changeset 0:460f0749aac5 draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
author yhoogstrate
date Thu, 05 Nov 2015 07:49:02 -0500
parents
children
files README.rst samtools-parallel-mpileup.xml test-data/example.bam test-data/example.fa test-data/example.fa.fai test-data/example.mpileup test-data/example.mpileup.parallel test-data/example.sam test-data/generate_reads.py tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 12 files changed, 2206 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,49 @@
+samtools-parallel-mpileup package for Galaxy
+============================================
+
+https://github.com/yhoogstrate/parallel-mpileup
+
+This wrapper is optimized for faster mpileup generation.
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+
+License
+-------
+
+**samtools-parallel-mpileup**:
+
+MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
+
+    MIT License:
+    
+    Copyright (c) 2008-2009 Genome Research Ltd.
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools-parallel-mpileup.xml	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,298 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup" version="0.1.19-a.a">
+    <description>Samtools mpileup (supporting parallelization)</description>
+    
+    <requirements>
+        <requirement type="package" version="0.1.19-a">samtools_parallel_mpileup</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+    </requirements>
+    
+    <version_command>samtools-parallel-mpileup 2&gt;&amp;1 | grep Version</version_command>
+    
+    <command>
+        #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
+            echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&amp;2
+        #else
+            #if $mpileup_parallelization.mpileup_parallelization_select == "true"
+                samtools-parallel-mpileup mpileup
+                -t $mpileup_parallelization.samtools_threads
+            #else
+                samtools mpileup
+            #end if
+                -f 
+                    #if $reference_genome_source.source_select == "indexed_filtered"
+                        "$reference_genome_source.reference_genome"
+                    #else if $reference_genome_source.source_select == "indexed_all"
+                        "$reference_genome_source.reference_genome"
+                    #else if $reference_genome_source.source_select == "history"
+                        "$reference_genome_source.reference_genome"
+                    #else
+                        <!--
+                            This is a workaround to obtain the "genome.fa" file that
+                            corresponds to the dbkey of the alignments.
+                            Because this file is "calculated" during run-time, it can
+                            be used in a workflow.
+                        -->
+                        "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+                    #end if
+            
+            #if $extended_parameters_regions.samtools_regions == "region"
+                -r $extended_parameters_regions.$samtools_r
+            #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
+                -l $extended_parameters_regions.$samtools_l
+            #end if
+            
+            #if $extended_parameters.parameters == "extended"
+                $extended_parameters.samtools_6
+                $extended_parameters.samtools_A
+                $extended_parameters.samtools_B
+                 -C $extended_parameters.samtools_C
+                 -d $extended_parameters.samtools_d
+                $extended_parameters.samtools_E
+                 -M $extended_parameters.samtools_M
+                $extended_parameters.samtools_R
+                 -q $extended_parameters.samtools_q
+                 -Q $extended_parameters.samtools_Q
+                
+                 -e $extended_parameters.samtools_e
+                 -F $extended_parameters.samtools_F
+                 -h $extended_parameters.samtools_h
+                $extended_parameters.samtools_I
+                 -L $extended_parameters.samtools_L
+                 -m $extended_parameters.samtools_m
+                 -o $extended_parameters.samtools_o
+                $extended_parameters.samtools_p
+                 -P $extended_parameters.samtools_P
+            #end if
+            
+            #for $alignment in $alignments
+                 ${alignment}
+            #end for
+            
+             2> stderr_1.txt
+            
+            #if $sort_mpileup
+             | sort -k1,1V -k2,2g 
+            #end if
+            
+             > $output ;
+             cat stderr_1.txt
+        #end if
+    </command>
+    
+    <inputs>
+        <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
+        
+        <!-- Find out how to access the reference genome from the BAM file(s) -->
+        <conditional name="reference_genome_source">
+            <param name="source_select" type="select" label="Fasta Source">
+                <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
+                <option value="history">Use reference from the history</option>
+                <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
+                <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
+            </param>
+            <when value="indexed_filtered">
+                <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" >
+                    <options from_data_table="all_fasta">
+                        <column name="name" index="2"/>
+                        <column name="dbkey" index="1"/>
+                        <column name="value" index="3"/><!-- Value is the path of the fasta file -->
+                        <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
+                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (fasta)" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
+            </when>
+            <when value="indexed_all">
+                <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" >
+                    <options from_data_table="all_fasta">
+                        <column name="name"  index="2"/>
+                        <column name="dbkey" index="1"/>
+                        <column name="value" index="3"/><!-- Value is the path of the fasta file -->
+                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
+                    </options>
+                </param>
+            </when>
+            <when value="attribute" />
+        </conditional>
+        
+        <conditional name="extended_parameters_regions">
+            <param name="samtools_regions" type="select" label="Region specific parameters" help="Let samtools target specific genomic locations.">
+                <option value="entire_genome">Entire genome</option>
+                <option value="region">Specific region</option>
+                <option value="regions_file_pos">Specific positions (file); list of positions</option>
+                <option value="regions_file_bed">Specific regions (file); list of regions in BED</option>
+            </param>
+            <when value="entire_genome">
+            </when>
+            <when value="region">
+                <param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="chr:pos or chr:start-end" />
+            </when>
+            <when value="regions_file_pos">
+                <param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" />
+            </when>
+            <when value="regions_file_bed">
+                <param type="data" name="samtools_l" format="bed"     label="Samtools: specific regions (BED)" />
+            </when>
+        </conditional>
+        
+        <conditional name="mpileup_parallelization">
+            <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance.">
+                <option value="false">No (uses original build of samtools)</option>
+                <option value="true" selected="true">Yes (uses samtools-parallel-mpileup)</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" />
+            </when>
+        </conditional>
+        
+        <param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." />
+        
+        <conditional name="extended_parameters">
+            <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings.">
+                <option value="default">Default settings</option>
+                <option value="extended">Extended settings</option>
+            </param>
+            <when value="default" />
+            <when value="extended">
+                <param type="boolean" name="samtools_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" />
+                <param type="boolean" name="samtools_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" />
+                <param type="boolean" name="samtools_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" />
+                <param type="integer" name="samtools_C" value="0"                     label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" />
+                <param type="integer" name="samtools_d" value="250"                   label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" />
+                <param type="boolean" name="samtools_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" />
+                <param type="integer" name="samtools_M" value="60"                    label="cap mapping quality at INT [60]" />
+                <param type="boolean" name="samtools_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" />
+                <param type="integer" name="samtools_q" value="0"                     label="Samtools: skip alignments with mapQ smaller than INT [0]" />
+                <param type="integer" name="samtools_Q" value="13"                    label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" />
+                
+                <param type="integer" name="samtools_e" value="20"                    label="Samtools: Phred-scaled gap extension seq error probability [20]" />
+                <param type="float"   name="samtools_F" value="0.002"                 label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
+                <param type="integer" name="samtools_h" value="100"                   label="Samtools: coefficient for homopolymer errors [100]" />
+                <param type="boolean" name="samtools_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" />
+                <param type="integer" name="samtools_L" value="250"                   label="Samtools: max per-sample depth for INDEL calling [250]" />
+                <param type="integer" name="samtools_m" value="1"                     label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" />
+                <param type="integer" name="samtools_o" value="40"                    label="Samtools: Phred-scaled gap open sequencing error probability [40]" />
+                <param type="boolean" name="samtools_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" />
+                <param type="text"    name="samtools_P" value="all"                   label="Samtools: comma separated list of platforms for indels [all]" />
+            </when>
+        </conditional>
+    </inputs>
+    
+    <outputs>
+        <data format="mpileup" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
+    </outputs>
+    
+    <tests>
+        <test><!-- Use classical samtools -->
+            <param name="alignments" value="example.bam" ftype="bam" />
+            
+            <param name="source_select" value="history" />
+            <param name="reference_genome" value="example.fa" ftypet="fasta" />
+            
+            <param name="samtools_regions" value="entire_genome" />
+            
+            <param name="mpileup_parallelization_select" value="false" />
+            <param name="sort_mpileup" value="true" />
+            
+            <param name="parameters" value="default" />
+            
+            
+            <output name="output" file="example.mpileup" /> 
+        </test>
+        <test><!-- Use parallelized samtools - @todo replace with sambamba! -->
+            <param name="alignments" value="example.bam" ftype="bam" />
+            
+            <param name="source_select" value="history" />
+            <param name="reference_genome" value="example.fa" ftypet="fasta" />
+            
+            <param name="samtools_regions" value="entire_genome" />
+            
+            <param name="mpileup_parallelization_select" value="true" />
+            <param name="samtools_threads" value="2" />
+            <param name="sort_mpileup" value="true" />
+            
+            <param name="parameters" value="default" />
+            
+            
+            <output name="output" file="example.mpileup.parallel" />
+        </test>
+    </tests>
+    
+    <help>
+**Samtools mpileup (supporting parallelization)**
+
+SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:
+
+Is flexible enough to store all the alignment information generated by various alignment programs;
+Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
+Is compact in file size;
+Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
+Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.
+SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
+
+SAMtools is hosted by SourceForge.net. The project page is http://samtools.sourceforge.net/. The source code releases are available from the download page. You can check out the most recent source code from the github project page with:
+git clone git://github.com/samtools/samtools.git 
+https://github.com/mydatascience/parallel-mpileup/
+
+Because samtools does not support parallization of the mpileup command, the project was forked to include paralellization support:
+
+
+However, since the project seems to lack support and contains fatal bugs this project was forked at:
+https://github.com/yhoogstrate/parallel-mpileup/
+
+
+**Input formats**
+
+Satmools accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.
+
+**Installation**
+
+The installation is fully automatic.
+
+**License**
+
+* parallel-mpileup: MIT License (https://github.com/yhoogstrate/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
+* samtool: MIT License
+
+
+Contact
+-------
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+
+http://toolshed.g2.bx.psu.edu/
+
+http://testtoolshed.g2.bx.psu.edu/
+</help>
+    <citations>
+        <citation type="bibtex">
+           @unpublished{samtools_parallel_mpileup,
+              author       = {Youri Hoogstrate}, 
+              title        = { Samtools parallel-mpileup, fork of classical samtools },
+              year         = 2014,
+              url          = { https://github.com/yhoogstrate/parallel-mpileup }
+            }
+        </citation>
+        <citation type="bibtex">
+            @misc{SAM_def,
+            title={Definition of SAM/BAM format},
+            url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+        </citation>
+        <citation type="bibtex">
+            @misc{SamTools_github,
+            title={SAMTools GitHub page},
+            url = {https://github.com/samtools/samtools},}
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file
Binary file test-data/example.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,11 @@
+>chr1
+aaataggtcccaaacgttacgcactctatgcctgacaaagttgcgaccacttcctctgcc
+ttgtgtgacacgccggagatagggcatcagcaagtacgttaagtacactgaacgaactgg
+aggtttctacatcgtgcgtgatggctctaggagaagtgggtgtatctgcacagcataagt
+tataagacggaagtaaagcgtcttcaccgttcagcaccccacgctcatagtcaatgctgg
+ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt
+gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg
+cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa
+tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga
+tgaacgttgaactatagctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca
+acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fa.fai	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,1 @@
+chr1	600	6	60	61
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.mpileup	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,540 @@
+chr1	1	a	5	^],^].^],^].^],	~~~~~
+chr1	2	a	6	,.,.,^],	~~~~~~
+chr1	3	a	7	,.,.,,^].	~~~~~~E
+chr1	4	t	8	,.,.,,.^].	~~~~~~RE
+chr1	5	a	12	,.,.,,..^],^],^].^].	~~~~~~UUEEEE
+chr1	6	g	13	,.,.,,..,,..^].	~~~~~~a`UUUUB
+chr1	7	g	17	,.,.,,..,,...^].^].^],^],	~~~~~~aaaaaaEEEEE
+chr1	8	t	21	,.,.,,..,,.....,,^].^],^],^].	~~~~~~~uuuuueUUUUEEEE
+chr1	9	c	23	,.,.,,..,,.....,,.,,.^],^],	~~~~~~~uuuuue]]]]UUUUAA
+chr1	10	c	26	,.,.,,..,,.....,,.,,.,,^].^].^],	~~~~~~~uuuuue]]]]]]]]BB>>>
+chr1	11	c	27	,.,.,,..,,.....,,.,,.,,..,^],	~~~~~~~uuuuue^^^^____EE>>>E
+chr1	12	a	28	,.,.,,..,,.....,,.,,.,,..,,^],	~~~~~~~uuuuue^^^^____^^]]]UA
+chr1	13	a	32	,.,.,,..,,.....,,.,,.,,..,,,^],^].^].^],	~~~~~~~uuuuue^^^^____^^]]]]B>>>>
+chr1	14	a	34	,.,.,,..,,.....,,.,,.,,..,,,,..,^].^].	~~~~~~~uuuuue^^^^____^^^^^_E>>>>EE
+chr1	15	c	36	,.,.,,..,,.....,,.,,.,,..,,,,..,..^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~uueeeeUUEE
+chr1	16	g	38	,.,.,,..,,.....,,.,,.,,..,,,,..,...,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeUUEE
+chr1	17	t	40	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,^].^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuee``UUBB
+chr1	18	t	41	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,..^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaEE@
+chr1	19	a	41	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB
+chr1	20	c	41	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB
+chr1	21	g	41	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB
+chr1	22	c	41	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB
+chr1	23	a	41	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB
+chr1	24	c	41	gGgGggGGggGGGGGggGggGggGGggggGGgGGGgGgGGG	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB
+chr1	25	t	47	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...,,,.^].^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB==11EE
+chr1	26	c	52	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...,,,...^].^].^],^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYB@@@ARRDDDDD
+chr1	27	t	53	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,...,,,.....,,,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuueeaaaaYYBIIIOUUIIIII~
+chr1	28	a	61	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,.^].^],^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuukkkkkkkkkppppp{{{arreeeee~~~~
+chr1	29	t	63	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuukkkkkkkkkpppqq{{{rttttttt~~~~~~
+chr1	30	g	66	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.,,^],^].^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	31	c	67	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.,,,..^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	32	c	68	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.,,,...^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	33	t	69	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.,,,...,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	34	g	71	,.,.,,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.,,,...,.^].^].	~~~~~~u~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	35	a	73	,$.$,$.$,$,..,,.....,,.,,.,,..,,,,..,...,.,......,.,,,.....,,,..,.,,,...,...^].^].	~~~~~~Ueqqqq{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1	243	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1	249	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	250	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	251	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1	253	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	254	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	255	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	256	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	257	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1	260	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	261	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1	387	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	388	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	389	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	390	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	391	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	392	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	393	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	394	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	395	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	396	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	397	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	398	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	399	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	400	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	401	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	402	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	403	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	404	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	405	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	406	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	407	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	408	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	409	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	410	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	411	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	412	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	413	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	414	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	415	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	416	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	417	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	418	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	419	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	420	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	421	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	422	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	423	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	424	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	425	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	426	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	427	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	428	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	429	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	430	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	431	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	432	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	433	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	434	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	435	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	436	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	437	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	438	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	439	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	440	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	441	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	442	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	443	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	444	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	445	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	446	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	447	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	448	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	449	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	450	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	451	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	452	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	453	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	454	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	455	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	456	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	457	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	458	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	459	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	460	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	461	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	462	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	463	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	464	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	465	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	466	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	467	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	468	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	469	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	470	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	471	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	472	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	473	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	474	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	475	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	476	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	477	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	478	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	479	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	480	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	481	t	82	,$..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E
+chr1	482	g	83	.$.$,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UEE
+chr1	483	a	84	,$,$.$.,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,^],^].^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`QQBBB
+chr1	484	a	82	.$,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,..^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a``EEEE
+chr1	485	c	83	,$.$,$.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rreeeUEE
+chr1	486	g	81	.$,$,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuueUUE
+chr1	487	t	83	,$...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.^],^],^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuue``UBBBB
+chr1	488	t	83	.$.$.,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuueaa`EEEEE
+chr1	489	g	83	.$,$...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,.^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeeeUEE
+chr1	490	a	81	.$..,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	491	a	80	.$.$,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	492	c	78	,$,$.$.$.,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	493	t	74	.$,$.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	494	a	72	.$,$,$,$.$,$.$,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	495	t	65	g$GggGggGGggGGggGgGGGgGgGgggGgGGggggGGGgGGGGGGggGggggGGGggGggggGGg	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	496	a	64	C$ccCccCCccCCccCcCCCcCcCcccCcCCccccCCCcCCCCCCccCccccCCCccCccccCCc	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	497	g	63	c$c$CccCCccCCccCcCCCcCcCcccCcCCccccCCCcCCCCCCccCccccCCCccCccccCCc	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	498	c	62	.$,$,$..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQE
+chr1	499	t	74	.$.$,$,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_]]___~~}}}TTDDDDUE
+chr1	500	g	72	,$.$.$,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~qqqqqqqqtts~~~~~~~TTTTeUE
+chr1	501	a	71	,$,$.$,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dduaUEE
+chr1	502	t	72	,$...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,^],^],^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{{~~~~ttzbbUUEEEE
+chr1	503	g	73	.$.$.$,$.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{{~~~~vv{eeeePPPPEE
+chr1	504	t	71	.$,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{{~~~~{{{wwqqUUUUUUEE
+chr1	505	a	71	,$.$,$,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^]]UUA
+chr1	506	a	72	,$,$.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,.^].^],^],^].	~~~~~~~~~~~~~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^]]]]B>>>>
+chr1	507	a	70	.$,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__E>>>>
+chr1	508	c	69	,$.$.$,$,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1	509	c	65	,$,$,$...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1	510	c	62	.$.$.,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1	511	c	60	.$,$.$.....,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\\\\\
+chr1	512	g	57	.$....,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~qsssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1	513	c	56	.$.$.$.$,$,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~eqqqqqvzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.mpileup.parallel	Thu Nov 05 07:49:02 2015 -0500
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+chr1	222	c	82	,$,$...,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,^].	DDUUrrrrrsssz{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	223	g	82	.$..,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.^],^],	EReeeeerrrz{{{{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	224	c	84	.$.,.,....,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,^].^],^],	DUUUUUUUUrvzz{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	225	t	86	.$,$.$,$.$...,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,^].^].^],	EEEEERRReezz{{{{{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	226	c	84	.$.$.$,,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,^],^].^].	EEEUbttzzzz{{{{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	227	a	84	,$,.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..^],^],^].	DUUUsssswww{{{{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	228	t	84	,$.....,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.^],	ERReeeeeeezzz{{{{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	229	a	87	.$.$...,,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,^].^].^].^],	EEUUUUbbbttttttt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	230	g	86	.$.$.$,$,.,..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,^].	EEEEUUUeeerrrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	231	t	85	,$.$,$..,.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.^],^].^],	EEEUUUeeeeuuuuu~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	232	c	84	.$.$,$.,...,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,^],^],	EEEUUUUeeeer~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	233	a	82	.$,$.$.$.,,,.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,^].	>>>>EEEE_aaeeeeeeee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	234	a	82	.$,$,$,$.,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.^],^].^].^],	BBBBU__eeeeeeee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	235	t	81	.$,..,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,^],^],^],	EQQeeeeeeee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	236	g	82	,$.$.,,,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,^].^].	EEUUUbbbbbuu~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	237	c	83	.$,$,$,,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,..^].^],^].	EEEUaaaarr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	238	t	81	,$,.,,,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,.^].	EUUUUee~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	239	g	85	,$.$,$,$,,,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,..^].^].^].^].^],	>>>>EE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	240	g	83	,$,$,..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,^],^].	BB~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	241	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	242	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	243	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	244	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	245	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	246	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	247	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	248	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	249	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	250	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	251	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	252	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	253	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	254	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	255	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	256	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	257	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	258	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	259	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	260	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	261	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	262	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	263	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	264	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	265	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	266	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	267	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	268	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	269	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	270	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	271	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	272	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	273	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	274	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	275	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	276	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	277	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	278	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	279	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	280	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	281	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	282	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	283	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	284	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	285	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	286	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	287	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	288	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	289	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	290	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	291	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	292	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	293	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	294	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	295	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	296	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	297	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	298	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	299	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	300	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	301	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	302	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	303	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	304	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	305	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	306	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	307	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	308	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	309	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	310	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	311	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	312	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	313	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	314	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	315	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	316	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	317	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	318	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	319	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	320	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	321	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	322	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	323	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	324	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	325	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	326	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	327	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	328	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	329	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	330	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	331	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	332	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	333	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	334	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	335	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	336	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	337	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	338	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	339	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	340	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	341	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	342	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+chr1	468	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	469	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	470	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	471	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	472	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	473	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	474	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	475	c	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	476	t	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	477	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	478	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	479	g	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	480	a	81	<>><<>><><><<>>><>>><<>>><><<<><><><<><<>><<>><<><>>><><><<<><>><<<<>>><>>>>>><<>	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	481	t	82	,$..,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	482	g	83	.$.$,,..,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~EE
+chr1	483	a	84	,$,$.$.,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,^],^].^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~QQBBB
+chr1	484	a	82	.$,.,.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,..^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~``EEEE
+chr1	485	c	83	,$.$,$.,,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rreeeUEE
+chr1	486	g	81	.$,$,...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuueUUE
+chr1	487	t	83	,$...,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.^],^],^],^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuue``UBBBB
+chr1	488	t	83	.$.$.,...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~uuuuueaa`EEEEE
+chr1	489	g	83	.$,$...,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,.^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeeeUEE
+chr1	490	a	81	.$..,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	491	a	80	.$.$,,...,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	492	c	78	,$,$.$.$.,.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	493	t	74	.$,$.,,,.,.,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	494	a	72	.$,$,$,$.$,$.$,.,,.,,..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	495	t	65	g$GggGggGGggGGggGgGGGgGgGgggGgGGggggGGGgGGGGGGggGggggGGGggGggggGGg	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	496	a	64	C$ccCccCCccCCccCcCCCcCcCcccCcCCccccCCCcCCCCCCccCccccCCCccCccccCCc	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	497	g	63	c$c$CccCCccCCccCcCCCcCcCcccCcCCccccCCCcCCCCCCccCccccCCCccCccccCCc	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQ
+chr1	498	c	62	.$,$,$..,,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_QQE
+chr1	499	t	74	.$.$,$,..,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eeeee_]]___~~}}}TTDDDDUE
+chr1	500	g	72	,$.$.$,,.,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~qqqqqqqqtts~~~~~~~TTTTeUE
+chr1	501	a	71	,$,$.$,...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dduaUEE
+chr1	502	t	72	,$...,.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,^],^],^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{~~~~ttzbbUUEEEE
+chr1	503	g	73	.$.$.$,$.,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{~~~~vv{eeeePPPPEE
+chr1	504	t	71	.$,.,,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,^].^],	~~~~~~~~~~~~~~~~~~~~~~~~~~~~{{{{{{{{{{{{{{{{{{{{{{{{~~~~{{{wwqqUUUUUUEE
+chr1	505	a	71	,$.$,$,,.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,^].	~~~~~~~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^]]UUA
+chr1	506	a	72	,$,$.,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,.^].^],^],^].	~~~~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^]]]]B>>>>
+chr1	507	a	70	.$,..,,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__E>>>>
+chr1	508	c	69	,$.$.$,$,,,...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1	509	c	65	,$,$,$...,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1	510	c	62	.$.$.,......,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\[[[[
+chr1	511	c	60	.$,$.$.....,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwqq^^^^^^__\\\\\
+chr1	512	g	57	.$....,,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~~sssssvzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1	513	c	56	.$.$.$.$,$,.,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~~~~~~qqqqqvzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1	514	g	51	,$.$,,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~~~UUooovzz{{{{{{{{{{{{{{{{~~~~{{{wwvvvvvvvvvvvvvvv
+chr1	515	t	49	,$,,,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	~RReeetzz{{{{{{{{{{{{{{{{~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	516	g	48	,$,$,...,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	EEUUUett{{{{{{{{{{{{{{{{~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	517	c	46	,$.$.$.,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	>>>E__aaaaaaaaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	518	c	43	.$,,.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	BUU_aaaaaaaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	519	a	42	,$,$.,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	>>E____aaaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	520	a	40	.$,,,,..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	BUUUU_aaaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	521	t	39	,$,$,$,$..,,...,,..,.,..,,,,.,,,.,.,.,..,,.	>>>>E__aaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	522	t	35	.$.,,...,,..,.,..,,,,.,,,.,.,.,..,,.	BUUaaaeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	523	c	34	.$,$,...,,..,.,..,,,,.,,,.,.,.,..,,.	>>__aeerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	524	c	32	,...,,..,.,..,,,,.,,,.,.,.,..,,.	UU_eerrr~~~~{{{{{{{{{{{{{{{{{{{{
+chr1	525	a	32	,$.$..,,..,.,..,,,,.,,,.,.,.,..,,.	EEUeerrr~~~~~~~~~~~~~~~~~~~~~~~~
+chr1	526	g	30	.$.,,..,.,..,,,,.,,,.,.,.,..,,.	>EE_____eeeez{~~~~~~~~~~~~~~~~
+chr1	527	g	29	.$,$,..,.,..,,,,.,,,.,.,.,..,,.	AAUUUUUeeeez{~~~~~~~~~~~~~~~~
+chr1	528	c	27	,$.$.$,.,..,,,,.,,,.,.,.,..,,.	EEERReeeez{~~~~~~~~~~~~~~~~
+chr1	529	g	24	,$.$,..,,,,.,,,.,.,.,..,,.	EEUUbbtz~~~~~~~~~~~~~~~~
+chr1	530	t	22	,$.$.,,,,.,,,.,.,.,..,,.	EEUUee~~~~~~~~~~~~~~~~
+chr1	531	c	20	.$,$,,,.,,,.,.,.,..,,.	EEUbu~~~~~~~~~~~~~~~
+chr1	532	a	18	,$,,.,,,.,.,.,..,,.	EUeuu~~~~~~~~~~~~~
+chr1	533	t	17	,$,.,,,.,.,.,..,,.	EUeeuuuu~~~~~~~~~
+chr1	534	g	16	,$.,,,.,.,.,..,,.	>>>>>>>>>EE[[[[[
+chr1	535	g	15	.$,$,,.,.,.,..,,.	;;;;;;;;BBXZZZZ
+chr1	536	g	13	,$,$.$,$.,.,..,,.	9999::AAXZZZZ
+chr1	537	g	9	.$,$.,..,,.	88??XZZZZ
+chr1	538	g	7	.$,$..,,.	>>TZZZZ
+chr1	539	c	5	.$.,,.	EUUUU
+chr1	540	a	4	.$,$,$.$	>>>>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.sam	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,610 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:600
+read_0.0.0	16	chr1	1	60	35M	*	0	0	AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA	*
+read_0.0.1	0	chr1	1	60	35M	*	0	0	AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA	*
+read_0.0.2	16	chr1	1	60	35M	*	0	0	AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA	*
+read_0.0.3	0	chr1	1	60	35M	*	0	0	AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA	*
+read_0.0.4	16	chr1	1	60	35M	*	0	0	AAATAGGTCCCAAACGTTACGCAGTCTATGCCTGA	*
+read_0.1.0	16	chr1	2	60	35M	*	0	0	AATAGGTCCCAAACGTTACGCAGTCTATGCCTGAC	*
+read_0.2.0	0	chr1	3	60	35M	*	0	0	ATAGGTCCCAAACGTTACGCAGTCTATGCCTGACA	*
+read_0.3.0	0	chr1	4	60	35M	*	0	0	TAGGTCCCAAACGTTACGCAGTCTATGCCTGACAA	*
+read_0.4.0	16	chr1	5	60	35M	*	0	0	AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA	*
+read_0.4.1	16	chr1	5	60	35M	*	0	0	AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA	*
+read_0.4.2	0	chr1	5	60	35M	*	0	0	AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA	*
+read_0.4.3	0	chr1	5	60	35M	*	0	0	AGGTCCCAAACGTTACGCAGTCTATGCCTGACAAA	*
+read_0.5.0	0	chr1	6	60	35M	*	0	0	GGTCCCAAACGTTACGCAGTCTATGCCTGACAAAG	*
+read_0.6.0	0	chr1	7	60	35M	*	0	0	GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT	*
+read_0.6.1	0	chr1	7	60	35M	*	0	0	GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT	*
+read_0.6.2	16	chr1	7	60	35M	*	0	0	GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT	*
+read_0.6.3	16	chr1	7	60	35M	*	0	0	GTCCCAAACGTTACGCAGTCTATGCCTGACAAAGT	*
+read_0.7.0	0	chr1	8	60	35M	*	0	0	TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT	*
+read_0.7.1	16	chr1	8	60	35M	*	0	0	TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT	*
+read_0.7.2	16	chr1	8	60	35M	*	0	0	TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT	*
+read_0.7.3	0	chr1	8	60	35M	*	0	0	TCCCAAACGTTACGCAGTCTATGCCTGACAAAGTT	*
+read_0.8.0	16	chr1	9	60	35M	*	0	0	CCCAAACGTTACGCAGTCTATGCCTGACAAAGTTG	*
+read_0.8.1	16	chr1	9	60	35M	*	0	0	CCCAAACGTTACGCAGTCTATGCCTGACAAAGTTG	*
+read_0.9.0	0	chr1	10	60	35M	*	0	0	CCAAACGTTACGCAGTCTATGCCTGACAAAGTTGC	*
+read_0.9.1	0	chr1	10	60	35M	*	0	0	CCAAACGTTACGCAGTCTATGCCTGACAAAGTTGC	*
+read_0.9.2	16	chr1	10	60	35M	*	0	0	CCAAACGTTACGCAGTCTATGCCTGACAAAGTTGC	*
+read_0.10.0	16	chr1	11	60	35M	*	0	0	CAAACGTTACGCAGTCTATGCCTGACAAAGTTGCG	*
+read_0.11.0	16	chr1	12	60	35M	*	0	0	AAACGTTACGCAGTCTATGCCTGACAAAGTTGCGA	*
+read_0.12.0	16	chr1	13	60	35M	*	0	0	AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC	*
+read_0.12.1	0	chr1	13	60	35M	*	0	0	AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC	*
+read_0.12.2	0	chr1	13	60	35M	*	0	0	AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC	*
+read_0.12.3	16	chr1	13	60	35M	*	0	0	AACGTTACGCAGTCTATGCCTGACAAAGTTGCGAC	*
+read_0.13.0	0	chr1	14	60	35M	*	0	0	ACGTTACGCAGTCTATGCCTGACAAAGTTGCGACC	*
+read_0.13.1	0	chr1	14	60	35M	*	0	0	ACGTTACGCAGTCTATGCCTGACAAAGTTGCGACC	*
+read_0.14.0	0	chr1	15	60	35M	*	0	0	CGTTACGCAGTCTATGCCTGACAAAGTTGCGACCA	*
+read_0.14.1	16	chr1	15	60	35M	*	0	0	CGTTACGCAGTCTATGCCTGACAAAGTTGCGACCA	*
+read_0.15.0	0	chr1	16	60	35M	*	0	0	GTTACGCAGTCTATGCCTGACAAAGTTGCGACCAC	*
+read_0.15.1	16	chr1	16	60	35M	*	0	0	GTTACGCAGTCTATGCCTGACAAAGTTGCGACCAC	*
+read_0.16.0	0	chr1	17	60	35M	*	0	0	TTACGCAGTCTATGCCTGACAAAGTTGCGACCACT	*
+read_0.16.1	0	chr1	17	60	35M	*	0	0	TTACGCAGTCTATGCCTGACAAAGTTGCGACCACT	*
+read_0.17.0	0	chr1	18	60	35M	*	0	0	TACGCAGTCTATGCCTGACAAAGTTGCGACCACTT	*
+read_0.18.0	0	chr1	19	60	35M	*	0	0	ACGCAGTCTATGCCTGACAAAGTTGCGACCACTTC	*
+read_0.19.0	0	chr1	20	60	35M	*	0	0	CGCAGTCTATGCCTGACAAAGTTGCGACCACTTCC	*
+read_0.19.1	0	chr1	20	60	35M	*	0	0	CGCAGTCTATGCCTGACAAAGTTGCGACCACTTCC	*
+read_0.20.0	16	chr1	21	60	35M	*	0	0	GCAGTCTATGCCTGACAAAGTTGCGACCACTTCCT	*
+read_0.20.1	0	chr1	21	60	35M	*	0	0	GCAGTCTATGCCTGACAAAGTTGCGACCACTTCCT	*
+read_0.21.0	16	chr1	22	60	35M	*	0	0	CAGTCTATGCCTGACAAAGTTGCGACCACTTCCTC	*
+read_0.21.1	16	chr1	22	60	35M	*	0	0	CAGTCTATGCCTGACAAAGTTGCGACCACTTCCTC	*
+read_0.22.0	16	chr1	23	60	35M	*	0	0	AGTCTATGCCTGACAAAGTTGCGACCACTTCCTCT	*
+read_0.23.0	0	chr1	24	60	35M	*	0	0	GTCTATGCCTGACAAAGTTGCGACCACTTCCTCTG	*
+read_0.24.0	0	chr1	25	60	35M	*	0	0	TCTATGCCTGACAAAGTTGCGACCACTTCCTCTGC	*
+read_0.24.1	0	chr1	25	60	35M	*	0	0	TCTATGCCTGACAAAGTTGCGACCACTTCCTCTGC	*
+read_0.25.0	0	chr1	26	60	35M	*	0	0	CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC	*
+read_0.25.1	0	chr1	26	60	35M	*	0	0	CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC	*
+read_0.25.2	16	chr1	26	60	35M	*	0	0	CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC	*
+read_0.25.3	16	chr1	26	60	35M	*	0	0	CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC	*
+read_0.25.4	16	chr1	26	60	35M	*	0	0	CTATGCCTGACAAAGTTGCGACCACTTCCTCTGCC	*
+read_0.26.0	0	chr1	27	60	34M0N1M	*	0	0	TATGCCTGACAAAGTTGCGACCACTTCCTCTGCCT	*
+read_0.27.0	0	chr1	28	60	33M0N2M	*	0	0	ATGCCTGACAAAGTTGCGACCACTTCCTCTGCCTT	*
+read_0.27.1	16	chr1	28	60	33M0N2M	*	0	0	ATGCCTGACAAAGTTGCGACCACTTCCTCTGCCTT	*
+read_0.27.2	0	chr1	28	60	33M0N2M	*	0	0	ATGCCTGACAAAGTTGCGACCACTTCCTCTGCCTT	*
+read_0.28.0	16	chr1	29	60	32M0N3M	*	0	0	TGCCTGACAAAGTTGCGACCACTTCCTCTGCCTTG	*
+read_0.28.1	16	chr1	29	60	32M0N3M	*	0	0	TGCCTGACAAAGTTGCGACCACTTCCTCTGCCTTG	*
+read_0.29.0	16	chr1	30	60	31M0N4M	*	0	0	GCCTGACAAAGTTGCGACCACTTCCTCTGCCTTGT	*
+read_0.29.1	0	chr1	30	60	31M0N4M	*	0	0	GCCTGACAAAGTTGCGACCACTTCCTCTGCCTTGT	*
+read_0.29.2	0	chr1	30	60	31M0N4M	*	0	0	GCCTGACAAAGTTGCGACCACTTCCTCTGCCTTGT	*
+read_0.30.0	0	chr1	31	60	30M0N5M	*	0	0	CCTGACAAAGTTGCGACCACTTCCTCTGCCTTGTG	*
+read_0.31.0	16	chr1	32	60	29M0N6M	*	0	0	CTGACAAAGTTGCGACCACTTCCTCTGCCTTGTGT	*
+read_0.32.0	0	chr1	33	60	28M0N7M	*	0	0	TGACAAAGTTGCGACCACTTCCTCTGCCTTGTGTG	*
+read_0.33.0	0	chr1	34	60	27M0N8M	*	0	0	GACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGA	*
+read_0.33.1	0	chr1	34	60	27M0N8M	*	0	0	GACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGA	*
+read_0.34.0	0	chr1	35	60	26M0N9M	*	0	0	ACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGAC	*
+read_0.34.1	0	chr1	35	60	26M0N9M	*	0	0	ACAAAGTTGCGACCACTTCCTCTGCCTTGTGTGAC	*
+read_0.35.0	16	chr1	36	60	25M0N10M	*	0	0	CAAAGTTGCGACCACTTCCTCTGCCTTGTGTGACA	*
+read_0.35.1	0	chr1	36	60	25M0N10M	*	0	0	CAAAGTTGCGACCACTTCCTCTGCCTTGTGTGACA	*
+read_0.35.2	16	chr1	36	60	25M0N10M	*	0	0	CAAAGTTGCGACCACTTCCTCTGCCTTGTGTGACA	*
+read_0.36.0	0	chr1	37	60	24M0N11M	*	0	0	AAAGTTGCGACCACTTCCTCTGCCTTGTGTGACAC	*
+read_0.36.1	0	chr1	37	60	24M0N11M	*	0	0	AAAGTTGCGACCACTTCCTCTGCCTTGTGTGACAC	*
+read_0.37.0	16	chr1	38	60	23M0N12M	*	0	0	AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG	*
+read_0.37.1	0	chr1	38	60	23M0N12M	*	0	0	AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG	*
+read_0.37.2	0	chr1	38	60	23M0N12M	*	0	0	AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG	*
+read_0.37.3	16	chr1	38	60	23M0N12M	*	0	0	AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG	*
+read_0.37.4	16	chr1	38	60	23M0N12M	*	0	0	AAGTTGCGACCACTTCCTCTGCCTTGTGTGACACG	*
+read_0.38.0	0	chr1	39	60	22M0N13M	*	0	0	AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC	*
+read_0.38.1	16	chr1	39	60	22M0N13M	*	0	0	AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC	*
+read_0.38.2	16	chr1	39	60	22M0N13M	*	0	0	AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC	*
+read_0.38.3	0	chr1	39	60	22M0N13M	*	0	0	AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC	*
+read_0.38.4	16	chr1	39	60	22M0N13M	*	0	0	AGTTGCGACCACTTCCTCTGCCTTGTGTGACACGC	*
+read_0.39.0	0	chr1	40	60	21M0N14M	*	0	0	GTTGCGACCACTTCCTCTGCCTTGTGTGACACGCC	*
+read_0.40.0	0	chr1	41	60	20M0N15M	*	0	0	TTGCGACCACTTCCTCTGCCTTGTGTGACACGCCG	*
+read_0.40.1	16	chr1	41	60	20M0N15M	*	0	0	TTGCGACCACTTCCTCTGCCTTGTGTGACACGCCG	*
+read_0.41.0	16	chr1	42	60	19M0N16M	*	0	0	TGCGACCACTTCCTCTGCCTTGTGTGACACGCCGG	*
+read_0.42.0	16	chr1	43	60	18M0N17M	*	0	0	GCGACCACTTCCTCTGCCTTGTGTGACACGCCGGA	*
+read_0.42.1	0	chr1	43	60	18M0N17M	*	0	0	GCGACCACTTCCTCTGCCTTGTGTGACACGCCGGA	*
+read_0.43.0	16	chr1	44	60	17M0N18M	*	0	0	CGACCACTTCCTCTGCCTTGTGTGACACGCCGGAG	*
+read_0.43.1	16	chr1	44	60	17M0N18M	*	0	0	CGACCACTTCCTCTGCCTTGTGTGACACGCCGGAG	*
+read_0.44.0	0	chr1	45	60	16M0N19M	*	0	0	GACCACTTCCTCTGCCTTGTGTGACACGCCGGAGA	*
+read_0.45.0	0	chr1	46	60	15M0N20M	*	0	0	ACCACTTCCTCTGCCTTGTGTGACACGCCGGAGAT	*
+read_0.45.1	0	chr1	46	60	15M0N20M	*	0	0	ACCACTTCCTCTGCCTTGTGTGACACGCCGGAGAT	*
+read_0.46.0	0	chr1	47	60	14M0N21M	*	0	0	CCACTTCCTCTGCCTTGTGTGACACGCCGGAGATA	*
+read_0.46.1	16	chr1	47	60	14M0N21M	*	0	0	CCACTTCCTCTGCCTTGTGTGACACGCCGGAGATA	*
+read_0.46.2	0	chr1	47	60	14M0N21M	*	0	0	CCACTTCCTCTGCCTTGTGTGACACGCCGGAGATA	*
+read_0.47.0	0	chr1	48	60	13M0N22M	*	0	0	CACTTCCTCTGCCTTGTGTGACACGCCGGAGATAG	*
+read_0.47.1	0	chr1	48	60	13M0N22M	*	0	0	CACTTCCTCTGCCTTGTGTGACACGCCGGAGATAG	*
+read_0.48.0	16	chr1	49	60	12M0N23M	*	0	0	ACTTCCTCTGCCTTGTGTGACACGCCGGAGATAGG	*
+read_0.49.0	0	chr1	50	60	11M0N24M	*	0	0	CTTCCTCTGCCTTGTGTGACACGCCGGAGATAGGA	*
+read_0.49.1	0	chr1	50	60	11M0N24M	*	0	0	CTTCCTCTGCCTTGTGTGACACGCCGGAGATAGGA	*
+read_0.50.0	16	chr1	51	60	10M0N25M	*	0	0	TTCCTCTGCCTTGTGTGACACGCCGGAGATAGGAC	*
+read_0.50.1	0	chr1	51	60	10M0N25M	*	0	0	TTCCTCTGCCTTGTGTGACACGCCGGAGATAGGAC	*
+read_0.50.2	0	chr1	51	60	10M0N25M	*	0	0	TTCCTCTGCCTTGTGTGACACGCCGGAGATAGGAC	*
+read_0.51.0	0	chr1	52	60	9M0N26M	*	0	0	TCCTCTGCCTTGTGTGACACGCCGGAGATAGGACA	*
+read_0.51.1	0	chr1	52	60	9M0N26M	*	0	0	TCCTCTGCCTTGTGTGACACGCCGGAGATAGGACA	*
+read_0.52.0	0	chr1	53	60	8M0N27M	*	0	0	CCTCTGCCTTGTGTGACACGCCGGAGATAGGACAT	*
+read_0.53.0	0	chr1	54	60	7M0N28M	*	0	0	CTCTGCCTTGTGTGACACGCCGGAGATAGGACATC	*
+read_0.53.1	0	chr1	54	60	7M0N28M	*	0	0	CTCTGCCTTGTGTGACACGCCGGAGATAGGACATC	*
+read_0.54.0	16	chr1	55	60	6M0N29M	*	0	0	TCTGCCTTGTGTGACACGCCGGAGATAGGACATCA	*
+read_0.54.1	16	chr1	55	60	6M0N29M	*	0	0	TCTGCCTTGTGTGACACGCCGGAGATAGGACATCA	*
+read_0.54.2	16	chr1	55	60	6M0N29M	*	0	0	TCTGCCTTGTGTGACACGCCGGAGATAGGACATCA	*
+read_0.55.0	16	chr1	56	60	5M0N30M	*	0	0	CTGCCTTGTGTGACACGCCGGAGATAGGACATCAG	*
+read_0.56.0	0	chr1	57	60	4M0N31M	*	0	0	TGCCTTGTGTGACACGCCGGAGATAGGACATCAGC	*
+read_0.56.1	0	chr1	57	60	4M0N31M	*	0	0	TGCCTTGTGTGACACGCCGGAGATAGGACATCAGC	*
+read_0.57.0	16	chr1	58	60	3M0N32M	*	0	0	GCCTTGTGTGACACGCCGGAGATAGGACATCAGCA	*
+read_0.58.0	0	chr1	59	60	2M0N33M	*	0	0	CCTTGTGTGACACGCCGGAGATAGGACATCAGCAA	*
+read_0.59.0	0	chr1	60	60	1M0N34M	*	0	0	CTTGTGTGACACGCCGGAGATAGGACATCAGCAAG	*
+read_0.59.1	16	chr1	60	60	1M0N34M	*	0	0	CTTGTGTGACACGCCGGAGATAGGACATCAGCAAG	*
+read_0.59.2	16	chr1	60	60	1M0N34M	*	0	0	CTTGTGTGACACGCCGGAGATAGGACATCAGCAAG	*
+read_1.60.0	16	chr1	61	60	35M	*	0	0	TTGTGTGACACGCCGGAGATAGGACATCAGCAAGT	*
+read_1.61.0	0	chr1	62	60	35M	*	0	0	TGTGTGACACGCCGGAGATAGGACATCAGCAAGTA	*
+read_1.61.1	0	chr1	62	60	35M	*	0	0	TGTGTGACACGCCGGAGATAGGACATCAGCAAGTA	*
+read_1.62.0	16	chr1	63	60	35M	*	0	0	GTGTGACACGCCGGAGATAGGACATCAGCAAGTAC	*
+read_1.62.1	16	chr1	63	60	35M	*	0	0	GTGTGACACGCCGGAGATAGGACATCAGCAAGTAC	*
+read_1.63.0	0	chr1	64	60	35M	*	0	0	TGTGACACGCCGGAGATAGGACATCAGCAAGTACG	*
+read_1.64.0	16	chr1	65	60	35M	*	0	0	GTGACACGCCGGAGATAGGACATCAGCAAGTACGT	*
+read_1.65.0	0	chr1	66	60	35M	*	0	0	TGACACGCCGGAGATAGGACATCAGCAAGTACGTT	*
+read_1.65.1	0	chr1	66	60	35M	*	0	0	TGACACGCCGGAGATAGGACATCAGCAAGTACGTT	*
+read_1.65.2	16	chr1	66	60	35M	*	0	0	TGACACGCCGGAGATAGGACATCAGCAAGTACGTT	*
+read_1.65.3	0	chr1	66	60	35M	*	0	0	TGACACGCCGGAGATAGGACATCAGCAAGTACGTT	*
+read_1.66.0	0	chr1	67	60	35M	*	0	0	GACACGCCGGAGATAGGACATCAGCAAGTACGTTA	*
+read_1.67.0	16	chr1	68	60	35M	*	0	0	ACACGCCGGAGATAGGACATCAGCAAGTACGTTAA	*
+read_1.67.1	16	chr1	68	60	35M	*	0	0	ACACGCCGGAGATAGGACATCAGCAAGTACGTTAA	*
+read_1.68.0	0	chr1	69	60	35M	*	0	0	CACGCCGGAGATAGGACATCAGCAAGTACGTTAAG	*
+read_1.69.0	0	chr1	70	60	35M	*	0	0	ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT	*
+read_1.69.1	0	chr1	70	60	35M	*	0	0	ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT	*
+read_1.69.2	16	chr1	70	60	35M	*	0	0	ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT	*
+read_1.69.3	16	chr1	70	60	35M	*	0	0	ACGCCGGAGATAGGACATCAGCAAGTACGTTAAGT	*
+read_1.70.0	16	chr1	71	60	35M	*	0	0	CGCCGGAGATAGGACATCAGCAAGTACGTTAAGTA	*
+read_1.70.1	16	chr1	71	60	35M	*	0	0	CGCCGGAGATAGGACATCAGCAAGTACGTTAAGTA	*
+read_1.71.0	0	chr1	72	60	35M	*	0	0	GCCGGAGATAGGACATCAGCAAGTACGTTAAGTAC	*
+read_1.71.1	0	chr1	72	60	35M	*	0	0	GCCGGAGATAGGACATCAGCAAGTACGTTAAGTAC	*
+read_1.71.2	16	chr1	72	60	35M	*	0	0	GCCGGAGATAGGACATCAGCAAGTACGTTAAGTAC	*
+read_1.72.0	16	chr1	73	60	35M	*	0	0	CCGGAGATAGGACATCAGCAAGTACGTTAAGTACA	*
+read_1.72.1	0	chr1	73	60	35M	*	0	0	CCGGAGATAGGACATCAGCAAGTACGTTAAGTACA	*
+read_1.72.2	16	chr1	73	60	35M	*	0	0	CCGGAGATAGGACATCAGCAAGTACGTTAAGTACA	*
+read_1.73.0	0	chr1	74	60	35M	*	0	0	CGGAGATAGGACATCAGCAAGTACGTTAAGTACAC	*
+read_1.73.1	0	chr1	74	60	35M	*	0	0	CGGAGATAGGACATCAGCAAGTACGTTAAGTACAC	*
+read_1.74.0	16	chr1	75	60	35M	*	0	0	GGAGATAGGACATCAGCAAGTACGTTAAGTACACT	*
+read_1.75.0	0	chr1	76	60	35M	*	0	0	GAGATAGGACATCAGCAAGTACGTTAAGTACACTG	*
+read_1.75.1	16	chr1	76	60	35M	*	0	0	GAGATAGGACATCAGCAAGTACGTTAAGTACACTG	*
+read_1.76.0	16	chr1	77	60	35M	*	0	0	AGATAGGACATCAGCAAGTACGTTAAGTACACTGA	*
+read_1.77.0	16	chr1	78	60	35M	*	0	0	GATAGGACATCAGCAAGTACGTTAAGTACACTGAA	*
+read_1.77.1	0	chr1	78	60	35M	*	0	0	GATAGGACATCAGCAAGTACGTTAAGTACACTGAA	*
+read_1.77.2	0	chr1	78	60	35M	*	0	0	GATAGGACATCAGCAAGTACGTTAAGTACACTGAA	*
+read_1.78.0	0	chr1	79	60	35M	*	0	0	ATAGGACATCAGCAAGTACGTTAAGTACACTGAAC	*
+read_1.79.0	0	chr1	80	60	35M	*	0	0	TAGGACATCAGCAAGTACGTTAAGTACACTGAACG	*
+read_1.80.0	0	chr1	81	60	35M	*	0	0	AGGACATCAGCAAGTACGTTAAGTACACTGAACGA	*
+read_1.81.0	0	chr1	82	60	35M	*	0	0	GGACATCAGCAAGTACGTTAAGTACACTGAACGAA	*
+read_1.81.1	0	chr1	82	60	35M	*	0	0	GGACATCAGCAAGTACGTTAAGTACACTGAACGAA	*
+read_1.81.2	0	chr1	82	60	35M	*	0	0	GGACATCAGCAAGTACGTTAAGTACACTGAACGAA	*
+read_1.82.0	16	chr1	83	60	35M	*	0	0	GACATCAGCAAGTACGTTAAGTACACTGAACGAAC	*
+read_1.82.1	16	chr1	83	60	35M	*	0	0	GACATCAGCAAGTACGTTAAGTACACTGAACGAAC	*
+read_1.82.2	16	chr1	83	60	35M	*	0	0	GACATCAGCAAGTACGTTAAGTACACTGAACGAAC	*
+read_1.83.0	16	chr1	84	60	35M	*	0	0	ACATCAGCAAGTACGTTAAGTACACTGAACGAACT	*
+read_1.83.1	0	chr1	84	60	35M	*	0	0	ACATCAGCAAGTACGTTAAGTACACTGAACGAACT	*
+read_1.83.2	16	chr1	84	60	35M	*	0	0	ACATCAGCAAGTACGTTAAGTACACTGAACGAACT	*
+read_1.83.3	16	chr1	84	60	35M	*	0	0	ACATCAGCAAGTACGTTAAGTACACTGAACGAACT	*
+read_1.84.0	0	chr1	85	60	35M	*	0	0	CATCAGCAAGTACGTTAAGTACACTGAACGAACTG	*
+read_1.84.1	0	chr1	85	60	35M	*	0	0	CATCAGCAAGTACGTTAAGTACACTGAACGAACTG	*
+read_1.85.0	16	chr1	86	60	35M	*	0	0	ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG	*
+read_1.85.1	0	chr1	86	60	35M	*	0	0	ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG	*
+read_1.85.2	16	chr1	86	60	35M	*	0	0	ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG	*
+read_1.85.3	16	chr1	86	60	35M	*	0	0	ATCAGCAAGTACGTTAAGTACACTGAACGAACTGG	*
+read_1.86.0	16	chr1	87	60	34M0N1M	*	0	0	TCAGCAAGTACGTTAAGTACACTGAACGAACTGGA	*
+read_1.87.0	16	chr1	88	60	33M0N2M	*	0	0	CAGCAAGTACGTTAAGTACACTGAACGAACTGGAG	*
+read_1.87.1	0	chr1	88	60	33M0N2M	*	0	0	CAGCAAGTACGTTAAGTACACTGAACGAACTGGAG	*
+read_1.88.0	0	chr1	89	60	32M0N3M	*	0	0	AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG	*
+read_1.88.1	0	chr1	89	60	32M0N3M	*	0	0	AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG	*
+read_1.88.2	16	chr1	89	60	32M0N3M	*	0	0	AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG	*
+read_1.88.3	16	chr1	89	60	32M0N3M	*	0	0	AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG	*
+read_1.88.4	0	chr1	89	60	32M0N3M	*	0	0	AGCAAGTACGTTAAGTACACTGAACGAACTGGAGG	*
+read_1.89.0	16	chr1	90	60	31M0N4M	*	0	0	GCAAGTACGTTAAGTACACTGAACGAACTGGAGGT	*
+read_1.89.1	16	chr1	90	60	31M0N4M	*	0	0	GCAAGTACGTTAAGTACACTGAACGAACTGGAGGT	*
+read_1.90.0	16	chr1	91	60	30M0N5M	*	0	0	CAAGTACGTTAAGTACACTGAACGAACTGGAGGTT	*
+read_1.90.1	16	chr1	91	60	30M0N5M	*	0	0	CAAGTACGTTAAGTACACTGAACGAACTGGAGGTT	*
+read_1.90.2	0	chr1	91	60	30M0N5M	*	0	0	CAAGTACGTTAAGTACACTGAACGAACTGGAGGTT	*
+read_1.91.0	0	chr1	92	60	29M0N6M	*	0	0	AAGTACGTTAAGTACACTGAACGAACTGGAGGTTT	*
+read_1.91.1	0	chr1	92	60	29M0N6M	*	0	0	AAGTACGTTAAGTACACTGAACGAACTGGAGGTTT	*
+read_1.92.0	0	chr1	93	60	28M0N7M	*	0	0	AGTACGTTAAGTACACTGAACGAACTGGAGGTTTC	*
+read_1.92.1	0	chr1	93	60	28M0N7M	*	0	0	AGTACGTTAAGTACACTGAACGAACTGGAGGTTTC	*
+read_1.92.2	0	chr1	93	60	28M0N7M	*	0	0	AGTACGTTAAGTACACTGAACGAACTGGAGGTTTC	*
+read_1.93.0	0	chr1	94	60	27M0N8M	*	0	0	GTACGTTAAGTACACTGAACGAACTGGAGGTTTCT	*
+read_1.93.1	16	chr1	94	60	27M0N8M	*	0	0	GTACGTTAAGTACACTGAACGAACTGGAGGTTTCT	*
+read_1.94.0	0	chr1	95	60	26M0N9M	*	0	0	TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA	*
+read_1.94.1	0	chr1	95	60	26M0N9M	*	0	0	TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA	*
+read_1.94.2	16	chr1	95	60	26M0N9M	*	0	0	TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA	*
+read_1.94.3	0	chr1	95	60	26M0N9M	*	0	0	TACGTTAAGTACACTGAACGAACTGGAGGTTTCTA	*
+read_1.95.0	0	chr1	96	60	25M0N10M	*	0	0	ACGTTAAGTACACTGAACGAACTGGAGGTTTCTAC	*
+read_1.96.0	0	chr1	97	60	24M0N11M	*	0	0	CGTTAAGTACACTGAACGAACTGGAGGTTTCTACA	*
+read_1.96.1	16	chr1	97	60	24M0N11M	*	0	0	CGTTAAGTACACTGAACGAACTGGAGGTTTCTACA	*
+read_1.97.0	16	chr1	98	60	23M0N12M	*	0	0	GTTAAGTACACTGAACGAACTGGAGGTTTCTACAT	*
+read_1.98.0	0	chr1	99	60	22M0N13M	*	0	0	TTAAGTACACTGAACGAACTGGAGGTTTCTACATC	*
+read_1.99.0	0	chr1	100	60	21M0N14M	*	0	0	TAAGTACACTGAACGAACTGGAGGTTTCTACATCG	*
+read_1.100.0	16	chr1	101	60	20M0N15M	*	0	0	AAGTACACTGAACGAACTGGAGGTTTCTACATCGT	*
+read_1.100.1	16	chr1	101	60	20M0N15M	*	0	0	AAGTACACTGAACGAACTGGAGGTTTCTACATCGT	*
+read_1.100.2	16	chr1	101	60	20M0N15M	*	0	0	AAGTACACTGAACGAACTGGAGGTTTCTACATCGT	*
+read_1.100.3	16	chr1	101	60	20M0N15M	*	0	0	AAGTACACTGAACGAACTGGAGGTTTCTACATCGT	*
+read_1.100.4	0	chr1	101	60	20M0N15M	*	0	0	AAGTACACTGAACGAACTGGAGGTTTCTACATCGT	*
+read_1.101.0	16	chr1	102	60	19M0N16M	*	0	0	AGTACACTGAACGAACTGGAGGTTTCTACATCGTG	*
+read_1.102.0	16	chr1	103	60	18M0N17M	*	0	0	GTACACTGAACGAACTGGAGGTTTCTACATCGTGC	*
+read_1.102.1	16	chr1	103	60	18M0N17M	*	0	0	GTACACTGAACGAACTGGAGGTTTCTACATCGTGC	*
+read_1.102.2	0	chr1	103	60	18M0N17M	*	0	0	GTACACTGAACGAACTGGAGGTTTCTACATCGTGC	*
+read_1.103.0	16	chr1	104	60	17M0N18M	*	0	0	TACACTGAACGAACTGGAGGTTTCTACATCGTGCG	*
+read_1.103.1	0	chr1	104	60	17M0N18M	*	0	0	TACACTGAACGAACTGGAGGTTTCTACATCGTGCG	*
+read_1.104.0	16	chr1	105	60	16M0N19M	*	0	0	ACACTGAACGAACTGGAGGTTTCTACATCGTGCGT	*
+read_1.104.1	0	chr1	105	60	16M0N19M	*	0	0	ACACTGAACGAACTGGAGGTTTCTACATCGTGCGT	*
+read_1.104.2	16	chr1	105	60	16M0N19M	*	0	0	ACACTGAACGAACTGGAGGTTTCTACATCGTGCGT	*
+read_1.105.0	0	chr1	106	60	15M0N20M	*	0	0	CACTGAACGAACTGGAGGTTTCTACATCGTGCGTG	*
+read_1.105.1	16	chr1	106	60	15M0N20M	*	0	0	CACTGAACGAACTGGAGGTTTCTACATCGTGCGTG	*
+read_1.105.2	16	chr1	106	60	15M0N20M	*	0	0	CACTGAACGAACTGGAGGTTTCTACATCGTGCGTG	*
+read_1.106.0	16	chr1	107	60	14M0N21M	*	0	0	ACTGAACGAACTGGAGGTTTCTACATCGTGCGTGA	*
+read_1.107.0	16	chr1	108	60	13M0N22M	*	0	0	CTGAACGAACTGGAGGTTTCTACATCGTGCGTGAT	*
+read_1.108.0	0	chr1	109	60	12M0N23M	*	0	0	TGAACGAACTGGAGGTTTCTACATCGTGCGTGATG	*
+read_1.108.1	0	chr1	109	60	12M0N23M	*	0	0	TGAACGAACTGGAGGTTTCTACATCGTGCGTGATG	*
+read_1.109.0	16	chr1	110	60	11M0N24M	*	0	0	GAACGAACTGGAGGTTTCTACATCGTGCGTGATGG	*
+read_1.109.1	0	chr1	110	60	11M0N24M	*	0	0	GAACGAACTGGAGGTTTCTACATCGTGCGTGATGG	*
+read_1.109.2	16	chr1	110	60	11M0N24M	*	0	0	GAACGAACTGGAGGTTTCTACATCGTGCGTGATGG	*
+read_1.110.0	16	chr1	111	60	10M0N25M	*	0	0	AACGAACTGGAGGTTTCTACATCGTGCGTGATGGC	*
+read_1.110.1	16	chr1	111	60	10M0N25M	*	0	0	AACGAACTGGAGGTTTCTACATCGTGCGTGATGGC	*
+read_1.111.0	0	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.111.1	0	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.111.2	16	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.111.3	16	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.111.4	16	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.111.5	0	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.111.6	0	chr1	112	60	9M0N26M	*	0	0	ACGAACTGGAGGTTTCTACATCGTGCGTGATGGCC	*
+read_1.112.0	16	chr1	113	60	8M0N27M	*	0	0	CGAACTGGAGGTTTCTACATCGTGCGTGATGGCCC	*
+read_1.113.0	16	chr1	114	60	7M0N28M	*	0	0	GAACTGGAGGTTTCTACATCGTGCGTGATGGCCCT	*
+read_1.113.1	16	chr1	114	60	7M0N28M	*	0	0	GAACTGGAGGTTTCTACATCGTGCGTGATGGCCCT	*
+read_1.114.0	0	chr1	115	60	6M0N29M	*	0	0	AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA	*
+read_1.114.1	0	chr1	115	60	6M0N29M	*	0	0	AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA	*
+read_1.114.2	16	chr1	115	60	6M0N29M	*	0	0	AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA	*
+read_1.114.3	0	chr1	115	60	6M0N29M	*	0	0	AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA	*
+read_1.114.4	16	chr1	115	60	6M0N29M	*	0	0	AACTGGAGGTTTCTACATCGTGCGTGATGGCCCTA	*
+read_1.115.0	16	chr1	116	60	5M0N30M	*	0	0	ACTGGAGGTTTCTACATCGTGCGTGATGGCCCTAG	*
+read_1.116.0	0	chr1	117	60	4M0N31M	*	0	0	CTGGAGGTTTCTACATCGTGCGTGATGGCCCTAGG	*
+read_1.117.0	0	chr1	118	60	3M0N32M	*	0	0	TGGAGGTTTCTACATCGTGCGTGATGGCCCTAGGA	*
+read_1.117.1	0	chr1	118	60	3M0N32M	*	0	0	TGGAGGTTTCTACATCGTGCGTGATGGCCCTAGGA	*
+read_1.118.0	0	chr1	119	60	2M0N33M	*	0	0	GGAGGTTTCTACATCGTGCGTGATGGCCCTAGGAG	*
+read_1.118.1	16	chr1	119	60	2M0N33M	*	0	0	GGAGGTTTCTACATCGTGCGTGATGGCCCTAGGAG	*
+read_1.119.0	0	chr1	120	60	1M0N34M	*	0	0	GAGGTTTCTACATCGTGCGTGATGGCCCTAGGAGA	*
+read_1.119.1	0	chr1	120	60	1M0N34M	*	0	0	GAGGTTTCTACATCGTGCGTGATGGCCCTAGGAGA	*
+read_1.119.2	16	chr1	120	60	1M0N34M	*	0	0	GAGGTTTCTACATCGTGCGTGATGGCCCTAGGAGA	*
+read_2.120.0	16	chr1	121	60	35M	*	0	0	AGGTTTCTACATCGTGCGTGATGGCCCTAGGAGAA	*
+read_2.121.0	16	chr1	122	60	35M	*	0	0	GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG	*
+read_2.121.1	16	chr1	122	60	35M	*	0	0	GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG	*
+read_2.121.2	0	chr1	122	60	35M	*	0	0	GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG	*
+read_2.121.3	0	chr1	122	60	35M	*	0	0	GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG	*
+read_2.121.4	0	chr1	122	60	35M	*	0	0	GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG	*
+read_2.121.5	0	chr1	122	60	35M	*	0	0	GGTTTCTACATCGTGCGTGATGGCCCTAGGAGAAG	*
+read_2.122.0	0	chr1	123	60	35M	*	0	0	GTTTCTACATCGTGCGTGATGGCCCTAGGAGAAGT	*
+read_2.122.1	0	chr1	123	60	35M	*	0	0	GTTTCTACATCGTGCGTGATGGCCCTAGGAGAAGT	*
+read_2.122.2	0	chr1	123	60	35M	*	0	0	GTTTCTACATCGTGCGTGATGGCCCTAGGAGAAGT	*
+read_2.123.0	0	chr1	124	60	35M	*	0	0	TTTCTACATCGTGCGTGATGGCCCTAGGAGAAGTG	*
+read_2.123.1	0	chr1	124	60	35M	*	0	0	TTTCTACATCGTGCGTGATGGCCCTAGGAGAAGTG	*
+read_2.124.0	16	chr1	125	60	35M	*	0	0	TTCTACATCGTGCGTGATGGCCCTAGGAGAAGTGG	*
+read_2.124.1	0	chr1	125	60	35M	*	0	0	TTCTACATCGTGCGTGATGGCCCTAGGAGAAGTGG	*
+read_2.124.2	16	chr1	125	60	35M	*	0	0	TTCTACATCGTGCGTGATGGCCCTAGGAGAAGTGG	*
+read_2.125.0	0	chr1	126	60	35M	*	0	0	TCTACATCGTGCGTGATGGCCCTAGGAGAAGTGGG	*
+read_2.126.0	0	chr1	127	60	35M	*	0	0	CTACATCGTGCGTGATGGCCCTAGGAGAAGTGGGT	*
+read_2.126.1	0	chr1	127	60	35M	*	0	0	CTACATCGTGCGTGATGGCCCTAGGAGAAGTGGGT	*
+read_2.126.2	0	chr1	127	60	35M	*	0	0	CTACATCGTGCGTGATGGCCCTAGGAGAAGTGGGT	*
+read_2.127.0	0	chr1	128	60	35M	*	0	0	TACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTG	*
+read_2.127.1	16	chr1	128	60	35M	*	0	0	TACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTG	*
+read_2.128.0	16	chr1	129	60	35M	*	0	0	ACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGT	*
+read_2.128.1	0	chr1	129	60	35M	*	0	0	ACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGT	*
+read_2.128.2	0	chr1	129	60	35M	*	0	0	ACATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGT	*
+read_2.129.0	0	chr1	130	60	35M	*	0	0	CATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTA	*
+read_2.129.1	0	chr1	130	60	35M	*	0	0	CATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTA	*
+read_2.129.2	0	chr1	130	60	35M	*	0	0	CATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTA	*
+read_2.130.0	0	chr1	131	60	35M	*	0	0	ATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTAT	*
+read_2.130.1	0	chr1	131	60	35M	*	0	0	ATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTAT	*
+read_2.130.2	0	chr1	131	60	35M	*	0	0	ATCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTAT	*
+read_2.131.0	16	chr1	132	60	35M	*	0	0	TCGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATC	*
+read_2.132.0	0	chr1	133	60	35M	*	0	0	CGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCT	*
+read_2.132.1	0	chr1	133	60	35M	*	0	0	CGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCT	*
+read_2.132.2	0	chr1	133	60	35M	*	0	0	CGTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCT	*
+read_2.133.0	0	chr1	134	60	35M	*	0	0	GTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTG	*
+read_2.133.1	16	chr1	134	60	35M	*	0	0	GTGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTG	*
+read_2.134.0	16	chr1	135	60	35M	*	0	0	TGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGC	*
+read_2.134.1	16	chr1	135	60	35M	*	0	0	TGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGC	*
+read_2.134.2	0	chr1	135	60	35M	*	0	0	TGCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGC	*
+read_2.135.0	0	chr1	136	60	35M	*	0	0	GCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCA	*
+read_2.135.1	16	chr1	136	60	35M	*	0	0	GCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCA	*
+read_2.135.2	0	chr1	136	60	35M	*	0	0	GCGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCA	*
+read_2.136.0	16	chr1	137	60	35M	*	0	0	CGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCAC	*
+read_2.136.1	0	chr1	137	60	35M	*	0	0	CGTGATGGCCCTAGGAGAAGTGGGTGTATCTGCAC	*
+read_2.137.0	0	chr1	138	60	35M	*	0	0	GTGATGGCCCTAGGAGAAGTGGGTGTATCTGCACA	*
+read_2.137.1	16	chr1	138	60	35M	*	0	0	GTGATGGCCCTAGGAGAAGTGGGTGTATCTGCACA	*
+read_2.137.2	0	chr1	138	60	35M	*	0	0	GTGATGGCCCTAGGAGAAGTGGGTGTATCTGCACA	*
+read_2.138.0	16	chr1	139	60	35M	*	0	0	TGATGGCCCTAGGAGAAGTGGGTGTATCTGCACAG	*
+read_2.139.0	0	chr1	140	60	35M	*	0	0	GATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGC	*
+read_2.139.1	16	chr1	140	60	35M	*	0	0	GATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGC	*
+read_2.139.2	16	chr1	140	60	35M	*	0	0	GATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGC	*
+read_2.140.0	16	chr1	141	60	35M	*	0	0	ATGGCCCTAGGAGAAGTGGGTGTATCTGCACAGCA	*
+read_2.141.0	16	chr1	142	60	35M	*	0	0	TGGCCCTAGGAGAAGTGGGTGTATCTGCACAGCAT	*
+read_2.141.1	0	chr1	142	60	35M	*	0	0	TGGCCCTAGGAGAAGTGGGTGTATCTGCACAGCAT	*
+read_2.142.0	16	chr1	143	60	35M	*	0	0	GGCCCTAGGAGAAGTGGGTGTATCTGCACAGCATA	*
+read_2.142.1	0	chr1	143	60	35M	*	0	0	GGCCCTAGGAGAAGTGGGTGTATCTGCACAGCATA	*
+read_2.142.2	16	chr1	143	60	35M	*	0	0	GGCCCTAGGAGAAGTGGGTGTATCTGCACAGCATA	*
+read_2.143.0	0	chr1	144	60	35M	*	0	0	GCCCTAGGAGAAGTGGGTGTATCTGCACAGCATAA	*
+read_2.144.0	0	chr1	145	60	35M	*	0	0	CCCTAGGAGAAGTGGGTGTATCTGCACAGCATAAG	*
+read_2.144.1	0	chr1	145	60	35M	*	0	0	CCCTAGGAGAAGTGGGTGTATCTGCACAGCATAAG	*
+read_2.145.0	16	chr1	146	60	35M	*	0	0	CCTAGGAGAAGTGGGTGTATCTGCACAGCATAAGT	*
+read_2.146.0	16	chr1	147	60	34M0N1M	*	0	0	CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT	*
+read_2.146.1	16	chr1	147	60	34M0N1M	*	0	0	CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT	*
+read_2.146.2	16	chr1	147	60	34M0N1M	*	0	0	CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT	*
+read_2.146.3	0	chr1	147	60	34M0N1M	*	0	0	CTAGGAGAAGTGGGTGTATCTGCACAGCATAAGTT	*
+read_2.147.0	0	chr1	148	60	33M0N2M	*	0	0	TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA	*
+read_2.147.1	0	chr1	148	60	33M0N2M	*	0	0	TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA	*
+read_2.147.2	16	chr1	148	60	33M0N2M	*	0	0	TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA	*
+read_2.147.3	0	chr1	148	60	33M0N2M	*	0	0	TAGGAGAAGTGGGTGTATCTGCACAGCATAAGTTA	*
+read_2.148.0	0	chr1	149	60	32M0N3M	*	0	0	AGGAGAAGTGGGTGTATCTGCACAGCATAAGTTAT	*
+read_2.148.1	0	chr1	149	60	32M0N3M	*	0	0	AGGAGAAGTGGGTGTATCTGCACAGCATAAGTTAT	*
+read_2.148.2	0	chr1	149	60	32M0N3M	*	0	0	AGGAGAAGTGGGTGTATCTGCACAGCATAAGTTAT	*
+read_2.149.0	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.1	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.2	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.3	0	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.4	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.5	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.6	0	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.7	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.8	16	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.149.9	0	chr1	150	60	31M0N4M	*	0	0	GGAGAAGTGGGTGTATCTGCACAGCATAAGTTATA	*
+read_2.150.0	0	chr1	151	60	30M0N5M	*	0	0	GAGAAGTGGGTGTATCTGCACAGCATAAGTTATAA	*
+read_2.150.1	0	chr1	151	60	30M0N5M	*	0	0	GAGAAGTGGGTGTATCTGCACAGCATAAGTTATAA	*
+read_2.150.2	0	chr1	151	60	30M0N5M	*	0	0	GAGAAGTGGGTGTATCTGCACAGCATAAGTTATAA	*
+read_2.151.0	16	chr1	152	60	29M0N6M	*	0	0	AGAAGTGGGTGTATCTGCACAGCATAAGTTATAAG	*
+read_2.151.1	0	chr1	152	60	29M0N6M	*	0	0	AGAAGTGGGTGTATCTGCACAGCATAAGTTATAAG	*
+read_2.151.2	0	chr1	152	60	29M0N6M	*	0	0	AGAAGTGGGTGTATCTGCACAGCATAAGTTATAAG	*
+read_2.152.0	16	chr1	153	60	28M0N7M	*	0	0	GAAGTGGGTGTATCTGCACAGCATAAGTTATAAGA	*
+read_2.152.1	16	chr1	153	60	28M0N7M	*	0	0	GAAGTGGGTGTATCTGCACAGCATAAGTTATAAGA	*
+read_2.153.0	16	chr1	154	60	27M0N8M	*	0	0	AAGTGGGTGTATCTGCACAGCATAAGTTATAAGAC	*
+read_2.154.0	0	chr1	155	60	26M0N9M	*	0	0	AGTGGGTGTATCTGCACAGCATAAGTTATAAGACG	*
+read_2.154.1	0	chr1	155	60	26M0N9M	*	0	0	AGTGGGTGTATCTGCACAGCATAAGTTATAAGACG	*
+read_2.155.0	16	chr1	156	60	25M0N10M	*	0	0	GTGGGTGTATCTGCACAGCATAAGTTATAAGACGG	*
+read_2.156.0	0	chr1	157	60	24M0N11M	*	0	0	TGGGTGTATCTGCACAGCATAAGTTATAAGACGGA	*
+read_2.157.0	0	chr1	158	60	23M0N12M	*	0	0	GGGTGTATCTGCACAGCATAAGTTATAAGACGGAA	*
+read_2.157.1	16	chr1	158	60	23M0N12M	*	0	0	GGGTGTATCTGCACAGCATAAGTTATAAGACGGAA	*
+read_2.158.0	0	chr1	159	60	22M0N13M	*	0	0	GGTGTATCTGCACAGCATAAGTTATAAGACGGAAG	*
+read_2.158.1	16	chr1	159	60	22M0N13M	*	0	0	GGTGTATCTGCACAGCATAAGTTATAAGACGGAAG	*
+read_2.159.0	16	chr1	160	60	21M0N14M	*	0	0	GTGTATCTGCACAGCATAAGTTATAAGACGGAAGT	*
+read_2.159.1	16	chr1	160	60	21M0N14M	*	0	0	GTGTATCTGCACAGCATAAGTTATAAGACGGAAGT	*
+read_2.160.0	16	chr1	161	60	20M0N15M	*	0	0	TGTATCTGCACAGCATAAGTTATAAGACGGAAGTA	*
+read_2.161.0	16	chr1	162	60	19M0N16M	*	0	0	GTATCTGCACAGCATAAGTTATAAGACGGAAGTAA	*
+read_2.161.1	16	chr1	162	60	19M0N16M	*	0	0	GTATCTGCACAGCATAAGTTATAAGACGGAAGTAA	*
+read_2.162.0	16	chr1	163	60	18M0N17M	*	0	0	TATCTGCACAGCATAAGTTATAAGACGGAAGTAAA	*
+read_2.162.1	16	chr1	163	60	18M0N17M	*	0	0	TATCTGCACAGCATAAGTTATAAGACGGAAGTAAA	*
+read_2.162.2	16	chr1	163	60	18M0N17M	*	0	0	TATCTGCACAGCATAAGTTATAAGACGGAAGTAAA	*
+read_2.163.0	0	chr1	164	60	17M0N18M	*	0	0	ATCTGCACAGCATAAGTTATAAGACGGAAGTAAAG	*
+read_2.164.0	16	chr1	165	60	16M0N19M	*	0	0	TCTGCACAGCATAAGTTATAAGACGGAAGTAAAGC	*
+read_2.165.0	16	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.165.1	0	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.165.2	16	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.165.3	16	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.165.4	0	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.165.5	0	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.165.6	0	chr1	166	60	15M0N20M	*	0	0	CTGCACAGCATAAGTTATAAGACGGAAGTAAAGCG	*
+read_2.166.0	0	chr1	167	60	14M0N21M	*	0	0	TGCACAGCATAAGTTATAAGACGGAAGTAAAGCGT	*
+read_2.166.1	0	chr1	167	60	14M0N21M	*	0	0	TGCACAGCATAAGTTATAAGACGGAAGTAAAGCGT	*
+read_2.167.0	0	chr1	168	60	13M0N22M	*	0	0	GCACAGCATAAGTTATAAGACGGAAGTAAAGCGTC	*
+read_2.168.0	16	chr1	169	60	12M0N23M	*	0	0	CACAGCATAAGTTATAAGACGGAAGTAAAGCGTCT	*
+read_2.168.1	0	chr1	169	60	12M0N23M	*	0	0	CACAGCATAAGTTATAAGACGGAAGTAAAGCGTCT	*
+read_2.169.0	0	chr1	170	60	11M0N24M	*	0	0	ACAGCATAAGTTATAAGACGGAAGTAAAGCGTCTT	*
+read_2.169.1	0	chr1	170	60	11M0N24M	*	0	0	ACAGCATAAGTTATAAGACGGAAGTAAAGCGTCTT	*
+read_2.169.2	0	chr1	170	60	11M0N24M	*	0	0	ACAGCATAAGTTATAAGACGGAAGTAAAGCGTCTT	*
+read_2.170.0	0	chr1	171	60	10M0N25M	*	0	0	CAGCATAAGTTATAAGACGGAAGTAAAGCGTCTTC	*
+read_2.170.1	0	chr1	171	60	10M0N25M	*	0	0	CAGCATAAGTTATAAGACGGAAGTAAAGCGTCTTC	*
+read_2.171.0	0	chr1	172	60	9M0N26M	*	0	0	AGCATAAGTTATAAGACGGAAGTAAAGCGTCTTCG	*
+read_2.171.1	0	chr1	172	60	9M0N26M	*	0	0	AGCATAAGTTATAAGACGGAAGTAAAGCGTCTTCG	*
+read_2.172.0	16	chr1	173	60	8M0N27M	*	0	0	GCATAAGTTATAAGACGGAAGTAAAGCGTCTTCGC	*
+read_2.172.1	16	chr1	173	60	8M0N27M	*	0	0	GCATAAGTTATAAGACGGAAGTAAAGCGTCTTCGC	*
+read_2.172.2	0	chr1	173	60	8M0N27M	*	0	0	GCATAAGTTATAAGACGGAAGTAAAGCGTCTTCGC	*
+read_2.173.0	0	chr1	174	60	7M0N28M	*	0	0	CATAAGTTATAAGACGGAAGTAAAGCGTCTTCGCC	*
+read_2.174.0	0	chr1	175	60	6M0N29M	*	0	0	ATAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCG	*
+read_2.175.0	0	chr1	176	60	5M0N30M	*	0	0	TAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGT	*
+read_2.175.1	16	chr1	176	60	5M0N30M	*	0	0	TAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGT	*
+read_2.175.2	0	chr1	176	60	5M0N30M	*	0	0	TAAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGT	*
+read_2.176.0	16	chr1	177	60	4M0N31M	*	0	0	AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT	*
+read_2.176.1	0	chr1	177	60	4M0N31M	*	0	0	AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT	*
+read_2.176.2	0	chr1	177	60	4M0N31M	*	0	0	AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT	*
+read_2.176.3	16	chr1	177	60	4M0N31M	*	0	0	AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT	*
+read_2.176.4	16	chr1	177	60	4M0N31M	*	0	0	AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT	*
+read_2.176.5	0	chr1	177	60	4M0N31M	*	0	0	AAGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTT	*
+read_2.177.0	0	chr1	178	60	3M0N32M	*	0	0	AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC	*
+read_2.177.1	16	chr1	178	60	3M0N32M	*	0	0	AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC	*
+read_2.177.2	16	chr1	178	60	3M0N32M	*	0	0	AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC	*
+read_2.177.3	0	chr1	178	60	3M0N32M	*	0	0	AGTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTC	*
+read_2.178.0	0	chr1	179	60	2M0N33M	*	0	0	GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA	*
+read_2.178.1	16	chr1	179	60	2M0N33M	*	0	0	GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA	*
+read_2.178.2	0	chr1	179	60	2M0N33M	*	0	0	GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA	*
+read_2.178.3	0	chr1	179	60	2M0N33M	*	0	0	GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA	*
+read_2.178.4	0	chr1	179	60	2M0N33M	*	0	0	GTTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCA	*
+read_2.179.0	0	chr1	180	60	1M0N34M	*	0	0	TTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAG	*
+read_2.179.1	0	chr1	180	60	1M0N34M	*	0	0	TTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAG	*
+read_2.179.2	16	chr1	180	60	1M0N34M	*	0	0	TTATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAG	*
+read_3.180.0	0	chr1	181	60	35M	*	0	0	TATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGC	*
+read_3.180.1	0	chr1	181	60	35M	*	0	0	TATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGC	*
+read_3.181.0	0	chr1	182	60	35M	*	0	0	ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA	*
+read_3.181.1	0	chr1	182	60	35M	*	0	0	ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA	*
+read_3.181.2	16	chr1	182	60	35M	*	0	0	ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA	*
+read_3.181.3	0	chr1	182	60	35M	*	0	0	ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA	*
+read_3.181.4	16	chr1	182	60	35M	*	0	0	ATAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCA	*
+read_3.182.0	16	chr1	183	60	35M	*	0	0	TAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCAC	*
+read_3.182.1	16	chr1	183	60	35M	*	0	0	TAAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCAC	*
+read_3.183.0	16	chr1	184	60	35M	*	0	0	AAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCACC	*
+read_3.183.1	16	chr1	184	60	35M	*	0	0	AAGACGGAAGTAAAGCGTCTTCGCCGTTCAGCACC	*
+read_3.184.0	0	chr1	185	60	35M	*	0	0	AGACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCC	*
+read_3.185.0	0	chr1	186	60	35M	*	0	0	GACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCC	*
+read_3.185.1	16	chr1	186	60	35M	*	0	0	GACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCC	*
+read_3.186.0	0	chr1	187	60	35M	*	0	0	ACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCA	*
+read_3.186.1	0	chr1	187	60	35M	*	0	0	ACGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCA	*
+read_3.187.0	16	chr1	188	60	35M	*	0	0	CGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCAC	*
+read_3.187.1	16	chr1	188	60	35M	*	0	0	CGGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCAC	*
+read_3.188.0	0	chr1	189	60	35M	*	0	0	GGAAGTAAAGCGTCTTCGCCGTTCAGCACCCCACG	*
+read_3.189.0	0	chr1	190	60	35M	*	0	0	GAAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGC	*
+read_3.190.0	0	chr1	191	60	35M	*	0	0	AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT	*
+read_3.190.1	16	chr1	191	60	35M	*	0	0	AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT	*
+read_3.190.2	0	chr1	191	60	35M	*	0	0	AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT	*
+read_3.190.3	16	chr1	191	60	35M	*	0	0	AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT	*
+read_3.190.4	0	chr1	191	60	35M	*	0	0	AAGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCT	*
+read_3.191.0	0	chr1	192	60	35M	*	0	0	AGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTC	*
+read_3.191.1	0	chr1	192	60	35M	*	0	0	AGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTC	*
+read_3.191.2	0	chr1	192	60	35M	*	0	0	AGTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTC	*
+read_3.192.0	16	chr1	193	60	35M	*	0	0	GTAAAGCGTCTTCGCCGTTCAGCACCCCACGCTCA	*
+read_3.193.0	16	chr1	194	60	35M	*	0	0	TAAAGCGTCTTCGCCGTTCAGCACCCCACGCTCAT	*
+read_3.194.0	0	chr1	195	60	35M	*	0	0	AAAGCGTCTTCGCCGTTCAGCACCCCACGCTCATA	*
+read_3.194.1	0	chr1	195	60	35M	*	0	0	AAAGCGTCTTCGCCGTTCAGCACCCCACGCTCATA	*
+read_3.195.0	0	chr1	196	60	35M	*	0	0	AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG	*
+read_3.195.1	0	chr1	196	60	35M	*	0	0	AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG	*
+read_3.195.2	0	chr1	196	60	35M	*	0	0	AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG	*
+read_3.195.3	16	chr1	196	60	35M	*	0	0	AAGCGTCTTCGCCGTTCAGCACCCCACGCTCATAG	*
+read_3.196.0	16	chr1	197	60	35M	*	0	0	AGCGTCTTCGCCGTTCAGCACCCCACGCTCATAGT	*
+read_3.196.1	0	chr1	197	60	35M	*	0	0	AGCGTCTTCGCCGTTCAGCACCCCACGCTCATAGT	*
+read_3.196.2	16	chr1	197	60	35M	*	0	0	AGCGTCTTCGCCGTTCAGCACCCCACGCTCATAGT	*
+read_3.197.0	0	chr1	198	60	35M	*	0	0	GCGTCTTCGCCGTTCAGCACCCCACGCTCATAGTC	*
+read_3.197.1	0	chr1	198	60	35M	*	0	0	GCGTCTTCGCCGTTCAGCACCCCACGCTCATAGTC	*
+read_3.197.2	16	chr1	198	60	35M	*	0	0	GCGTCTTCGCCGTTCAGCACCCCACGCTCATAGTC	*
+read_3.198.0	0	chr1	199	60	35M	*	0	0	CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA	*
+read_3.198.1	16	chr1	199	60	35M	*	0	0	CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA	*
+read_3.198.2	0	chr1	199	60	35M	*	0	0	CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA	*
+read_3.198.3	0	chr1	199	60	35M	*	0	0	CGTCTTCGCCGTTCAGCACCCCACGCTCATAGTCA	*
+read_3.199.0	0	chr1	200	60	35M	*	0	0	GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA	*
+read_3.199.1	16	chr1	200	60	35M	*	0	0	GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA	*
+read_3.199.2	16	chr1	200	60	35M	*	0	0	GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA	*
+read_3.199.3	16	chr1	200	60	35M	*	0	0	GTCTTCGCCGTTCAGCACCCCACGCTCATAGTCAA	*
+read_3.200.0	0	chr1	201	60	35M	*	0	0	TCTTCGCCGTTCAGCACCCCACGCTCATAGTCAAT	*
+read_3.201.0	16	chr1	202	60	35M	*	0	0	CTTCGCCGTTCAGCACCCCACGCTCATAGTCAATG	*
+read_3.201.1	0	chr1	202	60	35M	*	0	0	CTTCGCCGTTCAGCACCCCACGCTCATAGTCAATG	*
+read_3.202.0	0	chr1	203	60	35M	*	0	0	TTCGCCGTTCAGCACCCCACGCTCATAGTCAATGC	*
+read_3.202.1	16	chr1	203	60	35M	*	0	0	TTCGCCGTTCAGCACCCCACGCTCATAGTCAATGC	*
+read_3.202.2	16	chr1	203	60	35M	*	0	0	TTCGCCGTTCAGCACCCCACGCTCATAGTCAATGC	*
+read_3.203.0	16	chr1	204	60	35M	*	0	0	TCGCCGTTCAGCACCCCACGCTCATAGTCAATGCT	*
+read_3.204.0	16	chr1	205	60	35M	*	0	0	CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG	*
+read_3.204.1	0	chr1	205	60	35M	*	0	0	CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG	*
+read_3.204.2	16	chr1	205	60	35M	*	0	0	CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG	*
+read_3.204.3	16	chr1	205	60	35M	*	0	0	CGCCGTTCAGCACCCCACGCTCATAGTCAATGCTG	*
+read_3.205.0	16	chr1	206	60	35M	*	0	0	GCCGTTCAGCACCCCACGCTCATAGTCAATGCTGG	*
+read_3.205.1	16	chr1	206	60	35M	*	0	0	GCCGTTCAGCACCCCACGCTCATAGTCAATGCTGG	*
+read_3.206.0	16	chr1	207	60	34M240N1M	*	0	0	CCGTTCAGCACCCCACGCTCATAGTCAATGCTGGT	*
+read_3.207.0	0	chr1	208	60	33M240N2M	*	0	0	CGTTCAGCACCCCACGCTCATAGTCAATGCTGGTG	*
+read_3.207.1	0	chr1	208	60	33M240N2M	*	0	0	CGTTCAGCACCCCACGCTCATAGTCAATGCTGGTG	*
+read_3.208.0	16	chr1	209	60	32M240N3M	*	0	0	GTTCAGCACCCCACGCTCATAGTCAATGCTGGTGA	*
+read_3.208.1	16	chr1	209	60	32M240N3M	*	0	0	GTTCAGCACCCCACGCTCATAGTCAATGCTGGTGA	*
+read_3.208.2	0	chr1	209	60	32M240N3M	*	0	0	GTTCAGCACCCCACGCTCATAGTCAATGCTGGTGA	*
+read_3.209.0	0	chr1	210	60	31M240N4M	*	0	0	TTCAGCACCCCACGCTCATAGTCAATGCTGGTGAA	*
+read_3.210.0	16	chr1	211	60	30M240N5M	*	0	0	TCAGCACCCCACGCTCATAGTCAATGCTGGTGAAC	*
+read_3.210.1	0	chr1	211	60	30M240N5M	*	0	0	TCAGCACCCCACGCTCATAGTCAATGCTGGTGAAC	*
+read_3.210.2	16	chr1	211	60	30M240N5M	*	0	0	TCAGCACCCCACGCTCATAGTCAATGCTGGTGAAC	*
+read_3.211.0	0	chr1	212	60	29M240N6M	*	0	0	CAGCACCCCACGCTCATAGTCAATGCTGGTGAACG	*
+read_3.211.1	16	chr1	212	60	29M240N6M	*	0	0	CAGCACCCCACGCTCATAGTCAATGCTGGTGAACG	*
+read_3.212.0	16	chr1	213	60	28M240N7M	*	0	0	AGCACCCCACGCTCATAGTCAATGCTGGTGAACGT	*
+read_3.213.0	0	chr1	214	60	27M240N8M	*	0	0	GCACCCCACGCTCATAGTCAATGCTGGTGAACGTT	*
+read_3.213.1	0	chr1	214	60	27M240N8M	*	0	0	GCACCCCACGCTCATAGTCAATGCTGGTGAACGTT	*
+read_3.214.0	0	chr1	215	60	26M240N9M	*	0	0	CACCCCACGCTCATAGTCAATGCTGGTGAACGTTG	*
+read_3.214.1	16	chr1	215	60	26M240N9M	*	0	0	CACCCCACGCTCATAGTCAATGCTGGTGAACGTTG	*
+read_3.215.0	0	chr1	216	60	25M240N10M	*	0	0	ACCCCACGCTCATAGTCAATGCTGGTGAACGTTGA	*
+read_3.216.0	0	chr1	217	60	24M240N11M	*	0	0	CCCCACGCTCATAGTCAATGCTGGTGAACGTTGAA	*
+read_3.216.1	0	chr1	217	60	24M240N11M	*	0	0	CCCCACGCTCATAGTCAATGCTGGTGAACGTTGAA	*
+read_3.217.0	16	chr1	218	60	23M240N12M	*	0	0	CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC	*
+read_3.217.1	16	chr1	218	60	23M240N12M	*	0	0	CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC	*
+read_3.217.2	0	chr1	218	60	23M240N12M	*	0	0	CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC	*
+read_3.217.3	0	chr1	218	60	23M240N12M	*	0	0	CCCACGCTCATAGTCAATGCTGGTGAACGTTGAAC	*
+read_3.218.0	0	chr1	219	60	22M240N13M	*	0	0	CCACGCTCATAGTCAATGCTGGTGAACGTTGAACT	*
+read_3.218.1	16	chr1	219	60	22M240N13M	*	0	0	CCACGCTCATAGTCAATGCTGGTGAACGTTGAACT	*
+read_3.219.0	0	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.219.1	16	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.219.2	16	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.219.3	16	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.219.4	0	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.219.5	16	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.219.6	0	chr1	220	60	21M240N14M	*	0	0	CACGCTCATAGTCAATGCTGGTGAACGTTGAACTA	*
+read_3.220.0	16	chr1	221	60	20M240N15M	*	0	0	ACGCTCATAGTCAATGCTGGTGAACGTTGAACTAG	*
+read_3.221.0	0	chr1	222	60	19M240N16M	*	0	0	CGCTCATAGTCAATGCTGGTGAACGTTGAACTAGC	*
+read_3.222.0	16	chr1	223	60	18M240N17M	*	0	0	GCTCATAGTCAATGCTGGTGAACGTTGAACTAGCC	*
+read_3.222.1	16	chr1	223	60	18M240N17M	*	0	0	GCTCATAGTCAATGCTGGTGAACGTTGAACTAGCC	*
+read_3.223.0	0	chr1	224	60	17M240N18M	*	0	0	CTCATAGTCAATGCTGGTGAACGTTGAACTAGCCC	*
+read_3.223.1	16	chr1	224	60	17M240N18M	*	0	0	CTCATAGTCAATGCTGGTGAACGTTGAACTAGCCC	*
+read_3.223.2	16	chr1	224	60	17M240N18M	*	0	0	CTCATAGTCAATGCTGGTGAACGTTGAACTAGCCC	*
+read_3.224.0	0	chr1	225	60	16M240N19M	*	0	0	TCATAGTCAATGCTGGTGAACGTTGAACTAGCCCT	*
+read_3.224.1	0	chr1	225	60	16M240N19M	*	0	0	TCATAGTCAATGCTGGTGAACGTTGAACTAGCCCT	*
+read_3.224.2	16	chr1	225	60	16M240N19M	*	0	0	TCATAGTCAATGCTGGTGAACGTTGAACTAGCCCT	*
+read_3.225.0	16	chr1	226	60	15M240N20M	*	0	0	CATAGTCAATGCTGGTGAACGTTGAACTAGCCCTG	*
+read_3.225.1	0	chr1	226	60	15M240N20M	*	0	0	CATAGTCAATGCTGGTGAACGTTGAACTAGCCCTG	*
+read_3.225.2	0	chr1	226	60	15M240N20M	*	0	0	CATAGTCAATGCTGGTGAACGTTGAACTAGCCCTG	*
+read_3.226.0	16	chr1	227	60	14M240N21M	*	0	0	ATAGTCAATGCTGGTGAACGTTGAACTAGCCCTGA	*
+read_3.226.1	16	chr1	227	60	14M240N21M	*	0	0	ATAGTCAATGCTGGTGAACGTTGAACTAGCCCTGA	*
+read_3.226.2	0	chr1	227	60	14M240N21M	*	0	0	ATAGTCAATGCTGGTGAACGTTGAACTAGCCCTGA	*
+read_3.227.0	16	chr1	228	60	13M240N22M	*	0	0	TAGTCAATGCTGGTGAACGTTGAACTAGCCCTGAT	*
+read_3.228.0	0	chr1	229	60	12M240N23M	*	0	0	AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG	*
+read_3.228.1	0	chr1	229	60	12M240N23M	*	0	0	AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG	*
+read_3.228.2	0	chr1	229	60	12M240N23M	*	0	0	AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG	*
+read_3.228.3	16	chr1	229	60	12M240N23M	*	0	0	AGTCAATGCTGGTGAACGTTGAACTAGCCCTGATG	*
+read_3.229.0	0	chr1	230	60	11M240N24M	*	0	0	GTCAATGCTGGTGAACGTTGAACTAGCCCTGATGT	*
+read_3.230.0	16	chr1	231	60	10M240N25M	*	0	0	TCAATGCTGGTGAACGTTGAACTAGCCCTGATGTA	*
+read_3.230.1	0	chr1	231	60	10M240N25M	*	0	0	TCAATGCTGGTGAACGTTGAACTAGCCCTGATGTA	*
+read_3.230.2	16	chr1	231	60	10M240N25M	*	0	0	TCAATGCTGGTGAACGTTGAACTAGCCCTGATGTA	*
+read_3.231.0	16	chr1	232	60	9M240N26M	*	0	0	CAATGCTGGTGAACGTTGAACTAGCCCTGATGTAA	*
+read_3.231.1	16	chr1	232	60	9M240N26M	*	0	0	CAATGCTGGTGAACGTTGAACTAGCCCTGATGTAA	*
+read_3.232.0	0	chr1	233	60	8M240N27M	*	0	0	AATGCTGGTGAACGTTGAACTAGCCCTGATGTAAA	*
+read_3.233.0	16	chr1	234	60	7M240N28M	*	0	0	ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC	*
+read_3.233.1	0	chr1	234	60	7M240N28M	*	0	0	ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC	*
+read_3.233.2	0	chr1	234	60	7M240N28M	*	0	0	ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC	*
+read_3.233.3	16	chr1	234	60	7M240N28M	*	0	0	ATGCTGGTGAACGTTGAACTAGCCCTGATGTAAAC	*
+read_3.234.0	16	chr1	235	60	6M240N29M	*	0	0	TGCTGGTGAACGTTGAACTAGCCCTGATGTAAACC	*
+read_3.234.1	16	chr1	235	60	6M240N29M	*	0	0	TGCTGGTGAACGTTGAACTAGCCCTGATGTAAACC	*
+read_3.234.2	16	chr1	235	60	6M240N29M	*	0	0	TGCTGGTGAACGTTGAACTAGCCCTGATGTAAACC	*
+read_3.235.0	0	chr1	236	60	5M240N30M	*	0	0	GCTGGTGAACGTTGAACTAGCCCTGATGTAAACCC	*
+read_3.235.1	0	chr1	236	60	5M240N30M	*	0	0	GCTGGTGAACGTTGAACTAGCCCTGATGTAAACCC	*
+read_3.236.0	0	chr1	237	60	4M240N31M	*	0	0	CTGGTGAACGTTGAACTAGCCCTGATGTAAACCCC	*
+read_3.236.1	16	chr1	237	60	4M240N31M	*	0	0	CTGGTGAACGTTGAACTAGCCCTGATGTAAACCCC	*
+read_3.236.2	0	chr1	237	60	4M240N31M	*	0	0	CTGGTGAACGTTGAACTAGCCCTGATGTAAACCCC	*
+read_3.237.0	0	chr1	238	60	3M240N32M	*	0	0	TGGTGAACGTTGAACTAGCCCTGATGTAAACCCCG	*
+read_3.238.0	0	chr1	239	60	2M240N33M	*	0	0	GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC	*
+read_3.238.1	0	chr1	239	60	2M240N33M	*	0	0	GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC	*
+read_3.238.2	0	chr1	239	60	2M240N33M	*	0	0	GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC	*
+read_3.238.3	0	chr1	239	60	2M240N33M	*	0	0	GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC	*
+read_3.238.4	16	chr1	239	60	2M240N33M	*	0	0	GGTGAACGTTGAACTAGCCCTGATGTAAACCCCGC	*
+read_3.239.0	16	chr1	240	60	1M240N34M	*	0	0	GTGAACGTTGAACTAGCCCTGATGTAAACCCCGCG	*
+read_3.239.1	0	chr1	240	60	1M240N34M	*	0	0	GTGAACGTTGAACTAGCCCTGATGTAAACCCCGCG	*
+read_4.240.0	16	chr1	481	60	35M	*	0	0	TGAACGTTGAACTAGCCCTGATGTAAACCCCGCGT	*
+read_4.241.0	16	chr1	482	60	35M	*	0	0	GAACGTTGAACTAGCCCTGATGTAAACCCCGCGTG	*
+read_4.241.1	16	chr1	482	60	35M	*	0	0	GAACGTTGAACTAGCCCTGATGTAAACCCCGCGTG	*
+read_4.242.0	16	chr1	483	60	35M	*	0	0	AACGTTGAACTAGCCCTGATGTAAACCCCGCGTGC	*
+read_4.242.1	0	chr1	483	60	35M	*	0	0	AACGTTGAACTAGCCCTGATGTAAACCCCGCGTGC	*
+read_4.242.2	0	chr1	483	60	35M	*	0	0	AACGTTGAACTAGCCCTGATGTAAACCCCGCGTGC	*
+read_4.243.0	0	chr1	484	60	35M	*	0	0	ACGTTGAACTAGCCCTGATGTAAACCCCGCGTGCC	*
+read_4.244.0	16	chr1	485	60	35M	*	0	0	CGTTGAACTAGCCCTGATGTAAACCCCGCGTGCCA	*
+read_4.244.1	16	chr1	485	60	35M	*	0	0	CGTTGAACTAGCCCTGATGTAAACCCCGCGTGCCA	*
+read_4.245.0	0	chr1	486	60	35M	*	0	0	GTTGAACTAGCCCTGATGTAAACCCCGCGTGCCAA	*
+read_4.246.0	16	chr1	487	60	35M	*	0	0	TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT	*
+read_4.246.1	16	chr1	487	60	35M	*	0	0	TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT	*
+read_4.246.2	16	chr1	487	60	35M	*	0	0	TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT	*
+read_4.246.3	16	chr1	487	60	35M	*	0	0	TTGAACTAGCCCTGATGTAAACCCCGCGTGCCAAT	*
+read_4.247.0	0	chr1	488	60	35M	*	0	0	TGAACTAGCCCTGATGTAAACCCCGCGTGCCAATT	*
+read_4.248.0	0	chr1	489	60	35M	*	0	0	GAACTAGCCCTGATGTAAACCCCGCGTGCCAATTC	*
+read_4.248.1	16	chr1	489	60	35M	*	0	0	GAACTAGCCCTGATGTAAACCCCGCGTGCCAATTC	*
+read_4.250.0	16	chr1	491	60	35M	*	0	0	ACTAGCCCTGATGTAAACCCCGCGTGCCAATTCCA	*
+read_4.250.1	0	chr1	491	60	35M	*	0	0	ACTAGCCCTGATGTAAACCCCGCGTGCCAATTCCA	*
+read_4.251.0	0	chr1	492	60	35M	*	0	0	CTAGCCCTGATGTAAACCCCGCGTGCCAATTCCAG	*
+read_4.252.0	0	chr1	493	60	35M	*	0	0	TAGCCCTGATGTAAACCCCGCGTGCCAATTCCAGG	*
+read_4.252.1	16	chr1	493	60	35M	*	0	0	TAGCCCTGATGTAAACCCCGCGTGCCAATTCCAGG	*
+read_4.253.0	16	chr1	494	60	35M	*	0	0	AGCCCTGATGTAAACCCCGCGTGCCAATTCCAGGC	*
+read_4.253.1	0	chr1	494	60	35M	*	0	0	AGCCCTGATGTAAACCCCGCGTGCCAATTCCAGGC	*
+read_4.253.2	0	chr1	494	60	35M	*	0	0	AGCCCTGATGTAAACCCCGCGTGCCAATTCCAGGC	*
+read_4.254.0	16	chr1	495	60	35M	*	0	0	GCCCTGATGTAAACCCCGCGTGCCAATTCCAGGCG	*
+read_4.254.1	0	chr1	495	60	35M	*	0	0	GCCCTGATGTAAACCCCGCGTGCCAATTCCAGGCG	*
+read_4.255.0	16	chr1	496	60	35M	*	0	0	CCCTGATGTAAACCCCGCGTGCCAATTCCAGGCGT	*
+read_4.255.1	0	chr1	496	60	35M	*	0	0	CCCTGATGTAAACCCCGCGTGCCAATTCCAGGCGT	*
+read_4.256.0	0	chr1	497	60	35M	*	0	0	CCTGATGTAAACCCCGCGTGCCAATTCCAGGCGTC	*
+read_4.256.1	16	chr1	497	60	35M	*	0	0	CCTGATGTAAACCCCGCGTGCCAATTCCAGGCGTC	*
+read_4.257.0	16	chr1	498	60	35M	*	0	0	CTGATGTAAACCCCGCGTGCCAATTCCAGGCGTCA	*
+read_4.258.0	16	chr1	499	60	35M	*	0	0	TGATGTAAACCCCGCGTGCCAATTCCAGGCGTCAT	*
+read_4.259.0	16	chr1	500	60	35M	*	0	0	GATGTAAACCCCGCGTGCCAATTCCAGGCGTCATG	*
+read_4.260.0	0	chr1	501	60	35M	*	0	0	ATGTAAACCCCGCGTGCCAATTCCAGGCGTCATGG	*
+read_4.260.1	16	chr1	501	60	35M	*	0	0	ATGTAAACCCCGCGTGCCAATTCCAGGCGTCATGG	*
+read_4.261.0	16	chr1	502	60	35M	*	0	0	TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG	*
+read_4.261.1	16	chr1	502	60	35M	*	0	0	TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG	*
+read_4.261.2	0	chr1	502	60	35M	*	0	0	TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG	*
+read_4.261.3	16	chr1	502	60	35M	*	0	0	TGTAAACCCCGCGTGCCAATTCCAGGCGTCATGGG	*
+read_4.262.0	0	chr1	503	60	35M	*	0	0	GTAAACCCCGCGTGCCAATTCCAGGCGTCATGGGG	*
+read_4.262.1	16	chr1	503	60	35M	*	0	0	GTAAACCCCGCGTGCCAATTCCAGGCGTCATGGGG	*
+read_4.263.0	0	chr1	504	60	35M	*	0	0	TAAACCCCGCGTGCCAATTCCAGGCGTCATGGGGG	*
+read_4.263.1	16	chr1	504	60	35M	*	0	0	TAAACCCCGCGTGCCAATTCCAGGCGTCATGGGGG	*
+read_4.264.0	0	chr1	505	60	35M	*	0	0	AAACCCCGCGTGCCAATTCCAGGCGTCATGGGGGC	*
+read_4.265.0	0	chr1	506	60	35M	*	0	0	AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA	*
+read_4.265.1	16	chr1	506	60	35M	*	0	0	AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA	*
+read_4.265.2	16	chr1	506	60	35M	*	0	0	AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA	*
+read_4.265.3	0	chr1	506	60	35M	*	0	0	AACCCCGCGTGCCAATTCCAGGCGTCATGGGGGCA	*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generate_reads.py	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+
+import random
+import math
+
+
+__version_info__ = ('1', '0', '0')
+__version__ = '.'.join(__version_info__)
+
+
+class Region:
+	def __init__(self,start,stop,sequence):
+		self.start = start
+		self.stop = stop
+		self.sequence = sequence.strip().replace("\n","").replace(" ","")
+		if(len(self.sequence) != self.getSpanningLength()):
+			print "ERROR: sequence length: "+str(len(self.sequence))+", while spanning region is: "+str(self.getSpanningLength())
+			import sys
+			sys.exit()
+	
+	def getSpanningLength(self):
+		return abs(self.stop-self.start+1)
+
+class ReadSynthesizer:
+	def __init__(self,chromosome):
+		self.regions = []
+		self.chromosome = chromosome
+	
+	def addRegion(self,region):
+		self.regions.append(region)
+	
+	def produceReads(self,readDensity = 1,read_length = 50):
+		"""
+		Produces uniform reads by walking iteratively over self.regions
+		"""
+		
+		mRNA = self.getTotalmRNA()
+		spanning_length = self.getRegionSpanningLength()
+		n = spanning_length['total'] - read_length + 1
+		
+		j = 0
+		k = 0
+		
+		for i in range(n):
+			#  "alpha is playing the role of k and beta is playing the role of theta"
+			dd = max(0,int(round(random.lognormvariate(math.log(readDensity),0.5))))# Notice this is NOT a binomial distribution!!
+			
+			for d in range(dd):
+				sequence = mRNA[i:i+read_length]
+				
+				if(random.randint(0,1) == 0):
+					strand = 0
+				else:
+					strand = 16
+				flag = strand + 0
+				
+				print "read_"+str(j)+"."+str(i)+"."+str(d)+"\t"+str(flag)+"\t"+self.chromosome+"\t"+str(self.regions[j].start + k)+"\t60\t"+self.getMappingString(read_length,j,k)+"\t*\t0\t0\t"+str(sequence.upper())+"\t*"
+			
+			spanning_length['iter'][j] -= 1
+			if(k >= self.regions[j].getSpanningLength()-1):
+				j += 1
+				k = 0
+			else:
+				k += 1
+	
+	def getMappingString(self,length,j,offset):
+		m = 0
+		
+		out = ""
+		
+		for i in range(length):
+			k = i + offset
+			
+			if(k >= self.regions[j].getSpanningLength()):
+				j += 1
+				
+				out += str(m)+"M"
+				out += (str(self.regions[j].start - self.regions[j-1].stop-1))+"N"
+				m = 1
+				
+				offset = -k
+			else:
+				m += 1
+		
+		out += str(m) + "M"
+		
+		
+		return out
+	
+	def getRegionSpanningLength(self):
+		length = {'total':0,'iter':[]}
+		for r in self.regions:
+			l = r.getSpanningLength()
+			length['iter'].append(l)
+			length['total'] += l
+		return length
+	
+	def getTotalmRNA(self):
+		mRNA = ""
+		for r in self.regions:
+			mRNA += r.sequence
+		return mRNA
+
+
+
+if __name__ == "__main__":
+	# Artificial SNP
+	rs = ReadSynthesizer('chr1')
+	rs.addRegion(Region(  0+1, 59+1,'aaataggtcccaaacgttacgca'+'G'+'tctatgcctgacaaagttgcgaccacttcctctgcc'))#c -> G
+	rs.addRegion(Region( 60+1,119+1,'ttgtgtgacacgccggagatagg'+'A'+'catcagcaagtacgttaagtacactgaacgaactgg'))#g -> A
+	rs.addRegion(Region(120+1,179+1,'aggtttctacatcgtgcgtgatggc'+'C'+'ctaggagaagtgggtgtatctgcacagcataagt'))#t -> C
+	rs.addRegion(Region(180+1,239+1,'tataagacggaagtaaagcgtcttc'+'G'+'ccgttcagcaccccacgctcatagtcaatgctgg'))#a -> G
+	#rs.addRegion(Region(240+1,299+1,'ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt'))
+	#rs.addRegion(Region(300+1,359+1,'gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg'))
+	#rs.addRegion(Region(360+1,419+1,'cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa'))
+	#rs.addRegion(Region(420+1,479+1,'tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga'))
+	rs.addRegion(Region(480+1,539+1,'tgaacgttgaacta'+'GCC'+'ctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca'))#tag -> gcc
+	#rs.addRegion(Region(540+1,599+1,'acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat'))
+	rs.produceReads(2,35)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Thu Nov 05 07:49:02 2015 -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	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,9 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<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/tool_dependencies.xml	Thu Nov 05 07:49:02 2015 -0500
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="samtools_parallel_mpileup" version="0.1.19-a">
+        <repository changeset_revision="7dd0c6a9be41" name="package_samtools_parallel_mpileup_0_1_19_a" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>