGTAAAAAGGAACGAAGCACAGCATATAGGCAAACAGAAAAATGAATAAGACTCGGAAGATCTGGAAATAACATTATTATT :DFBFEDEBGFFEGGEGEGGGGDGG?FGEEDEGGBGGDGEGGEGGGGGGGGGEGDGGGGGGGGGGFGGGGEGGGGGGGGGGGGGGGGGEGGGFGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:82:4792:16460/1 0 chrIV 19447 60 101M * 0 0 ATCAATGATTTGTTACAAGAAATTTTAGAATTTGTCCGACACAATTCTTAGATTTTTGAAAATACTGTTCAAACATTATAAAAATATATTTAAGTTGCACT DGGGFGBFGGDGGGFGGFGGGGGGGGGEFGGFGEEGGGFGFFDGEGGGCGGGFGGGGEEGGGEFGBFAEFGGFGEEEFEEEEEE>C@EDEEEGEECEF=@C PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:12255:61856 99 chrIV 19979 60 100M = 20074 195 TCTTGATACTGCATGAATTTTCTTTCTGCCAAAAATGAAAAAGTTGAGGCATAATCAGCTTTCAATGCTTCCATCGCTTGACGCGGTCCCTTGACTCCAT BBBFDDDFHHHHHJIJIIIJJHIJJJIGIJIJJIJJJJJIJJIGHGJIJJGHHIJIJGBGIGIIJJJJJJEHHJJJHGHEFFFFDDBB;BCCDDDDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:12255:61856 147 chrIV 20074 60 100M = 19979 -195 TCCATTCAAGTTGAGATGATTGATAACTTTACACGCGAGTTCTTCAAGTTGTCTTTAAAATCAGAAATGGCCGTACACTTGCAAACGAGAAAACCTACTC AC@DDDDDCDDDDDDDDDDDEDEDCDCCCCAEEGJJJJIHEJIJJJJJJJJJIJJIJJJJGJJIJJJIJJJIIIHHCJJJJJJJJIJHHHHHDFFDBC@B PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2307:13742:62661 99 chrIV 20173 60 100M = 20424 334 TCTTGAGTTGAGCGTAATCATTGCGCTTTAAAACTTGCCCGAAATCCTTAGCGTCTAATAATCGTTTCATAGAATGCGCCACGAAGCACATTACCATTAT ?@@DDBDADDHFBE<CEBHBHICH?FAEH@@?CGH@F<9BFEF@HGECEGI>B';AEFEFEHC?;B566>;;>6>;5'9''3;?5?9CCCCCACCC>:A3 PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2307:13742:62661 147 chrIV 20424 60 17S83M = 20173 -334 AAAAAATGACGACACCAACACTTTGAATTTAGTACGTACTCTTGCTTTTTGCATTGCAAATTTTTCTTAATTTGAATGTTGAGTTCATCCTTTCTACAAT #################@;)CHC;CC=:ED@EECHDCB2G>F?(0)?9?9E??:IHDH?);HE9BEFBH@IHFA<3CFFA3322++<++:<HFDB=BBB8 PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:75:4143:14945/1 0 chrIV 22397 60 101M * 0 0 GTTCAAATCAACCAAAGTTCAGTTACGCAGTGTAAAACTGGATTTTGACCATGGTGCATCTATTGAAAGTTTGTATATTGTCTCACCAAAAAATCGTTTCA GGGGGGDGGGGGGGGGGFGGGFFGDFEFAFEFFCFGGGGGGFGEGGAEGGGFGGCFFFEFGEEGGEEG?@EFADEFGEEFEFEGEEFEEDFDCBEE>C=E@ PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1207:8708:89857 99 chrIV 22773 60 100M = 23094 421 ATACAGTATATTAGTTTTTAAAAGTTTTGTGCCAAACGAAATTTTGTCGAAAGTTGACAACTTTTTTGTCTAGAATTGGCAATTTTTTAAAAATTTAAAT CCCFFFFFHHHHHJHGIJJJJJJJJJJJJHJJJJJJJJJJJJIJJJIJIIHIIIIIJJJJJJJJJJHHHHFFFFFFB@CEE>ACCDDDDDDDDDDDDEDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1207:8708:89857 147 chrIV 23094 60 100M = 22773 -421 GTTTTTGAATTGAAATTGAAAGAAATCGAGCAACTTGAAGCCGAGGCCGAAAACACAATTCCAAAAATACCCAAGAAAGCAGCTGGCTCATCTTCAGAGC @DDDDCCEEDDCDEEDCDDDDDBCA<DFFFFFDHHHHHJJIJJJJJJIJJJJJIHJJJIGJJJJJIHF?JJJJJJJJJJJIJJIJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2108:16786:19522 99 chrIV 23918 60 100M = 24045 227 GTAATGTACGTATCAAAAATTTTTCTATTATATATTATTTATAGTAATTTGTTTGCGACCCTATCGTATTTTAATGAAGGATGTAAAGTAACAGACTACA BBCFFFFFHHFHHJJJJJIJJJJJJJJJJIJJJJJJJIJJIJJJIICIIJJJJJJJJJJJJJJJJJHIIJJHHHHHHHFFFFFEEEECCEDDDCDDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2108:16786:19522 147 chrIV 24045 60 100M = 23918 -227 CCATTTTGCAAACTTTCAGTAGAAAATTTTCAACTTTCTAAAGCACAACTTTGAGTCGATAACAAACAAAAAAGATATCCCTCATTTATTTTTCCACACT ADDDDCDCCDDCDDDDDEDEDECDEFDFFFFHHHHHHJIJJJJJIJGIHIJJJJIJJIJJIHJJIIIJJJJJJJIIIIJJJIJJJJJHGHHHFFDADBB@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:49:4402:14093/1 16 chrV 2002 60 101M * 0 0 ATTAGTCTTGCATGCAAGACTAATTTTCAATTGACCCGTAGGGGTGCAAGACAAATAGGGGTGCAAGACTAATAGAGGCTGCAAGACTAATAGAGGAAATA DBEDEEDCCEA@DEDDEGEEGDDEED=FEDGEFBEDFGFEGGGGGGEGFEECGFGGFFGGGGGFGGGEGGGGGFGGGG=GGGGGGGFGGGEGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:42:2639:3086/1 16 chrV 2123 60 101M * 0 0 GCGATAGCATTTCGAGAGAAAAATATTCTTAAATGTGCTCAATATGGCTGATACAGATAGGTTTTTCATTACAGACAGGTTTTTCATTTCAATTTTAAAAA EBEEEBEEB:BEBEEA;A=EEBE?CEE?EEEEED?D?EEE:DDEEEEEEE=DAD:DEE=DEBEEAEEEDEEEBDEBDEEDEAEEEEGGEGFGGGGD;FD?F PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:20321:98700 99 chrV 3178 60 100M = 3335 257 GTCTATGAAAATGCTTTTATTTGGTATTACAGTTCTTTTCAAAGGCACACATATTTTTCCCATTTAACAAAAAATCGTCGTGACCTTATATCGTATTTTC CCCFFFFFHHHHHJJJJJIJJJJGCHIJJJJJIGIJJJJIIJJJJJJJIIDHIJJJJJJJJJJJJJJJGHJJJJJGHFFEDDEDECDDDDFEDCDDDEEE PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2310:20321:98700 147 chrV 3335 60 100M = 3178 -257 GCAATAATACAACACCGGGTCTCGACGTGGCAAACGATTGTTTATTGATTTTCACGGGATTCTCGCCTTTCTCATTGAATTTTCGCGCTCCATTGGCAAT CDEEDEDDCDD@@<DDDDDDDDDBBDDDDCDDDDDDDDDDDEEEEECFFFFFHHHJJJJJJJJJIJIJJJJIJJJJJJJIJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2201:16390:41463 99 chrV 3761 60 100M = 3998 337 AAATAGAATTCATGATACACGATCTTGAGAAGAGCTCTGTCCTCCAGGCTGCGAACTGGAGCGTAGAAAGTTTTCATATTGTTAAAAACTGCAAAGAAAT CCCFFFFFHHHHHJJIJJJJJJJJJJJJIJJIJJGIIJHHIJJJJJJJJIHIJJJJJJJIJJHHFFFFEECEEEDDEEFEEEDDEDDDDDDDD@CCC1?> PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:71:9405:4095/1 0 chrV 3773 60 101M * 0 0 TGATACACGATCTTGAGAAGAGCTCTGTCCTCCAGGCTGCGAACTGGAGCGTAGAAAGTTTTCATATTGTTAAAAACTGCAAAGAAATGTTCGATTCCTTG DA=DADDBB:;?@@@=DDDDDDD?DDDBDDCDDDDDDDDDDB?C=DDADDD=DDB?AA:ADCDDCCBCDB=:@ACDBCA=ABCBDB@>A@ABC??BB=BBB PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:65:16164:2544/1 16 chrV 3846 60 101M * 0 0 AAACTGCAAAGAAATGTTCGATTCCTTGTTCTGACGTGTGATGCTTTCTCAAATATGGAATTAAATGACAGACAAGGAGATGAAGTTTCGGAGTGACTCAT @?@C@B;>EDDBDDBEEEABBA@B=C:EFEFFDBFEEEEEEADDCBEDBDBFD5FFFFFBFFFEBEFEAFFFAFFFFFFFFEEDEE?D=GGGGFGGGFGFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1214:8214:10158 99 chrV 3997 60 100M = 4220 323 GTTAAAGCAAAACTTCAATTTTGTCAATCTCTTGGTCTAAATACGTTCTATCGTTAGATAAATCTAACTATCTAACTGAAACGAGTACAACTATATTGTA C@@FFFFFHGHHHJJJJIJJJJJIIJIJJJJJJJJFHIJJJJJIJGIJJJIJJJJJJJJJJJJJJIJIIIJIIIIDGDHHEHGFFB>CCCEEDDDDEEAC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2201:16390:41463 147 chrV 3998 60 100M = 3761 -337 TTAAAGCAAAACTTCAATTTTGTCAATCTCTTGGTCTCAATACGTTCTATCGTTAGATAAATCTAACTATCTAACTGAAACGAGTACAACTATATTGTAA DDCCC>DC@ECEEC@EEFFEFHHE>HGIIIGHCEC=/)FIHFHIJIIGIHIJJJIHIIIJJIIIIGGJIJJJJJJIIJIHIJJIIGGHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1214:8214:10158 147 chrV 4220 60 100M = 3997 -323 AAAATTAGTTTAATCTCCTCGCAAGATTTTTTTCTCCGAAATTTAAGATTGGGCGCTTAGTGATATCATAACTCTGCAGCCATCAGAAAAACTGAAATGT CDEDDDDCCDCCA@BBDD@BC>CCDB@CEFHHFIJIJHIIIGJIJIIIIHJJIJGHIIJJIGJJIJIHGHHGFJJJJJIJJIEJJJJHGHHGFDFFF@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:76:4095:13262/1 16 chrV 4714 60 101M * 0 0 ATCGTAAGGCGGTACTTTTTAAAATTTCGTTTCCATTCTTCCCCAGGGATCCCGTAAAAAACCAATTTTTCGACTAGGTCTCACATTTTGCCCTACAAGAG B=BC:CACBCACA=ECD:CDGA?AA:ADA:A@EEEBCGDAGGGGEGGGEDGGGGFFGGFGBFFFFFFGGEGGGGEGGGGGFGDGGGGFGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:89:14779:18797/1 0 chrV 4998 60 101M * 0 0 TGTGTTTGGTTTCATTCAGACGCTACTTGCCTGATCTATCAGTCTAACAATTTTTGTTTAATTTTCTTCACTATCCGCCGTTTATAGTTCGTTCTTCCGTA EEE=FEFEEEFFGGGFGGFGGGGDGGGGGGGFD?DFFEFCFGDGGEGGEEGGGGGGEGG=FGGFFFGEEGGFEGGEGGGGEGG@EDDADDEEEBGDDEDCE PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1302:16740:19201 99 chrV 5929 60 100M = 6103 274 CTCCAGGAAGACGAAAATTCCACAGACTGAGTATCCACGTAAGTATACGATTTTTCTATGCGCTATAAAATTCTTTAAAATCCGCTATTTTCCAGCTGAT CCCFFFFFGHGHGJJJJJJJJJJJIIJIIGGCGIIJIIJHIJJDHIIJJIIIJJJJJJJJJJJHGFFFFFFFCEEEEEEDEDDDDD=BDEEEDEDDDDCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2115:16987:87976 99 chrV 5959 60 82M18S = 6130 228 GAATCCACGTAAGTATACGATTTTTCTATGCGCTATAAAATTCTTTAAAATCCGCTATTTTCCAGCTGATTACGCATCTAACGACCTGATGAACAGTTTC 1++=+2+22+2A:HD?E,A+++32+++2A@*:8C):BBGD4*9B9*?*099/?6(6@'.@E;)).==)7;7?),5;ACA53@################## PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:85:10419:2317/1 0 chrV 5963 60 101M * 0 0 CCACGTAAGTATACGATTTTTCTATGCGCTATAAAATTCTTTAAAATCCGCTATTTTCCAGCTGATTACGCATCTAACGACCTGATGAACAGTTTCAATGG GGGGGGGGGEFFFFFBDGGGGGGGGGGGGGGGGGEGGDGGGGGFEFGFEFEEBEGFDGEEGEGGBEGEBGGDEEEEBEEE?DCDCEE?EECE;CCACCCC? PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1302:16740:19201 147 chrV 6103 60 100M = 5929 -274 CACCTATGCGTCACGCTATGGTCCCGCATATCTTCGCGAACGATTCGGAAGCCATGATTCCCAACTTGAGCGTATGCTTTATGGCGGCAGTGGACCACAG @:CCDDBBDDDB<BDDDDDDDDBBBDCC@CDDDDDDFFFEHHHJHIJJJJIJJJJJIGHJIGIJJJJJJJJJJJJIJJJJJJJJJJJHHHHHFDFDFCCB PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2115:16987:87976 147 chrV 6130 60 43S57M = 5959 -228 CACTTCGCGAGCTTGCCCCCTATGCGTCACGCTATGGTCCCGCATATCTTCGCGAACGATTCGGAAGCCATGATTCCCAACTTGAGCGTATGCTTTATGG ###########################################D@;'/FFF;-(/8(0)B:):9:)8:??*1?DG@C<A<:IEE?@;DBAC?DDDD?@?8 PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1213:12756:79582 165 chrV 7559 0 * = 7559 0 GATGAGGAACGAGCCGTCGCGTCCTTGGGAACTTCATATCTGGAAATCATTTACAAAGATAGCTTATAATAAAATTGAAAAATTTCCTCATAATAACAGT :+1++2+++<)<0B<C2@D)1:0889B3(8?##################################################################### PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:1213:12756:79582 89 chrV 7559 60 100M = 7559 0 GTGATTGTACAGCGACCAGAAGTCCTAGACAATGTCGAAAAGTGAAACCAACTGGAAAAAAACGATAAAAGGCGTATTTAAAAATCTTCTTCCTTCAGAC ########################################################?);?00:*?*DC:):)FA,CBA3A:C<<A2;:<2+B?;A7B?:? PG:Z:SNAP RG:Z:000 NM:i:6 +EAGLE:2:47:13418:12913/1 16 chrV 8644 60 101M * 0 0 CGTCGTCGTCAGGAATTCATGAGCCGTCCCGGTGTCTCGAGCTCTTGTGAGCATACACACAGACACATACAGCAGCAGCCTCCACAACATGCACATATAAA A=6=857::?9AAAAB?????8@=:>5A:?BADADA???5@DA:EEBEFBFBBBACAEA?EEBCBBBABEEFGBGGGFGGGFFEFFDBGGGGFDGFGFGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:47:2986:6932/1 16 chrV 10038 60 101M * 0 0 GAAGATCTAATAGCTTTGTAAAATTGATAATTTATCGTCAAAAATTTGACTTGAAACAGTCTAAATCGTGCAAAATACATACTTTTCTATTGTTTTATCAA EEEEEEEEEEEBBFEBGEEEGEFF?EEGEEGGGGEGGGEGFEEE?EFFCFFFF=FCGFGGGGFGG?GGGGGECCEDEGGFDGDGFFGDGEFGGGGGFFGGF PG:Z:SNAP RG:Z:266-1 NM:i:2 +EAGLE:2:104:13973:5102/1 0 chrV 10071 60 101M * 0 0 ATTATCAAAAATTTGACTTGAAACAGTCTAAATCGTGAAAAATACATACTTTTCTATTGTTTTATCAATTATTTGAACACTTTAAAATTTAATTTAGCTAA FGGGGGGGGGGGEGGGGGEGGFGGG=EFFFEGGFGGGGBGGGGAGGFFGGGGFGGGGGGEGGGGFGFGGGGGGG?DDGEGGBGFGGFFGAGFGGGGFFGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:113:10088:6922/1 0 chrV 10199 60 101M * 0 0 CAAAATGCTGCTGGTCTGGCAAGAATAGGGCTGCAAGACTATTACCGTATTTCCTCTATTAGTCTTGCATGCAATACTAACAGAGGCTGCAAGACTAATTT GGGGFGGGGGGGGGEGGGGGGFFGGGFGGFGGGFDFGEGEGDGGGFFDBFGEGGEE=E?EFGBGBEEEEDFCEEEEEEBDGEE?EEE@ED:@B59ADDACD PG:Z:SNAP RG:Z:266-1 NM:i:7 +BS-DSFCONTROL03:121:D0M8KACXX:5:2313:7454:29242 99 chrV 11315 60 100M = 11637 422 GTCTACGGGAGGGGGATCCTCTTGTGTAATACGTTATTAAATTATGCCTGTCAGAGCAGCAACACACACAGACAAGTGAGTCGTCGACTCAAAAAAAGAA CCCFFFFFHHFHHJJGIHIGIJIICHGGIIJJGEHIIJGGIDHIJGIIGIHHHCEHFFFFFEEEDDDDDDBDBDCACDCDACBBDDDDDBDDDD8>>5?? PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2313:7454:29242 147 chrV 11637 60 100M = 11315 -422 ATGCGGGAGGAAATCGTAGACATCTCAACTGATTTCGCATGGTTAAGAGTGTGCTGACGTCACAATTTTTCTGGGAAAAAATTCCGCATTTTTGTAGATC @DD@BCDDEDDB?=BDEDDDDDDDDCDEDDDDDDFFDDGGHHHHJJJIGHIJJJJIIGGJJGIJJJJIIJJJJIJJJJJJJHJJJJJHHHHHFFFFF@@C PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:5368:22825 73 chrV 11689 60 36M1I5M1I17M40S = 11689 0 GGTGACGTTACAATTTTTCTGGGAAAAAATTCCCCAATTTTTTGCAGATGAAACCGCAATGAGACTTTCTGATAAAACGTCAGTACTCCACACGGCCGAA ++:+AD7D<+A,++AFE:F:,+++2++<:DB4:?)))0*000?'=8=/CFC;@@6@:A6B######################################## PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:5368:22825 133 chrV 11689 0 * = 11689 0 TTTCTCAAAAATGTCACGTCAGCACGTTCTTCATAATGAAAAATCAATTGAGAATCCCGCATTTGTTTGTAGATCTCCGTAGATCAAACCGAAATCGGGC ################################@@DAA>D?@??;)==.)==.7E@8FD@FFFB>BBB::0?01))1)?CF<94BE?E<<FDFDD=?D@@@ PG:Z:SNAP RG:Z:000 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:14381:50677 99 chrV 12587 60 100M = 12708 221 CTCAACATCCTGAAATAAGTTTTTGTCAGTTTGGTCTCCATTTTTTTGTCTGCAAACGATAAAATCTAAAGATCCAAAAATAAAATTAGTTAGTTTTAAC CCCFFFFFHHHHHJJJIJJHHIJJGGIIJHIJJIFHIJJIIJJJJJIJIJJJGIIIGIJ?EEFHGGEFFFFFDCC@CEDDDDDDDEDDDDDED>CDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:14381:50677 147 chrV 12708 60 100M = 12587 -221 TTAAAAAAAACAATGTGACTTGACATCACCGTCTGTGTTCGTCTAATGAAAAACAGCAGACCGAAAAAAAAACGGGTCTGTTTTAATTAAAAACTGATAG :1DB@DCC>@>AADCCA@CC>:>>>22&902?A<?@B@@DAC>:E@;;D@FEEHE>@GEDF;;JJIIGGGGEIJJJIJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:100:2124:19174/1 0 chrV 13308 60 101M * 0 0 TTTGATTTTCCTCTAGAATGTTGCTTCCGTCTCCTCAATCCATTTTCATTCCACATAGATTCTAAAACAGAAAAAAATCGATTCAGAAAAAAGTTAACAAA ?EEDEAFFFFFFGEGGAGDGGGGFGGGGGDEGGGDGGGDDE5EDEEFEAFGGGDDB?GGFGFGDDGGFGA?GGBFCDAEAGEEFBAED?EA>A=ADDAEEG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2305:14519:87038 73 chrV 14262 60 100M = 14262 0 ATATTAGGTCTCCAAATAAGTTCCGGGTCAAAAATCATAACTTTGTTCGCTGCGTATCGATTTTTATGAAATTGTGGGAATTTATGTTATCAACCATGAT CCCFFFFFHHHHHJJJJJJJJIJJJJJHIJJJJJJJJJJJJJJJJJJJJJJJJJHIJJJEHHHHFFFFEDEEEEEABDBDDDDDFDFEEECDDDDDDDDC PG:Z:SNAP RG:Z:000 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2305:14519:87038 133 chrV 14262 0 * = 14262 0 TTCATTTGACAATACTCACAAAATTTTTTTGCCGTCCGAAGTGCCCTAACTCGGAGCCAAATTTTTCAGGCATTTTTCAGATCTCGCTTCTTTTACGCTT DDDDDDEEEDEDC@DDDDDDDDDDDDDDDDDDDDFFFHHHHJJJJJIIGFIJJJIJJJJJJIJJJJJJJJJJJJJJJJJJJIIHJJJHHHHHFDDDFCC@ PG:Z:SNAP RG:Z:000 +EAGLE:1:73:5284:8999/1 0 chrV 14265 60 101M * 0 0 TTAGGTCTCCAAATAAGTTCCGGGTCAAAAATCATAACTTTGTTCGCTGCGTATCGATTTTTATGAAACTTTGGGAATTTATGTTATCAACCATGATCTTT GGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGEGCGGGGGGGGGGFFDGGFGGGDGEDBGGGGGEGGGGCGGGGGGEBFFGF PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:83:17647:3047/1 0 chrV 14268 60 101M * 0 0 GGTCTCCAAATAAGTTCCGGGTCAAAAATCATAACTTTGTTCGCTGCGTATCGATTTTTATGAAACTTTGGGAATTTATGTTATCAACCATGATCTTTCAT =E?DEDE?EDBDDD=DBDBDAAAACDFFFFFDEFF?CDD@DE=?BAA??A=EEEE?FFFF@EFFDBFBEFFEDF=BE?BE=@C?CBE@EEEEBE@EEADDD PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:24:16337:8220/1 16 chrV 14278 60 101M * 0 0 TAAGTTCCGGGTCAAAAATCATAACTTTGTTCGCTGCGTATCGATTTTTATGAAACTGTGGGAATTTATGTTATCAACCATGATCTTTCATTTGACAATAG =DD@ECEBCEC?DFGGFFEFFEE5DEFEDDDGEGGGDGBGGGFFGGEGFGFGGGEGAGGGGEEEE?DGGGGFGGFGGGGGGGGDGGGAGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:7:10444:9975/1 16 chrV 14287 60 101M * 0 0 GGTCAAAAATCATAACTTTGTTCGCTGCTTATCGATTTTTATGAAACTGTATGAATTTACGTTATCAATCATGATCTTTCATTTGACAATAGTCACAAAAT BBEEDEEBEEDBEE:E=EEEEAD:BD?EEAEEEBABEEDBDDDEA?EEDEADBDBDDEBEBEE?EEE==EECA=;=DDB?AEBC=EDDD=DE:EBEDE=AE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:59:15165:16923/1 0 chrV 14304 60 88M1I12M * 0 0 TTGTTCGCTGCGTATCGATTTTTATGAAACTTTGGGAATTTATGTTATCAACTATGATCTTTCATTTGACAATAGTCACAACATTTTTTGACCACCCCAAG EGFGGEGDEDFFFBFGGAGGFGGGG@FFEFGGGAGGEFDGGBGGGG=GEFGFGCGAGFEGGFBGGCEEEE?C@BBAFEEFFFEBFFGDB?=FEDEGEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:42:11999:2677/1 0 chrV 14317 60 75M1I25M * 0 0 ATCGATTTTTATGAAACTTTGGGAATTTATGTTATCAACCATGATCTTTCAATTGACAATAGTCACAACATTTTTTGACCACCCCAAGTGTCCTAACTCGG GBGFDGGGDFAECFEFFGGFFEFDFEFF?EGAFGGGGGGG=EBBBEFFFFABCC=EDFEDEE@EBEFEEDEEEDGEB:?EEEEB=8BB:E5AA@:@@AAAD PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:2:11:9361:9333/1 16 chrV 14441 60 53M1D48M * 0 0 CACGGCAAATTCGGCAAATTTGCCGTGCTTAACAAACTCCAAAAAATGTGACATTTTTTGATGTTTTTTGGAGCACCAAAACTACTGAGTTCTGAACAAAA =CEEDBGFGEBGEEFGEGDEEGGGGDGGGDFEGGGEGFGGGGGGGGGGGGGGGGGE=FGGGGGGFGDGGGGEGAEFGGGGGAGGGGGGGGGGGGFGGGG?F PG:Z:SNAP RG:Z:266-1 NM:i:7 +EAGLE:1:82:11123:16509/1 16 chrV 14444 60 53M1D13M1I34M * 0 0 GGCAAATTCGGCAAATTTACCGTGCTTAACAAACTCCGAAAAATTTGATACTTTTTGATGTTTTTTTGGAGCACCAAAACTACTAAATTCTGAACAAAAAG BCBCACB=EEEAFGFEDFDFGGFFGFFF?FFEBEEADGGDGGGGGFGGGEGBDDGGGF@GDC@C@@5EFFFGFEEGDFFFFEFDFF=EEEBCCCEDGFGDD PG:Z:SNAP RG:Z:266-1 NM:i:8 +EAGLE:2:120:10149:2029/1 16 chrV 17145 60 101M * 0 0 TTTTTTTTGTTGTTTTTTTGTTTTGCGAAAAACTTTTGAAAGTGTGATCCCACGTTCTTTTCTTGTCTGCGTCTCTTTTAAATTTGGGTTCTCTCGATAAA <C<8;AD?ACCC?ACA:AEGFEGDFFBFFFFBEEAAEDDDBGGGEGBFFEFCEAB?FDFGFGGGFAFGDGGGFGFGGGDDDE?FGGGEEFDFFFFFBCAEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:3:16562:7761/1 0 chrV 18570 60 101M * 0 0 ATTTTCAACTCCGGCAAATTGCCGATTTGCCGTTTGCCGGAAATTTTTAGAGAAATTTTTATAAGACGGAAGCATTTAAAGCTATATCATTCGGAAGAATT GGFGGGGGGEGGGGGGGFGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGEBGEGGGGGGGGGF=EEFGGFGGFEGGGGFGGGGEDFGEEGEFGFEBGDDFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:88:4071:9423/1 0 chrV 19829 60 101M * 0 0 ATTGAGTTTTTCTCCCCATAAAAGAAGCGTTGACTAGGAAAAATGAATGCAATTTTTTAGTTAGCAGGTACACATTATTATTCAAAAGTATTTAGAAGTTT EFFFFBBDEECDB>?DDCDDADEE?CCED:DD5DDEF?FE?DEAEFFF:F??:DDFDFDFFF==DCBEEEB?EDEFD=DEFBFDFFFF?FFAFDFD:EB5C PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:42:18060:2997/1 16 chrV 23388 60 101M * 0 0 TTTTTCCGATTTAATTTTTGATAGGTTTTCTCCGCAAATTTTCCACTTCAGTGCATGGCACACAAACGGCATGTTATAGTAATTTTCCAATTTTCCAAAAG FDDECFADDB@FEEGED?EGGGFBEGFG?GEGGFGGFFGFGGGDCGGCGGEFGGDGGGFEGDFFFDGGGGEGGGFFGGGGDGGGGGGGGFGGEGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:13:6904:13626/1 0 chrV 24494 60 101M * 0 0 GGTTTTTCTTGAAATATCGTTTTTAAGGTCAATTGATATGATAATAAAATATATTGTTGACCTTAAAACACATTAAAAAAACTTCGACAAGAACCGACAAA EDEDABDA8BCF=FF=EEEDFFDFFFDA=FFEDEFBFADF:EDEED=FEEEFFD?DAEEB=DEDEFEDFCEABEEFFE?B8CDBFAFDFFFEFEBFEFEDE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:47:11060:17697/1 0 chrV 24606 60 101M * 0 0 CGGTTGAAAACGATAAAGATAAAACATTTCGTAAATATACACAAATCTCGTAAATCGACACATGGCGTTTTTGGCGCGAAAATTCGGCGTTTGAAAAACTT GGGEGGGFAGGGGADGFDDGGGGGGGGGFGGEGEGDGGGGGGDFDGGGFEDGGGFGEFGGGGBF=EE@BCFEFFDFEFEEEEEEGEBAFB=E==BFEDE@B PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:2411:63807 99 chrV 24799 60 100M = 24916 217 AAGAGTACCTAACCAAAGAGCGACTCATCAATTTTCTGAATGAAGAACAACGTGATCCACGACTCAACGAGATCCTCTTCCCATTTTTTGATTCTCAGCG @BCFFDDFFHGHHJJJJJJIJJIIGIGGGHGIJJJJJIIJJJIJJJJJIJJICGGGHGIEHGFHFFFFFDC>BDDCDC@CCCCCDEDDDDBCDDDDDD<@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:2411:63807 147 chrV 24916 60 100M = 24799 -217 AAAAACACGAAAACGACATAAAATATCAAGAAGATGGAAAAATGTCCGGTGACGGTTTTCTCCGATTCCTGATGTCAGACGAGAACCCGCCAGTGTTTCT ?CC?8<<-:BB<?AABA>4DC@::A@@CCAC>:44>(DDDC@5=;??@;;;;8?;)B6/:55()@=)@8)==.))6DB6?990B?JJHHGHHFFFFF@C@ PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:45:11954:18961/1 0 chrX 1563 60 76M2I23M * 0 0 TCACAAAGTTGCAGCTCCGAAAAGAGAATCCGTCTGGAATTCTGGAAGTTCACAAGAATTGTGAGTACTTACCTTTTTCAAGTGAAACTAGAGGAAAAATT GGGGGGGGGGGFGGGGGGGGGGGGFGGGGGG=GGFGGFFGGGGFGEDFBDGFGGGGAGGGFCFEFCDDEEGGGFGFGGEAFFBFCEEFEDDCDGAADEBDB PG:Z:SNAP RG:Z:266-1 NM:i:6 +BS-DSFCONTROL03:121:D0M8KACXX:5:1311:7062:60667 99 chrX 5712 60 100M = 5891 279 AATAAAGTCCTGCCGCGAATGCTTCAAGGTTACTGTAGTTTTTGGTGGTGAGACCCGGAAATTTCTTTATTTTTCAAAAATTTCAGAACCCGGTCATGAT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJGIJJJJHIJIIJJJJIHIJAGIJIHHHFFBDDDDDDEDDDDDEEDDCDDDDDDDDECDDDDDDDBBDDDDC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1311:7062:60667 147 chrX 5891 60 100M = 5712 -279 TCTTGGTGGGTCCCGTCACGAATTTTTGGAAATTATAGTAAAACGCCAATTTCATACTGATTTTGATGAATTTTAACAATAAATTAGCAGTATTTTAAGA DBBDDDDDDDB>DDFFFFHHHHJJIGGJJJJJIJJIJIJJJIHHJJIJJIJJJJIIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1306:15859:17118 99 chrX 5939 60 100M = 6055 216 ATTTCATACTGATTTTGATGAATTTTAACAATAAATTAGCAGTATTTTAAGATTCTGAAATTAATTTTTTACTGAATTTGGCGAAAAATTGCAAATTTTT CCCFFFFFGHHHHJJJIIGGIGIIJJCHHJII@HHIIJIGJJHIIJGICB?GGHIIJGHHJBGEIFIHHJIJJJIJGIJ;@CHD<><?ACCDCACC>@@A PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1306:15859:17118 147 chrX 6055 60 1M1I3M1D95M = 5939 -216 AACCTGGTGGTTTTCGTGGCGGGACCCGGAAATTTCTGAATTTACGCAAACCTGGTCATGATTGTACTTAAATGAAAGCTCCTAGCGAACTGAAATCGAA @CBA@BDDBDDBBB=BDBBBAAADDDDHHGHEGIGIJIIIJIGGGEHHF?IHJIIIJJJJIJJIIIHHDIIIHIIIGJIIJJJJIIHFFHGHFFDFDCCC PG:Z:SNAP RG:Z:000 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:6622:23752 99 chrX 6879 60 100M = 7127 348 TTTTCAAATTTTTTTGGAAGTTTTCCAAAAAATCTCTGTTTTTCCCGCCGCTCAAAACCCTCAATTTTTCAGATTTCCCTGCTGGAAATGCTCGATTGCA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJIJJJJJIJJJJJIJIJJJJEFFDEEEEDDDDDDDEDDDDDDCDDDDEDDDDDDDDACCACCCBBDDDA: PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:77:8575:6989/1 0 chrX 6976 60 101M * 0 0 GCATTGAAATTATCACTGAAGAATTCAAATCTCCAAAAATGACGTCTCCGTTCTCATCGCCATCTACCCGACAATCAATCACTTATATTCAAGCGAAAATC GGGGGGFFGFGGGGGGGGGGGGGGGGGFCGGGGGGFBGFGGFGGEGEFGFEGGEGGGGEGEEEGEEEGGECD@CCFCD@FAECC@CAACECDBCDA?CCCB PG:Z:SNAP RG:Z:266-1 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:6622:23752 147 chrX 7127 60 100M = 6879 -348 CACAATGTCATCGAAACCACTCTCTTAAAACTGCAAATTTCTGGATTTTCGACCTTAAAATTTTTAAAAATTCCCAAAAAATCAAATTTCTGTCAAAATT CEDDDDDDDDDDDDDCDCCDEEEEDEFFFDFFFHHHHHHJJJJJJIJIIHGIJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:118:7183:17666/1 16 chrX 7624 60 101M * 0 0 AAACTTTCTTGGGTTATGAGTCTCAACGTATCCACGTGCATGACGGAAGAATTGGCTCAAATGCTCGCGAAGCTGCTCGGCAGACGTGTAAACGTCCAAAA 9=:?7@?C@CACA?ECCC=CCC:B?5B@BA:A=CCEACDDBEEFFGFBBGGEGGDDGGGGF=EGFGFFGGGGGGEGGBEGGGGGGGGGGDGGGGFGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:2:55:11225:9062/1 16 chrX 7903 60 101M * 0 0 CAAAAAATGAAAATTTGGGCATAGCTTCCGCATCTCCAGTGACAAATGTGCTCTATTGCACAAATTGTTGGTTGGAATACGGTATTTATTGCATGTTTCAG EGEEEEEEEEEADBBDGGFEEEDBEBCEFDGEEGEGGGFAFEEGGGFGGGEGFGGEFGGEGFEEFGFGGGGAGGGGGFGGGGFGGGEGGFGGGDGFDGFGG PG:Z:SNAP RG:Z:266-1 NM:i:3 +EAGLE:2:78:6338:2856/1 0 chrX 7939 60 101M * 0 0 CGGTGACAAATGTGCTCTATTGCACAAATTGTTGGTTGGAATACGGTATTTATTGCATATTTCAGCCGAGAATACCACTATTCAAACCATCAATTTGGATA DDD@DEEEEEGBDEGFGGFGGGGEGGFGEGGEBFEBEFFADDEFFFEEEEEDEEEEEDEEEEGBEEEEEEEEEEEEEEAEEEEEEEEE@EEEEAECCCABE PG:Z:SNAP RG:Z:266-1 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:1115:15278:33162 73 chrX 7942 60 100M = 7942 0 TGACAAGTGTGCTCTATTGCACAAATTGTTGGTTGGAATACGGTATTTATTGCATATTTCAGCCGAGAATACCACTATTCAAACCATCAATTCGGATAGA @@@FDDDDFDDDAGFHJJGIDHICFHEFCBFGGBDA@BDDGEH:?GA>GEFG<?DGHDFGGGGEB<BHHHEEC>DCDEEEFDEE??>CA@A@C@B@DBA> PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1115:15278:33162 133 chrX 7942 0 * = 7942 0 TAATAAGCCACTTTTCAAATAATCGCTGAATTCTAAGTAAAACATGTTTATTTTCAGTATATTTATCAGATTTAAAAAAAAAAGTGAGATTGTGTTAGTT ##########A:3CC;<DC?A?B@CCDCDCC@;C>AB;)7)))3=.7.))=D=.))));=;=)8B<FB89FB(GDHFA@HCA2E4?A+2+3FA+2A+1+1 PG:Z:SNAP RG:Z:000 +EAGLE:1:50:11162:12440/1 16 chrX 7960 60 101M * 0 0 GCACAAATTGTCGGTTGGAATACGGTATTTATTGAATATTTCAGCCGAGAATACCACTATTCAAACCATCAATTCGGATAGAGAAACACACAAGTCACAGA FAEEGGDGFFEGGGGGGGGGGEGGDGDGGFGGGFGEGFGGGEFFAFGGGGFGEGFEDFFFCBGGEFGFGEGEGGFGGGGGGGGGGGFGFGGGGGEGGGEGE PG:Z:SNAP RG:Z:266-1 NM:i:2 +EAGLE:2:103:14619:17650/1 0 chrX 8476 60 101M * 0 0 ATTGTTTAATTTTTCCGGAAAAAAACTGAAAAATCCAAAATTTTTGAATTTTCTTCATAAAAAGTCGGGAAAACCCAGAAATTTTCCAATTTTTTCCGGAA GGGGGGGGBGGGGEGGGEGGFGGFGGGGDGGGGFGGGGEGGFGGGFGGGGGGGGGGGGG?FACEDGGEGDDGBGGGFFFGCFEGGGGGBGGGGGGE?DGEG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:5:12119:5229/1 0 chrX 8820 60 101M * 0 0 TTTCTGAAATCCATAATTTTTCCAATTTTTTTGGGAAAAAATCCAGTAAAAGCCAGTTTTTCGCAAATTTCCATCCAATTTTCACCCTTAACGGCACAACA EG?EGGAFGGGDGDDAGGGDFFFEGGGGFGGEGEEGEGGEGDEGGGFGDFFFFDGGFGAGFDG?GEB?FFGFGGGDDEGEEAFDF5DECE:CE=E=CCECD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:73:11201:4957/1 0 chrX 10521 60 1D6M1I94M * 0 0 GTTTTCCGGGAAAACTGAAAATTTGGTCATAGCTTCCGCATCTCCGAGTGACAAATGTGCTCTATTGTCAAATTGTTGGCAGAAATGCGGTATTTATTCAC GGGGEGGFGEBCECEGGDGGGGDGGGGGGDGGEFGEGGGDGEGGGFFFFFDFFFFGEGFFFGFGGGGEFGBC?DDFFGDFFFAFFEEAEE?ADE=DEEEDE PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:46:5340:5404/1 0 chrX 10534 60 101M * 0 0 AAAGAAAATTTGGGCATAGCTTCCGCATGTCCGAGTGACAAATGTGCTCTATTGTCAAATTGTTGCCAGAAATACGGTATTTATTCACATTTTCAGCCCAA GGFGGDFGDG?F=FFGEEGGEGGGGBCDGEGGEEFEFCFDEEEEBGFGEGGFEFEGGBEFFF@DEFFFDD??BBC???@?EEEEEBBBBBEEEE?EEEEEB PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:2:10:12798:8231/1 0 chrX 10540 60 90M1D11M * 0 0 AATTTGGGCATAGCTTCCGCATCTCCGAGTGACAAATGTGCTCTGTTGTCAAATTGTTGGCAGAAATACGGTATTTATTCACATTTTAAGCCAATTTAAGG GGGGGFFFFFGGGGGGGGGGGGGGGGGFGEEGGGGFGGEGGFGGGGGGGGGGGGGGGGGGGGGEE?EEEEGEGGGGGGFGGGDGGEDGBAEGGEFDGEAGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:113:16640:19734/1 0 chrX 10540 60 90M1D11M * 0 0 ATTTTGGGCATAGCTTCCGCATCTCCGAGTGACAAATGTGCTCCATTGCCAAATTGTTGGCAGAAATACGGTATTTATTCCCATTTTCAGCCAATTTAAGG FGGGGGGFGAFDFFFGGGGGDGGGGGGGGDFEEDBFFFEFGGGGFGGFGGBBGGGGGGGGFBGEEGFFECF??EECCEECEFEEEEE>CB:@BAACEEDEF PG:Z:SNAP RG:Z:266-1 NM:i:6 +EAGLE:1:75:12666:4476/1 0 chrX 10543 60 87M1D12M1I1M * 0 0 TTGGGCATAGCTTCCGCATGTCCGAGTGACAAATGTGCTCTATTGTCAAATTGTTGGCAGAAATACGGTATTTATTCACATTTTCAGCCAATTTAAGGCTG GGGFDGFFFGGGGGGGGGGFDGGGGGBGGGFFFFFFFDGGGGGGFGGFGFGEDGGAEGGGDGGGGGFFEEFFFEDGGEGGGGGGGDFGGEBDFG=EEFFCB PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:56:15981:20326/1 0 chrX 10549 60 81M1D20M * 0 0 ATAGGTTCCGCATCTCCGAGTGACAAATGTGCTCTATTGTCAAATTGTTGGCAGAAATACGGTATTTATTCACATTTTCAGCCAATTTAAGGCTGAAAATG FFFFFEGGGEFGGGGGGGCEBGGGGGDFEDGFFEGFGFGEEEEEGGGEEEBFAEADDBDBEE>EEEEBEE?:???ABA??AAA@AABB?B88A>?BBBB<A PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:26:17260:3333/1 16 chrX 10550 60 101M * 0 0 TAGCTTCCGCATCTCCGAGTGACAAATGTGCTCTATTGTCAAATTGTTGGCAGAAATACGGTATTTATTCACATTTTCAGGCCAATTTAAGACTGAAAATG BB=BB?=B=BB:B=BDCBB:B?BABBCD?BDBAC=BBDCAAA:AD:DCBDBB@?BDA>C:C;C?@;:C?:@CCAC?CA>AA=5BB;:5A?:D=?DDDD5?D PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:2213:8832:90154 99 chrX 11838 60 100M = 12309 571 GTCTCCAGCTTCAAAATGACCCCCATCATGCCCTGTTTCCGTGCAATTTGAAAAATTCGGGTCTCGCCACGCGTTTTTTTTTGCAATTTTCGAACGAACT CCCFFFFFHHGHHJJIJJJJJJJJJJJIIIIJJIJFHIJJIIIIHIIIJJBGGGJJJJFIIEHGEFHFFFDDDD6;@BDBDDDDECDDDDCBBBDDDDBA PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2213:8832:90154 147 chrX 12309 60 100M = 11838 -571 TCAAAAATATTGAAAAGCCACCGATAGAGAGGATTTAGTGTGAAGAAAAAGGGGTGAAAAAACACCGGAATTGGGAGAGATATAGGACACGTCCATATCT 05CDEECD@C:5C>??@BD?@DCCEEEEDDFFCDFHHHHHED@7)JJJIIJJIJIJJIHGIGHGIHGJIJIJJJIGIIIJIGIJIIJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1101:20052:62684 99 chrX 12814 60 94M6S = 12857 139 CTGTATAACAGTGTGTAATTTCAAAAAAATCGGACGCACACACGCTGACTTGTGAGGCTTCAAAAAAAAAGTTGAAATAGTCAAAAAAAAAATCCATCAT CCCFFFFFHHHFHHHIHIJJJJJJJJJJJHGHJIJJJJJJJJIHIHHHFEFFFFDEECDDDDDDDDDDDB>:CCC@CACC:CCDDDDDDDDD<A###### PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1101:20052:62684 147 chrX 12857 60 4S96M = 12814 -139 CCACGCTGACTTGTGAGGCTTCAAAAAAAAAGTTGAAATAGTCAAAAAAAAAATCCATCATTTTTCTGCCCAAAAATTGAAAAAACGGGCACCTATGCAC ####CC@::<DCDCCCA>>:8-BDDDDDDDDCCA>DDC:C><=DDFHHGFG@IGGJJJJJJJGHEIGIIHBIJJJJIIIGJJIHGIIHHHFHFFFFDB@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:61:3791:13082/1 0 chrX 13027 60 101M * 0 0 AAAATATGAAAATGTGATAGAGTGAATCATTGCGATTCCAATGAGGTAAAAAACTTGGCAAAATTCGACAAAAATTTCATTTTGACACTAAACACTTTATT GGGGGEFE?GEEDBEEEEEEFGFGGEFFEADGGGGE?GFFGGFGGGDGFGFFGFFFFBGGBFEEFGGGFGGDGEEBGEEEFFGDBEBGFEGFEEEGEEBGD PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2313:12490:88378 99 chrX 13038 60 100M = 13177 239 ATGTGATAGAGTGAATCATTGCGATTCCAATGAGGTAAAAAACTTGGCAAAATTCGACAAAAATTTCATTTTGACACTAAACACTTTATTCAAAACACTA CCCDFFFFHHHHHJJJJIJJJIJJJJJJJJJJJJJHIJJJJJJJJJJJJJJJJJI7FHJJJIJJHHHHHHHFFFFFFEEEEEDDDDDDDDEEEDDDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2313:12490:88378 147 chrX 13177 60 100M = 13038 -239 TATTTCTCAAAAAAGATTATCTTAAAATGTTGAAAATGATTATCTTAAAGATTATCTTAAAATGTTGAAAAAAAAAACACCGACTACCGTAACCCAGAAC @DCCBB?BDDDDDDDDDDDCDCDDDDCDDDDEEFDCCCDDDDDEEDEEECEFFFEFFHHHHEAGIGGJJJJJJJJGGGFJIIIIHGJHHHHFFFFFFBBB PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:84:6328:7727/1 0 chrX 15454 60 49M1I37M2I12M * 0 0 CAGTAACCTGACGCTGAATTTCGCGGCGAGACCCAAAAATTCCGAAAAAACCATCAAAAACAATCAAAATCTGCCAAGAAGGAAGGGGGTTTGATTTAAGT GFGFGGGGGGEGGGGGGFDFGGGGBGGFFBEGEGBGGGFBBGFEDGFGBG?GGEFFGGGFGEE7EBDEFDDDECFEECEE@EACCCCCC6:AA@:AC?C@; PG:Z:SNAP RG:Z:266-1 NM:i:5 +BS-DSFCONTROL03:121:D0M8KACXX:5:1205:12522:62956 99 chrX 21169 60 100M = 21409 340 GTATAATCATGACTAGGTTCCGGTAATTTCGGAAAATATTGGGTCCCGAAGCGAAATTCCCCGGGTTACTGTAGGCCTTCGCGGCGAGACCCAAAAATTT @?@FFFFFHHHGHJIJJCFIIJFIJIGIJIIGDGGIFIIJGIJDFHIIBG>HEDGHFHFFFFDDBBBDDDCCC>C>>CAC@BB9999>09@ABBDDA<:> PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1205:12522:62956 147 chrX 21409 60 100M = 21169 -340 ACCTAAAATTTCGCGAGAAATTCAATTTTCAAGCGAAAAATTTTAATGTCCGAACGCAGATCGTCGAGAGCTTTCATTTAAGTATAACCATGCCTTAGTT CCC@DC@B>@@BB?<ECCA@>>CCCADDDDDDBEEFCEAEECDJIIGHGGIHF?GEGJIIEIHD<EBGFGIIIHIJ@GGIJIIIGBAGGHHGFFFFFCB@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:18264:40909 99 chrX 23955 60 100M = 24075 220 ACCGTAACCCGAAATGTTCAAAATTTCGCCGCGCCGGGGGTGAAAAATGACGGAAAAATTGAATTTCGCACTACTTTTTGCGTATTTCGATTGGATTTCG CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJHFD=@DDDDDDDDCBDDDDDDDDDDDDEDDDDDDDDDDDEDDDDDDBDDEEDDDDDDACDDDA PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2112:18264:40909 147 chrX 24075 60 100M = 23955 -220 TTCTTAATTGGCGGATATTCGACTTTGAGCGGATTTGAGGTTCTAACAATATCAGAGTCGGCGAGCGACAGCCGCGAGAAGTTGTTCCAGTCTTTGTGCA CCACDDDDDDDDCCEDDDDDCADDCDDDDDDDDDDCDDDDDDDDDEEFEEECEEDFFEGJJIJIJIIIJJJJJJIJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:62:3773:4884/1 0 chrX 24873 60 101M * 0 0 CCCGAAAATTTGAAAATGTCCGCTAGAGACCCGGTAAAAAGACGTTCTAATGTGAAATTTGGCGAGGAATTCGAATTTCATATTAAAATATGTTAACATCA GGGGGGGGGG?FFEFEGGFGGGGFGF?DFFFFFFCGGGFGGEGFEAEEBEDFCEBEEDDE5BEECCEACCCDECAEEEEEECDEEBEDCCACACCEEE@EE PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:2:111:17901:21150/1 16 MtDNA 148 60 101M * 0 0 TAGGATTATTAGATATATTAATATTGACCCTATAAAAAGAAGTTTTTTTCTTATCTTTTCACTACTTTTTAGTATACCAGTTATTTCAATGAGAATACATA CB???CA=AC=BBCADBDC?B?B?BA5DCAA8C?ADDABDC?CAACDDDDBDDDDDDADDBD=5DDDDBDDCDDDBDDDDDDDBDD=DDBD:DDDB>AACC PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:24:11474:6931/1 16 MtDNA 422 60 101M * 0 0 GGTTTAAGAGGTTTTTATTATAGTATTTACTGGTTTATTTTTTGTTTTATTTTAGTATGTTTATTATTTTTTATAAATTTTAGTAGTTATTTTTTACATTT DCCCA5:DDBC>BCD5D:DD=:D6DDDDBDD?CCCCACCCCCDC<CC>B=DDDBDDCDDDDBCCCC<CBDBDADDDD=::D=EED@CBBBE:DBDD5CC@A PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1215:12199:50114 99 MtDNA 542 60 100M = 651 209 GTTTAAAATTATGTTTTTATTTGTTAGATTATTTATATTTATTTTTAAATGACAACGTTTAATTTTTATTCTAATTTCTTTAGAATTTATAATGTTGAGA @@CFFFFFHHHHHJJJJJJJJJJJJJJGIJJJJJJJIIJJIIJJJJJIIJJIIIHIIIJJJIIJIJIJJJHJJIJHHGIJJJIDFHHGFHFDEFFFFEC= PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:37:4190:5792/1 0 MtDNA 597 60 101M * 0 0 CGTTTAATTTTTATTCTAATTTCTTTAGAATTTATAATGTTGAGATTATTTTTAAAATTTTCTTATGTTTTAGGGGAAATAATGTTTTTTTATTTTATGTG GDEGGGGGFGGGEFGGFGFGGFGGGEGEGGGGGGGDFGGFGGEFGGGEFGGGGGGGGGGEGGGEEFGEGGGGGGGGEEEGEDGG?EEEAAE7EEEC?EFAA PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1215:12199:50114 147 MtDNA 651 60 100M = 542 -209 AAATTTTCTTATGTTTTAGGGGAAATAATGTTTTTTTATTTTATGTGTTTTTCTGTTATTTCAAGAATCCTGGGTATGGTAGTTATAGTAGGTAATATAA ADCCDDDCDDDDDDDDDDDDEEDFDEFFFFHJJJIJJIJJJJIJJJJIIHJIIIJIIGIGDIJJIJIGIJJJJJJIJJJJIJJJIJJHHHHFFDDFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:51:1652:7346/1 16 MtDNA 726 60 101M * 0 0 ATGGTAGTTATAGTAGGTAATATAAAATTTTTTGGTAGTGATAATTGTATTTTTTAGTAACAGATATAAGTTAAGTTTAAACTATTGATCTTCAAAATCAA BEEFEFEEEEBEFBFEEEAFEFFEFFAFFF?EFFFFFFEFFFFFFFFFFAFFFFBFFEFFEFFFBFFEFFEDEDFDFAFFFFFFFFF?FFEFFD?FEFFFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2207:3477:80131 99 MtDNA 800 60 100M = 937 237 GTTTAAACTATTGATCTTCAAAATCAAAAATTTATTTCTGTAGAGATAATAGTATAAATAAGTATGTTTCTTTTTCGCAGAAATGGTTTTTTATCTTATA CBCFFFFFHHHHHJJJJJJJJJIIJJJJJIJJJIJJJJJJGIJJJJJJJJJJIJJJJJJJJJHFHIGIJJIJJJJJIIIIIHHHHHFFFFDDDDDDDDCD PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:77:16898:20473/1 0 MtDNA 800 60 101M * 0 0 GTTTAAACTATTGATCTTCAAAATCAAAAATTTATTTCTGTAGAGATAATAGTATAAATAAGTATGTTTCTTTTTCGCAGAAATGGTTTTTTATCTTATAA ECEE?FFFFFGGGGGGGGGGFGGGGGGGGGGGGFGGGFGGFFGEFEGFEGEGFDGEEFGEEGEEEEEEFEFGEFEEEEBG?ACDEFBDDEEDCB=FEEFEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2207:3477:80131 147 MtDNA 937 60 100M = 800 -237 TAAGATGATTTAAAATGTTATTATCTAAATTTGATTTACAGAGTAGGCAATAAAAATTTACCTCGGCAATTTATCGCTTGTAAAATACTTGTTCCAGAAT DDDDDCCECDFEEDEEEEEEFFFFFFFHHHHHHJJJJJJJJJJJIIIHIGJJJJJJIHF?IJJJJJIJJJJJJJJIJJJJJJJJIGCHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:46:4245:14190/1 16 MtDNA 952 60 101M * 0 0 TGGTATTATCTAAATTTGATTTACAGAGTAGGCAATAAAAATTTACCTCGGCAATTTATCGCTTGTAAAATACTTGTTCCAGAATAATCGGCTAGACTTGT CGBEEDEDEFEGEGEGEDDGFEEBDGGGDBGEE@EFGGGGGGFECEGGGGEBFFGGFGFGGGGGGFGGDGGEFFFFEBGGFGGFFEDFGGGFGFGEFGGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:27:7941:4769/1 16 MtDNA 1010 60 101M * 0 0 TCGCTTGTAAAATACTTGTTCCAGAATAATCGGCTAGACTTGTTAAAGCTTGTACTTTAATTGATGTTAATTATGAAATTATTATATTTTCTTTTAGATCT CG?BGGGAFGFDDCFBGGGFFEGGGGDGGEFGEGFGGGGGGGFGFGGBEGGFFDADGGEGGGGGGDGGGGGGGGGFGGGFGGGGFGGGGFGGGGGFGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:84:2306:5557/1 16 MtDNA 1132 60 101M * 0 0 TTAGTGAATTTTCATAATTTTAAGATTTGTTGAACAAAGCAGATTAGTACCTGGTTAGACAAAAATTAAAAGAGCAGGAGTAAAGTTGTATTTAAACTGAA CCE?EEACBBEBFFFBEEE5EABF?FFEFFFEDAE=EFFECEDEEDDD@DDEEEDDDECFFFFAFFDEBE?DFFDFFFFFDDEEDA=EEEED:DDDEEBEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:111:11302:7630/1 16 MtDNA 1137 60 101M * 0 0 GAATTTTCATAATTTTAAGATTTGTTGAACAAAGCAGATTAGTACCTGGTTAGACAAAAATTAAAAGAGCAGGAGTAAAGTTGTATTTAAACTGAAAAGAT AEEAEE:EAECD?BB?DGGGAGDFAGGDDGGGGGGGFF:FFGGDGGEEEDEAGGEGGGFGDGEFDGGAFGFFGFGGDEDGGGGDDGGAG=GGGGFGEGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1205:2947:30776 99 MtDNA 1208 60 100M = 1331 223 GGAGTAAAGTTGTATTTAAACTGAAAAGATATTGGCAGACATTCTAAATTATCTTTGGAGGCTGAGTAGTAACTGAGAACCCTCATTAACTACTTAATTT BCCFDDFFHHHHHJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJIIIJJIJJJJJJJJJJJJJJJIJFFHHIIJJIHHIJHHHHFFFFFDEEDDEDEDEEE PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:43:15776:12730/1 16 MtDNA 1242 60 101M * 0 0 GCAGACATTCTAAATTATCTTTGGAGGCTGAGTAGTAACTGAGAACCCTCATTAACTACTTAATTTTTTGACTCGTGTATGATCGTTTATTTTATTCTTAA EDDC:EDDCEBGEEEEDEEEEEGFGEEEGGGEFGGGGDGFGFFACEAGGDFFFECFGCGEGCEGGFEF?GDGGGFGGGGGGFFGGFGDFGGGGGEGGGDGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1205:2947:30776 147 MtDNA 1331 60 100M = 1208 -223 TTTTATTCTTAAGGATTATAATAAAAAATTTTTAATTTATTAAAATAGATATATACCCGGTTTATGATTTAAGAAACATTTGGCCTACAATATTTTATAT @DDDDCDACDDEDEFEEEFFFFFHHJJJIJJJIJJJIIJJJJJJJJIIHDJIGD?JJIJJJJJJJJGJJJJJJJJJJJJJJJJJJIHHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1208:16741:52367 99 MtDNA 1375 60 100M = 1446 171 ATAGATATATACCCGGTTTATGATTTAAGAAACATTTGGCCTACAATATTTTATATTATGGATTTTAGTTTTAGTTAACTAAATGAAATTGTAAAAGACA CCCFFFFFHHHHHJIICHHJJJIJJJIIGIJJICHJJIJGJGIJJJJEHIJIHIJJIIIIIJJIIIJJFHIJJIDCEEEHHHHFFFFFFEEEEECECBDC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:51:9770:4736/1 0 MtDNA 1428 60 101M * 0 0 TATTATGGATTTTAGTTTTAGTTAACTAAATGAAATTGTAAAAGACAGTAAAAAATTCTTAATGTATTTTTGAAGATTATCTAGAAGTGGTACAAATCATC FFEEFDFDFFFFFDFBD5DDEEEEEEEE=EEEEEEEEE?EEEEEEEEEEEEEEEBCEEEDEEDEEEEEEEEDEABEDDEEEEEDEEEBEEDEEEEEAEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1208:16741:52367 147 MtDNA 1446 60 100M = 1375 -171 TAGTTAACTAAATGAAATTGTAAAAGACAGTAAAAAATTCTTAATGTATTTTTGAAGATTATCTAGAAGTGGTACAAATCATCCATCAATTGCCCAAAGG DDDEEECEEEFEFFFFFFFHHH@FFHJJJJJJJIIJJJJIJJJJJJJIIIJJIJJJJJJJIJJIGIJJJJJIGGJIJJJJIIJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2306:21063:70183 99 MtDNA 1578 60 96M4S = 1595 108 ACCTGAATCTAGTAATAAAACTATTTTTAAATATGTTTTGAAAACATGTTTTGAGGTAACTCGTAGTTTTTAAGAGTTAGTTTAATATAGAATTGTTGAT @CCFFFFFGHFGBGGGHJGFHIHGIJJICGHIEIHGIJGIFDDDGHIG@D?FEHHIHHHHIJGGB@CF@GC@DHE3.?EHHHCF7@37.6>6>>;@#### PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2306:21063:70183 147 MtDNA 1595 60 9S91M = 1578 -108 CTAGTAATAAAACTATTTTTAAATATGTTTTGAAAACATGTTTTGAGGTAACTCGTAGTTTTTAAGAGTTAGGTTAATATAGAATTGTTGACTGTTAATC #########@B>67;3@;B?<HC;==JJIHGGFFHF=89B@GGHFB8DBB?8)?*C<>JIIIGFC9A2?C<++JJJJIIEIHFC;EJHHHHHFFEDDBB@ PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:62:8987:8931/1 0 MtDNA 1620 60 101M * 0 0 AACATGTTTTGAGGTAACTCGTAGTTTTTAAGAGTTAGTTTAATATAGAATTGTTGACTGTTAATCAAAAGGTGTACCTCTTAATATAAGAGTTTAGTTTA GGGGGGGGGGGGGGFGGGGGGGGGEFGGGGEGDGEFFFDFGGGGGGGGGGGGGEGFEGGGEFDFGGFFFEFFAFECEEEFEGEEGEGEEGBFBEEEDCDEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:58:15307:9170/1 0 MtDNA 1657 60 101M * 0 0 GTTTAATATAGAATTGTTGACTGTTAATCAAAAGGTGTACCTCTTAATATAAGAGTTTAGTTTAAGTTAAAACGTTAGATTGTAAATCTAAAGATTATTGC DBDD:CDCBCEBAEEEC=EEEBCBBB=BBB@>>CC5C>AA?>>;>@@FBD@@E:B@@@BB@@5B?B>BBBAAA:A@BB@@@D@@@@@A?BA?@>@@@@@@? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:87:9699:18394/1 16 MtDNA 1707 60 101M * 0 0 AAGAGTTTAGTTTAAGTTAAAACGTTAGATTGTAAATCTAAAGATTATTGCTCTTGATAATTTTAGTTTTACTTATAGTTATTTTAATGATGATTTTTATT BEFGEBEEGEEEEEEGBEGGEEFGEGGGGGGGGGDGFEGEGGGGGFDGGGGGGGDGGBGGBGGGGGFGGGEGGGEGGGGGGGGFGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:100:3634:12538/1 16 MtDNA 1809 60 101M * 0 0 TTCAAAGAATCGCTTTTATTACTCTATATGAGGGTCATTTATTGGGAAGAAGACAAAATCGTCTAGGGCCCACCAAGGTTACATTTATGGGATTAGCACAA EA=EE??ED:EA<?:A=EED5EEE=E<<>B>8;;9?EE?EEEEEDDDEAEEEBEDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA?FGGGGDDGEGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1111:21372:42529 99 MtDNA 1832 60 100M = 1878 -100 CTATATGAGCGTCATTTATTGGGAAGAAGACAAAATCGTCTAGGGCCCACCAAGGTTACATTTATGGGATTAGCACAAGCTTTATTGGATGGGGTTAAAC @B@FFFFFHHHHHJIIJFHIIJJHGIIHHGJJJJJIIHGHIIJJJBFHJIFGGFHEIHIIIHHACHHFEFFFEEEECEBBCDDCDDDCCDDD@DBB?CAC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1111:21372:42529 147 MtDNA 1878 60 46S53M1S = 1832 -100 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCACCAANGTTACATTTATGGGATTAGCACAAGCTTTATTGGATGGGGTTAAAN ##############################################IHGFF?0#IIGEIIJIIJJJJJIIIJJJIIJJJIHHHHIJJHHGHHFDFDD=1# PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1109:13191:17203 99 MtDNA 1898 60 100M = 1981 183 GGATTAGCACAAGCTTTATTGGATGGGGTTAAACTTTTAAAAAAAGAACAAATAACACCCTTAAATTCCTCTGAAGTATCATTTTTACTTGTACCAGGAA BCCFFFFFHHHHHJJJJIJJJJJJJJJJFHIJJJIIIJIIIJJIJJJJJJGIIJJJJJHHHFFFFFFEEEEEDEDDCDFEEEEEEDBDDDDDCEDDDDD< PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:73:15682:20928/1 0 MtDNA 1914 60 101M * 0 0 TATTGGATGGGGTTAAACTTTTAAAAAAAGAACAAATAACACCCTTAAATTCCTCTGAAGTATCATTTTTACTTGTACCAGGAATTTCTTTTGTTGTAATA GGGGGGGGGGGGEGGGGDGGGGFGGGEGEGEGGEGGFGFGGGGGBE?GFFEEGEGEECEC=CCCCEEEEECC@D?ACEC:CDACCEEEEEEE;EE6<AA?? PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2108:8075:44880 99 MtDNA 1923 60 100M = 2060 237 GGGTTAAACTTTTAAAAAAAGAACAAATAACACCCTTAAATTCCTCTGAAGTATCATTTTTACTTGTACCAGGAATTTCTTTTGTTGTAATATATTTAGA @@@DDDFFFHHFHGIIJJIJIGGIJJJGIIIIIDIIIDGEHIGEGGIECHHFHACFHIIIIJGIFFCEEHEFFE>;ACECCCACBCBDDDDDFDDEDDDA PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:64:1358:10984/1 0 MtDNA 1931 60 101M * 0 0 CTTTTAAAAAAAGAACAAATAACACCCTTAAATTCCTCTGAAGTATCATTTTTACTTGTACCAGGAATTTCTTTTGTTGTAATATATTTAGAATGATTTAC GGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGFGGGGGGGFGGGGEEGGEGGEEEGEGGEGGAEF@D@CDDE@FDFEDDDDE@EEC?@ PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2301:3386:87325 99 MtDNA 1965 60 100M = 2135 270 CCTCTGAAGTATCATTTTTACTTGTACCAGGAATTTCTTTTGTTGTAATATATTTAGAATGATTTACGTTACCATATTTTTTTGATTTTATTAGTTTTGA CCCFFFFFHFHHHIJJJJJJJJJJIIJJJJJJJJJJJIJJJJIJJIJJJJJJJJJJJJIJJIJJJJJJJJJJJJJIJIJIIHDDBECEDECDCDCDDDD< PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1109:13191:17203 147 MtDNA 1981 60 100M = 1898 -183 TTTACTTGTACCAGGAATTTCTTTTGTTGTAATATATTTAGAATGATTTACGTTACCATATTTTTTTGATTTTATTAGTTTTGAGTATTCAGTTTTATTT DDCCDDDDDCDDDDDCEEDDEFFDBHFHEHHHJJJJJJJIJJJJIHFGHFIIIHGJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:118:10385:6513/1 16 MtDNA 2048 60 101M * 0 0 GATTTTATTAGTTTTGAGTATTCAGTTTTATTTTTTTTATGTTTAATTGGATTTTCTGTTTATACAACTTTAATTAGCGGTATCGTAAGAAAATCAAAATA DEEFGGFGABGGEEFGEGGFGEGGGGGGGEGEAGGEFGGGGGDGGAGGGGGGGGGGGGGGGGFGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2108:8075:44880 147 MtDNA 2060 60 100M = 1923 -237 TTTGAGTATTCAGTTTTATTTTTTTTATGTTTAATTGGATTTTCTGTTTATACAACTTTAATTAGCGGTATCGTAAGAAAATCAAAATATGGTATAATTG >>CCDCEDCC@CCDDDCDDBDEGHHHHHGCGGHIGHGGIIHEIGIGHGIFHHIGGHIGIIH@GIIHGGGGHJIIIJJIIHEA4IIIIFHHHHFFFFF@CC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2301:3386:87325 147 MtDNA 2135 60 100M = 1965 -270 AGAAAATCAAAATATGGTATAATTGGGGCCATCCGTGCTAGAAGACAAAGAATTTCTTATGAAATTGCTTTTTCTTTATATGTTTTGTGTATTATTATTC CCCEDDDDEEEDDCCEEEEECCBFFHHHHJJIIJJJIIJIJJJJIJJJJJJJJJJJJJJJJJJJIHGJJJJJJIJJJJJJJJJJJJJHHHHGFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:44:5556:17346/1 0 MtDNA 2177 60 101M * 0 0 AGACAAAGAATTTCTTATGAAATTGCTTTTTCTTTATATGTTTTGTGTATTATTATTCATAATAATGTTTTTAATTTTGTTTCAAAATTTAATTTGAGACT FFEGGGDFGGGGGGGGDGGGEGEGGGEDGFFGFGGFGFDGGGEGGEDFGGGGGG?GGGGEDEFGGGEGGGGGGGGGFFGEGGE?EGEFGGEEGGDFBBAGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:90:16871:20538/1 0 MtDNA 2198 60 101M * 0 0 ATTGCTTTTTCTTTATATGTTTTGTGTATTATTATTCATAATAATGTTTTTAATTTTGTTTCAAAATTTAATTTGAGACTTTTAATTATTTACATCCCATT FGGGGGEGGGGFGGGGGGGGGGGGGGGGGGGGG?GFGGGGGGFGGGGGGGGFGGGGF?GGGGDGDGGGEGGEFGGEGEGGGGGACGGGGFGDGGGFGFGFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:1:15979:20440/1 0 MtDNA 2341 60 101M * 0 0 TTTTTCTGAAGGTGAAAGGGAGTTAGTTAGAGGATTTAATGTGGAGTTTGCCAGAGTAGCTTTTGTTTTATTATTTTTAAGGGAATATGGAAGATTAATTT GGGGGGGGEFGGEGEEFEEEFFFFFFFFDFFGGEGGGGDGGFGFEFEFFFGGDGDGCEGFGDGGGEEGGEGG=FGGEG?AGGG?DAEBEE=CFAEDDDDEG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:8192:26387 99 MtDNA 2360 60 100M = 2687 427 GAGTTAGTTAGAGGATTTAATGTGGAGTTTGCCAGAGTAGCTTTTGTTTTATTATTTTTAAGGGAATATGGAAGATTAATTTTTTTTAGGGTACTTTCTT B@BDFDEEHGHHHIFHIJIIIJBHHFHGFHIJJIIFHCBHGIJJJJGIJJHHJIJJJJJIEIJIEBGHIJJHHGEGHIEGGHGHDDDBCDD>CDDEEDC@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:86:11924:13707/1 0 MtDNA 2394 60 101M * 0 0 GAGTAGCTTTTGTTTTATTATTTTTAAGGGAATATGGAAGATTAATTTTTTTTAGGGTACTTTCTTCTGCTATATTTTTTAAATTTTCAATTTTTATAGCA GGFGGGGFGEFGDFGGFGGEGGGGGGFGGGEDFFGFDDEFGGGFFGGGGGGGGEGDFAFFFGGGGGGEGGEDFDDGGGGGEEEEGFGGEEEGEFGDC:=F5 PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:23:12390:3932/1 16 MtDNA 2447 60 101M * 0 0 AGGGTACTTTCTTCTGCTATATTTTTTAAATTTTCAATTTTTATAGCATTTAGTATTTTTTCATTATTAATTTTTATTCGTAGTTCATACCCTCGTTATCG @A?A?:EE:?E==FGBDGEEGFFFB?DFBDEGG:FD>EGGBFGGFEFFGGEG@GEEFFE:BGFDFG?GDFGEGGGEEFFFEEF?FFEE@BDDFDFFDFDFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:69:4343:18981/1 0 MtDNA 2510 60 101M * 0 0 TTATTAATTTTTATTCGTAGTTCATACCCTCGTTATCGTTATGATTTAATAATAAGTTTATTTTGATTTAAACTTTTACCAATCTCTTTAATTATATTGTG EECCCDDEEEFFEEECDDADEEEEDFGGFFGGGGAGGGGFEEE:EEEEEEF?GDDGEGGGGGGDGBFGDFFEGGGFGBGCDDFDFGEDGGAGGAGBFEBE? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:106:17241:4836/1 0 MtDNA 2631 60 101M * 0 0 ATTATTAATCAAGTTTATTTTTTAGACATTTTTATATTTGTTTTTGTTTTACAATTTTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAA GGGGGGEEFGGGGGGGDGGGGGGGEGGGGGGGGAFGGFGEGDGGGFFGGFFEFGGGGGGDGGFFGGGGGFDGG?ACEEFFGDGEDFDD=FBAEEEFBF?FF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:118:1597:14954/1 16 MtDNA 2633 60 101M * 0 0 TATTAATCAAGTTTATTTTTTAGACATTTTTATATTTGTTTTTGTTTTACAATTTTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAAAT FGGGEEGGBECG?GEGGGGGFGGBGEGGBFGGGEFGGFFGEAEDAEBGDGGGEGFGGGGFGGGBGGEEGDFGAGGFGFGFDFGGGEGFGEGGGEFGDGAGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:30:9587:17311/1 0 MtDNA 2647 60 101M * 0 0 ATTTTTTAGACATTTTTATATTTGTTTTTGTTTTACAATTTTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAAATTTCTTAATAGGTTA GGGGGGFFEDGGEGEGFGGGGGGGG;EEEEFGGGGGGGEGGEGGEEGFGEGGGGEGDGDGCCEEBFDFFFGGGDGGGGGGFGGDGGGFGGFGGGGGGFDGC PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:90:16079:8007/1 16 MtDNA 2653 60 101M * 0 0 TAGACATTTTTATATTTGTTTTTGTTTTACAATTTTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAAATTTCTTAATAGGTTAGTAGGA GEEBEA5GFGGGGGAEGGGGGGGGGFGFDFGGGGCGDG>GEGGFGGAGGGGDFDGGGGGFGFFFFBFFFDFGGGGFGGGGFGGFGGG?GDGDDGGGGEGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:48:1800:14293/1 16 MtDNA 2661 60 101M * 0 0 TTTATATTTGTTTTTGTTTTACAATTTTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAAATTTCTTAATAGGTTAGTAGGAGTATTTAG FFDFBAC?ACC>E5FFFFFFFEFACCACE?C@ADE=FEFFFFFDFFFDFFFFFFFFFDEBFFFFFB?FFDF?F=ADFFFFFEEAEEDEEEFEFABDGGDG= PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:83:16330:7076/1 16 MtDNA 2681 60 101M * 0 0 ACAATTTTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAAATTTCTTAATAGGTTAGTAGGAGTATTTAGATATACAAATACTTTACCAT BEE@@<AC??C>>?FD:FCFFBFEFDFFFDFFBFFFBFFFF=FFBFFFFFFFDFBFFDFFFD=D=:FFDEFFFDFF?FFFFE=EEDDDEEEC@?ACCCBD= PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:8192:26387 147 MtDNA 2687 60 100M = 2360 -427 TTTGTTTTATTTTAAAGAAAGTATATTAAATACTTTAGTGAAAAAATTTCTTAATAGGTTAGTAGGAGTATTTAGATATACAAATACTTTACCATTAAGG ECDEEFFFFFFHHHHFGHJIIIGHEEIJIJHHJIIJJHGJJJJJJJIIJIIIJJJJIIJIJJJJJJJIFIIIIJJJIJHJJJJIHFJGHFFHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:23:17204:14243/1 0 MtDNA 2720 60 101M * 0 0 TTTAGTGAAAAAATTTCTTAATAGGTTAGTAGGAGTATTTAGATATACAAATACTTTACCATTAAGGTCAGTAATTTCTATTTTTACTTTTATTGTTCTTT ;;;9;:===:C;CCA=?DDDDDDDD6>C>>@@??B:D=DDDDDDDDDDD=DDDDDDDDDDDDDDD=DADDDABBBDDD=5DCD?C<DD?:DDDCCB=DCDD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:42:2835:3423/1 0 MtDNA 2726 60 101M * 0 0 GAAAAAATTTCTTAATAGGTTAGTAGGAGTATTTAGATATACAAATACTTTACCATTAAGGTCAGTAATTTCTATTTTTACTTTTATTGTTCTTTTAACTT @C@@=AAACCEDDEED?A=?C?A>C>AAABCDDDD=CCCA:AA?CDDDDDDABDBDDB?DC=C@??ACDD:CA9ABDC=>CCCDD=D8>BBBBBDC5BBCD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:73:15087:6864/1 0 MtDNA 2787 60 101M * 0 0 TCAGTAATTTCTATTTTTACTTTTATTGTTCTTTTAACTTGTTGTTTTGGAGGTTATTTTACTTACTCTTTTTGTCCTTGTGGAATGGTTGAATTTACTTT ==?;B;C>=;CC?CC?>:8CA=?C:;==CBD?DDCB?B?DDBDD@ABA>ABDDBBCDAD>>CDDCDCDDDCD@A>>CDDDCDA5BC=D5DDB:B5@=>CCD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:41:4283:1044/1 16 MtDNA 2804 60 101M * 0 0 TACTTTTATTGTTCTTTTAACTTGTTGTTTTGGAGGTTATTTTACTTACTCTTTTTGTCCTTGTGGAATGGTTGAATTTACTTTTGTTTATGCTGCTGTAG FBCCFDEEGEEAEGEEEEFEGEGGGFGFGGGGGFFFAGGGGFFCFFDEGGGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGFGFGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2212:11575:96550 99 MtDNA 2839 60 100M = 2949 210 GTTATTTTACTTACTCTTTTTGTCCTTGTGGAATGGTTGAATTTACTTTTGTTTATGCTGCTGTAGCGTGATTAAGTACTTTGTTAACTTTTATTTCAAG @@@DFFFFHHHHHGIGHIIJJJIIIJIIDHGHDHHGEGHIEIJJIGIIIJGHGGGIIIGEEHEDGGI<AAHHIIFHHFHFHG>DFD;7>CEECACDCDCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:83:6736:2885/1 0 MtDNA 2866 60 101M * 0 0 GTGGAATGGTTGAATTTACTTTTGTTTATGCTGCTGTAGCGTGATTAAGTACTTTGTTAACTTTTATTTCAAGAGAAAAATTTTCAGTTTATATAAGAAAA EEEEEFFFFDDGEGFGGGGGGGGFEEEEEGGEBGEGEEFGGEGEEEEEBBCEDEEEEEEEEEEGEEEEEEEEEEEGEBEEEEEEEEEEEEEEEEDEEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:62:11372:10324/1 0 MtDNA 2896 60 101M * 0 0 CTGCTGTAGCGTGATTAAGTACTTTGTTAACTTTTATTTCAAGAGAAAAATTTTCAGTTTATATAAGAAAACCAGGAGACACATATTTGAAAACTCTTAGA F?FFBDB?=D@:@@@CC:>5:;A;;DC>DDDD:ADDA@>B=DA?D?DDC@>=?AD?DBCBBDDCDBCBDB>>DA=??5?B?C?@?@=>@CBBBBC=>@>>B PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:91:13282:2427/1 16 MtDNA 2915 60 101M * 0 0 TACTTTGTTAACTTTTATTTCAAGAGAAAAATTTTCAGTTTATATAAGAAAACCAGGAGACACATATTTGAAAACTCTTAGAATGCTATTAATTGAAATCG CEEEEEEEEEEEEEEEEBBEEEEEEEEEEEEGGEEGEGGEGEGF>EFGEGEEEEEFGFGEGEGGGDEGEGGGFEFGGGGGGGGGGFGGGGGGEEGFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:53:2586:12076/1 0 MtDNA 2916 60 101M * 0 0 ACTTTGTTAACTTTTATTTCAAGAGAAAAATTTTCAGTTTATATAAGAAAACCAGGAGACACATATTTGAAAACTCTTAGAATGCTATTAATTGAACTCGT GGGGGFGGFBGGGGGGGGGGFGGGGFGGD8EEEFFGGGEGGGGGG?GGGFFGGGGGFGGGGG?GAGEGGEDAFGFFEGGGEEEBGEAEEEEEEDE=::?>C PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2212:11575:96550 147 MtDNA 2949 60 100M = 2839 -210 TCAGTTTATATAAGAAAACCAGGAGACACATATTTGAAAACTCTTAGAATGCTATTAATTGAAATCGTTAGAGAATTTTCTCGTCCACTTGCTTTAACAG ACDDDDDDDDEEECDEFDFFFHHHHHHCJIJIJIJJIHG@GHCJJJIHGGCIGIJJIIGIIJIHHGGJJIIIDIGGIGGEIIGIHG@HGHHFFFFFF@C@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:54:12110:15974/1 0 MtDNA 2950 60 101M * 0 0 CAGTTTATATAAGAAAACCAGGAGACACATATTTGAAAACTCTTAGAATGCTATTAATTGAAATCGTTAGAGAATTTTCTCGTCCACTTGCTTTAACAGTG GFGGGGGGGGGGDGGGGGGEFGGGDFGFGGGGGFGGFEEGFFGGEGEEBGFEGFGDGGFGEGFGGEEEDEEEEAEEEFEEGEEEEEEEEEEEEEBCCADA? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:80:9039:4187/1 16 MtDNA 3058 60 101M * 0 0 CAGTTAATATTACTGTTGGTCATTTAGTTAGAATAATGCTTTATCAAGGATTAGAATTAAGAATAGGTGATCAGTATATTTGATTATCAATTTTAGCCATT :@?A@<BB;BB@AAAABBBB><AAAA@AAAAEE<EEAAAAAAAAAAEEE?EBBBB?EBEEEEEEBEBAAAAA?EBAE@EEEECEEEEEEEECBCAB=<;>@ PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:24:5066:4097/1 0 MtDNA 3060 60 101M * 0 0 GTTAATATTACTGTTGGTCATTTAGTTAGAATAATGCTTTATCAAGGATTAGAATTAAGAATAGGTGATCAGTATATTTGATTATCAATTTTAGCCATTAT DGGGGGGGEAFFFFFFFFFFEAEEEEF?FEFEBFFFFGBBDEEEBGGEE=FFDFFGGEGEFFEFFAFDFEBFAEEDGEFGEEBGEGGEGEGDEDEEEFBEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:105:7673:2329/1 16 MtDNA 3249 60 101M * 0 0 GTTAACTTAAGTTTTAAAGTGCCAAACTTTTAATTTGGAAATGGTGGACCACATCTTAGTTGATATAGCATAAGAAGTGCATTTGTTTTAAGCGCAAAAGA EE5DEE5FFEEFBAEFD@?==D5:C?F5FFFGGBGFFFDFF=EEEECBEEBDE:DD?:GGGDGGEGGGGGEGGGGDGGGGGFGGGGGGGGDGFFGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1113:17155:40031 99 MtDNA 3295 60 100M = 3421 226 GACCACATCTTAGTTGATATAGCATAAGAAGTGCATTTGTTTTAAGCGCAAAAGATATCCGTCAACTAACGAGTTCATAAAGCAAGTCTTCTAAATTTGT @BCFFFFFHHHHHHIJJJJJJJJJJJJJIIIEHIJJJJJEHIJJJJJJJJJJJJJJJIJJJHIJJIIGHHGDFBCAEEEEEDDDDDACEEDDDEDDEDDE PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1305:16341:33179 99 MtDNA 3300 60 100M = 3308 108 CATCTTAGTTGATATAGCATAAGAAGTGCATTTGTTTTAAGCGCAAAAGATATCCGTCAACTAACGAGTTCATAAAGCAAGTCTTCTAAATTTGTTCTAG CCCFFFFFHHHHHJJJJJJJJIJIJJH>HIIJJJHIIJEGJIJJJJJJJIIJJJIJIJIJJIJJJJHHADFFFFFDCECEECDDEDDDEDDEDDDDDEED PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1305:16341:33179 147 MtDNA 3308 60 100M = 3300 -108 TTGATATAGCATAAGAAGTGCATTTGTTTTAAGCGCAAAAGATATCCGTCAACTAACGAGTTCATAAAGCAAGTCTTCTAAATTTGTTCTAGGTTAAATC CEEEEEDEDDDDDDCDDDC@EEEDFFFFFFHHIFJIJJJJJJJIJJJIHHJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFC@C PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:61:8761:13140/1 0 MtDNA 3309 60 101M * 0 0 TGATATAGCATAAGAAGTGCATTTGTTTTAAGCGCAAAAGATATCCGTCAACTAACGAGTTCATAAAGCAAGTCTTCTAAATTTGTTCTAGGTTAAATCCT FFFFF?EGGGGD=FGGFFGGDFDFFGGGGDFDGGGD?BDFFGBGGGGDGFDFFFFGGBDDEFEFFGDEFEEGBGEBBC?BBBBBCADBEDCB:CA?@B@@: PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:72:9498:11197/1 16 MtDNA 3343 60 101M * 0 0 CAAAAGATATCCGTCAACTAACGAGTTCATAAAGCAAGTCTTCTAAATTTGTTCTAGGTTAAATCCTGCTCGTTTTTGATTGTTTTTATTTCTTTATTTAC EED=DF?>>A?A=>5@?CDBBFB=EFFEEDBBFDDFEDFFFFFDDFFD;FF?FEDFDFDFFEEEBDEFDFDDBFFFDFDFEFFFFFD>EFAB>EAADDDCB PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:30:13606:9054/1 16 MtDNA 3373 60 101M * 0 0 AAAGCAAGTCTTCTAAATTTGTTCTAGGTTAAATCCTGCTCGTTTTTGATTGTTTTTATTTCTTTATTTACCTTGTTTTTAACATTATTAAGAATTTTGAC EA5B??:EEEEEEEDEDE=DBBEEB=FBEDEEEEEFDEGGEEGGFEEGA5DEGEGGEAEGGECB=FEFF=FFGEGFGFFDGFFFFDEFGFDGGGGGFGDGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1113:17155:40031 147 MtDNA 3421 60 100M = 3295 -226 ATTGTTTTTATTTCTTTATTTACCTTGTTTTTAACATTATTAAGAATTTTGACTAATAACGTTATTGTTTGATGAAGAATTTTTTTATTGATAACTGTAG CDDDDDDDDDDDDEEEEEEEDCFFFHHHHJIJJIJJJJJJJJJJJJJHGDIIJJIIJIHJJJJIJIJJJJJJJJJIGIIJJJJJJJJHHHHHDDFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:79:5551:14500/1 16 MtDNA 3442 60 101M * 0 0 ACCTTGTTTTTAACATTATTAAGAATTTTGACTAATAACGTTATTGTTTGATGAAGAATTTTTTTATTGATAACTGTAGTTTTTATTCTATTAAATAAAAG 5DGEGGGGEGGGEGFGGFFFGFGGGGGGGGEFGFGGGEFGGFGGGGEDGGFGGGFGDEGGGEGEGFGGGGGFAGGGGGGGGGGGGGCGGEGCGGGGGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:118:9818:14692/1 0 MtDNA 3448 60 101M * 0 0 TTTTTAACATTATTAAGAATTTTGACTAATAACGTTATTGTTTGATGAAGAATTTTTTTATTGATAACTGTAGTTTTTATTCTATTAAATAAAAGCAGCAA GGEGGEGGGEFGGGBGGFGGGGGGGGFGBFEGGGGFFGGGGGGEGGGGGGEGEGADGGGEGFEGGGGGBGEFFEFGGFGGGGEGGGGGG?GFGAGEGGGCB PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:50:8060:11985/1 0 MtDNA 3466 60 101M * 0 0 ATTTTGACTAATAACGTTATTGTTTGATGAAGAATTTTTTTATTGATAACTGTAGTTTTTATTCTATTAAATAAAAGCAGCAAGAGATATACCAGAATTTT EEAEAC=D=D:AACA@;@=@>@<@@DDDD?CA5C?DDDDDCABCADD=DDDDDDDA=ADA?>><DCCD:DD:DD>AADDACCCCBBCAD?CBCDC?B:=BD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:56:13819:18497/1 0 MtDNA 3542 60 101M * 0 0 GCAGCAAGAGATATACCAGAATTTTTAATTATTTTGTTATTCAAGAGTCTTTAGGTTTATTATTTCTTCTTTGTAGAGGAGGTCTATTACAATTTTTTATT GGGGGGFGGGGGFGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGEGFGGGGGGGEGGGGGGGGGGGGGGGGGFGGBEGEGEEGEEGFEFEEEFEGEEFEA PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:69:5893:18114/1 0 MtDNA 3759 60 101M * 0 0 TATTTTATTACAAATTTTTTGGTTAAGATCCGTGTATATTTTGTTATTTGGTTTATTGATTTGTTATGTTCAAATTTTTGTCATAAAAAGTTATAAAAATT FGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGGDAGGGGFFFEEAGGGDGEDGDGGGDGGGFBGDFGFGGDAGGGGGGGGGGGAEFGGFEFBGGEGDCCG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:67:1744:8605/1 0 MtDNA 3773 60 101M * 0 0 TTTTTTGGTTAAGATCCGTGTATATTTTGTTATTTGGTTTATTGATTTGTTATGTTCAAATTTTTGTCATAAAAAGTTATAAAAATTTGTTAATTATTTCA GGGGGGGGGGFGGEGFFFFFBDEBEGGGGFG8DGGDE@EEEEEE?GGGFFG?GBEGFEGEEGGGGFCCAGEEFFEDDBEFEGEFEEGGGEGEEGEEAFGFB PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1310:8213:55897 99 MtDNA 3943 60 100M = 4215 372 ATTTATTACTTTGTATTAATAGTTTTATTAATTTCTAAGTTTTCTAAAACTAGGGGTTATAATTTTATTAATTGAGAAACAACATTAGTATTTTTAAATA CCCFFFFFHHHHHFHHIJJJJJJIJJJJJJIJJJJIJJJHIIJJJJIJJJIJIJJJGIIIJHIIJJIIJJIIIJEGGIJJIIHHHHHHCEFFFFFDEEEC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:77:12526:7315/1 0 MtDNA 3981 60 101M * 0 0 GTTTTCTAAAACTAGGGGTTATAATTTTATTAATTGAGAAACAACATTAGTATTTTTAAATATTCCATTTAGAGTTTCATTTTTTGTAAAAATTTTCTCAT EEEEEEEDEBDDFFFFEFAEFFFFFFFFFFFFFFFFFDFFEFFFFFEFFDEFEFEFFFFFFDEFFFEFFFAEBE@EEFEFFFFFEBEEFEEDFEEEE?EBF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2311:10246:30315 99 MtDNA 3984 60 100M = 4165 281 TTCTAAAACTAGGGGTTATAATTTTATTAATTGAGAAACAACATTAGTATTTTTAAATATTCCATTTAGAGTTTCATTTTTTGTAAAAATTTTCTCATTG CCCFFFFFHHHHHJJIIJJJIJJJJJJJJIJJIJJJJJJJJJGJJJIBGIJJJJJJJJJJJJJIJJJJIJIHIJJEHIJJHFFFEDDEEEDDDE@CCDEC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:12:4535:13471/1 16 MtDNA 4089 60 101M * 0 0 AATTTTTAAATATGATAGATTCTTTACTCTATTTTTGCTTTTTACAATATTTTTATCTGTATTGGCATTTAGATTTTGATTAATTAACTTGAGAATGAAAA GGGGDADGFGFEGEBEFEFFFEEEEBEBC@EGGGGGEGFGGGGFGFG<GGGEEGGGGGGFGGGGFGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGFEGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2311:10246:30315 147 MtDNA 4165 60 100M = 3984 -281 TGATTAATTAACTTGAGAATGAAAAATAATGAAGAAACTTCAAATAATAATAAAATAAATTATTTTATTATTTTTCCGTTAATAGTTATTTCTATTATTT EEEDFFFDFFHFGHHHHHHGHJJIJJIIHDIJJJJIHJJJJJJJJJJJIIJJJJJJIJJJJJJJJIJJJJJJJJHJIJJJJJIJIJJHHHGHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1310:8213:55897 147 MtDNA 4215 60 100M = 3943 -372 TAAAATAAATTATTTTATTATTTTTCCGTTAATAGTTATTTCTATTATTTAATTACTTTTCTAGTAAAATATATTATATTATCTTGATAAGGTAAAGTTC @AECC@BDEDFFFGHHECHJIJJJJJJIEJIHJIJHEGIJJJJIHIJJIIJIIHFIJIJIJJJJJJJJJJJJJJJJIIJJJIIJJJIHHGHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:6:13139:10288/1 16 MtDNA 4217 60 101M * 0 0 AAATAAATTATTTTATTATTTTTCCGTTAATAGTTATTTCTATTATTTAATTACTTTTCTAGTAAAATATATTATATTATCTTGATAAGGTAAAGTTCCAG EDCE=C==?B=DD?5@=CDDDBBDEEDEECE5EGGDEBDFEEBFGBEEEECE=AEEADGFFGF?GFGGGGFB?BE=BGDEFGGGFDFGGGDDFFFF?DEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:35:11810:7389/1 16 MtDNA 4285 60 101M * 0 0 ATATTATATTATCTTGATAAGGTAAAGTTCCAGTTGGGAGAAGTAAGATGTAAAATAGATATTACTATGTTTGGTTACGGTCCAAAAAGATGCACATCTTT DB===?B?EEB5B5EDC?:@EABB:?B@BCBAF5BFFFFFD=DDDFEFDFFFDDFEEE:BECE?=C=AE?EABE5EEFFFEEA8EE=BECEEBB=EFFEFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:9:13349:5289/1 16 MtDNA 4305 60 101M * 0 0 GGTAAAGTTCCAGTTGGGAGAAGTAAGATGTAAAATAGATATTACTATGTTTGGTTACGGTCCAAAAAGATGCACATCTTTGCGATCTAGTTTAGAAAAAA =GEGGFGGEEGGGGFAFFGEGGGFGEGGAFGGGGFGDGGFEGFGGGFFGGGGGGAEFFFFBDGGGGGGGGDGFGGDGGGGGGGGGGGEGGGFAGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:31:10170:14522/1 16 MtDNA 4388 60 101M * 0 0 GATCTAGTTTAGAAAAAATATTTGTTTTTGGTGCAAAAGAGTTTGATTGCATTTAGTTTACTCTTTTAGTTTATAATTAAAATATGGCCCTGAAGAGGCTA EEE?DE5FDECCCC=FEE?AGEGGFFGGGFGGGFFGFGGEBBGGGGFGGBGGGDGGDDGGGGGGEGDGFGGDGGGFGDGGGGGFEGGGEGGGFGGGEGEGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:59:7488:8665/1 0 MtDNA 4539 60 101M * 0 0 TGGGATGTTGGTGACATTGCCATCTAGAAAAACTTTAACATTAAGATGAAATTTTGGTAGTATATTGGGTATAGTTTTAATCTTTCAGATTTTAACAGGTA GGGFGFGFFGFEFDFFDFFEGEGGGGFGEFGGGD?GGDGGGGGGGGFFGAGEFDGDDBEEDFFFEGGGE@DEEEBCDFBEFGGFGFGFEDE?E?GFDEFAF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:49:13216:3175/1 0 MtDNA 4636 60 90M1D11M * 0 0 GGTACATTTTTAGCATTTTATTATACGCCCGATAGGTTAATAGCATTTTCAACAGTGCAGTATATTATGTATGAGGTAAATTTTGGATGAACTTTTTAATT DD@DDAEEEDGGFDGFGGGDGGGGGGEGFGBDFEFEDFFFEFFFDGGGFGADFFFBDDCECEECEFEFDCEFGEGEA?C=DDECED?EF@EAEEEEEEEFB PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:21:4522:8165/1 0 MtDNA 4827 60 101M * 0 0 AGTATGAATGTCTGGTTTAACAATTTATTTATTAGTAATAATAGAAGCTTTTATAGGTTATGTTTTAGTTTGAGCTCAAATAAGATTTTGAGCAGCAGTAG DEEDECBEEEBEEE=?EEEEFDAFFEFEE<EEDEEFEFDFDFFF?FFFBFEDDEEFFBF5D:BDDD>=ADEC:DAFFE=FFFBFBF?FFD:FDFFFDFADE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:84:1391:9200/1 0 MtDNA 4874 60 101M * 0 0 CTTTTATAGGTTATGTTTTAGTTTGAGCTCAAATAAGATTTTGAGCAGCAGTAGTTATTACTAGACTTTTAAGAGTTATTCCAATTTGAGGGCCAACGATT GFGGGFFGDDEBEEEFFFFEFFFFFGGGGGGGGEDGFGGFGGGGEGBGGGGFGGGGAG?EFFDGGFGGGG:EEAD=ECEEEGFGGFFFFEA?CEABB7BB@ PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:2:107:7520:19689/1 0 MtDNA 4896 60 101M * 0 0 TTGAGCTCAAATAAGATTTTGAGCAGCAGTAGTTATTACTAGACTTTTAAGAGTTATTCCAATTTGAGGGCCAACTATTGTTACTTGAATTTGAAGAGGTT BGGGGADGGGGDGGFFAGGF:FFFFGFGFFFACDEFFFEBGF?GGGFGBEEC5DED==D??ECEEEFGGGFFEFBD=BAEDDBFBD:?BDEEDB?===D@? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:31:10465:15263/1 0 MtDNA 4937 60 101M * 0 0 GACTTTTAAGAGTTATTCCAATTTGAGGGCCAACTATTGTTACTTGAATTTGAAGAGGTTTTGGTGTTACAGGGGCAACATTAAAATTCTTTTTTGTATTA GGGGGGGGDGGGEGGE=EEEDGDGGFGDGGGBGFGGGGGEGDGEEGEGGGGEDEGEEE=EEEDE=FAEFAEEFDEBGFEDEEEEBEBEEBEGEE7C:=5AB PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:29:14125:10562/1 16 MtDNA 5109 60 101M * 0 0 AACATCTAGGTTATATTGCCACGGTGATTATGATAAAGTTTGTTTTAGACCTGAGTACTTAGGTAAAGATGCTTATAATATTGTTATTTGATTATTATTTA ECGDEGEGEGB?FBGFEGGGCGEGDGFGFG?GGGGFEGG6GGGGDGGGEGGEEEE=EGGGEGGGGFBEGEGGBFGGGGDFFGFFGGGEDGGEGGGGGGGFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:37:12921:1122/1 16 MtDNA 5174 60 101M * 0 0 AAGATGCTTATAATATTGTTATTTGATTATTATTTATTGTGTTAAGGTTGATTTACCCGTTTAATTTAGGTGATGCAGAGATGTTTATTGAAGCTGACCCT DAB=?B=BGGEGBEDGEGEGGGGDGEGGFAFBGEGGG5EGGEBGGGCE?E?GGECGDEFGGEGGGGFGGDGGGFGDGGGGFFGGGGDGFGGGFFGGDFFFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2215:6882:11082 99 MtDNA 5381 60 100M = 5391 110 GGATCGTAACATTTTATTTTTTTGCTTTAGTTAATAATTATACCTCTTGTTTAACCAAATTAAATAAATTTTTAGTATTTATATTTATTATCTCATCTAC @@=DDDDDFHFDHIIHIJJJJJIJIIIJJJGIGIJGJJJIJJJJJIIJJH=FGHJICHHIJJGIJJIIHEEHHHF@EFFFFEEEEEEEEEFDDDCCCDD: PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2215:6882:11082 147 MtDNA 5391 60 100M = 5381 -110 ATTTTATTTTTTTGCTTTAGTTAATAATTATACCTCTTGTTTAACCAAATTAAATAAATTTTTAGTATTTATATTTATTATCTCATCTACTATTTTAAGA =CCCCBBBEEHEHCFIEAGGHIFGC@IGGHFCIIIGIGD@IHGIGIHEEIHFGIIIIIDIIIIIIIIGFC:IIIIHECIGEFEC<GIHFFB?DDDDD@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:70:6358:2346/1 0 MtDNA 5567 60 101M * 0 0 CTTATTTAATATTGTTTATTTTTATAAGAAGTAAATTGTTATTTAAATAATAAAACATGTCTAGTATAAGTTAATACATTAGATTTAGGTTCTAAAGATTT FFGBFGFGGDGGDFGGGDEACCACAGGGGEDEGFGGDFFGDEGGDGGFG?GGGGGGEGGAEEDEBFDFDFEEGDBFFFFFDGEEDEBEE@EGEEEDEDDEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:5:6773:20401/1 0 MtDNA 5728 60 101M * 0 0 ATTTTTTGCCTCAGCCGGAATGTTAAGATCTTTAGTAATATTTTTTAAATTTGGACTATACGAATTATTTATTTTTACACTATTTTCTGTGTTATTTATTT GGGFFFEFFGGGDGGGGGGFGGGFGGGGGGGGGEFFGGFGGGGGGGGDFGFFFFDEFDFBEEEDBEEEEEAGGGGDCEGGEDGGDGGDGFGGGDGGGDGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:39:10545:13693/1 16 MtDNA 5756 60 101M * 0 0 TCTTTAGTAATATTTTTTAAATTTGGACTATACGAATTATTTATTTTTACACTATTTTCTGTGTTATTTATTTCTTTTGCTTGAGGTAAGGATATTGCTAT FADAAEEEF;CDFAEEEEFEAEEEB@>CCCA:EE?EF=A@ECFFFFD?EEEEDEE:EFFEFEEEBAC;FECCDBDEEEBA??F?DFAFFFEEDDE=DDAD: PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:96:18019:19876/1 16 MtDNA 5769 60 101M * 0 0 TTTTTAAATTTGGACTATACGAATTATTTATTTTTACACTATTTTCTGTGTTATTTATTTCTTTTGCTTGAGGTAAGGATATTGCTATAGAAGGTTTAAGA GEBBFGGFEEGEE=EBGFEGGEEEEADDGGGEEEEBEAFFEFFDEDGG?GGGFGFG@DGGFGGBGFGGEGFFGGGGGGDFFGBGBGGGGGFGFGGFDDFEF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:28:5015:7424/1 0 MtDNA 5798 60 101M * 0 0 ATTTTTACACTATTTTCTGTGTTATTTATTTCTTTTGCTTGAGGTAAGGATATTGCTATAGAAGGTTTAAGAGGTTACCATAATTTTTTCGTTATAGACGG GGGGGGFGDGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGBFFFFFGGGGGGGGGGGGGGGBGGFGFEFFCFAEFFDDGFGGFGFEGEGFFDFDDFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:30:5276:1934/1 0 MtDNA 5801 60 101M * 0 0 TTTACACTATTTTCTGTGTTATTTATTTCTTTTGCTTGAGGTAAGGATATTGCTATAGAAGGTTTAAGAGGTTACCATAATTTTTTCGTTATAGACGGGTT GGGDGGGGEGGGGGGGFGGGEGGGGGGGGGFGGGGGGGGGGDGDGFCFCFGGGGGGDGDGGGDGG=EDBEFAFDEDEFBEGGGGEGEGEFCECEC?EEECC PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:14433:23059 99 MtDNA 5853 60 100M = 5996 243 CTATAGAAGGTTTAAGAGGTTACCATAATTTTTTCGTTATAGACGGGTTTAAATTCGGAGTAATTTTATTTGTGTTTAGGGAGTTTATATTCTTCTTTTG BCCFFFFFHHDFHIJJIHJFHJJJJJJJJJJJJJJJIJIJJJIJJII@FIHIIIIIJJHH?AEHHHFDFFFFFEA6@>CDD;?<CCCDDDFEEEDDCDD: PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:83:3624:6531/1 16 MtDNA 5868 60 101M * 0 0 GAGGTTACCATAATTTTTTCGTTATAGACGGGTTTAAATTCGGAGTAATTTTATTTGTGTTTAGGGTGTTTATATTCTTCTTTTGTATTTTTTGAACATTT BEEDFDEGDEEFEEDBDFEGFGGFGGFBGFGFAGGFGGGFGGGEGGG>EGGGGGGFGGGGFEEEEF;EFEEGGGGFGGGGGGGGGGFGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:76:4139:2647/1 16 MtDNA 5966 60 101M * 0 0 TTTTTTGATGCTGATCTAGTACCAGTACACGAGTTGGGAGAGACTTGATCACCTTTTGGAATGCACTTAGTTAATCCATTTGGTGTACCGTTATTAAATAC EBBEEEEEEEE@B@BEB@@B?BC?BB@B?DEEEDEFDBEEEB=CCCE@EE@FFFFDECEEDEDEBEFFEFDFFFEFEAFDFFEFCFBDFFFFFFAFGGGBG PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1104:14433:23059 147 MtDNA 5996 60 100M = 5853 -243 GAGTTGGGAGAGACTTGATCACCTTTTGGAATGCACTTAGTTAATCCATTTGGTGTACCGTTATTAAATACAATTATTTTATTAAGGAGTGGTGTTACAG CDDDCCAECEC@EEFFFFFDAHHGJJJJJIJIJJIJJJJJJJJJJJJIGHHGJJJIGJIJJJJJIJJIIHJJJJJJJJJJIJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:99:8553:16567/1 0 MtDNA 6020 60 101M * 0 0 TTTGGAATGCACTTAGTTAATCCATTTGGTGTACCGTTATTAAATACAATTATTTTATTAAGGAGTGGTGTTACAGTAACTTGAGCACATCACAGATTACT :FDGBFGFGDDGFDGFFGGFBGGDGFFFF=EAEEEDEEAEFDFDFGFG?GG?FEGGGFGGGGGFFDFFEFEAFFFGEGGGGAGEFGEFGGFGGECBEDDFG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2201:8667:82934 99 MtDNA 6028 60 100M = 6185 257 GCACTTAGTTAATCCATTTGGTGTACCGTTATTAAATACAATTATTTTATTAAGGAGTGGTGTTACAGTAACTTGAGCACATCACAGATTACTTAGAAAT CCCFFFFFHHHHHJJJJJJJJFHGHIIJIJJJJGJJIIJJJIIJJJJJIJJIIJJJJBFIBFGHIEIGEGHJJJJJHHHHGHFFFFFDECECEEEDDDDC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:83:16211:16889/1 0 MtDNA 6029 60 101M * 0 0 CACTTAGTTAATCCATTTGGTGTACCGTTATTAAATACAATTATTTTATTAAGGAGTGGTGTTACAGTAACTTGAGCACATCACAGATTACTTAGAAATAA EAEEBGFGGFGGGGEFFFAFEFFGEGFEDGDEECCGFDFBGGEGFGG@FGCBFDDFDFDBBDDBBBEBEFBAEEBFBDFEEGEEEB=B@BBEB?BAABDBE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:8:8735:6148/1 16 MtDNA 6076 60 101M * 0 0 ATTAAGGAGTGGTGTTACAGTAACTTGAGCACATCACAGATTACTTAGAAATAAAAGATGTACTAATAGTATAATTTTAACATGTTTATTGGCAGCTTATT DB:DDDB?D:BDCDDDD?DDDD=DADDADDBDDDDBDDDDDDADDDBC>CDDADADDD:DBCCBDDDDADDDDDBD5DDDDE?DEE:EFFEEEBDD;EEE: PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2201:8667:82934 147 MtDNA 6185 60 100M = 6028 -257 ATTCAATTAATAGAGTATATAGAAGCTAGATTTTCTATTGCAGACGGAGTATTTGGAAGGATTTTTTATTTATCTACGGGATTTCACGGAATTCATGTCT CCACEEFEECDCDEEEEEEEDEFFFFFFEGHHHHIJJIGJJHHDJIJJIHHJJJJJJJIGGJJJJJJJIJJJIIHGJIJJJJIIIGJHGHGHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:105:1340:12432/1 0 MtDNA 6235 60 101M * 0 0 ATTTGGAAGGATTTTTTATTTATCTACGGGATTTCACGGAATTCATGTCTTGTGTGGTGGTTTGTTCTTAGCATTTAATTTTTTACGTCTTCTAAAAAATC FFFD@DGGEEEFGGGGGGDFGGGGGGGEGGFEFFEEDEE:EADDEFF5FBEE=EEDDADDB?DE=><:6>EEDEE:D5EDEEBB5:ECAC:?B:CEBEEEC PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:54:12468:5717/1 16 MtDNA 6304 60 101M * 0 0 AGCATTTAATTTTTTACGTCTTCTAAAAAATCATTTTAATTATAATCATCATCTGGGGTTGGAATTTGCTATTTTATATTGACATTTTGTTGATGTAGTGT BBB:DDC?CBCB@AB:BDDDD@C?>CACB::?DCD=CC:?A=D:DB?DDAD:?CCCD=D:DDDDA?ADDDA;C:AAC?=A??:@<DC5CC=A5CCA6;@=; PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:41:9266:7772/1 0 MtDNA 6313 60 101M * 0 0 TTTTTTACGTCTTCTAAAAAATCATTTTAATTATAATCATCATCTGGGGTTGGAATTTGCTATTTTATATTGACATTTTGTTGATGTAGTGTGATTATTTT GGGGGGGGGGEDFGGGGGFGGDGGEGFFEGFGFGEGGGGGGFGGGGGGGEFGFDEDGGGGGEFGGFBGGGGGAEBBFFFEEEEBEEBBEAEAEABGEEDGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:65:9093:5871/1 16 MtDNA 6392 60 101M * 0 0 GTTGATGTAGTGTGATTATTTTTATTTGTGTTTGTTTATTGATGATCTTACTAATATAGCTATGATAGTTTAATTTAGAATATATAACTTGTAATTATAAG FBEEBE??:B@D:FAFFEAAFFFFFFFFFAEFFEFCFFFFF?FEFFDEEEDDFFEFCCCC:DDDDADEEEEDDBEEEEED=FFFFEEFDGGGGDGGEGGBG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:89:15660:12072/1 16 MtDNA 6413 60 101M * 0 0 TTATTTGTGTTTGTTTATTGATGATCTTACTAATATAGCTATGATAGTTTAATTTAGAATATATAACTTGTAATTATAAGGTTTCTAGTAGCTTTGTTAGA BEEAEEEGEGEEFGEGFGBGDFGEBFGEEGFGGFGGGGGFFFFEDCEGGGGEDEFFGGGGDEEED?AGFGGEGDGFGEFGGEGGGFGGGGGDGBGGGAFGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:8873:86961 99 MtDNA 6488 60 100M = 6541 153 ATAAGGTTTCTAGTAGCTTTGTTAGAATTTCTTTTTATCTCCTTATTATGACTTTTTAAACCTATTTATTTTTTATTATTTACAGTGATGTTTAGGTTTT @B@FFFBDBHHFHEGGIGIECEHIJGHIIGGIIIJIGIJIJGDHHHIJJEDEEGIIIIIIJJJJJJJJJIGGIIJJIHDECHEEE?DFF@?CFECE>CCB PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:35:14137:12613/1 0 MtDNA 6539 60 101M * 0 0 CTTTTTAAACCTATTTATTTTTTATTATTTACAGTGATGTTTAGGTTTTTAATTTTTAATAATTTTTCATGAGGCGGACTATTTTTAGTATTAGATTCATA GGGGGGGGGGGGDGGGGGFGGGGGGGGGGFFGFGDGCGGECFFFF?FEFDEAGGGAGGGGGGGGGGDGFGGEFFGGGEEGEGDGGE@GEEGEEFEEAEED@ PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1210:8873:86961 147 MtDNA 6541 60 100M = 6488 -153 TTTTAAACCTATTTATTTTTTATTATTTACAGTGATGTTTAGGTTTTTAATTTTTAATAATTTTTCATGAGGCGGACTATTTTTAGTATTAGATTCATAT CACCCCCCCDA@CCA<EEEHFHEA=>CAIGIGH@;F9EEFC1EIHHCEHGBCIHFAGD9HD?9DCFFCGCCA@A,ACGEIIGGGEDE?F?DFABD7D@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:80:12688:9364/1 0 MtDNA 6564 60 101M * 0 0 TATTTACAGTGATGTTTAGGTTTTTAATTTTTAATAATTTTTCATGAGGCGGACTATTTTTAGTATTAGATTCATATAGATTTATTTTATTGATTGTTATA GGGEGAFCDDFAFDFEECDE@EEDEEFFFBDDDD:A?AC?GDGEFFGFEACEB:C=EEEE>:C@BEEEE=DEFA?DFEE?DE??EFC>5B;?AAEDAD9D= PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:83:3138:12153/1 16 MtDNA 6612 60 101M * 0 0 GCGGACTATTTTTAGTATTAGATTCATATAGATTTATTTTATTGATTGTTATAAGATTATTTATTTTAGGTATTATTGTTATTAGAGAAAAAAATAATAAT GGGFEEGFEEEBEDGGFGFFGGGGGFGFGGEGFGDGGGGGGAGGFGGGGGGGGGGGGGGFGGGFGGGGGGGDGGGGFGGBFGGGGFGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:59:15380:6072/1 16 MtDNA 6635 60 101M * 0 0 TCATATAGATTTATTTTATTGATTGTTATAAGATTATTTATTTTAGGTATTATTGTTATTAGAGAAAAAAATAATAATTTATTGATTTTATCTGAAATTTT EDGEEBEE@EEGEEEEEEEAEEE?EEEEAEBFEEFEEEGGGEEGDEEFEDDGFEECGGEDGEGEDGEGDGEGFGEGGGFEECDCD;G=GFFAGGGGGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2109:14592:38248 73 MtDNA 6659 60 87M1I5M1I1M1I4M = 6659 0 GTTATAAGATTATTTATTTTAGGTATTATTGTTATTAGAGAAAAAAATAATAATTTATTGATTTTATCTGAAATTTTAGTATTTATTCTGTCTCTTATAC CCCFFFFFHHHHHJJIJJJJIIICHJJIJJIJJIJJJJJJJJJJJJJJIIJJIJJJJJJIEIJJIIJJJJIGGHJGHHHFHHHFFFFFFFEEEEEEDEDD PG:Z:SNAP RG:Z:000 NM:i:6 +BS-DSFCONTROL03:121:D0M8KACXX:5:2109:14592:38248 133 MtDNA 6659 0 * = 6659 0 AATAAATACTAAAATTTCAGATAAAATCAATAAATTATTATTTTTTTCTCTAATAACAATAATACCTAAAATAAATAATCTTATAACCTGTCTCTTATAC CCCFFFFFHHHHHJJJJJJJIJJJJJJIJJJJJJJJJJJJJJJJJJJJJJHIJJJJJJJJJJJJJJJJIJJJJHHHHHHHFFFFFFFDDECEDDDDDDDC PG:Z:SNAP RG:Z:000 +EAGLE:1:39:10037:14104/1 16 MtDNA 6823 60 101M * 0 0 TATAATTCTAGGTTATGGTTCTCAAATTGAAAAAATTAACTCCTCTTATTATTTAATATTTTATGCAGCTTTTTGTTCATTCCCATTTTTATTTGTATATT E?F?FDFGF?FGAGAGFFFEDGGDGGGFGFGFFF?FG?EGGDDBDBAF>EFEGGGGCGDGFGGFGGFGGGFGGFGGFGGGEDGGFGGDDGFFGEGFFGFDF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:51:9949:15014/1 16 MtDNA 6862 60 1M1D6M1I87M1I5M * 0 0 CGATCTTTATTATTTAATATTTTATGCAGCTTTTTGTTCATTCCCATTTTTATTTGTATATTTTAAGAGTAATTTTTTATTGGTTTTTTCTTACTTATTAC EEEEEEEBEEEEEE=EEEEEBEEEEEEEE=C?EEDDEEDEE?EEECCCCEDDEEEEBEEEEEEEEAECEBACAC<EEEEE=ECDEED?DDBE5AEEEEEDE PG:Z:SNAP RG:Z:266-1 NM:i:8 +BS-DSFCONTROL03:121:D0M8KACXX:5:2210:19195:39418 83 MtDNA 6948 60 100M = 6949 101 GTACTTACTATAATTTTGTTATTTCTTGAGAAATATTTTTTATTCTTAGTTTAAGATTTATAATAAAATTTCCAATTTATTTTTTACATCTTTGATTACC CCBDFDDDEEEDEDEFFFFFFHHFHHIJJJJIJJJJIJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIHIJHHHHHFFFDD@BB PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2210:19195:39418 163 MtDNA 6949 60 100M = 6948 -101 TACTTACTATAATTTTGTTATTTCTTGAGAAATATTTTTTATTCTTAGTTTAAGATTTATAATAAAATTTCCAATTTATTTTTTACATCTTTGATTACCC CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHIGIJJJJJJJJJJJJJJJJJJJIIJJJJIJJJJJFFFFFFEEEECEEEC>; PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:1:86:3647:16273/1 16 MtDNA 6985 60 101M * 0 0 TTTTATTCTTAGTTTAAGATTTATAATAAAATTTCCAATTTATTTTTTACATCTTTGATTACCTAAAGCTCATGTAGAGGCTCCTACAACAGCTAGAATAC <DEBBBEEEEBEBBEEEEEEEEEEEG?FGEEDD?EBEEEEEEEFEDEDAFEBDDEEEDFFADCBCCFABFEGFGDGEFEDGEFFFEFDFFFEFFFFDEEBE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1204:10706:29128 99 MtDNA 7118 60 100M = 7195 177 GCGGGATTTTTACGTATTTTAGGTAGTTTAAGATTTGTAAAAAACAATGTATGAATTTTTATTGCATTTTTAGGGATAATTTTTGGATTTTTTTGTTGTT ;;<@################################################################################################ PG:Z:SNAP RG:Z:000 NM:i:6 +EAGLE:2:99:13522:17668/1 0 MtDNA 7120 60 101M * 0 0 GGGATTTTTACGTATTTTAGGTAGTTTAAGATTTGTACACAACAATGTATGAATTTTAATTGCATTTTTAGGGATAATTTTAGGATCTTTTTGTTGTGTGT GFDGFGGEAFEFBFF?FFFFDBDF?ECECEEGDFGEGGGGFEEDDFGEGEBDEFDBEEFBEGFDEFEEE9EEC@?EEEEEDEGEEEEFEEGGEEEABBAFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1204:10706:29128 147 MtDNA 7195 60 100M = 7118 -177 AATTTTAGGATCTTTTTGTTGTGTGTTTCAAAGAGATTCAAAGGCTTTAGCAGCTTATTCTTCAGTCACTCATATAAGGTTTTTATTATTATCACTGGTA CEDDDCC@;DBCCDEBFDFHFFJGEGIGGIJJJIEIIGHEIHGJGJJIHFIHACGGEGIJIGIIHHEFIGEJIJGIHEJIJJIGIGGGGHHHED>FDC@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:102:7363:18384/1 0 MtDNA 7214 60 101M * 0 0 TGTGTGTTTCAAAGAGATTCAAAGGCTTTAGCAGCTTATTCTTCAGTCACTCATATAAGGTTTTTATTATTATCACTGGTATTTATCACAATGAGTAGTAA D:BDDCEDEEBFFFFGGEGGGGGGGGGGG:EEEEEGGGGFGFGGCGEGGFGDGGGGGEEGBEEEEFGGEGEAFE:FFDFCGGGGGFFADDFFFFFAFFEEF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:38:3103:6670/1 16 MtDNA 7304 60 101M * 0 0 ATGAGTAGTAAAATTAGAAGAGTTATGCTTATGCTAGCACACGGTTATACATCTACACTTATGTTTTACCTTATTGGTGAATTTTATCATACAACTGAAAA FGGEGGGGGGGGGAGGGGFGGGEEGGGGGGEEGGGGGGFGGGGGGGGGFGGFFFDFEGGGGFGGGGGEGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:4 +EAGLE:1:55:13359:5768/1 0 MtDNA 7379 60 101M * 0 0 GGTGAATTTTATCATACATCTGGGAGGCGTATAATTTATTTTATAAGTAGATTTTTTAGATCTAGAATAATTATAGGTATTTTGTTTTCAGTTGTATTTTT FBFEFFFADEGBGDGDGGGGGFFGGGGFGDGEBBGGGFFGGGGAGEEBFFFGEGFGGEBEGGGBGEEGDFDGFGEGGEAGFGGGDGFEEBCEEECEFGGG? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:40:8204:14676/1 16 MtDNA 7463 60 101M * 0 0 TTTTCAGTTGTATTTTTATCAAATAGGGGTGTACCACCTTCTTTGTCATTTTTATCAGAATTTTTAGTTATTTCTAATAGTATATTAATTAGAAAAAGTAT DDBEBGED?FGGECGGECDE;FGEGGFGGDGFDFFCFF>FFGGGGGDGGGEGGGGGGGGGFDGGDGGD?GGDGGGGGGGGGFGGGGGGGEGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:17139:67717 99 MtDNA 7469 60 100M = 7536 167 GTTGTATTTTTATCAAATAGGGGTGTACCACCTTCTTTGTCATTTTTATCAGAATTTTTAGTTATTTCTAATAGTATATTAATTAGAAAAAGTATATTTG CBCFFFFFHHHHHIJJJJJJJJJEHGHIIIIJIIJJJJJIJJJJJJJJJIIIIHIJJIJIIGIJJJJJJEGHGGCCEHHHHHHHFFDFDDCD;CCBDDE> PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:17139:67717 147 MtDNA 7536 60 100M = 7469 -167 CTAATAGTATATTAATTAGAAAAAGTATATTTGTAATAATTTTTATTTATTTTGTAGTATCTTTTTACTATTCTTTATTTTTGATTACAAGATCTTTAAT DEEEEFFFFFFFFHHHHHHJJJJIJIJJJJJJJJJJJJJIJJJJJJJJJJJIJJJJJJIIJJJJJIGJJJJJJJJJJJJJJJJJJJIHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:57:7347:8572/1 0 MtDNA 7620 60 101M * 0 0 TTACAAGATCTTTAATAGGAAAAGGTTACCATAATTTTAATACTTGAAATGTAGGGTTTTCAGCACCATTAGTCTTAATAATATATAATGTATTTTGATTA FEFFDEBE??EEDEAFEDFDFFFDEBBDEEC?CCD=EEEBFFEEFF?FF=?:?ACE?BCEFFFFDFEFDEFEEEDEBDDEEEDEEEDDED@B=ABEDDBEB PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:12015:97588 99 MtDNA 7885 60 100M = 7994 209 GATTAGAGAGATCTAATCATAAAGATATCGGAACTCTTTATTTTATTTTTGGACTTTGATCTGGTATGGTTGGTACTAGATTTTCTTTATTAATTCGTTT B@@FFDFE>FFHHIJJIGIIJJIGHGJJJFIIIJJJJJJHJIJJGIJJJIGHIGIIJJIIIJIGCGHGDEHIE?CEFFFEFFEDEEEEDEDCDEEDDDDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:9064:66647 99 MtDNA 7912 60 100M = 8034 222 TCGGAACTCTTTATTTTATTTTTGGACTTTGATCTGGTATGGTTGGTACTAGATTTTCTTTATTAATTCGTTTAGAATTAGCTAAACCAGGTTTTTTTCT BB<1:=@BFHFH>CFHB<F<CHD@:FB?HEA<?CADHI@DFHHBEB0?FGCFHEAFEEEHI@FFDHJJ@;@=@@>>EC;=;@EEB;@>ACD555=?=BDC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2114:12015:97588 147 MtDNA 7994 60 100M = 7885 -209 TAAACCAGGTTTTTTTCTTAGGAATGGACAGTTGTATAATTCAGTTATTACAGCTCATGCTATTTTAATAATTTTTTTTATGGTAATACCTACTATAATC CBC@DBCBDDDDDEDEEEEFFFFC?BDAFHHEIJJJJIHGGGIIGIIIIHJIIIGFJIIGJJJJJJIIGIIIJJJIIIIJIJJJJIGFGHHFFFFFFC@C PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:9064:66647 147 MtDNA 8034 60 100M = 7912 -222 TCAGTTATTACAGCTCATGCTATTTTAATAATTTTTTTTATGGTAATACCTACTATAATCGGTGGTTTTGGTAACTGATTATTACCACTTATGTTAGGAG :::@@B;5AA:@:@5:A>>A>;B@@@>DA>@?6AC;7C@=8B<FCF>D<FF?IIG@GG?@DGEGD@EA<4@F?<AC3,<F:<:A@C:FBF8?AD?DB@@= PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:86:14256:19867/1 16 MtDNA 8225 60 101M * 0 0 TATAGGTTGTGGGACTAGGTGAACAGTCTACCCACCTTTAAGAACAATGGGGCACCCTGGAAGTAGAGTAGATTTAGCTATTTTTAGTTTACATGCAGCAG =BBB@BBBBBDBDBBBAD@ABDADBDABA6BBDBDBDDDDEEGEEGDDFEFEE@EEEGGGFDGGFGGGGGGGGGFGGGFGGEGGGGGEGGFGGGEGGEGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2214:18868:93712 99 MtDNA 8250 60 100M = 8386 236 GTCTACCCACCTTTAAGAACAATGGGGCACCCTGGAAGTAGAGTAGATTTAGCTATTTTTAGTTTACATGCAGCAGGGTTAAGATCTATCTTAGGTGGTA 11:BA::2220CFH@>94:<<:H@BBEHHGHHGGI?GEH>?FADFGIGIICGGEGIBAHGIICFHEEC>DGEHGGHFF@BDEE@CACCCCDDDDD::<?3 PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2214:18868:93712 147 MtDNA 8386 60 100M = 8250 -236 GTTCTATTTCATTAGAACATATAACTTTATTTGTTTGAACTGTGTTTGTAACAGTGTTTTTACTGGTTTTATCTCTACCGGTTTTAGCAGGGGCTATTAC AB>:>A>@A>@;EEEEDDEEEDAB@DDDDDB;?=?:IEECAEC;@CBDF==FCFB?FBBD<G=BDDDBAGEG@FGC<GFAHI<AEA;C:<==;D?DB@=@ PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:2:39:11175:12286/1 0 MtDNA 8405 60 101M * 0 0 TATAACTTTATTTGTTTGAACTGTGTTTGTAACAGTGTTTTTACTGGTTTTATCTCTACCGGTTTTAGCAGGGGCTATTACTATGTTGTTAACTGATCGTA BDDD?BDDDDEEEEFFFFEFFFFBFEEDEBEEEEEDFEFFFCCF:EE@EEFDEFDFFEFFFFDEFBEDEBDD:FBEEEEBEEEEAADDBABDADFB?C=<B PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:2:113:8946:21007/1 0 MtDNA 8550 60 101M * 0 0 CTTATTTATCAACATTTGTTTTGATTTTTTGGTCATCCTGAAGTATATATTTTGATTTTACCAGCTTTTGGTATTGTCAGACAATCTACACTTTATTTAAC GGDGGGGGGGDAGBEGGGFGGFGGFGGGEGDGEG=FFFEFGEFGEGFEEGGGGGFDGGGGG?FGEGGGGGECEFFFEEEGBEE?DFEADC?DEE=BE?<B5 PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:81:3391:15213/1 16 MtDNA 8553 60 101M * 0 0 ATTTATCAACATTTGTTTTGATTTTTTGGTCATCCTGAAGTATATATTTTGATTTTACCAGCTTTTGGTATTGTCAGACAATCTACACTTTATTTAACAGG ?DEDDDGEBE@EEFEFFGGGEGGGFGGGGEFEEGGGGGFGEGGGGGGGGGGFGGGGEGGFEEFFGGGGDGGGGFGGFEGGGGGGEFFGGDEGGGGGGFEGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1207:2101:11733 99 MtDNA 8591 60 100M = 8633 142 AGTATATATTTTGATTTTACCAGCTTTTGGTATTGTCAGACAATCTACACTTTATTTAACAGGAAAAAAAGAAGTTTTTGGTGCTTTGGGTATAGTTTAT BC@DFFFFHHHHGGJGJJJJJJIJJJJJJGDHIJGIEGIIIHGGIICGCDDG>GIJIIGG@DHHG9FGIBHFBEDDFEDD?BDDDDDDCB5>>CEDCDCA PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1207:2101:11733 147 MtDNA 8633 60 100M = 8591 -142 ATCTACACTTTATTTAACAGGAAAAAAAGAAGTTTTTGGTGCTTTGGGTATAGTTTATGCAATTTTAAGAATTGGTTTAATTGGTTGTGTAGTATGAGCT DDA>@C@DCAEECC>CDCDDDDDHHHHHHEGHEEGGJJIJHGGJIGGGIIHCIGIIJIIGHAIJJIJJJJIGIIIJJJJJIIIJJJIHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:25:12122:5259/1 0 MtDNA 8665 60 101M * 0 0 TTTTTGGTGCTTTGGGTATAGTTTATGCAATTTTAAGAATTGGTTTAATTGGTTGTGTAGTATGAGCTCACCATATGTATACAGTAGGTATAGATTTGGAT FGFAGFDBFD:EEEEEB5AEEEEEAFFFAFDF=FEFEFFFFDAEEFFFFFD:FFACEB:E?:BD?B?EBAFADBBDDBCEBBBAEBEE@EBBE@BFFE?AF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:82:4393:14891/1 0 MtDNA 8674 60 101M * 0 0 CTTTGGGTATAGTTTATGCAATTTTAAGAATTGGTTTAATTGGTTGTGTAGTATGAGCTCACCATATGTATACAGTAGGTATAGATTTGGATTCACGTGCT DGFDDEEAEEEECEEFFEDFGGGGGGEGDFEEEDEDEDBEGEGDGEEEEEFDFFFGGGCBFGGGBFFFDDFDFEFCEEE5@B?D:?CBDB5@B?@CFCF?B PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:3:4300:2958/1 0 MtDNA 8776 60 101M * 0 0 ATTTTTCGGCTGCTACTATAGTTATTGCAGTGCCAACAGGTGTTAAAGTGTTTAGATGATTGGCTACATTATTTGGTATAAAAATGGTATTTAATCCACTT GGGGGGGGGGGGGGGGGGGFGFGGGGGGGDDFFGGEEEEECEEEEECE@EFFFBFAEGBFGGFFFFDEDGCGGGBD=@@D:AA;9EE??=AA@C55>;<?E PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:75:3836:14170/1 0 MtDNA 8880 60 101M * 0 0 TTGTGAGTATTGGGTTTTATTTTTTTGTTTACTTTAGGTGGGTTGACAGGTGTTGTATTATCTAATTCAAGATTGGATATTATTTTACATGATACTTATTA EEECEEEEEEDDDDBGGGDGGGGGEFGDFGFGGGFGFG@ACC<CCBEEEE?EEAEDFFFFGGGFGGGGFEGBEGGDEGGEGEGGGGGGGGGEGGFFGGFGD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:57:17429:11489/1 0 MtDNA 8902 60 101M * 0 0 TTTTGTTTACTTTAGGTGGGTTGACAGGTGTTGTATTATCTAATTCAAGATTGGATATTATTTTACATGATACTTATTATGTAGTTAGACATTTTCATTAT GGGGGGGGEGGGFAGFDFFFEEFFFFFFCFFFFDFEBBFEGFGGGEEEGECGGGCGEGEAEGGEGGBGGEDEEFEDGGDGACCECFDBBCFEFEFD@AFA@ PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2312:8770:13442 99 MtDNA 9086 60 100M = 9229 243 ACTTATGATATCTGCAGTATTTATTTTATTATTTATTGGGGTAAATTTAACATTTTTCCCGCTACATTTTGCAGGACTACACGGGTTCCCACGTAAATAT CCCFFFFFHHHHHJJJJFHHJJJJJJJIJJIJJJJJJJJJJCFHIJJJJIGJJJJJJJJJIJJIJJJJJJIIIGHEHHHFFFFDDDDDDDDDDD?ABFDC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:14393:27976 99 MtDNA 9087 60 100M = 9151 164 CTTATGATATCTGCAGTATTTATTTTATTATTTATTGGGGTAAATTTAACATTTTTCCCGCTACATTTTGCAGGACTACACGGGTTCCCACGTAAATATT @C@FFFFFFHHHHJJJGIIIJIJIIJGHIGIGIIIIJGIJ?AGHJGIIJHIIJIJJJJJIJJIJJJJJJIGIGGEAEHEDFDDD>?BDDCDDBDDBDEDC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:50:14046:18753/1 16 MtDNA 9087 60 101M * 0 0 CTTATGATATCTGCAGTATTTATTTTATTATTTATTGGGGTAAATTTAACATTTTTCCCGCTACATTTTGCAGGACTACACGGGTTCCCACGTAAATATTT BEEEEEEEEEGEEEEEEEE?D@EGGGEEEEGEEEEEGEGEEGDEGGEEEGEGGFGEGGGGGGEGGGGGDGGGGGEGGEGGGGGGGGGGGGGGGGGGGAGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:10705:30822 99 MtDNA 9102 60 100M = 9126 124 GTATTTATTTTATTATTTATTGGGGTAAATTTAACATTTTTCCCGCTACATTTTGCAGGACTACACGGGTTCCCACGTAAATATTTAGATTACCCTGATG CBCFFFFFHHHHHJIJJJIJJJJJJCFHIJJJJJGHIJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJIHBEFFFEBBDDDDEEFFEFDDDEDDDDDDDDA PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:72:10661:11179/1 16 MtDNA 9109 60 101M * 0 0 TTTTATTATTTATTGGGGTAAATTTAACATTTTTCCCGCTACATTTTGCAGGACTACACGGGTTCCCACGTAAATATTTAGATTACCCTGATGTTTATTCG ;EEBEEEEEEEAEEEEEEEEEEEEEEBEDDD@E?EEGEEBEEDEEGDEEDEDCFFCECFFEGGEEGDEEGEFGGGGEFGFGGFGCGGDGGGGGGFGGFFGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:10705:30822 147 MtDNA 9126 60 100M = 9102 -124 GTAAATTTAACATTTTTCCCGCTACATTTTGCAGGACTACACGGGTTCCCACGTAAATATTTAGATTACCCTGATGTTTATTCGGTATGAAATATTATTG EDDEEDEEEDDDDDDBBDBAADEFFFFFBHHHHHHGJIHIIJJJJJJIIHJJJJJJJJJJJJJJIHG?JJJJJJJJJJJJIJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1314:14393:27976 147 MtDNA 9151 60 100M = 9087 -164 ATTTTGCAGGACTACACGGGTTCCCACGTAAATATTTAGATTACCCTGATGTTTATTCGGTATGAAATATTATTGCCTCTTATGGTTCTATTATTAGAAC CCC@DDCDDEDCCDDBDDDFDBFGFEIJIIGIGJJIJJIHGC=HIIIGFCJJJIIIIGJFIJJIJJJJFIHGJIGDHGIIIGHGIGIHHHHFFFFDD@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:52:2501:13323/1 0 MtDNA 9191 60 101M * 0 0 TTACCCTGATGTTTATTCGGTATGAAATATTATTGCCTCTTATGGTTCTATTATTAGAACTGCAGGACTATTCTTATTTATTTATGTATTATTAGAGTCTT GGFFGGFGEGGGFGGAFFFFGGGGGGGGEGGGGDGGGGGGGGGGFEGGGGGGGGGGGGGGGGGGGGEGGEGGGGGGGGGEGGGEGGEGGGGGGEFEFCFGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:46:14009:4930/1 0 MtDNA 9196 60 101M * 0 0 CTGATGTTTATTCGGTATGAAATATTATTGCCTCTTATGGTTCTATTATTAGAACTGCAGGACTATTCTTATTTATTTATGTATTATTAGAGTCTTTCTTT EEDBEDEFEFFFFFFEDEEBFFFDFECBE?BEEEEDCCEAEGDG=FEEDFAA:BEB=BBCA=AAAEAFBFFEGGBDF?=FABCCBEAGD=????@EEABE; PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2312:8770:13442 147 MtDNA 9229 60 100M = 9086 -243 CTTATGGTTCTATTATTAGAACTGCAGGACTATTCTTATTTATTTATGTATTATTAGAGTCTTTCTTTAGTTATCGTTTAGTAATTAGAGATTATTATTC CDEEDDEFFFFFFFHHFHHHFJJJJJJIHJJJJJJJJJJJJJJJJJJIIIJJJJJJJJJJJJIJJJJJJJJJJJJIJJJJJJJJJJJHHHHGFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:8985:17141 99 MtDNA 9258 60 100M = 9340 182 CTATTCTTATTTATTTATGTATTATTAGAGTCTTTCTTTAGTTATCGTTTAGTAATTAGAGATTATTATTCTAATAGAAGACCTGAGTATTGTATGAGTA CC@FFFFFHGHHHJJJIJJJGJJIJJIIJJHJJJJJIJJHIHIJIJIHHIHIIJJJJJIHIJJJJJJJGIJJGHGHIDHIIIIIIGIEHDHFHGFFDFDC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:77:4177:11048/1 16 MtDNA 9303 60 101M * 0 0 CGTTTAGTAATTAGAGATTATTATTCTAATAGAAGACCTGAGTATTGTATGAGTAATTATGTATTTGGTCACAGTTATCAGTCTGAGATTTATTTTAGAAC DGEGEEGDEEDGFGEGGEGGGFFGDGGFFFFFFFFAGFDGGFGGDFGGGGGGGGGFGFGGGGGFDGGGGGEGGGGFGGGGGGGGGGGGGGFGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:8985:17141 147 MtDNA 9340 60 100M = 9258 -182 CTGAGTATTGTATGAGTAATTATGTATTTGGTCACAGTTATCAGTCTGAGATTTATTTTAGAACTACTAGATTAAAAAATTAGAAACCTTAGTATAATTT CDDEEEEEFFFFFFFHHHHHHJIHDJJIJJJJIHJJJJJJJJJJJIJJJJJJJJJIJJJJIIIJIHJJJJJJJJJJJJJIIJJJIHJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1305:20758:28262 99 MtDNA 9506 60 100M = 9991 585 GTTCATACCCTTGAGGTGGTTTTCTCTTATTAAAAGTTTTAGTATAAAAAAGTATATTTTATTGTCAATAAAAAGGTAAAAACTTTAGATTCTTTAGTAT CCCFFFFFHHHHHFHJAEHCDHIGJJIJHIJGIHIJFHIJHJGIIJDGHJJGBFHIJJJIGHIGIIIHBDHGGIEACHHFFFFFEEEEEEEDCEDDCCA; PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:76:8573:4029/1 0 MtDNA 9566 60 101M * 0 0 ATTGTCAATAAAAAGGTAAAAACTTTAGATTCTTTAGTATAATTCAGTATGTTTGACTTCCAATCAAAAGGTTTTGAGGATTAATTAATAATTTTTTTCAA DDDDDDD=DDDAB>CD?DDDDDDDDDDBDDDDDDDDDBDDCDDDDDDBDDDBDDDDDADDDDCCDBB=BDDBDDDD?DDBBCCCCCCDDBCBCDBDBCCCB PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:59:16574:9800/1 0 MtDNA 9610 60 101M * 0 0 CAGTATGTTTGACTTCCAATCAAAAGGTTTTGAGGATTAATTAATAATTTTTTTCAAGGATATAATTTACTATTTCAGCATAGTTTATTTGCTAGTTATAT GFAFGFDFFEFFFDDFGGGGGFGCGED=EEDDDDDEGGCGEGGGGGDFGDEFFCE?EGFEGGGDGGFGBGGCGEDGGFG?FDFBFFDGC=AEEAEDDFFDD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:39:12621:19315/1 0 MtDNA 9636 60 101M * 0 0 GTTTTGAGGATTAATTAATAATTTTTTTCAAGGATATAATTTACTATTTCAGCATAGTTTATTTGCTAGTTATATAGATTGATTTCATAGGTTTAATTGTA DBEEEEEEEB?E:EEFFFFB:CDCEFFACFAEEBEBCB?CFEFEFEFFFFFFFDBAC@BC=C;?<EBBEEBDCBBDFDEEB5ACC??B:BE@E?@@A@AA: PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:97:3517:19360/1 16 MtDNA 9687 60 101M * 0 0 GCATAGTTTATTTGCTAGTTATATAGATTGATTTCATAGGTTTAATTGTAGTTTATTGTTGGGAGTTTTAGTGTTTGTTACTTTATTGTTTGGATATTTAA =DF=DEGGGGFGDGFGFF?FGGEGFG?GGGFFGGGGDBGGGFFFEGGGGGGGGGGGFGEEGGFGGGGFGGGGGGGFGGGEGGGGGGGGGFFGGAGGGGGGF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:113:4491:15082/1 16 MtDNA 9710 60 101M * 0 0 TAGATTGATTTCATAGGTTTAATTGTAGTTTATTGTTGGGAGTTTTAGTGTTTGTTACTTTATTGTTTGGATATTTAATTTTTGGTACTTTTTATTTTAAA =BEE?EEE=EEA=5EEEEEEEAEEEEDD;EE;AEE?=EEDDCE=EED?BEEEEE?EEEBDEEEE?A=DEE6EEE=EEEAEEDDEEE?@EEEGFGDGEFF:F PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:73:1194:5250/1 16 MtDNA 9720 60 101M * 0 0 TCATAGGTTTAATTGTAGTTTATTGTTGGGAGTTTTAGTGTTTGTTACTTTATTGTTTGGATATTTAATTTTTGGTACTTTTTATTTTAAAAGAAAAAAAA FF=FBFEEFFFEFFFDFDFCFEEFFDEFFFBFFAFFDFFFFFFFFFEEFFFFFEFFFFFBFFFDFFDFFFDEEEEEEECDEFFFFDFDFFFFFFFFAFFDD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:24:12750:7270/1 16 MtDNA 9752 60 1I5M1D95M * 0 0 GATTTAACTTTGTTACTTTATTGTTTGGATATTTAATTTTTGGTACTTTTTATTTTAAAAGAAAAAAAATTGAGTATCAGTTTGGTGAATTATTGTGTAGT =5EAEE@EEE?FFFAFED:DBEGDEEGDFFGBFEGGFBFFFEED?>C:E8FG:GDCGGG<GF<GAGBGGDGGDGGGD=GGFFGGGFGGGGGGEBGGGGDGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:1:39:6442:9317/1 16 MtDNA 9797 60 101M * 0 0 CTTTTTATTTTAAAAGAAAAAAAATTGAGTATCAGTTTGGTGAATTATTGTGTAGTATTTTTCCAACTATTATTTTATTAATACAAATAGTTCCTTCACTT D8@=CADGEBDGGEEEGGFFEEEFAFG=EFEGGFFDGGGGDGGGGGGEAGGGFGGGFFGGGFFFEDBEGEGGGEGGGFGGDGDGGGEGFGGEGGGGFDFFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1305:20758:28262 147 MtDNA 9991 60 100M = 9506 -585 GATATTCCTGGGTTAGAATTTGACTCTTATATAAAATCACTAGATCAATTAAGTTTAGGTGAACCACGTTTATTAGAAGTTGATAATCGTTGTGTTATTC DEDDDDBBB?;DFFFFFFFEHHEGHIHEGIJJJJIIGHHIGIJIGIJJIGJJJJGHJJIIHHBIGFGBJJJIHEIFJJJJJJJIJJIHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2105:2690:5126 99 MtDNA 10115 60 100M = 10123 108 GTATTACATCTGCTGATGTTATTCATGCTTGGGCATTAAATTCTTTATCTGTAAAATTAGATGCTATAAGAGGAATTTTAAGAACATTTAGTTACAGGTT C@@FFFFFHHHFHJJJJJJIIJJ>FHIIJJEHIIJIJJJJJJIJIJJJJJIFGGIIIJIIIJIIJJIJJIHHGGIFHIIIIHCAEHFHEFFEFFEDEC>@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2105:2690:5126 147 MtDNA 10123 60 100M = 10115 -108 TCTGCTGATGTTATTCATGCTTGGGCATTAAATTCTTTATCTGTAAAATTAGATGCTATAAGAGGAATTTTAAGAACATTTAGTTACAGGTTTCCTATAG DEEDEDFFFFFFHHGFGHJGGIJHGDJIJJJJIGJJJIIIJHIIJJJJIGJJJIJJJJJJJIJJJJJIJJIJJJIHJJIJJJJJJJJHHHFBFFFFFCC@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:95:13542:11427/1 0 MtDNA 10154 60 101M * 0 0 ATTCTTTATCTGTAAAATTAGATGCTATAAGAGGAATTTTAAGAACATTTAGTTACAGGTTTCCTATAGTGGGAGTTTTTTATGGTCAATGTTCAGAGATT GGGGDFGFDGEGGGGGFDGGGGGGGGEFGDGGDGFGEGFGFGGGGGGGDGFFEEGEFGBCGGGGGEGFBEEEECEBEEFFGE=EGEECDEEEEGGDCEDDB PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:56:15270:6191/1 16 MtDNA 10392 60 101M * 0 0 ATATAGAGCTTTAAATTTTACTTGTTTAAATATTGGTATTGCATACTATTACAATAAAATTTCATGTTAATGAAAAATAGAAACAAAGGGTAGAGTAAATA GEEEEGEEEEEDBGEFEGEEGGFEGGFGGEEFEGGGEGFGGDEGEGGEGCDFGGGGGGGGGGGGGGFAGGGGGGGGGGGGGGGGFDGGGGGGGEGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:51:14694:9582/1 16 MtDNA 10415 60 101M * 0 0 GTTTAAATATTGGTATTGCATACTATTACAATAAAATTTCATGTTAATGAAAAATAGAAACAAAGGGTAGAGTAAATATTAGTTTTATTGTTTCATACTAA DEDEFEFEDAEEFF?EFFFEEBEAEE=ECCDDFFFFFFFFEFFEFFD=E@DFFFFFFFFFFFDBFFFEAFEFDFFFDEFFFEGGEGGFEGGGGGFFDFDDE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:69:16487:9482/1 0 MtDNA 10798 60 101M * 0 0 TAGGCTTTATATTAAAGCTGGCTTCTGCCCTATGATATTTAAATGGCAGTCTTAGCGTGAGGACATTAAGGTAGCAAAATAATTTGTGCTTTTATTGAGTT GGGGGGEGGGDEGFGGGGGEGGFGGGGGGGGGGFGDGFGGDGGGEGGFGEGGGGDFEDFBFDEEEEGEFFGCDDFEEGEEEE=GGB@FFDFDGAGAA5EC5 PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:65:19066:9962/1 16 MtDNA 10886 60 101M * 0 0 CTTTTATTGAGTTCCAGTATGAATGAAGTTATTGGTTAGTTCTATTTATGTTTTATGTTTGAATTTAATTTTTATTTAAGAAAAAATAAATATATTTATAC E=@BBD@BEEEE@EE@EEEEEEEBEEBDDDE?FEEBEFFFDDBEBFEEFEDEEEFEBBEAEEFDADFF8CCEEE=??CCCCAFFBFCBEDCB=DEEEEEEE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:57:11714:20002/1 0 MtDNA 11269 60 101M * 0 0 TTTATCTTGATAAATATTTATATTTAATACATTTAGTACGAAAGGAACATTGTAAAAGTTTTAAACTTTAAAGATTTTGAAATCTTTATTTTAGTGCTATT FFFFFEFFFAFFF?FFFFFFFFFFFDFFFFFEFFFFEFFFFDFFBDEFFDFDFFFFFFFFFFFEBFFFFDF=FFFFFFCEEEEFEFFFEFEEE=@BECBBD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:39:7418:8959/1 0 MtDNA 11394 60 101M * 0 0 TTTATTATTTGCTTTTTATTTGATTAATTTTTTATTAAGAATTAAGGATATAGGAAAAAATAAAATTAGAGCGTTTGAATGTGGTTTTGTAAGAGTTGGAA GGGDGG?GGFFGGEGFFDFEFFFAFFFEFFFFFEFFFFFDEFFFDFFFF:E?EEEFACFFFFEEEFFFFAFFBFBFFBFFEBEC=ECEEBBBA=D=?CDAF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:41:12959:4517/1 16 MtDNA 11405 60 101M * 0 0 CTTTTTATTTGATTAATTTTTTATTAAGAATTAAGGATATAGGAAAAAATAAAATTAGAGCGTTTGAATGTGGTTTTGTAAGAGTTGGAAAAATATGATTT EGGEFGGEBGFDGGGGG@GFGGGFEGGGFGGGDGGGGGGDFGGGGGFEGBGFFFD?GFGFEGGGEGGGGEGGGGGGFGDGFGGGGGGGGEGGFGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:5 +EAGLE:2:94:12001:2695/1 0 MtDNA 11494 60 101M * 0 0 AAAATTCAAAATTCTTTTAGAATTCATTTTTTTATTATGATATTGATATTTGTTATTTTTGATTTAGAAATTGTTATGTTTTTAGGTATTTTAGTATCAGA ?EEDEAEEEEDFEFFDEFEDFFEAFDFFFFFFCFDFCFEFF?FFFFFFFAFFDFAFFDFFFFFDFFFDFFFFF=F?DFEFFFA@FF?EFFF?FFEFFF=?: PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:26:8245:3800/1 0 MtDNA 11527 60 101M * 0 0 ATTATGATATTGATATTTGTTATTTTTGATTTAGAAATTGTTATGTTTTTAGGTATTTTAGTATCAGATTTAAGTTCGTATATCAGGTTTTTAATAATATT :FGEEFGFFGGEGGGEFFFFDFFFFGFEGBFFEFEEEEEEDE?EEDEEEBAE?EAEEEECFEDFF=FBFEEA??EEEEEEFEEG?DFF?DEFF?AB;EDDD PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:70:14381:7815/1 0 MtDNA 11624 60 101M * 0 0 TATTCATCTTCATCTTGGGAGGATTTTACATAGAGTGATGATATGGTAAATTAGTTTGAGTAATTTAATTAATATTTCTATTTTTTTGATTGGATTTGTTT GGGGGEGGGGGGFGGEGGGGFGFGGGGAGGGFGGGEGFGFGFEGFGEG?GGGFGFFFFBF@EEDEGEEGBADGFGGGGGGGBGGGDGC@F?EECDFFFDAC PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:41:9505:15324/1 16 MtDNA 11679 60 101M * 0 0 TTGAGTAATTTAATTAATATTTCTATTTTTTTGATTGGATTTGTTTTTTTTATAGGTGGAATTAGTGTTTGGCTTATACCCACATTTAAATTAGGAATCTT EBE=E=EEEEEEEEEE=BEEDEEEEEDEEB?EEEEEEE>EEECCC;EEEEEEEDEEEEE5EDEEEEDDAEEEDDEEDADDD:EEDEDF?AFEBDEDDDBD? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:1:16170:13381/1 0 MtDNA 11707 60 101M * 0 0 TTTTGATTGGATTTGTTTTTTTTATAGGTGGAATTAGTGTTTGGCTTATACCCACATTTAAATTAGGAATCTTTTTTTTAGAATGAGATTTTTTAAGGTTA FFFFFBFFFFFDFDFGEGGGDG>@GAED=EDCCDA:DADCE?EEEFD==FFFEDB?FFFFC:EC:ECCBBC?EEECAFC8=C:=D?E5ECFEFDB:E:CAE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:85:11274:20902/1 0 MtDNA 11790 60 101M * 0 0 TGAGATTTTTTAAGGTTAAAATTTAATTTTTATTTTAATAGAATCTTATTTTCGTTTATTCTTTTTTTGGTAACGTTTAGAGTTTTAGTTTTTAGTAGTTA GGGGFGGGGGGGGGGDGGGFGGGGGFGGFGGGGGGGGGGGGEGGGGFEGGGGGGGGGEGGGGGGGGGGEFCEFFGFFEEEEGEGGGCFDEGFEEF=:6??: PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:45:6186:13482/1 0 MtDNA 11795 60 101M * 0 0 TTTTTTAAGGTTAAAATTTAATTTTTATTTTAATAGAATCTTATTTTCGTTTATTCTTTTTTTGGTAACGTTTAGAGTTTTAGTTTTTAGTACTTATTATT DFFFEBAEEEDDADDEDED==CCCCE=EEEEEEDBEEE?EEDDEEAB@EEDDEEDEEAEECEECA>:ACC@DCCB?DAABEBEBCEEEB?EBBEEB=E@EE PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:26:5376:8009/1 0 MtDNA 11861 60 101M * 0 0 AACGTTTAGAGTTTTAGTTTTTAGTACTTATTATTTAAATAGTGAGTTAAACTTTAATTATTATTATTTTGTATTGTTAATTTTCGTAGGTAGAATGTTTA ADC<DCEDBEAF?D:DBEEAFBBDBAE?EEDG?GEEGEEFEE??ED:AD?EEEEEBBGGD?FADFDGGGFEBDEDDEAEEDGFGBE5CEE=DD=?:B>ABB PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1301:9999:63927 99 MtDNA 11891 60 100M = 11969 178 TTATTTAAATAGTGAGTTAAACTTTAATTATTATTATTTTGTATTGTTAATTTTCGTAGGTAGAATGTTTAGGCTAAATTTTAGAAACAGTATTTTTACA CCCFFFFFHHHHFHIJJJIJGIJJJJIJJJJJJJJJJJJJJIJJJJIJJJJJJJJJHIJIFGIIJJJIJJJIJIJHGIJJJJJIIHHHHHADFFFFFDCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:18436:71346 99 MtDNA 11949 60 100M = 12056 207 GGTAGAATGTTTAGGCTAAATTTTAGAAACAGTATTTTTACAATGTTACTAAGATGAGATTTATTGGGTATTTCTAGGTTTTTTTTAGTTTTATTTTATA BCBDFFFFHHHHHJJJJJIJJJJJIIIJJJJJCHIIJJJIIIJJJGIIJJJJIIJIGIFHHIHIJIJIFHHJJJJEIJEHIJHFDDDDDDEDDDDEEEDD PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:74:13913:12442/1 16 MtDNA 11959 60 101M * 0 0 TTAGGCTAAATTTTAGAAACAGTATTTTTACAATGTTACTAAGATGAGATTTATTGGGTATTTCTAGGTTTTTTTTAGTTTTATTTTATAATAATTGAGAT GGGEEEFFBEEDGFGGFEDGFGGFGDGGGEGGGGGGGEGGFGFGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGFGGCAAA@D9EEEGGGGGGGGGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1301:9999:63927 147 MtDNA 11969 60 100M = 11891 -178 TTTTAGAAACAGTATTTTTACAATGTTACTAAGATGAGATTTATTGGGTATTTCTAGGTTTTTTTTAGTTTTATTTTATAATAATTGAGATAGATGTAGG ADEEDDDCCEDDDDDDEEEEDEEEFFFFFFFHHHHHHJJJJJJJJJJJIIJJJIJJJJIIIJJJJJJIJJJJJJJJJJJIIIJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:27:3003:10682/1 16 MtDNA 12043 60 101M * 0 0 TTTATAATAATTGAGATAGATGTAGGGGTGCAATAAATACAGCATTAACTAATCGTCTAGGTGATTATTTTATATTTGTCTTTTTTGGTTTGTCGGTTTTT FB?CEACEE=EDEEE==?EE=DFFEAEEEE;FCEFEBAF?F?FFDFBEDGGFBEGGGGFGGGGEGFF?;FFFFDDDGDEGEFGEGGGGDAFGGGFGDFGGB PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:2202:18436:71346 147 MtDNA 12056 60 100M = 11949 -207 AGATAGATGTAGGGGTGCAATAAATACAGCATTAACTAATCGTCTAGGTGATTATTTTATATTTGTCTTTTTTGGTTTATCGGTTTTTAGAGGTTATTAT DDEDDDDDDDDDDDDDDDDFEFEDCDDDDDEEDCCEDFFFHHHHJJJJJJJJJJJJJIJJIIJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1116:18352:37917 99 MtDNA 12193 60 100M = 12359 266 TATTATTACTTTTAACAGCTTTTACTAAAAGAGCACAATTTCCATTTAGATCTTGGTTACCCAAAGCTATAAGAGCCCCCACACCGGTGAGGTCTTTGGT @@@FFFDDHGHHHII@FGGGGGGIIIIIIJJIIGGIIJIJFHIGGIJFEHDBGHHGBGIJIHGIAEHIIIJCG@ACCDHEB<?A=>@,8<995<CCDD?B PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2313:14435:43021 99 MtDNA 12276 60 100M = 12492 316 CCGGTGAGGTCTTTGGTTCATAGTAGAACTTTAGTTACAGCAGGATTAATTCTATTAATAAATTTTAATAATTTAGTAATACAGAAAGATTTTATCAGTT B@@DADBDFCFHHIGGIIJGIJJJJJJJJJJJGIHGIGHJJIIJJJGHIIFFFICIIJIJICHJGGGFHHIIJIIIHIIJIHGGEHGF@BCFFECCDE@@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1116:18352:37917 147 MtDNA 12359 60 100M = 12193 -266 GAAAGATTTTATCAGTTTTGTTCTGATTATTGGCCTATTTACTATATTTTTTTCTAGCTTAGCAAGTTTGGTCGAAGAAGATTTGAAGAAGGTGGTAGCC DDDDCEDDDCCADCDDDDCAC>CACA@C>FFFFHGHHHEE@>CDAHFEGIEIJIGIGHIIGIGHGJIIIHIGIHIJGGHDJJIIHEIHHHHHFDFDF@@@ PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:4:6493:13587/1 0 MtDNA 12373 60 101M * 0 0 GTTTTGTTCTGATTATTGGCCTATTTACTATATTTTTTTCTAGCTTAGCAAGTTTGGTCGAAGAAGATTTGAAGAAGGTGGTAGCCTTGAGGACACTTTCA B88:7D??>BGFGDFEDDEFEDBEEEGEEBE=DEEEEEEEEEEGED@EDE5BABBEE>AAA?@?@@?5??BB?BBABA>B?7:??AAABAAAA?A<:>A>? PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:1:5:16925:17939/1 0 MtDNA 12403 60 101M * 0 0 TATTTTTTTCTAGCTTAGCACGTTTGGTCGAAGAAGATTTGAAGAAGGTGGTAGCCTTGAGGACACTTTCACAAATAGGTTTTTCAATAGTTACTTTGGGC FFF5FFEEECGGGEGEDEEE=EEEEEEEEEEEDEEEEEEEEEEEEEEDDEEE=E?BEEEEEEDEEEEEEEEEEEE6CCB>AEEEEEE?BADEEBEEAE=EE PG:Z:SNAP RG:Z:266-1 NM:i:1 +EAGLE:1:79:6338:4546/1 0 MtDNA 12420 60 101M * 0 0 GCAAGTTTGGTCGAAGAAGATTTGAAGAAGGTGGTAGCCTTGAGGACACTTTCACAAATAGGTTTTTCAATAGTTACTTTGGGCCTAGGGCTTAGGTTTAT FFDFFFFFFDEFBFFGGGGGFGEEGGEFFFECEECFFFFFGGGGFGGGGGGGGGFGEFEGGGEGEFFF?DFDFCFEEFEFEBFGEEEEBGEEEEDGEEEEF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1313:2251:84798 99 MtDNA 12449 60 100M = 12482 133 GGTGGTAGCCTTGAGGACACTTTCACAAATAGGTTTTTCAATAGTTACTTTGGGCCTAGGGCTTAGGTTTATTTCATTTATTCATTTAGTTAGACATGCT BCBDFDFFHHHHHJIJIJJJJJJJJJJJIJJIJEFHJJJGIGHJIIJJIJJJIIGHJIIIJJJJJJIEHHIGHHHFHHHFFFFFFFFEEEEEEEDCDDDC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1313:2251:84798 147 MtDNA 12482 60 100M = 12449 -133 TTTTTCAATAGTTACTTTGGGCCTAGGGCTTAGGTTTATTTCATTTATTCATTTAGTTAGACATGCTTTGTTCAAAAGATGTTTATTTATACAAGTAGGT ADDDDDEECEC>CDFFFDHHHHIJJJJJIIJJJJJJJJJJJIJJJJJJJJJJJJIJJIJIIJJJIJJJIIGIJJJJJJJJJJJJJJJHHGHGFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2313:14435:43021 147 MtDNA 12492 60 100M = 12276 -316 GTTACTTTGGGCCTAGGGCTTAGGTTTATTTCATTTAATCATTTAGTTAGACATGCTTTGTTCAAAAGATGTTTATTTATACAAGTAGGTTACATTATTC ACC@CEDCDBDDFFHHHFIGHGIIGIJGIIIJHGHD?4JJJJIHIJJIGIHJIJJJJJIJIIJJJJIJJJJJJJJJJJJIHJJJIJJHHHHHFFFFFC@C PG:Z:SNAP RG:Z:000 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:13602:38947 99 MtDNA 12495 60 100M = 12781 386 ACTTTGGGCCTAGGGCTTAGGTTTATTTCATTTATTCATTTAGTTAGACATGCTTTGTTCAAAAGATGTTTATTTATACAAGTAGGTTACATTATTCATT ?????DD::C:2<3C?;EECFFEIEFIEDE9?@E@DA<DDCDCDEEDAECDDDDA@DEDCEAC>C;CA7=ACCEDCEIEED>)=?A7?7?DDD@>BD@AD PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:102:10210:8668/1 0 MtDNA 12538 60 101M * 0 0 TTAGACATGCTTTGTTCAAAAGATGTTTATTTATACAAGTAGGTTACATTATTCATTGTTCATTTGGACAACAAGATGGACGTAATTATAGGAATAATGGT GFGGGGGGGG:FF?FGGGFGGGFGEBFGGGGFFDDGGGGGGGGAGDEEEEGFFBGGDED;EAGGGDGEEG?FDFFBEG5EEDCEEFDA5FEEBEF?EEB:: PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2214:8352:14578 99 MtDNA 12620 60 100M = 12676 156 TAAGTATAGGAATAATGTTAATTTACCAAATTTTATTCAGTTACAAATATTAGTAACCCTATTTTGTTTATGTGGATTAATTTTCTCAAGGGGTGCTGTA @CC1BDFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJIJJJJJJJJJJJJJJIGHJGIIIGHIFGIJJJJIGHHHFDBABCDDD PG:Z:SNAP RG:Z:000 NM:i:2 +BS-DSFCONTROL03:121:D0M8KACXX:5:2214:8352:14578 147 MtDNA 12676 60 100M = 12620 -156 CCCTATTTTGTTTATGTGGATTAATTTTCTCAAGGGGTGCTGTAAGAAAAGATTTTATTTTAGAATTATTTTTTTCTAATAACTATATAATGTTTTTTAG ?CCDDBDDDDDDDDDDDDDEDDEDEEEAFFFFFHHIIEJJJGIJJJJIHFGJJIJJIIGIJJJJIIJJJIJJJJJJJJJIJJJJJJJHHHHHFFFFFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:101:7524:6107/1 0 MtDNA 12685 60 101M * 0 0 GTTTATGTGGATTAATTTTCTCAAGGGGTGCTGTAAGAAAAGATTTTATTTTAGAATTATTTTTTTCTAATAACTATATAATGTTTTTTAGATTAATATTT BEEEEDD5DDEEEDEFEDFFAFBDFFFFDFFFFAFEED=E:CBEEFFEDFFEEFEDFFFFDFFFFDF@EFBDFFBEFEFABCD:EFFCCCDD:EADFEFFF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:73:3706:15683/1 0 MtDNA 12685 60 101M * 0 0 GTTTATGTGGATTAATTTTCTCAAGGGGTGCTGTAAGAAAAGATTTTATTTTAGAATTATTTTTTTCTAATAACTATATAATGTTTTTTAGATTAATATTT DDDD:DDBDBBEEEEGFFFGGGFGGGFGDF?ADCEFF=EB?CE:BFF=FCCE>FDEDEAAGAGCCEEGEEGGFEFEFEGD@EFADEFCC>E?E=BBBAEBF PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:35:14999:3587/1 0 MtDNA 12745 60 101M * 0 0 TTTTTTCTAATAACTATATAATGTTTTTTAGATTAATATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTC DEFFFFFFFFBFD?FFFBFFFFFAFEEBECFDFFFFFDAFFFFFFCFFFBECECEFFEC?FBFFFDDEE??CDBEFFFFEEFFFFABFFFE8CFFFFFFE; PG:Z:SNAP RG:Z:266-1 NM:i:1 +BS-DSFCONTROL03:121:D0M8KACXX:5:1101:18737:28666 99 MtDNA 12755 60 100M = 12783 128 TAACTATATAATGTTTTTTAGATTAATATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAAT CCCFFFFEHHHHHJJJJJJGJGHJJJIGIIJJJJJHIJIIIGHIJJJJJHIIJJJJJIJJJJJIGHHHHFFFFEECECEDDBDDDDDDDDBCCDCCDDDA PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:1:53:16100:4061/1 0 MtDNA 12755 60 101M * 0 0 TAACTATATAATGTTTTTTAGATTAATATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATA FFDFFDEFDFAFE=FDFE@AFB?DFFF5FF?D@<@ACAEEE:ECEEEAA=FFDFDFADDFEEE@EEEEE@AABBB=AEEEDCCFDBEFE@@@DBADEDBBF PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1303:13602:38947 147 MtDNA 12781 60 100M = 12495 -386 TATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATAAAGTAATAAATCATTACAGTAGCAC :?BBBB?CC@5CCCA9'=>>5(;>C;;A>>?;B@BFEFHEBG@=@>FB;BCGB?<GDEDC9<F<EEA<4D>HEGJHE<C<?<?A<2,,?B=2A4DDD8@? PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1101:18737:28666 147 MtDNA 12783 60 100M = 12755 -128 TTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATAAAGTAATAAATCATTACAGTAGCACAG BDBDDDDCCDDDDBBDDDDEDCDDDDEEEFFFFFFHHFIJJJJJJJJIIHJIIJJJJJJJHGJJJJIJIJJIJJJJIJJJJJJJJJJGHHHHFFFDFCCC PG:Z:SNAP RG:Z:000 NM:i:0 +EAGLE:2:109:6839:9395/1 16 MtDNA 12786 60 101M * 0 0 TTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATAAAGTAATAAATCATTACAGTAGCACAGTATT GGGGGFEFFGGGGGGDGGDGFDGGGGGGFGGGGGGFFGGGFGGGGGGGGGGGGGGGGGGFBGGGGGDGGGGGGGGGGGGGGFGGGGGGGGEGGFGGGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:89:16184:15896/1 16 MtDNA 12850 60 101M * 0 0 TTAATAAAGTAATAAATCATTACAGTAGCACAGTATTTATAAATTTTTTAAGTTTAGTATTAGTTATTTTTTCTATTAGATTTTTATGATGAATAAATTTT EEEEFEEDFEEEGEBEEGEEBEGEEFGEGEGDGBFGFGGFGDFGEGGFEGGGFGEGGGGGFFGCEGGGGGGDGFFGDEGDGGGEGFDGGGGEGFGFGGGGG PG:Z:SNAP RG:Z:266-1 NM:i:0 +EAGLE:2:73:18789:5004/1 0 MtDNA 12862 60 97M1I3M * 0 0 TAAATCATTACAGTAGCACAGTATTTATAAATTTTTTAAGTTTAGTATTAGTTATTTTTTCTATTAGATTTTTATGATGAATAAATTTTAATCTAATAGAA GFEGFGGF=FEADEEEEEEDEEDEEFFFFFGGGGGGDGGGEGDFABE:EEBA=BBFFCCCGE@FF?BBBCACCB8>BEEEFFFGGFFGGE?EEEBD5?BBE PG:Z:SNAP RG:Z:266-1 NM:i:4 +BS-DSFCONTROL03:121:D0M8KACXX:5:1114:11635:22812 99 MtDNA 12940 60 100M = 13083 243 GAATAAATTTTAATCTTCTTAACATCCCAAGACTTTTCTTATACGTAGATTTTTTTGGTCCTCTAGTATTTTTATTTATAATAATTTTTTTATCTTTTTT CCCFFFFFHHHHHJJJJIJJJJJJJIJJJJJJJJJJJJJJJJIIJHIJIJGHJJJJJIHHIJJJFHEHHHHHFFFFFFFEEFEEEFEDDDDDDDDDDDD< PG:Z:SNAP RG:Z:000 NM:i:1 +EAGLE:1:50:13913:15312/1 16 MtDNA 13005 60 101M * 0 0 GTATTTTTATTTATAATAATTTTTTTATCTTTTTTAATTTTAAAAATATTATTTAAGGAGTTAATATACAAGTTTTTAGTTGATTATTTGGCTAAAAATAG ?>:>;::BCBB::FFF@@8<96BABC=@DFFBF=EDFDEFCAE=?EE?FAFEEC?=EEEC=FDEEBEEDAFF?EFFEBEDDEEEEBCDDD?E@<DDDEECE PG:Z:SNAP RG:Z:266-1 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:1114:11635:22812 147 MtDNA 13083 60 100M = 12940 -243 GTTGATTATTTGGCTAAAAATAGTATTTATAAAATAAAGAATTTAAAATTTATAGATTTATTTTTAAATAATATTAATTCTAAGGGGTACACCTTATTTT @CFEDEFFFHGHGIJJJJJJJIHEGJJIHCJJJJJJJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHDHFFFFFCC@ PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2115:12001:40456 99 MtDNA 13159 60 100M = 13242 183 ATTCTAAGGGGTACACCTTATTTTTAAGCAGTGGTATATTTAAAAATTACTATTTAAAAAGGTTAAATTTTAATAGTGTAGTAGTTTTAATTTTTATTTT @@@FFFFDFFHDFGGEB;AB<EHGGGBH@FH?CC?F@GGIII>DGHGEDBDHHEDHGHIIGCHGI@@FGHIHGGIC==EC>)=A?CD>DDDEEECAACDD PG:Z:SNAP RG:Z:000 NM:i:0 +BS-DSFCONTROL03:121:D0M8KACXX:5:2115:12001:40456 147 MtDNA 13242 60 100M = 13159 -183 GTTTTAATTTTTATTTTTTTTATAATTTGTTAAGGGATTTTAGTTTAATAAAAATATATGTTTTGCATACATAAGATAATAATTCTAGATAGTTTTACAC @DDDDDDDCACDDDFGJIIJIJIIG@HIIJIHIHJJIIGJJIHGGIEIIGIIIIJIGIJJJJIGGCIIIGJIJJJIJJJIHIIJJJJHHFDGFFDDD@@@ PG:Z:SNAP RG:Z:000 NM:i:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.vcf Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,192 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/wolma/galaxy_2017/database/files/000/dataset_35.dat +##contig=<ID=chrI,length=25050> +##contig=<ID=chrII,length=25050> +##contig=<ID=chrIII,length=25050> +##contig=<ID=chrIV,length=25050> +##contig=<ID=chrV,length=25050> +##contig=<ID=chrX,length=25050> +##contig=<ID=MtDNA,length=13794> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)"> +##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes 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=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases"> +##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled Genotype Quality"> +##source=MiModD varcall (version 0.1.8.0) +##MiModDCommand=mimodd varcall /home/wolma/galaxy_2017/database/files/000/dataset_35.dat /home/wolma/galaxy_2017/database/files/000/dataset_54.dat --index-files /home/wolma/galaxy_2017/database/files/_metadata_files/000/metadata_14.dat --ofile /home/wolma/galaxy_2017/database/files/000/dataset_58.dat --depth 250 --verbose --quiet +##samtoolsCommand=n.a. (wrapped by MiModD) +##bcftools_callCommand=n.a. (wrapped by MiModD) +##rginfo=<ID=0,Rgid="000",Name="N2"> +##rginfo=<ID=1,Rgid="266-1",Name="ot266",Description="mutant strain carrying the vab-3 allele ot266"> +##samtoolsVersion=1.2+htslib-1.2.1 +##bcftools_callVersion=1.2+htslib-1.2.1 +##bcftools_concatVersion=1.2+htslib-1.2.1 +##bcftools_viewVersion=1.2+htslib-1.2.1 +##bcftools_viewCommand=view /home/wolma/galaxy_2017/database/files/000/dataset_58.dat +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N2 ot266 +chrI 855 . G C 231.0 . DP=27;VDB=2.48853e-13;SGB=13.8822;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,11,13;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:255,72,0:24:0,24:86 +chrI 885 . t tTCT 69.0 . INDEL;IDV=4;IMF=0.0769231;DP=56;VDB=2.27029e-09;SGB=1.27626;MQSB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=16,17,3,1;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,3,60:1:1,0:11 0/1:105,0,255:36:32,4:96 +chrI 912 . A T 195.0 . DP=92;VDB=0.233506;SGB=-8.71232;RPB=0.810719;MQB=1;MQSB=1;BQB=0.974933;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=30,38,9,13;MQ=60 GT:PL:DP:DPR:GQ 0/1:26,0,54:2:1,1:25 0/1:204,0,255:88:67,21:127 +chrI 921 . G A 341.0 . DP=101;VDB=0.0381167;SGB=14.497;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=4;AN=4;DP4=0,1,41,52;MQ=60 GT:PL:DP:DPR:GQ 1/1:110,6,0:2:0,2:25 1/1:255,239,0:92:1,91:127 +chrI 942 . A T 182.0 . DP=147;VDB=0.486211;SGB=-13.0084;RPB=0.177913;MQB=1;MQSB=1;BQB=0.00895523;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=42,63,15,21;MQ=60 GT:PL:DP:DPR:GQ 0/1:20,0,116:4:3,1:17 0/1:198,0,255:137:102,35:127 +chrI 945 . G A 396.0 . DP=144;VDB=0.936097;SGB=17.553;RPB=0.198891;MQB=1;MQSB=1;BQB=0.921548;MQ0F=0;ICB=0.3;HOB=0.125;AC=3;AN=4;DP4=7,15,50,66;MQ=60 GT:PL:DP:DPR:GQ 1/1:177,12,0:4:0,4:19 0/1:255,0,86:134:22,112:78 +chrI 962 . G T 379.0 . DP=141;VDB=0.0554366;SGB=20.8365;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,58,75;MQ=60 GT:PL:DP:DPR:GQ 1/1:148,12,0:4:0,4:36 1/1:255,255,0:129:0,129:127 +chrI 973 . A G,T 329.0 . DP=140;VDB=0.0208629;SGB=18.7462;RPB=0.14071;MQB=1;MQSB=1;BQB=0.978744;MQ0F=0;ICB=0.3;HOB=0.125;AC=3,0;AN=4;DP4=7,12,44,71;MQ=60 GT:PL:DP:DPR:GQ 1/1:110,6,0,110,6,110:2:0,2,0:14 0/1:255,0,65,255,255,255:132:19,112,1:56 +chrI 974 . A T 9.21175 . DP=139;VDB=0.000145084;SGB=10.9211;RPB=0.0841531;MQB=1;MQSB=1;BQB=0.939818;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=44,72,7,11;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:14 0/1:45,0,255:132:114,18:36 +chrI 998 . A T 99.0 . DP=98;VDB=0.00196934;SGB=10.9211;RPB=0.976264;MQB=1;MQSB=1;BQB=0.993458;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=33,40,5,13;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:12 0/1:134,0,255:89:71,18:127 +chrI 1000 . A T 93.0 . DP=108;VDB=0.000325892;SGB=11.6141;RPB=0.945574;MQB=1;MQSB=1;BQB=0.923217;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=34,48,9,10;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:13 0/1:128,0,255:99:80,19:120 +chrI 1028 . G A 105.0 . DP=63;VDB=0.000108954;SGB=6.07412;RPB=0.732968;MQB=1;MQSB=1;BQB=0.91987;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=18,30,6,5;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:12 0/1:140,0,255:57:46,11:127 +chrI 1041 . C T 6.52941 . DP=40;VDB=0.00951951;SGB=1.94933;RPB=0.416648;MQB=1;MQSB=1;BQB=0.652425;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=13,21,3,2;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,71:2:2,0:14 0/1:42,0,255:37:32,5:33 +chrI 1045 . T A 273.0 . DP=36;VDB=1.8168e-09;SGB=2.16465;RPB=0.578971;MQB=1;MQSB=1;BQB=0.637911;MQ0F=0;ICB=0.3;HOB=0.125;AC=3;AN=4;DP4=4,1,11,18;MQ=60 GT:PL:DP:DPR:GQ 1/1:54,6,0:2:0,2:13 0/1:255,0,51:32:5,27:43 +chrI 1048 . G A 266.0 . DP=30;VDB=1.83438e-10;SGB=2.65329;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,10,18;MQ=60 GT:PL:DP:DPR:GQ 1/1:35,3,0:1:0,1:20 1/1:255,81,0:27:0,27:98 +chrI 1053 . c cT 8.64418 . INDEL;IDV=1;IMF=0.047619;DP=21;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:32,3,0:1:0,1:16 +chrI 1054 . A T 231.0 . DP=18;VDB=4.22339e-07;SGB=7.05893;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,5,9;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:255,42,0:14:0,14:54 +chrI 1412 . T C 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrI 1414 . G A 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrI 1421 . G A 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrI 2752 . C T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrI 13851 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13856 . T A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13874 . A G 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13876 . C T 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrI 13901 . C A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13919 . C A 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrI 13921 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 13944 . T A 11.8912 . DP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:6 +chrI 13952 . G T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13958 . C T 8.01478 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:32,3,0:1:0,1:4 +chrI 13970 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 13993 . A G 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrI 14201 . G A 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14223 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14242 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14246 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14247 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 22325 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 23943 . g gG 41.4034 . INDEL;IDV=2;IMF=1;DP=2;VDB=0.94;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:66,6,0:2:0,2:9 +chrII 239 . A G 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrII 252 . A T 44.4523 . DP=11;VDB=0.0411132;SGB=0.620439;RPB=0.916482;MQB=0.916482;MQSB=1.00775;BQB=0.366593;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,3,2,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:75,0,160:10:7,3:74 +chrII 265 . A G 161.0 . DP=14;VDB=0.00228484;SGB=4.69269;RPB=0.965069;MQB=1;MQSB=0.966012;BQB=0.686908;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,1,3,6;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:191,0,96:14:5,9:96 +chrII 278 . A T 167.0 . DP=14;VDB=0.000574122;SGB=4.69269;RPB=0.249352;MQB=1;MQSB=0.966012;BQB=0.867428;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,3,5,4;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:197,0,111:14:5,9:111 +chrII 279 . A T,G 38.2143 . DP=14;VDB=0.0501588;SGB=1.94933;RPB=0.448332;MQB=1;MQSB=0.966012;BQB=0.118179;MQ0F=0;ICB=1;HOB=0.5;AC=1,0;AN=2;DP4=7,2,0,5;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0,0,0,0:0:0,0,0:0 0/1:69,0,186,71,175,247:14:9,4,1:67 +chrII 291 . A G 86.0 . DP=14;VDB=0.0340507;SGB=1.94933;RPB=1;MQB=1;MQSB=0.966012;BQB=0.197899;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=6,3,1,4;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:116,0,189:14:9,5:116 +chrII 300 . A C 231.0 . DP=14;VDB=3.24567e-05;SGB=7.05893;MQSB=0.966012;MQ0F=0;AC=2;AN=2;DP4=0,0,7,7;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:255,42,0:14:0,14:53 +chrII 304 . A T 137.0 . DP=14;VDB=0.000156924;SGB=4.00342;RPB=0.991701;MQB=1;MQSB=0.966012;BQB=0.703221;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,5,6,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:167,0,107:14:6,8:108 +chrII 305 . A T 27.2811 . DP=14;VDB=0.0785113;SGB=0.620439;RPB=0.973096;MQB=1;MQSB=0.966012;BQB=0.738577;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=6,5,1,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:59,0,236:14:11,3:56 +chrII 317 . A G 101.0 . DP=14;VDB=0.00324086;SGB=2.63044;RPB=0.94925;MQB=1;MQSB=0.966012;BQB=0.997919;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,4,3,3;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:131,0,172:14:8,6:127 +chrII 331 . A T 121.0 . DP=14;VDB=0.0126037;SGB=3.31571;RPB=0.497296;MQB=0.966012;MQSB=0.966012;BQB=0.834543;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,2,5;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:151,0,154:14:7,7:127 +chrII 343 . A G 90.0 . DP=9;VDB=0.00476095;SGB=1.97062;RPB=0.346719;MQB=0.924584;MQSB=0.924584;BQB=0.462292;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,5,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:120,0,74:9:3,6:74 +chrII 11921 . A T 7.18923 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:31,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrII 17381 . G A 4.14838 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:32,0,34:2:1,1:32 ./.:0,0,0:0:0,0:0 +chrII 17518 . A T 14.9987 . DP=3;VDB=0.5;SGB=0.0985265;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,2,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:45,0,29:3:1,2:30 ./.:0,0,0:0:0,0:0 +chrII 19959 . T A 7.18923 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:31,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrIII 7994 . C T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrIII 8004 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrIII 8023 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 8026 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 8027 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 8039 . C A 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrIII 9659 . C T 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrIII 9662 . G T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 9700 . A T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrIV 9450 . A G 4.78389 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:33,0,27:2:1,1:28 ./.:0,0,0:0:0,0:0 +chrIV 16467 . T C 4.14182 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:32,0,25:2:1,1:26 ./.:0,0,0:0:0,0:0 +chrIV 16478 . C G 4.58205 . DP=3;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=0,2,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:35,0,23:2:1,1:28 0/0:0,3,29:1:1,0:5 +chrIV 16499 . A G 3.42278 . DP=3;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=1,1,0,1;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,79:2:2,0:4 0/1:35,3,0:1:0,1:3 +chrIV 16537 . aaga a 25.8002 . INDEL;IDV=1;IMF=1;DP=3;VDB=0.206307;SGB=-0.516033;MQSB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=1,1,0,1;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,120:2:2,0:4 0/1:60,3,0:1:0,1:3 +chrIV 16633 . C A 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrIV 16697 . C T 52.0 . DP=2;VDB=0.48;SGB=-0.759771;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:40,3,0:1:0,1:9 1/1:36,3,0:1:0,1:9 +chrIV 16709 . C G 5.30774 . DP=3;VDB=0.98;SGB=0.0985265;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=3;AN=4;DP4=0,1,2,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:0,3,39:1:1,0:3 1/1:38,6,0:2:0,2:4 +chrIV 16729 . C T 4.14943 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:0,3,37:1:1,0:3 0/1:35,3,0:1:0,1:3 +chrIV 16769 . A T 13.7861 . DP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:6 +chrIV 16814 . A G 3.03341 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:30,0,31:2:1,1:30 +chrIV 16815 . C A 48.4033 . DP=2;VDB=0.42;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:73,6,0:2:0,2:9 +chrIV 16823 . A C 4.14995 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,28:2:1,1:29 +chrIV 16829 . T C 3.56356 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:31,0,32:2:1,1:31 +chrIV 16833 . A T,G 14.5409 . DP=2;VDB=0.42;SGB=0.0985265;MQSB=1;MQ0F=0;AC=1,1;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0,0,0,0:0:0,0,0:0 1/2:65,34,31,34,0,31:2:0,1,1:29 +chrIV 16834 . T A 3.56452 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:31,0,27:2:1,1:28 +chrIV 16894 . T C 55.0 . DP=2;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:9 1/1:38,3,0:1:0,1:9 +chrIV 16899 . T A 49.5769 . DP=2;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:9 1/1:33,3,0:1:0,1:9 +chrIV 16902 . T G 55.0 . DP=2;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:9 1/1:38,3,0:1:0,1:9 +chrIV 16921 . A G 68.0 . DP=3;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:54,3,0:1:0,1:11 1/1:38,3,0:1:0,1:11 +chrIV 16951 . C A 76.0 . DP=3;VDB=0.740702;SGB=-0.8159;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,2,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:35,3,0:1:0,1:11 1/1:65,6,0:2:0,2:13 +chrIV 17000 . T C 149.0 . DP=7;VDB=0.103091;SGB=-0.680382;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,6,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:14 1/1:132,18,0:6:0,6:29 +chrIV 17020 . C G,A 99.0 . DP=8;VDB=0.391417;SGB=2.55596;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0;AC=1,1;AN=4;DP4=0,1,7,0;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,3,34,3,34,34:1:1,0,0:3 1/2:150,33,15,125,0,122:7:0,6,1:10 +chrIV 17024 . T C 14.4249 . DP=7;VDB=0.48;SGB=0.00473136;RPB=0.6;MQB=1;BQB=0.8;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:45,0,103:7:5,2:44 +chrIV 17037 . T A 37.8983 . DP=7;VDB=0.460446;SGB=0.620439;RPB=1.01283;MQB=1.01283;BQB=0.810265;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,0,3,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:68,0,95:7:4,3:69 +chrIV 17051 . C T 103.0 . DP=6;VDB=0.534935;SGB=1.41704;MQ0F=0;AC=2;AN=2;DP4=0,0,5,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:127,15,0:5:0,5:22 +chrIV 17112 . T A 3.03494 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:30,0,30:2:1,1:30 +chrV 5001 . T G 4.94666 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:28,3,0:1:0,1:4 +chrV 10045 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrV 10095 . T A 50.0 . DP=2;VDB=0.56;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:75,6,0:2:0,2:9 +chrV 10108 . C A 4.15167 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,32:2:1,1:32 +chrV 10158 . C T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrV 10166 . G A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10205 . A G 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10229 . G C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10249 . G T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10250 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrV 10251 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10257 . A T 6.39934 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:30,3,0:1:0,1:4 +chrV 10279 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 14271 . T C 39.4036 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:64,6,0:2:0,2:9 +chrV 14273 . G C 39.4036 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:64,6,0:2:0,2:9 +chrV 14285 . T C 76.0 . DP=3;VDB=0.074936;SGB=0.461295;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:100,9,0:3:0,3:13 +chrV 14335 . T G 19.5632 . DP=6;VDB=0.18;SGB=0.00473136;RPB=1;MQB=1;MQSB=1;BQB=0.875;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,0,0,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:50,0,98:6:4,2:49 +chrV 14337 . A G 100.0 . DP=6;VDB=0.405004;SGB=1.41704;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,4,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:132,0,14:6:1,5:9 +chrV 14339 . A G 154.0 . DP=6;VDB=0.189016;SGB=1.97062;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,4,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:178,18,0:6:0,6:25 +chrV 14346 . C T 100.0 . DP=6;VDB=0.405004;SGB=1.41704;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,4,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:132,0,18:6:1,5:14 +chrV 14367 . C A 104.0 . DP=5;VDB=0.220638;SGB=0.908071;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:128,12,0:4:0,4:19 +chrV 14445 . A G 21.4343 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:46,6,0:2:0,2:9 +chrV 14481 . G A 4.15167 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,32:2:1,1:32 +chrV 14488 . G T 4.15167 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,32:2:1,1:32 +chrV 14528 . G A 3.56356 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:31,0,32:2:1,1:31 +chrV 14530 . A G 4.13076 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,22:2:1,1:23 +chrV 14538 . T C 32.4055 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:57,6,0:2:0,2:9 +chrX 1592 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 1622 . G T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 1648 . A C 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrX 1650 . T A 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrX 6015 . A T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:38,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6032 . G A 8.01478 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:32,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6058 . ta t 15.3937 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:40,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6118 . A G 15.394 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:40,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6143 . G A 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:37,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6984 . T A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 7025 . A G 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrX 10527 . c cC 8.86989 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:33,3,0:1:0,1:4 +chrX 10535 . T C 11.8912 . DP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:6 +chrX 10562 . C G 18.2649 . DP=7;VDB=0.18;SGB=0.00473136;RPB=0.8;MQB=1;MQSB=1;BQB=0.9;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,1,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:49,0,131:7:5,2:48 +chrX 10595 . T G 148.0 . DP=7;VDB=0.00429645;SGB=2.55596;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,6,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:172,21,0:7:0,7:29 +chrX 10629 . gt g 45.8065 . INDEL;IDV=4;IMF=0.666667;DP=6;VDB=0.14;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:70,6,0:2:0,2:13 +chrX 10630 . T C,G 10.4616 . DP=2;VDB=0.32;SGB=0.0985265;MQSB=1;MQ0F=0;AC=1,1;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0,0,0,0:0:0,0,0:0 1/2:58,29,26,32,0,29:2:0,1,1:25 +chrX 10643 . G T 34.5919 . DP=3;VDB=0.02;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:59,6,0:2:0,2:11 +chrX 15480 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 15495 . G C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 24890 . C G 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 24935 . A C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +MtDNA 954 . G T 4.79534 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ 0/1:36,3,0:1:0,1:3 0/1:0,3,33:1:1,0:3 +MtDNA 5979 . C A 7.18923 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:31,3,0:1:0,1:4 +MtDNA 8429 . A G 38.5774 . DP=2;VDB=0.36;SGB=-0.759771;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:26,3,0:1:0,1:9 1/1:37,3,0:1:0,1:9 +MtDNA 12134 . A G 6.22224 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ 0/1:0,3,41:1:1,0:3 0/1:38,3,0:1:0,1:3 +MtDNA 12637 . G T 8.72328 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=1,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:41,3,0:1:0,1:3 0/1:0,3,25:1:1,0:3 +MtDNA 12998 . C T 14.4264 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:39,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ce11ToCe10.over.chain Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,871 @@ +chain 1420037770 chrI 15072434 + 0 15072434 chrI 15072423 + 0 15072423 5 +288367 0 1 +49582 0 1 +3348 0 1 +884584 1 0 +731267 0 1 +203378 1 0 +1324625 0 1 +399852 13 13 +122370 1 0 +213502 1 0 +782497 1 0 +39234 0 3 +867656 1 0 +595979 1 0 +295566 2 0 +147478 1 1 +23 1 1 +191487 13 13 +8983 1 0 +213892 1 0 +58238 1 0 +125173 11 11 +206247 1 0 +126100 1 1 +46 1 1 +281857 1 0 +118832 1 0 +67661 0 1 +470697 1 0 +457535 1 0 +70047 4 4 +38252 0 1 +84452 1 0 +164033 1 0 +319488 1 0 +78543 1 0 +82353 0 1 +129773 0 1 +246657 1 0 +5362 1 0 +354010 0 4 +296600 1 0 +240963 1 0 +37688 1 0 +81200 0 1 +883251 1 0 +528183 1 0 +98784 1 1 +39 1 1 +65027 1 0 +20874 0 1 +542549 1 0 +216555 1 1 +30 1 1 +489109 1 0 +27002 0 1 +222382 0 1 +473092 + +chain 1440101603 chrII 15279421 + 0 15279421 chrII 15279345 + 0 15279345 4 +523340 1 0 +72281 0 8 +1033090 1 0 +219329 1 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/header_only.sam Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,2 @@ +@HD VN:1.5 +@RG ID:000 SM:N2 DS:C. elegans wt CN:ABC DT:2017-06-27 LB:XYZ PI:400 PL:ILLUMINA PU:SEQ123
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rebased.vcf Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,186 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/wolma/galaxy_2017/database/files/000/dataset_35.dat +##contig=<ID=chrI,length=15072423> +##contig=<ID=chrII,length=15279345> +##contig=<ID=chrIII,length=13783700> +##contig=<ID=chrIV,length=17493793> +##contig=<ID=chrM,length=13794> +##contig=<ID=chrV,length=20924149> +##contig=<ID=chrX,length=17718866> +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> +##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> +##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> +##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)"> +##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes 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=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases"> +##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled Genotype Quality"> +##source=MiModD varcall (version 0.1.8.0) +##MiModDCommand=mimodd varcall /home/wolma/galaxy_2017/database/files/000/dataset_35.dat /home/wolma/galaxy_2017/database/files/000/dataset_54.dat --index-files /home/wolma/galaxy_2017/database/files/_metadata_files/000/metadata_14.dat --ofile /home/wolma/galaxy_2017/database/files/000/dataset_58.dat --depth 250 --verbose --quiet +##samtoolsCommand=n.a. (wrapped by MiModD) +##bcftools_callCommand=n.a. (wrapped by MiModD) +##rginfo=<ID=0,Rgid="000",Name="N2"> +##rginfo=<ID=1,Rgid="266-1",Name="ot266",Description="mutant strain carrying the vab-3 allele ot266"> +##samtoolsVersion=1.2+htslib-1.2.1 +##bcftools_callVersion=1.2+htslib-1.2.1 +##bcftools_concatVersion=1.2+htslib-1.2.1 +##bcftools_viewVersion=1.2+htslib-1.2.1 +##bcftools_viewCommand=view /home/wolma/galaxy_2017/database/files/000/dataset_58.dat +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N2 ot266 +chrI 855 . G C 231.0 . DP=27;VDB=2.48853e-13;SGB=13.8822;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,11,13;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:255,72,0:24:0,24:86 +chrI 885 . t tTCT 69.0 . INDEL;IDV=4;IMF=0.0769231;DP=56;VDB=2.27029e-09;SGB=1.27626;MQSB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=16,17,3,1;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,3,60:1:1,0:11 0/1:105,0,255:36:32,4:96 +chrI 912 . A T 195.0 . DP=92;VDB=0.233506;SGB=-8.71232;RPB=0.810719;MQB=1;MQSB=1;BQB=0.974933;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=30,38,9,13;MQ=60 GT:PL:DP:DPR:GQ 0/1:26,0,54:2:1,1:25 0/1:204,0,255:88:67,21:127 +chrI 921 . G A 341.0 . DP=101;VDB=0.0381167;SGB=14.497;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=4;AN=4;DP4=0,1,41,52;MQ=60 GT:PL:DP:DPR:GQ 1/1:110,6,0:2:0,2:25 1/1:255,239,0:92:1,91:127 +chrI 942 . A T 182.0 . DP=147;VDB=0.486211;SGB=-13.0084;RPB=0.177913;MQB=1;MQSB=1;BQB=0.00895523;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=42,63,15,21;MQ=60 GT:PL:DP:DPR:GQ 0/1:20,0,116:4:3,1:17 0/1:198,0,255:137:102,35:127 +chrI 945 . G A 396.0 . DP=144;VDB=0.936097;SGB=17.553;RPB=0.198891;MQB=1;MQSB=1;BQB=0.921548;MQ0F=0;ICB=0.3;HOB=0.125;AC=3;AN=4;DP4=7,15,50,66;MQ=60 GT:PL:DP:DPR:GQ 1/1:177,12,0:4:0,4:19 0/1:255,0,86:134:22,112:78 +chrI 962 . G T 379.0 . DP=141;VDB=0.0554366;SGB=20.8365;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,58,75;MQ=60 GT:PL:DP:DPR:GQ 1/1:148,12,0:4:0,4:36 1/1:255,255,0:129:0,129:127 +chrI 973 . A G,T 329.0 . DP=140;VDB=0.0208629;SGB=18.7462;RPB=0.14071;MQB=1;MQSB=1;BQB=0.978744;MQ0F=0;ICB=0.3;HOB=0.125;AC=3,0;AN=4;DP4=7,12,44,71;MQ=60 GT:PL:DP:DPR:GQ 1/1:110,6,0,110,6,110:2:0,2,0:14 0/1:255,0,65,255,255,255:132:19,112,1:56 +chrI 974 . A T 9.21175 . DP=139;VDB=0.000145084;SGB=10.9211;RPB=0.0841531;MQB=1;MQSB=1;BQB=0.939818;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=44,72,7,11;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:14 0/1:45,0,255:132:114,18:36 +chrI 998 . A T 99.0 . DP=98;VDB=0.00196934;SGB=10.9211;RPB=0.976264;MQB=1;MQSB=1;BQB=0.993458;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=33,40,5,13;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:12 0/1:134,0,255:89:71,18:127 +chrI 1000 . A T 93.0 . DP=108;VDB=0.000325892;SGB=11.6141;RPB=0.945574;MQB=1;MQSB=1;BQB=0.923217;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=34,48,9,10;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:13 0/1:128,0,255:99:80,19:120 +chrI 1028 . G A 105.0 . DP=63;VDB=0.000108954;SGB=6.07412;RPB=0.732968;MQB=1;MQSB=1;BQB=0.91987;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=18,30,6,5;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,110:2:2,0:12 0/1:140,0,255:57:46,11:127 +chrI 1041 . C T 6.52941 . DP=40;VDB=0.00951951;SGB=1.94933;RPB=0.416648;MQB=1;MQSB=1;BQB=0.652425;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=13,21,3,2;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,71:2:2,0:14 0/1:42,0,255:37:32,5:33 +chrI 1045 . T A 273.0 . DP=36;VDB=1.8168e-09;SGB=2.16465;RPB=0.578971;MQB=1;MQSB=1;BQB=0.637911;MQ0F=0;ICB=0.3;HOB=0.125;AC=3;AN=4;DP4=4,1,11,18;MQ=60 GT:PL:DP:DPR:GQ 1/1:54,6,0:2:0,2:13 0/1:255,0,51:32:5,27:43 +chrI 1048 . G A 266.0 . DP=30;VDB=1.83438e-10;SGB=2.65329;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,10,18;MQ=60 GT:PL:DP:DPR:GQ 1/1:35,3,0:1:0,1:20 1/1:255,81,0:27:0,27:98 +chrI 1053 . c cT 8.64418 . INDEL;IDV=1;IMF=0.047619;DP=21;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:32,3,0:1:0,1:16 +chrI 1054 . A T 231.0 . DP=18;VDB=4.22339e-07;SGB=7.05893;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,5,9;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:255,42,0:14:0,14:54 +chrI 1412 . T C 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrI 1414 . G A 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrI 1421 . G A 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrI 2752 . C T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrI 13851 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13856 . T A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13874 . A G 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13876 . C T 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrI 13901 . C A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13919 . C A 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrI 13921 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 13944 . T A 11.8912 . DP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:6 +chrI 13952 . G T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrI 13958 . C T 8.01478 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:32,3,0:1:0,1:4 +chrI 13970 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 13993 . A G 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrI 14201 . G A 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14223 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14242 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14246 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 14247 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 22325 . T C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrI 23943 . g gG 41.4034 . INDEL;IDV=2;IMF=1;DP=2;VDB=0.94;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:66,6,0:2:0,2:9 +chrII 239 . A G 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrII 252 . A T 44.4523 . DP=11;VDB=0.0411132;SGB=0.620439;RPB=0.916482;MQB=0.916482;MQSB=1.00775;BQB=0.366593;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,3,2,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:75,0,160:10:7,3:74 +chrII 265 . A G 161.0 . DP=14;VDB=0.00228484;SGB=4.69269;RPB=0.965069;MQB=1;MQSB=0.966012;BQB=0.686908;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,1,3,6;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:191,0,96:14:5,9:96 +chrII 278 . A T 167.0 . DP=14;VDB=0.000574122;SGB=4.69269;RPB=0.249352;MQB=1;MQSB=0.966012;BQB=0.867428;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,3,5,4;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:197,0,111:14:5,9:111 +chrII 279 . A T,G 38.2143 . DP=14;VDB=0.0501588;SGB=1.94933;RPB=0.448332;MQB=1;MQSB=0.966012;BQB=0.118179;MQ0F=0;ICB=1;HOB=0.5;AC=1,0;AN=2;DP4=7,2,0,5;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0,0,0,0:0:0,0,0:0 0/1:69,0,186,71,175,247:14:9,4,1:67 +chrII 291 . A G 86.0 . DP=14;VDB=0.0340507;SGB=1.94933;RPB=1;MQB=1;MQSB=0.966012;BQB=0.197899;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=6,3,1,4;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:116,0,189:14:9,5:116 +chrII 300 . A C 231.0 . DP=14;VDB=3.24567e-05;SGB=7.05893;MQSB=0.966012;MQ0F=0;AC=2;AN=2;DP4=0,0,7,7;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:255,42,0:14:0,14:53 +chrII 304 . A T 137.0 . DP=14;VDB=0.000156924;SGB=4.00342;RPB=0.991701;MQB=1;MQSB=0.966012;BQB=0.703221;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,5,6,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:167,0,107:14:6,8:108 +chrII 305 . A T 27.2811 . DP=14;VDB=0.0785113;SGB=0.620439;RPB=0.973096;MQB=1;MQSB=0.966012;BQB=0.738577;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=6,5,1,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:59,0,236:14:11,3:56 +chrII 317 . A G 101.0 . DP=14;VDB=0.00324086;SGB=2.63044;RPB=0.94925;MQB=1;MQSB=0.966012;BQB=0.997919;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,4,3,3;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:131,0,172:14:8,6:127 +chrII 331 . A T 121.0 . DP=14;VDB=0.0126037;SGB=3.31571;RPB=0.497296;MQB=0.966012;MQSB=0.966012;BQB=0.834543;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,2,5;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:151,0,154:14:7,7:127 +chrII 343 . A G 90.0 . DP=9;VDB=0.00476095;SGB=1.97062;RPB=0.346719;MQB=0.924584;MQSB=0.924584;BQB=0.462292;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,5,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:120,0,74:9:3,6:74 +chrII 11921 . A T 7.18923 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:31,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrII 17381 . G A 4.14838 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:32,0,34:2:1,1:32 ./.:0,0,0:0:0,0:0 +chrII 17518 . A T 14.9987 . DP=3;VDB=0.5;SGB=0.0985265;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,2,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:45,0,29:3:1,2:30 ./.:0,0,0:0:0,0:0 +chrII 19959 . T A 7.18923 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:31,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrIII 7994 . C T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrIII 8004 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrIII 8023 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 8026 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 8027 . A G 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 8039 . C A 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrIII 9659 . C T 9.75336 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:34,3,0:1:0,1:4 +chrIII 9662 . G T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrIII 9700 . A T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrIV 9450 . A G 4.78389 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:33,0,27:2:1,1:28 ./.:0,0,0:0:0,0:0 +chrIV 16467 . T C 4.14182 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:32,0,25:2:1,1:26 ./.:0,0,0:0:0,0:0 +chrIV 16478 . C G 4.58205 . DP=3;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=0,2,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:35,0,23:2:1,1:28 0/0:0,3,29:1:1,0:5 +chrIV 16499 . A G 3.42278 . DP=3;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=1,1,0,1;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,79:2:2,0:4 0/1:35,3,0:1:0,1:3 +chrIV 16537 . aaga a 25.8002 . INDEL;IDV=1;IMF=1;DP=3;VDB=0.206307;SGB=-0.516033;MQSB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=1,1,0,1;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,6,120:2:2,0:4 0/1:60,3,0:1:0,1:3 +chrIV 16633 . C A 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrIV 16697 . C T 52.0 . DP=2;VDB=0.48;SGB=-0.759771;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:40,3,0:1:0,1:9 1/1:36,3,0:1:0,1:9 +chrIV 16709 . C G 5.30774 . DP=3;VDB=0.98;SGB=0.0985265;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=3;AN=4;DP4=0,1,2,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:0,3,39:1:1,0:3 1/1:38,6,0:2:0,2:4 +chrIV 16729 . C T 4.14943 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ 0/1:0,3,37:1:1,0:3 0/1:35,3,0:1:0,1:3 +chrIV 16769 . A T 13.7861 . DP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:6 +chrIV 16814 . A G 3.03341 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:30,0,31:2:1,1:30 +chrIV 16815 . C A 48.4033 . DP=2;VDB=0.42;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:73,6,0:2:0,2:9 +chrIV 16823 . A C 4.14995 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,28:2:1,1:29 +chrIV 16829 . T C 3.56356 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:31,0,32:2:1,1:31 +chrIV 16833 . A T,G 14.5409 . DP=2;VDB=0.42;SGB=0.0985265;MQSB=1;MQ0F=0;AC=1,1;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0,0,0,0:0:0,0,0:0 1/2:65,34,31,34,0,31:2:0,1,1:29 +chrIV 16834 . T A 3.56452 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:31,0,27:2:1,1:28 +chrIV 16894 . T C 55.0 . DP=2;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:9 1/1:38,3,0:1:0,1:9 +chrIV 16899 . T A 49.5769 . DP=2;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:9 1/1:33,3,0:1:0,1:9 +chrIV 16902 . T G 55.0 . DP=2;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:9 1/1:38,3,0:1:0,1:9 +chrIV 16921 . A G 68.0 . DP=3;VDB=0.58;SGB=-0.759771;MQ0F=0;AC=4;AN=4;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:54,3,0:1:0,1:11 1/1:38,3,0:1:0,1:11 +chrIV 16951 . C A 76.0 . DP=3;VDB=0.740702;SGB=-0.8159;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,2,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:35,3,0:1:0,1:11 1/1:65,6,0:2:0,2:13 +chrIV 17000 . T C 149.0 . DP=7;VDB=0.103091;SGB=-0.680382;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,6,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:41,3,0:1:0,1:14 1/1:132,18,0:6:0,6:29 +chrIV 17020 . C G,A 99.0 . DP=8;VDB=0.391417;SGB=2.55596;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0;AC=1,1;AN=4;DP4=0,1,7,0;MQ=60 GT:PL:DP:DPR:GQ 0/0:0,3,34,3,34,34:1:1,0,0:3 1/2:150,33,15,125,0,122:7:0,6,1:10 +chrIV 17024 . T C 14.4249 . DP=7;VDB=0.48;SGB=0.00473136;RPB=0.6;MQB=1;BQB=0.8;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:45,0,103:7:5,2:44 +chrIV 17037 . T A 37.8983 . DP=7;VDB=0.460446;SGB=0.620439;RPB=1.01283;MQB=1.01283;BQB=0.810265;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,0,3,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:68,0,95:7:4,3:69 +chrIV 17051 . C T 103.0 . DP=6;VDB=0.534935;SGB=1.41704;MQ0F=0;AC=2;AN=2;DP4=0,0,5,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:127,15,0:5:0,5:22 +chrIV 17112 . T A 3.03494 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:30,0,30:2:1,1:30 +chrV 5001 . T G 4.94666 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:28,3,0:1:0,1:4 +chrV 10045 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrV 10095 . T A 50.0 . DP=2;VDB=0.56;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:75,6,0:2:0,2:9 +chrV 10108 . C A 4.15167 . DP=2;SGB=-0.516033;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,32:2:1,1:32 +chrV 10158 . C T 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrV 10166 . G A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10205 . A G 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10229 . G C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10249 . G T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10250 . C T 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4 +chrV 10251 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 10257 . A T 6.39934 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:30,3,0:1:0,1:4 +chrV 10279 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrV 14271 . T C 39.4036 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:64,6,0:2:0,2:9 +chrV 14273 . G C 39.4036 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:64,6,0:2:0,2:9 +chrV 14285 . T C 76.0 . DP=3;VDB=0.074936;SGB=0.461295;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:100,9,0:3:0,3:13 +chrV 14335 . T G 19.5632 . DP=6;VDB=0.18;SGB=0.00473136;RPB=1;MQB=1;MQSB=1;BQB=0.875;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,0,0,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:50,0,98:6:4,2:49 +chrV 14337 . A G 100.0 . DP=6;VDB=0.405004;SGB=1.41704;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,4,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:132,0,14:6:1,5:9 +chrV 14339 . A G 154.0 . DP=6;VDB=0.189016;SGB=1.97062;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,4,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:178,18,0:6:0,6:25 +chrV 14346 . C T 100.0 . DP=6;VDB=0.405004;SGB=1.41704;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,4,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:132,0,18:6:1,5:14 +chrV 14367 . C A 104.0 . DP=5;VDB=0.220638;SGB=0.908071;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,2,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:128,12,0:4:0,4:19 +chrV 14445 . A G 21.4343 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:46,6,0:2:0,2:9 +chrV 14481 . G A 4.15167 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,32:2:1,1:32 +chrV 14488 . G T 4.15167 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,32:2:1,1:32 +chrV 14528 . G A 3.56356 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:31,0,32:2:1,1:31 +chrV 14530 . A G 4.13076 . DP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:32,0,22:2:1,1:23 +chrV 14538 . T C 32.4055 . DP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:57,6,0:2:0,2:9 +chrX 1592 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 1622 . G T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 1648 . A C 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrX 1650 . T A 10.6576 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:35,3,0:1:0,1:4 +chrX 6015 . A T 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:38,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6032 . G A 8.01478 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ 1/1:32,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6058 . ta t 15.3937 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:40,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6118 . A G 15.394 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:40,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6143 . G A 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL:DP:DPR:GQ 1/1:37,3,0:1:0,1:4 ./.:0,0,0:0:0,0:0 +chrX 6984 . T A 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 7025 . A G 12.5173 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:37,3,0:1:0,1:4 +chrX 10527 . c cC 8.86989 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:33,3,0:1:0,1:4 +chrX 10535 . T C 11.8912 . DP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:6 +chrX 10562 . C G 18.2649 . DP=7;VDB=0.18;SGB=0.00473136;RPB=0.8;MQB=1;MQSB=1;BQB=0.9;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,1,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 0/1:49,0,131:7:5,2:48 +chrX 10595 . T G 148.0 . DP=7;VDB=0.00429645;SGB=2.55596;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,6,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:172,21,0:7:0,7:29 +chrX 10629 . gt g 45.8065 . INDEL;IDV=4;IMF=0.666667;DP=6;VDB=0.14;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:70,6,0:2:0,2:13 +chrX 10630 . T C,G 10.4616 . DP=2;VDB=0.32;SGB=0.0985265;MQSB=1;MQ0F=0;AC=1,1;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0,0,0,0:0:0,0,0:0 1/2:58,29,26,32,0,29:2:0,1,1:25 +chrX 10643 . G T 34.5919 . DP=3;VDB=0.02;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:59,6,0:2:0,2:11 +chrX 15480 . T C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 15495 . G C 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 24890 . C G 13.4669 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:38,3,0:1:0,1:4 +chrX 24935 . A C 11.5799 . DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL:DP:DPR:GQ ./.:0,0,0:0:0,0:0 1/1:36,3,0:1:0,1:4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/so_queryname.sam Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,2 @@ +@HD VN:1.5 SO:queryname +@RG ID:000 SM:N2 DS:C. elegans wt CN:ABC DT:2017-06-27 LB:XYZ PI:400 PL:ILLUMINA PU:SEQ123
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_pair_reads_1.fastqsanger Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAA ++HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?h +@HWI-EAS91_1_30788AAXX:7:45:408:807/1 +TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT ++HWI-EAS91_1_30788AAXX:7:45:408:807/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +CTAACTCTATTTATTGTATTTCAACTAAAAATCTCA ++HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:64:947:234/1 +TATCAAAAAAGAATATAATCTGAATCAACACTACAA ++HWI-EAS91_1_30788AAXX:7:64:947:234/1 +hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJ
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_pair_reads_2.fastqsanger Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 +GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 +hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +@HWI-EAS91_1_30788AAXX:7:22:1621:462/2 +ACTAGCCCCAATATCAATCCTATATCAAATCTCACC ++HWI-EAS91_1_30788AAXX:7:22:1621:462/2 +hJhhhhChhhJhhhRhhKhePhc\KhhV\KhXhJhh +@HWI-EAS91_1_30788AAXX:7:45:408:807/2 +ATGAGTGCTAGGATCAGGATGGAGAGGATTAGGGCT ++HWI-EAS91_1_30788AAXX:7:45:408:807/2 +hhhhhhhhhhhhhhhhhh`hhhZh`hhhhhRXhhYh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/2 +TAGGTTTATTGATAGTTGTGTTGTTGGTGTAAATGG ++HWI-EAS91_1_30788AAXX:7:49:654:1439/2 +hhhhhhhhhhhhhhhhhhhhhhhhhdhh_hG\XhU@ +@HWI-EAS91_1_30788AAXX:7:64:947:234/2 +CCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG ++HWI-EAS91_1_30788AAXX:7:64:947:234/2 +hhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varextract.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,184 @@ +<tool id="mimodd_varextract" name="MiModD Extract Variant Sites" +version="@MIMODD_WRAPPER_VERSION@"> + <description>from a BCF file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd varextract '$ifile' + #if $len($sitesinfo) + -p + #for $source in $sitesinfo + '${source.pre_vcf}' + #end for + #end if + --ofile '$output_vcf' + $keep_alts + --verbose + ]]></command> + + <inputs> + <param name="ifile" type="data" format="bcf" label="BCF input file" + help="Use the MiModD Variant Calling tool to generate the input for this tool."/> + <repeat name="sitesinfo" title="include information from pre-calculated vcf dataset" default="0"> + <param name="pre_vcf" type="data" format="vcf" + label="independently generated vcf datset" /> + </repeat> + <param name="keep_alts" type="boolean" truevalue="-a" falsevalue="" checked="false" + label="keep all sites with alternate bases" + help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." /> + </inputs> + <outputs> + <data name="output_vcf" format="vcf" + label="Variants extracted with MiModd from ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="ifile" value="a.bcf" /> + <output name="output_vcf" ftype="vcf"> + <assert_contents> + <has_line_matching expression="#CHROM.POS.ID.REF.ALT.QUAL.FILTER.INFO.FORMAT.N2.ot266" /> + </assert_contents> + </output> + <assert_command> + <not_has_text text="-a" /> + </assert_command> + </test> + <test> + <param name="ifile" value="a_part2.bcf" /> + <param name="keep_alts" value="true" /> + <param name="pre_vcf" value="a.vcf" /> + <output name="output_vcf" ftype="vcf"> + <assert_contents> + <has_line_matching expression="#CHROM.POS.ID.REF.ALT.QUAL.FILTER.INFO.FORMAT.ot266.external_source_1_N2.external_source_1_ot266" /> + </assert_contents> + </output> + <assert_command> + <has_text text="-a" /> + </assert_command> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool takes as input a BCF dataset like the ones produced by the +*MiModD Variant Calling* tool, extracts just the variant sites from it and +reports them in VCF format. + +If the BCF input file specifies multiple samples, sites are included if they qualify as variant sites in at least one sample. + +---------- + +**Options:** + +**keep all sites with alternate bases** + +By default, a variant site is considered to be a position in the genome for +which a non-reference allele appears in the inferred genotype of any sample. + +You can select the *keep all sites with alternate bases* option, if instead +you want to extract all sites, for which at least one non-reference base has +been observed (whether resulting in a non-reference allele call or not). +Using this option should rarely be necessary, but could be occassionally +helpful for closer inspection of candidate genomic regions. + + +**include information from pre-calculated vcf dataset** + +During the process of variant extraction the tool can take into account +genome positions specified in one or more independently generated VCF datasets. +If such additional VCF input is provided, the tool output will contain the +samples found in these files as additional samples and sites from the main BCF +dataset will be included not only if they qualify as variant sites in at least +one sample specified in the BCF, but also if they are listed in any of the +additional VCF datasets. + +Optional VCF input can be particularly useful in one of the following +situations: + +1) you have prior information that leads you to think that certain genome + positions are of special relevance for your project and, thus, you are + interested in the statistics produced by the variant caller for these + positions even if they are not considered variant sites. In this case you + can use a minimal VCF dataset to guide the variant extraction process to + include these positions. This dataset needs a minimal header of the form: + + ``##fileformat=VCFv4.2`` + + followed by positional information like in this example:: + + #CHROM POS ID REF ALT QUAL FILTER INFO + chrI 1222 . . . . . . + chrI 2651 . . . . . . + chrI 3659 . . . . . . + chrI 3731 . . . . . . + + , where columns are tab-separated and . serves as a placeholder for missing + information. + +2) you have actual variant calls from an additional sample, but you do not + have access to the original sequenced reads data (if you had, the + recommended approach would be to include that data in the + *MiModD Variant Calling* step. + + This situation is often encountered with published datasets. Assume you + have obtained a list of known single nucleotide variants (SNVs) found in + one particular strain of your favorite model organism and you would like + to know which of these SNVs are present in the related strains you have + sequenced. You have aligned the sequenced reads from your samples and have + used the *MiModD Variant Calling* tool, which has generated a BCF dataset + ready for variant extraction. If the SNV list for the previously sequenced + strain is in VCF format already, you can now just plug it into the + analysis process by specifying it in the tool interface as an + *independently generated vcf dataset*. + The resulting vcf output will contain all SNV sites along with the variant + sites found in the BCF alone. You can then proceed to the + *MiModD VCF Filter* tool to look at the original SNV sites only or to + investigate any other interesting subset of sites. If the SNV list is in + some other format, you will have o convert it to VCF first. At a minimum, + the dataset must have a ``##fileformat`` header line like the previous + example and have the ``REF`` and ``ALT`` column filled in like so:: + + #CHROM POS ID REF ALT QUAL FILTER INFO + chrI 1897409 . A G . . . + chrI 1897492 . C T . . . + chrI 1897616 . C A . . . + chrI 1897987 . A T . . . + chrI 1898185 . C T . . . + chrI 1898715 . G A . . . + chrI 1898729 . T C . . . + chrI 1900288 . T A . . . + + , in which case the tool will assume that the corresponding sample is + homozygous for each of the SNVs. + If you need to distinguish between homozygous and heterozygous SNVs you + will have to extend the format to include a format and a sample column + with genotype (GT) information like in this example:: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sampleX + chrI 1897409 . A G . . . GT 1/1 + chrI 1897492 . C T . . . GT 0/1 + chrI 1897616 . C A . . . GT 0/1 + chrI 1897987 . A T . . . GT 0/1 + chrI 1898185 . C T . . . GT 0/1 + chrI 1898715 . G A . . . GT 0/1 + chrI 1898729 . T C . . . GT 0/1 + chrI 1900288 . T A . . . GT 0/1 + + , in which sampleX would be heterozygous for all SNVs except the first. + +.. class:: warningmark + + If the optional VCF input contains INDEL calls, these will be ignored by the + tool. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varreport.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,140 @@ +<tool id="mimodd_varreport" name="MiModD Report Variants" +version="@MIMODD_WRAPPER_VERSION@"> + <description> + in a human-friendly format that simplifies data exploration + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + #if $str($formatting.oformat) == 'html': + mkdir '$ofile.files_path' && + #end if + mimodd varreport + '$inputfile' --oformat ${formatting.oformat} + #if $str($formatting.oformat) == 'html': + #if $str($formatting.species): + --species '${formatting.species}' + #end if + #if $formatting.link_formatter: + --link '${formatting.link_formatter}' + #end if + --ofile '${ofile.files_path}/variant_report.html' + && echo + '<html><body><p>MiModD has generated the variant report you requested, but for technical reasons, we have to take you through this little detour to display the report in Galaxy.</p><p>Proceed to <a href="variant_report.html">the variant report</a>.</p></body></html>' + > '$ofile' + #else + --ofile '$ofile' + #end if + ]]></command> + + <inputs> + <param name="inputfile" type="data" format="vcf" + label="The VCF input with the variants to be reported" /> + <conditional name="formatting"> + <param name="oformat" type="select" + label="Format to use for the report"> + <option value="html">HTML</option> + <option value="text">Tab-separated plain text</option> + </param> + <when value="html"> + <param name="species" type="text" label="Species" + help="If you declare the species your input data comes from, variant reports in html format can have hyperlinks to species-specific databases and genome browsers added. If you have used the MiModD Variant Annotation tool to generate the input dataset, the species information will already be recorded in the dataset, but you can overwrite it if you wish." /> + <param name="link_formatter" type="data" format="txt" optional="true" + label="Optional file with species-specific hyperlink formatting instructions" + help="If the tool has no built-in support for your species, i.e., it does not know how to generate hyperlinks for it, you can provide a custom recipe here." /> + </when> + <when value="text"> + <param name="species" type="hidden" value="" /> + </when> + </conditional> + </inputs> + + <outputs> + <data name="ofile" format="html"> + <change_format> + <when input="formatting.oformat" value="text" format="tabular"/> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="inputfile" value="a.vcf" /> + <conditional name="formatting"> + <param name="oformat" value="html" /> + <param name="species" value="C. elegans" /> + </conditional> + <output name="ofile" ftype="html"> + <extra_files type="file" name="variant_report.html" ftype="html"> + <assert_contents> + <has_line_matching expression=".+tools/genome/gbrowse/c_elegans_PRJNA13758.+" /> + </assert_contents> + </extra_files> + </output> + </test> + <test> + <param name="inputfile" value="a.vcf" /> + <conditional name="formatting"> + <param name="oformat" value="text" /> + </conditional> + <output name="ofile" ftype="tabular"> + <assert_contents> + <has_n_columns n="11" /> + <has_line_matching expression="Chromosome	Position	Affected Gene	Transcript	Effects	genotype N2	.+genotype ot266	.+" /> + <has_line_matching expression="chrI	.+" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool turns a variant list in VCF format into a more readable summary table +listing variant sites and effects. + + +**Html output enriched with species-specific hyperlinks** + +If you select html as the output format, the tool can insert species- and +variant-specific hyperlinks to public genome browsers and databases into the +report. This is a useful feature to explore medium-size lists of variants, but +requires that the tool knows: + +1) the species that you are analyzing data for + + The tool can autodetect the species if the input dataset has been generated + with the *MiModD Variant Annotation* tool. Alternatively, you can declare + the species you are working with explicitly. + +2) how to generate hyperlinks for this species + + The tool has built-in support for a number of standard model organisms. + If your organism is not in that list or if you find that the default + hyperlinks for a supported species are outdated, you can provide your own + recipe to generate correct hyperlinks through a `custom hyperlink template + file`_. + + **TIP:** + MiModD's built-in hyperlink formatting tables are actively maintained and + extended with every new version! If you find the tool produces outdated + hyperlinks for any supported species or if you would like to see additional + species supported, do not hesitate to `tell us about it`_. + If you have a custom hyperlink template file that is working for you, that + is even better. We may use it as a starting point for a built-in recipe and, + while we are working on that and with your permission, we can post it on the + package home page for other users who may need it. + +.. _custom hyperlink template file: http://mimodd.readthedocs.io/en/@MIMODD_REAL_VERSION@/recipes.html#hyperlink-template-file +.. _tell us about it: mailto:mimodd@googlegroups.com + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf_filter.xml Sat Nov 11 18:19:22 2017 -0500 @@ -0,0 +1,191 @@ +<tool id="mimodd_vcf_filter" name="MiModD VCF Filter" version="@MIMODD_WRAPPER_VERSION@"> + <description> + extracts lines from a vcf variant file based on field-specific filters + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd vcf-filter + '$inputfile' -o '$outputfile' + #if len($datasets): + -s + #for $i in $datasets + '$i.sample' + #end for + --gt + #for $i in $datasets + ## remove whitespace from free-text input + '#echo ("".join($i.GT.split()) or "ANY")#' + #echo " " + #end for + --dp + #for $i in $datasets + $i.DP + #end for + --gq + #for $i in $datasets + $i.GQ + #end for + --af + #for $i in $datasets + '#echo ($i.AF or "::")#' + #end for + #end if + #if len($regions): + -r + #for $i in $regions + #if $i.stop: + '$i.chrom:$i.start-$i.stop' + #else: + '$i.chrom:$i.start' + #end if + #end for + #end if + #if $vfilter: + --vfilter + ## remove ',' and replace with ' ' + '#echo ('" "'.join($vfilter.split(',')))#' + #end if + $vartype + ]]></command> + + <inputs> + <param name="inputfile" type="data" format="vcf" label="VCF input file" /> + <repeat name="datasets" title="Sample-specific Filter" default="0" min="0"> + <param name="sample" type="text" label="sample" + help="name of a sample as it appears in the VCF input file and that indicates the sample that this filter should be applied to." /> + <param name="GT" type="text" + label="genotype pattern(s) for the inclusion of variants" + help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." /> + <param name="DP" type="integer" value="0" + label="depth of coverage for the sample at the variant site" + help="keep only variants with at least this sample-specific coverage at the variant site" /> + <param name="GQ" type="integer" value="0" + label="genotype quality for the variant in the sample" + help="keep only variants for which the genotype prediction for the sample has at least this quality" /> + <param name="AF" type="text" + label="allelic fraction filter" + help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" /> + </repeat> + <repeat name="regions" title="Region Filter" default="0" min="0" + help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported."> + <param name="chrom" type="text" label="Chromosome" /> + <param name="start" type="text" label="Region Start" /> + <param name="stop" type="text" label="Region End" /> + </repeat> + <param name="vartype" type="select" + label="Select the types of variants to include in the output"> + <option value="">all types of variants</option> + <option value="--no-indels">exclude indels</option> + <option value="--indels-only">only indels</option> + </param> + <param name="vfilter" type="text" label="sample" + help="Filter output by sample name; only the sample-specific columns with their sample name matching any of the comma separated filters will be retained in the output." /> + </inputs> + + <outputs> + <data name="outputfile" format="vcf" /> + </outputs> + + <tests> + <test> + <param name="inputfile" value="a.vcf" /> + <repeat name="datasets"> + <param name="sample" value="N2" /> + <param name="GT" value="0/0" /> + </repeat> + <output name="outputfile" ftype="vcf" compare="diff"> + <assert_contents> + <has_text text="GT:PL:DP:DPR:GQ	0/0" /> + <not_has_text text="GT:PL:DP:DPR:GQ	1/1" /> + <not_has_text text="GT:PL:DP:DPR:GQ	0/1" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputfile" value="a.vcf" /> + <repeat name="regions"> + <param name="chrom" value="chrX" /> + </repeat> + <output name="outputfile" ftype="vcf"> + <assert_contents> + <has_text text="chrX	" /> + <not_has_text text="chrI	" /> + <not_has_text text="chrII	" /> + <not_has_text text="chrIII	" /> + <not_has_text text="chrIV	" /> + <not_has_text text="chrV	" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputfile" value="a.vcf" /> + <param name="vartype" value="--no-indels" /> + <param name="vfilter" value="ot266" /> + <output name="outputfile" ftype="vcf"> + <assert_contents> + <not_has_text text="INDEL;" /> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ot266" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool filters a variant file in VCF format to generate a new VCF file with only a subset of the original variants. + +The following types of variant filters can be set up: + +1) Sample-specific filters: + + Filter variants based on their characteristics in the sequenced reads of a specific sample. Multiple sample-specific filters are combined by logical AND, i.e., only variants that pass ALL sample-specific filters are kept. + +2) Region filters: + + Filter variants based on the genomic region they affect. Multiple region filters are combined by logical OR, i.e., variants passing ANY region filter are kept. + +3) Variant type filter: + + Filter variants by their type, i.e. whether they are single nucleotide variations (SNVs) or indels + +In addition, the *sample* filter can be used to reduce the samples encoded in a multi-sample VCF file to just those specified by the filter. +The *sample* filter is included mainly for compatibility reasons: if an external tool cannot deal with the multisample file format, but instead looks only at the first sample-specific column of the file, you can use the filter to turn the multi-sample file into a single-sample file. Besides, the filter can also be used to change the order of the samples since it will sort the samples in the order specified in the filter field. + +**Examples of sample-specific filters:** + +*Simple genotype pattern* + +genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant + +*Complex genotype pattern* + +genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype + +*Multiple sample-specific filters* + +Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1: +==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant + +*Combining sample-specific filter criteria* + +genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9 +==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9 +**and** at least three reads from the sample cover the variant site + +**TIP:** + +As in the example above, genotype quality is typically most useful in combination with a genotype pattern. +It acts then, effectively, to make the genotype filter more stringent. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>