# HG changeset patch
# User dereeper
# Date 1436539091 14400
# Node ID feb40a9a8eae45166c09e5ffcce10c75e5b62b9a
# Parent  420b57c3c185659c868f39fad44244edb3b1e85f
Uploaded

diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/MDSbasedOnIBSmatrix.pl
--- a/MDSplot/MDSbasedOnIBSmatrix.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-use Bio::SeqIO;
-
-my $PLINK_EXE= "plink";
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -i, --in         <input>
-    -o, --out        <output>
-~;
-$usage .= "\n";
-
-my ($in,$out);
-
-
-GetOptions(
-	"in=s"        => \$in,
-	"out=s"       => \$out
-);
-
-die $usage
-  if ( !$in || !$out);
-  
-	
-my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1";
-system($plink_command);
-
-my $awk_cmd = "awk \{\'print \$1\'\} $in.ped";
-my $inds = `$awk_cmd`;
-my @individuals = split("\n",$inds);
-
-my %populations;
-if (-e "$in.individual_info.txt")
-{
-	open(my $I,"$in.individual_info.txt");
-	while(<$I>)
-	{
-		my $line = $_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		my ($ind,$pop) = split(/;/,$line);
-		$populations{$ind} = $pop;
-	}
-	close($I);
-}
-
-open(my $OUT,">$out.mds_plot.txt");
-my $go = 0;
-open(my $O,"$out.mds");
-while(<$O>)
-{
-	if ($go)
-	{
-		my $line = $_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		my @i = split(/\s+/,$line);
-		if ($line =~/^ /)
-		{
-			my $ind = $i[1];
-			my $pop = "Pop1";
-			if ($populations{$ind})
-			{
-				$pop = $populations{$ind};
-			}
-			print $OUT "$pop	$ind	".$i[4]."	".$i[5]."\n";
-		}
-		if ($line =~/^\w/)
-		{
-			my $ind = $i[0];
-			my $pop = "Pop1";
-			if ($populations{$ind})
-			{
-				$pop = $populations{$ind};
-			}
-			print $OUT "$pop	$ind	".$i[3]."	".$i[4]."\n";
-		}
-		
-	}
-	if (/C1/){$go = 1;}
-}
-close($O);
-close($OUT);
-
-
-my $j = 0;
-open(my $IBS,">$out.ibs_matrix.txt");
-print $IBS "Individuals	" . join("\t",@individuals)."\n";
-open(my $O2,"$out.mibs");
-while(<$O2>)
-{
-	my $line = $_;
-	$line =~s/\n//g;
-	$line =~s/\r//g;
-	my @i = split(/\s+/,$line);
-	print $IBS $individuals[$j]. "	". join("\t",@i)."\n";
-	$j++;
-}
-close($O2);
-close($IBS);
-
-
-	
-	
-
-
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/MDSbasedOnIBSmatrix.pl.org
--- a/MDSplot/MDSbasedOnIBSmatrix.pl.org	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-use Bio::SeqIO;
-
-my $PLINK_EXE= "/apps/www/sniplay.cirad.fr/tools/plink/plink-1.07-x86_64/plink";
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -i, --in         <input>
-    -o, --out        <output>
-~;
-$usage .= "\n";
-
-my ($in,$out);
-
-
-GetOptions(
-	"in=s"        => \$in,
-	"out=s"       => \$out
-);
-
-die $usage
-  if ( !$in || !$out);
-  
-	
-my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1";
-system($plink_command);
-
-my $awk_cmd = "awk \{\'print \$1\'\} $in.ped";
-my $inds = `$awk_cmd`;
-my @individuals = split("\n",$inds);
-
-
-open(my $OUT,">$out.mds_plot.txt");
-my $go = 0;
-open(my $O,"$out.mds");
-while(<$O>)
-{
-	if ($go)
-	{
-		my $line = $_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		my @i = split(/\s+/,$line);
-		my $ind = $i[1];
-		print $OUT "$ind	".$i[4]."	".$i[5]."\n";
-	}
-	if (/C1/){$go = 1;}
-}
-close($O);
-close($OUT);
-
-
-my $j = 0;
-open(my $IBS,">$out.ibs_matrix.txt");
-print $IBS "Individuals	" . join("\t",@individuals)."\n";
-open(my $O2,"$out.mibs");
-while(<$O2>)
-{
-	my $line = $_;
-	$line =~s/\n//g;
-	$line =~s/\r//g;
-	my @i = split(/\s+/,$line);
-	print $IBS $individuals[$j]. "	". join("\t",@i)."\n";
-	$j++;
-}
-close($O2);
-close($IBS);
-
-
-	
-	
-
-
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/mdsplot.sh
--- a/MDSplot/mdsplot.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-tool_path=$(dirname $0)
-ped=$1
-map=$2
-fileout_label=$3
-fileout_matrix=$4
-fileout_plot=$5
-fileout_log=$6
-
-rsync -a $ped input.ped 
-rsync -a $map input.map
-
-perl $tool_path/MDSbasedOnIBSmatrix.pl --in input --out $fileout_label
-
-rm -f input.ped input.map
-
-cp $fileout_label.ibs_matrix.txt $fileout_matrix
-cp $fileout_label.mds_plot.txt $fileout_plot
-cp input.plink.log $fileout_log
-
-
-rm -f $fileout_label.ibs_matrix.txt $fileout_label.mds_plot.txt input.plink.log
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/mdsplot.xml
--- a/MDSplot/mdsplot.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,232 +0,0 @@
-<tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1">
-    
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
-    <description> IBS matrix / multi-dimensional scaling</description>
-    
-    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
-    <requirements>
-        <requirement type="binary">perl</requirement>
-	<requirement type="package" version="1.07">plink</requirement>
-    </requirements>
-    
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
-    
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="bash">
-	mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log
-    </command>
-   
-    <!-- [REQUIRED] Input files and tool parameters -->
-    <inputs>
-	<param name="fileped" type="data" format="txt" optional="false" label="PED input" />
-	<param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
-	<param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
-    </inputs>
-    
-    <!-- [REQUIRED] Output files -->
-    <outputs>
-	<data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" />
-	<data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" />
-	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
-    </outputs>
-    
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-
-        <test>
-         <param name="fileped" value="input.ped" />
-	 <param name="filemap" value="input.map" />
-         <output name="fileout_matrix" file="output.ibs_matrix.txt" />
-	 <output name="fileout_plot" file="output.mds_plot.txt" />
-	 <output name="fileout_log" file="output.log" />
-        </test>
-
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-    
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
-
-
-.. class:: infomark
-
-**Authors** plink_
-
-.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
-
-  | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007.
-
-
-.. class:: infomark
-
-**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
-
-.. class:: infomark
-
-**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
-
-.. class:: infomark
-
-**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
----------------------------------------------------
-
-
-
-========
-MDS plot
-========
-
------------
-Description
------------
-
-  Compute an IBS matrix and a multi-dimensional scaling.
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ========================== ===============
-Name            output file(s)             format 
-=============== ========================== ===============
-VCFtools Filter PED and MAP file	   tabular and MAP
-=============== ========================== ===============
-
-
-
-----------
-Input file
-----------
-
-PED file
-
-MAP file
-	4 columns tabular file: chromosome, snp id, genetic distance, bp position 
-
-
-----------
-Parameters
-----------
-
-Output name
-        Output base name for the ouput files
-
-
-------------
-Output files
-------------
-
-Output_name.ibs_matrix.txt
-	Tabular file with IBS matrix 
-
-Output_name.mds_plot.txt
-	File to construct mds plot
-
-Output_name.log
-	Log file
-
-------------
-Dependencies
-------------
-plink 
-	version 1.07
-	
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-PED file
------------
-
-::
-
-	IRAT112	1	0	0	1	1	1 1	4 4	...
-	IAC25	1	0	0	1	1	1 1	4 4	...
-	CIRAD409	1	0	0	1	1	3 3	1 1	...
-
-
-MAP file
------------
-
-::
-
-	Chr1	Chr1:4299	0	4299
-	Chr1	Chr1:26710	0	26710
-	Chr1	Chr1:56184	0	56184
-	Chr1	Chr1:93272	0	93272
-
-
-
-Parameters
-==========
-
-Output name -> densities
-
-
-Output files
-============
-
-densities.ibs_matrix.txt
-------------------------
-
-::
-
-	Individuals	IRAT112	IAC25	IAC165	KARASUKARASURANKASU	DOURADOPRECOCE	...
-	IRAT112	1	0.93691	0.937407	0.734724	0.943368	...
-	IAC25	0.93691	1	0.958768	0.723299	0.965723	...
-
-
-densities.mds_plot.txt
-----------------------
-
-::
-
-	IRAT112	-0.0969382	0.0376036
-	IAC25	-0.0918126	0.0501177
-
-	
-
-    </help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-    
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/test-data/analyse.ibs_matrix.txt
--- a/MDSplot/test-data/analyse.ibs_matrix.txt	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-Individuals	IRAT112	IAC25	IAC165	KARASUKARASURANKASU	DOURADOPRECOCE	CUIABANA	BICOBRANCO	CAAWA/FORTUNA6	CANELADEFERRO	CIRAD358	COLOMBIA1	CIRAD409	BAGANANASALAO	BAKUNGH	FOHISOMOTRA	KAKANI2	GUARANI	DOURADOAGULHA	IRAT13	DAWASANRED	GRAZI	IRAT144	IAC47	MOROBEREKAN	IRAT362	GIZA171	IDSA77	IRAT216	IRAT177	CHAPHUMA	CIRAD392	ARROZCEBADA	INDANE	DINORADO	63-104	IR63380-16	CANAROXA	CICIHBETON	IR68704-145-1-1-B	HAWMOM	IRAT364	IRAT212	KHAODAM	62667	IRAT234	NIPPONBARE_D	JUMULA2	CUBA65	BABER	CIRAD488	BENGALYVAKARINA	ESPERANZA	BULUPANDAK	ARIAS	GOMPA2	CT13582-15-5-M	IRAT335	M202	IR65907-188-1-B	IR71525-19-1-1	CNA-7_BO_1_1_33-13-6-1	IRAT257	IRAT109	KANIRANGA	IR66421-096-2-1-1	GOGO	GEMJYAJYANAM	DANGREY	BINULAWAN	CAIAPO	IGUAPECATETO	IRAT170	IRAT380	ARAGUAIA	GOGOLEMPAK	JAOHAW	CHALOYOE	GANIGI	GUNDILKUNING	IRAT2	IRAT366	IRAT104	DAVAO	HD1-4	CURINCA	DAM	CIRAD403	JUMALI	JIMBRUKJOLOWORO	GOGOLEMPUK	CIRAD394	IR63372-08	IR60080-46A
-IRAT112	1	0.93691	0.937407	0.734724	0.943368	0.819672	0.903626	0.850969	0.842524	0.802285	0.717834	0.836562	0.804272	0.832588	0.81073	0.614009	0.946846	0.943368	0.944362	0.688525	0.807253	0.712866	0.929955	0.782414	0.902136	0.692499	0.817188	0.796821	0.943865	0.697963	0.790859	0.787879	0.704918	0.833582	0.917039	0.769001	0.938897	0.682563	0.814704	0.707402	0.859911	0.787879	0.709389	0.945355	0.883259	0.703924	0.697963	0.843517	0.725286	0.725782	0.84302	0.876304	0.69995	0.74466	0.651267	0.836066	0.958271	0.651764	0.755092	0.859911	0.861898	0.905614	0.892201	0.739692	0.828117	0.80924	0.650273	0.644312	0.860407	0.853949	0.922504	0.944858	0.81073	0.908097	0.756085	0.674118	0.744163	0.785892	0.698957	0.944858	0.80775	0.857427	0.838053	0.931446	0.831098	0.721311	0.798808	0.592151	0.739692	0.757079	0.767014	0.781918	0.899155
-IAC25	0.93691	1	0.958768	0.723299	0.965723	0.825137	0.93691	0.836562	0.850969	0.772976	0.713363	0.807253	0.791853	0.819175	0.814208	0.602583	0.934426	0.966716	0.904123	0.676105	0.817685	0.706408	0.948336	0.811724	0.892697	0.693989	0.819672	0.784401	0.902633	0.677596	0.806259	0.812221	0.717337	0.813214	0.876801	0.757576	0.923497	0.706905	0.806259	0.69995	0.833582	0.777447	0.693989	0.904123	0.896672	0.703428	0.694486	0.813214	0.728763	0.747144	0.82464	0.864878	0.710383	0.758073	0.643815	0.834575	0.925981	0.674118	0.745653	0.839543	0.845504	0.900149	0.851962	0.764034	0.817685	0.814704	0.655738	0.644809	0.819175	0.834575	0.90313	0.90462	0.838053	0.928465	0.751615	0.666667	0.733731	0.800298	0.707402	0.902633	0.805266	0.846995	0.822653	0.955787	0.809737	0.700944	0.788376	0.591654	0.750124	0.751615	0.790363	0.769498	0.879781
-IAC165	0.937407	0.958768	1	0.722802	0.929459	0.839543	0.932439	0.862891	0.85544	0.786388	0.739692	0.817685	0.790363	0.817685	0.822653	0.596125	0.968703	0.929459	0.920517	0.677596	0.832091	0.704918	0.9846	0.822156	0.92002	0.688525	0.834078	0.794834	0.921013	0.685047	0.805763	0.823646	0.717834	0.826627	0.895181	0.769995	0.945852	0.688525	0.825633	0.694486	0.846001	0.77993	0.697466	0.920517	0.90611	0.694983	0.689021	0.809737	0.723299	0.745653	0.810233	0.87233	0.692002	0.76155	0.636364	0.849975	0.91853	0.66766	0.755092	0.866865	0.855936	0.916542	0.868356	0.746647	0.822156	0.813214	0.651267	0.632389	0.82464	0.844014	0.927471	0.921013	0.832588	0.963736	0.774963	0.661202	0.743169	0.796821	0.702931	0.921013	0.800795	0.864382	0.80924	0.98609	0.821162	0.709389	0.797814	0.588177	0.735718	0.774963	0.783905	0.780924	0.901143
-KARASUKARASURANKASU	0.734724	0.723299	0.722802	1	0.73075	0.748137	0.745653	0.766518	0.747144	0.796324	0.673125	0.738202	0.774466	0.753105	0.780924	0.630899	0.731247	0.73075	0.769498	0.802782	0.769498	0.677099	0.73224	0.749627	0.754098	0.817685	0.715847	0.721311	0.769001	0.837059	0.777943	0.775956	0.827124	0.740189	0.778937	0.707402	0.743169	0.675609	0.704421	0.80775	0.780427	0.748137	0.879285	0.770492	0.759066	0.828117	0.731744	0.743169	0.761053	0.669151	0.764531	0.71237	0.693989	0.737705	0.668157	0.735718	0.723795	0.781918	0.728266	0.764531	0.750621	0.741679	0.731247	0.689021	0.768505	0.751615	0.760556	0.754595	0.731247	0.806259	0.736711	0.769995	0.758073	0.699454	0.709389	0.858917	0.825633	0.753105	0.701937	0.769001	0.733234	0.769001	0.735718	0.731744	0.710879	0.874317	0.725286	0.598112	0.688028	0.710383	0.761053	0.735221	0.753105
-DOURADOPRECOCE	0.943368	0.965723	0.929459	0.73075	1	0.808743	0.9384	0.816195	0.837556	0.773472	0.71386	0.799801	0.789369	0.81073	0.813711	0.604074	0.911078	0.998013	0.89071	0.686538	0.841033	0.689021	0.942871	0.811227	0.874317	0.688525	0.79533	0.773969	0.88922	0.684054	0.795827	0.823646	0.724789	0.802782	0.862394	0.74615	0.898162	0.702434	0.792846	0.707402	0.832091	0.76304	0.700447	0.89071	0.895181	0.69697	0.698957	0.816692	0.721311	0.733731	0.841033	0.864382	0.705912	0.764531	0.634377	0.825137	0.929459	0.671634	0.733234	0.82613	0.834078	0.880775	0.838549	0.754595	0.806259	0.816195	0.664183	0.653254	0.821659	0.820169	0.882762	0.890214	0.82464	0.901143	0.755092	0.674118	0.736215	0.783905	0.701937	0.890214	0.804769	0.833582	0.818182	0.941381	0.810233	0.705415	0.77695	0.582216	0.74764	0.756085	0.778937	0.76006	0.867362
-CUIABANA	0.819672	0.825137	0.839543	0.748137	0.808743	1	0.833582	0.771982	0.780427	0.799801	0.652757	0.726776	0.741182	0.793343	0.82315	0.613512	0.828117	0.809737	0.82762	0.731744	0.791853	0.716344	0.831098	0.829608	0.782414	0.697963	0.705415	0.709886	0.828117	0.819672	0.781421	0.789369	0.800795	0.770492	0.82613	0.708892	0.819175	0.700944	0.715847	0.804272	0.829608	0.791356	0.818182	0.828614	0.853949	0.705415	0.708395	0.801292	0.724789	0.754098	0.767014	0.759563	0.704421	0.754098	0.644809	0.742176	0.800795	0.676105	0.71386	0.834575	0.76304	0.817685	0.780427	0.79384	0.802782	0.820666	0.711376	0.700447	0.802285	0.806756	0.80775	0.828117	0.793343	0.812221	0.791356	0.801788	0.773472	0.820169	0.71237	0.827124	0.800298	0.853949	0.809737	0.826627	0.720318	0.825137	0.712866	0.605564	0.771982	0.791356	0.725782	0.712866	0.807253
-BICOBRANCO	0.903626	0.93691	0.932439	0.745653	0.9384	0.833582	1	0.850969	0.864382	0.773472	0.717834	0.789866	0.824143	0.843517	0.835569	0.613015	0.925981	0.939394	0.882762	0.71237	0.866865	0.701937	0.941878	0.831098	0.885246	0.701441	0.783408	0.764034	0.882265	0.719821	0.809737	0.856433	0.742673	0.838549	0.886239	0.769001	0.901143	0.721311	0.801788	0.730253	0.824143	0.773969	0.73224	0.883756	0.902136	0.707899	0.718828	0.811724	0.736215	0.745653	0.847988	0.843517	0.725782	0.783408	0.651267	0.838053	0.89071	0.679583	0.754098	0.831098	0.827124	0.885743	0.831595	0.776453	0.832091	0.839046	0.686041	0.670144	0.832588	0.827124	0.879781	0.883259	0.850472	0.902136	0.782911	0.69697	0.750124	0.805763	0.721808	0.882265	0.82464	0.845504	0.808246	0.942375	0.782414	0.743169	0.768008	0.598112	0.74764	0.783905	0.783905	0.778937	0.869349
-CAAWA/FORTUNA6	0.850969	0.836562	0.862891	0.766518	0.816195	0.771982	0.850969	1	0.869349	0.793343	0.733731	0.828614	0.851962	0.818679	0.81073	0.615002	0.886239	0.817188	0.892697	0.697466	0.830104	0.703924	0.854446	0.765524	0.881272	0.713363	0.783408	0.795827	0.892201	0.727769	0.755092	0.838549	0.73075	0.816692	0.884252	0.785892	0.88922	0.68455	0.817685	0.725286	0.802285	0.775956	0.753105	0.892697	0.850472	0.719821	0.694983	0.813711	0.741182	0.69697	0.77546	0.796821	0.707899	0.785395	0.665176	0.817188	0.842027	0.673621	0.769001	0.847988	0.84302	0.860904	0.843517	0.73075	0.84302	0.796324	0.669151	0.655241	0.835569	0.825137	0.858917	0.893194	0.772976	0.837556	0.780924	0.717834	0.768008	0.82464	0.717834	0.891207	0.796821	0.847491	0.799305	0.855936	0.769498	0.751118	0.797814	0.591157	0.715847	0.780924	0.742176	0.796821	0.878291
-CANELADEFERRO	0.842524	0.850969	0.85544	0.747144	0.837556	0.780427	0.864382	0.869349	1	0.829608	0.697466	0.769498	0.85842	0.859911	0.832091	0.655241	0.87382	0.838549	0.860407	0.71386	0.883259	0.679583	0.846995	0.778937	0.852956	0.712866	0.741182	0.733731	0.859911	0.71535	0.764531	0.897665	0.720318	0.863885	0.888723	0.777447	0.880775	0.743666	0.787382	0.723795	0.785892	0.762543	0.726776	0.861401	0.853949	0.720318	0.707402	0.818182	0.729757	0.679583	0.81073	0.782414	0.762047	0.831595	0.702434	0.80775	0.831595	0.692002	0.718828	0.811724	0.802782	0.864382	0.808246	0.752111	0.825633	0.799801	0.693492	0.675609	0.867859	0.818679	0.862394	0.860904	0.768505	0.828117	0.770492	0.702434	0.74466	0.868852	0.765027	0.860904	0.841033	0.831098	0.832588	0.846498	0.72926	0.740686	0.735718	0.617486	0.707402	0.771485	0.750621	0.74764	0.845007
-CIRAD358	0.802285	0.772976	0.786388	0.796324	0.773472	0.799801	0.773472	0.793343	0.829608	1	0.644312	0.738202	0.783408	0.79384	0.851465	0.644809	0.794834	0.773472	0.816195	0.738202	0.866865	0.690015	0.795827	0.827124	0.77993	0.736215	0.717834	0.703428	0.815698	0.770492	0.752111	0.861401	0.737705	0.774963	0.795827	0.71237	0.805763	0.71535	0.723299	0.720318	0.848982	0.769001	0.774963	0.817188	0.783905	0.750621	0.680079	0.794834	0.706408	0.647293	0.786388	0.733234	0.732737	0.788376	0.682067	0.723795	0.787382	0.689518	0.704421	0.827124	0.752608	0.816195	0.76304	0.76155	0.743666	0.759563	0.702931	0.688028	0.820666	0.817188	0.802285	0.816692	0.711376	0.762047	0.800795	0.762543	0.77993	0.846498	0.741679	0.815698	0.895181	0.842524	0.791356	0.797317	0.703924	0.783905	0.706408	0.598112	0.739692	0.801788	0.693492	0.697466	0.808743
-COLOMBIA1	0.717834	0.713363	0.739692	0.673125	0.71386	0.652757	0.717834	0.733731	0.697466	0.644312	1	0.837556	0.678092	0.658718	0.68157	0.597119	0.742176	0.714853	0.729757	0.663686	0.674118	0.682067	0.737208	0.659215	0.774963	0.66766	0.863885	0.87531	0.730253	0.665176	0.728266	0.66468	0.650273	0.68455	0.723299	0.822653	0.740189	0.570293	0.822653	0.628912	0.672131	0.716344	0.658718	0.73075	0.73224	0.667163	0.599603	0.674615	0.659712	0.689021	0.661202	0.781918	0.567809	0.629409	0.609538	0.79533	0.714853	0.637854	0.836562	0.692996	0.782414	0.71386	0.736215	0.608544	0.777447	0.701937	0.634377	0.629409	0.686538	0.707899	0.701937	0.730253	0.694486	0.751118	0.635867	0.624441	0.692499	0.661699	0.578738	0.72926	0.622951	0.679583	0.660209	0.738698	0.864878	0.666667	0.87531	0.594138	0.60159	0.63686	0.725286	0.868356	0.738202
-CIRAD409	0.836562	0.807253	0.817685	0.738202	0.799801	0.726776	0.789866	0.828614	0.769498	0.738202	0.837556	1	0.767014	0.749627	0.746647	0.619473	0.834078	0.800795	0.887233	0.701937	0.735221	0.678589	0.815201	0.719324	0.87382	0.692002	0.93691	0.958271	0.88773	0.69846	0.742673	0.745653	0.707402	0.762543	0.859911	0.881769	0.847988	0.609538	0.871833	0.69697	0.790859	0.756582	0.722802	0.888227	0.783408	0.707402	0.685544	0.774466	0.701937	0.688525	0.738202	0.810233	0.620964	0.695479	0.651764	0.881272	0.809737	0.670144	0.916542	0.814704	0.843517	0.80775	0.850969	0.669647	0.820666	0.734228	0.654744	0.666667	0.774466	0.814704	0.794834	0.88773	0.740686	0.829111	0.698957	0.688525	0.718828	0.711873	0.630899	0.88773	0.69995	0.794337	0.753105	0.816692	0.921013	0.711873	0.959265	0.598609	0.655738	0.69995	0.755589	0.944362	0.861898
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-BAKUNGH	0.832588	0.819175	0.817685	0.753105	0.81073	0.793343	0.843517	0.818679	0.859911	0.79384	0.658718	0.749627	0.918033	1	0.805266	0.626428	0.84004	0.811724	0.845504	0.723795	0.814704	0.700447	0.821162	0.80775	0.820169	0.728763	0.730253	0.714853	0.846001	0.745156	0.77844	0.821162	0.739195	0.879781	0.87382	0.756582	0.863885	0.742673	0.755589	0.738698	0.816692	0.777447	0.753602	0.846498	0.839046	0.734228	0.736215	0.797317	0.737705	0.696473	0.847491	0.781421	0.766021	0.82762	0.679583	0.787879	0.817685	0.710879	0.700944	0.806756	0.788872	0.82464	0.801292	0.79384	0.820666	0.805763	0.704421	0.697466	0.852956	0.825633	0.825633	0.846001	0.757576	0.791356	0.793343	0.741182	0.740686	0.806259	0.771982	0.846995	0.779434	0.836066	0.803775	0.821659	0.711376	0.752608	0.716841	0.621461	0.766021	0.79533	0.742673	0.729757	0.817188
-FOHISOMOTRA	0.81073	0.814208	0.822653	0.780924	0.813711	0.82315	0.835569	0.81073	0.832091	0.851465	0.68157	0.746647	0.783905	0.805266	1	0.640338	0.834078	0.814704	0.822653	0.728763	0.860407	0.733234	0.833085	0.902136	0.820169	0.743666	0.727273	0.715847	0.822156	0.780924	0.789369	0.853949	0.765027	0.802285	0.814208	0.69697	0.834078	0.720815	0.773472	0.758569	0.859414	0.785395	0.77546	0.823646	0.874814	0.749131	0.736215	0.827124	0.732737	0.706408	0.833582	0.752608	0.739195	0.797814	0.68455	0.775956	0.815698	0.68306	0.751615	0.861401	0.786885	0.878291	0.773472	0.805763	0.806756	0.84153	0.714357	0.685544	0.82315	0.795827	0.834575	0.82315	0.796324	0.796324	0.835072	0.758073	0.779434	0.860904	0.748137	0.822156	0.891704	0.862891	0.82762	0.836562	0.71535	0.783408	0.718828	0.613512	0.812717	0.835072	0.705912	0.717834	0.84004
-KAKANI2	0.614009	0.602583	0.596125	0.630899	0.604074	0.613512	0.613015	0.615002	0.655241	0.644809	0.597119	0.619473	0.620964	0.626428	0.640338	1	0.614506	0.604074	0.624938	0.610532	0.649776	0.640835	0.591654	0.608048	0.602583	0.702931	0.597119	0.597615	0.623448	0.627919	0.669151	0.629409	0.613015	0.633383	0.627422	0.623448	0.61848	0.610532	0.60457	0.630402	0.613015	0.654247	0.608544	0.624938	0.631396	0.68455	0.737208	0.645306	0.627422	0.642822	0.630899	0.619473	0.625931	0.627919	0.894188	0.63388	0.606061	0.655241	0.610532	0.604074	0.590164	0.610035	0.628415	0.618977	0.628912	0.644809	0.587183	0.602086	0.659215	0.640835	0.617983	0.624441	0.61848	0.611525	0.597615	0.61699	0.620467	0.657228	0.643815	0.623448	0.624441	0.61848	0.637854	0.593145	0.604074	0.617486	0.597615	0.845007	0.595132	0.597615	0.677099	0.605564	0.617486
-GUARANI	0.946846	0.934426	0.968703	0.731247	0.911078	0.828117	0.925981	0.886239	0.87382	0.794834	0.742176	0.834078	0.813711	0.84004	0.834078	0.614506	1	0.912072	0.943865	0.69697	0.815698	0.730253	0.961252	0.801788	0.944362	0.694983	0.814704	0.79533	0.944362	0.705415	0.785395	0.80924	0.71237	0.850969	0.916542	0.769498	0.963239	0.691008	0.847988	0.714853	0.845504	0.802285	0.717834	0.944858	0.882762	0.703428	0.708395	0.832091	0.742673	0.741182	0.817685	0.875807	0.710383	0.747144	0.656731	0.869349	0.927968	0.651267	0.754595	0.887233	0.878291	0.925981	0.893691	0.740189	0.845504	0.81073	0.671634	0.652757	0.847988	0.865375	0.928962	0.944362	0.812221	0.936413	0.788376	0.68157	0.746647	0.821162	0.719324	0.943368	0.808246	0.888723	0.830601	0.961749	0.805763	0.729757	0.798311	0.603577	0.716344	0.789369	0.764531	0.781421	0.924491
-DOURADOAGULHA	0.943368	0.966716	0.929459	0.73075	0.998013	0.809737	0.939394	0.817188	0.838549	0.773472	0.714853	0.800795	0.790363	0.811724	0.814704	0.604074	0.912072	1	0.89071	0.686538	0.842027	0.690015	0.942871	0.811227	0.87531	0.687531	0.79533	0.774963	0.890214	0.685047	0.796821	0.82464	0.725782	0.804769	0.863388	0.747144	0.899155	0.702434	0.79384	0.708395	0.832091	0.764034	0.701441	0.891704	0.895181	0.69697	0.69995	0.817685	0.721311	0.734724	0.841033	0.865375	0.705912	0.765524	0.63537	0.82613	0.929459	0.670641	0.734228	0.827124	0.835072	0.881769	0.839543	0.755589	0.807253	0.817188	0.665176	0.653254	0.822653	0.821162	0.882762	0.891207	0.82464	0.901143	0.755092	0.675112	0.736215	0.785892	0.701937	0.891207	0.804769	0.834575	0.820169	0.941381	0.80924	0.706408	0.777943	0.582216	0.74764	0.756085	0.778937	0.761053	0.868356
-IRAT13	0.944362	0.904123	0.920517	0.769498	0.89071	0.82762	0.882762	0.892697	0.860407	0.816195	0.729757	0.887233	0.819175	0.845504	0.822653	0.624938	0.943865	0.89071	1	0.716344	0.805266	0.762543	0.913065	0.794337	0.942871	0.713363	0.830104	0.848485	0.997516	0.729757	0.802782	0.820666	0.736711	0.857427	0.970691	0.821659	0.958768	0.683557	0.839543	0.728266	0.875807	0.840537	0.759066	0.999006	0.878291	0.723795	0.725782	0.857427	0.726279	0.750621	0.821162	0.866369	0.701937	0.768505	0.677099	0.877794	0.907601	0.690512	0.806756	0.909588	0.909588	0.917536	0.943865	0.751615	0.85693	0.815201	0.673125	0.670144	0.873323	0.906607	0.902633	0.999503	0.801788	0.890214	0.782911	0.723795	0.759066	0.791853	0.711873	0.997516	0.777943	0.905117	0.857923	0.914555	0.814208	0.754098	0.853453	0.621957	0.723795	0.782911	0.803775	0.834575	0.946846
-DAWASANRED	0.688525	0.676105	0.677596	0.802782	0.686538	0.731744	0.71237	0.697466	0.71386	0.738202	0.663686	0.701937	0.743169	0.723795	0.728763	0.610532	0.69697	0.686538	0.716344	1	0.697466	0.637854	0.687034	0.69846	0.704918	0.741679	0.695479	0.694983	0.717834	0.820666	0.745653	0.695976	0.767014	0.722802	0.734724	0.675112	0.707899	0.642325	0.706905	0.76155	0.721311	0.710879	0.813214	0.717337	0.693989	0.758073	0.68455	0.728763	0.723795	0.629906	0.719324	0.661202	0.660705	0.689518	0.647789	0.707402	0.68455	0.707899	0.707899	0.703428	0.714357	0.708395	0.688028	0.659712	0.76006	0.721311	0.898162	0.914059	0.703924	0.74615	0.68455	0.716841	0.707899	0.663189	0.726776	0.79384	0.789369	0.701937	0.66766	0.717834	0.673125	0.706905	0.709389	0.688525	0.68455	0.806259	0.69697	0.605564	0.61997	0.727769	0.700944	0.707899	0.702931
-GRAZI	0.807253	0.817685	0.832091	0.769498	0.841033	0.791853	0.866865	0.830104	0.883259	0.866865	0.674118	0.735221	0.810233	0.814704	0.860407	0.649776	0.815698	0.842027	0.805266	0.697466	1	0.653254	0.840537	0.842027	0.802782	0.725286	0.728763	0.714357	0.804769	0.728763	0.777943	0.957774	0.749627	0.801788	0.808743	0.750124	0.815698	0.757079	0.74615	0.706408	0.821162	0.72926	0.736215	0.806259	0.881272	0.729757	0.697963	0.786885	0.727273	0.670144	0.824143	0.761053	0.76155	0.857923	0.675112	0.762543	0.80924	0.701441	0.71535	0.813214	0.760556	0.820169	0.756085	0.797317	0.773472	0.831098	0.678092	0.659215	0.837556	0.768505	0.822156	0.805763	0.77695	0.806756	0.801788	0.709886	0.750124	0.864382	0.768505	0.804769	0.879285	0.82762	0.790363	0.84302	0.722802	0.755092	0.717337	0.608048	0.77546	0.801788	0.727273	0.728266	0.799801
-IRAT144	0.712866	0.706408	0.704918	0.677099	0.689021	0.716344	0.701937	0.703924	0.679583	0.690015	0.682067	0.678589	0.673125	0.700447	0.733234	0.640835	0.730253	0.690015	0.762543	0.637854	0.653254	1	0.700447	0.754595	0.736215	0.660705	0.628415	0.648783	0.761053	0.66617	0.745156	0.657725	0.625435	0.704421	0.753105	0.647789	0.74615	0.608048	0.672628	0.661699	0.741679	0.898162	0.672628	0.762543	0.710383	0.656234	0.642325	0.714357	0.631893	0.867859	0.746647	0.733234	0.627422	0.655241	0.644312	0.700944	0.703924	0.624938	0.668654	0.757576	0.720815	0.776453	0.81073	0.728763	0.720815	0.712866	0.646299	0.645306	0.719324	0.763537	0.718828	0.76304	0.709389	0.678589	0.686538	0.682067	0.672628	0.68455	0.634377	0.761053	0.688525	0.782911	0.742673	0.702931	0.616493	0.656731	0.651764	0.668654	0.692002	0.685544	0.718331	0.642822	0.769001
-IAC47	0.929955	0.948336	0.9846	0.73224	0.942871	0.831098	0.941878	0.854446	0.846995	0.795827	0.737208	0.815201	0.800795	0.821162	0.833085	0.591654	0.961252	0.942871	0.913065	0.687034	0.840537	0.700447	1	0.831595	0.915549	0.689021	0.823646	0.79235	0.914555	0.691505	0.800298	0.837059	0.725286	0.824143	0.885743	0.765524	0.93542	0.691008	0.82315	0.703924	0.844511	0.773472	0.705912	0.914059	0.898659	0.695479	0.695479	0.803279	0.717834	0.741182	0.820666	0.868852	0.694486	0.771982	0.629906	0.847491	0.911078	0.668157	0.749627	0.859414	0.854446	0.90611	0.859911	0.749131	0.816692	0.80775	0.659712	0.638847	0.821162	0.835569	0.917039	0.913562	0.827124	0.950323	0.786388	0.670641	0.751615	0.793343	0.705415	0.913562	0.811227	0.857923	0.805763	0.989568	0.814704	0.71386	0.79533	0.582712	0.730253	0.787382	0.781421	0.77844	0.898659
-MOROBEREKAN	0.782414	0.811724	0.822156	0.749627	0.811227	0.829608	0.831098	0.765524	0.778937	0.827124	0.659215	0.719324	0.772479	0.80775	0.902136	0.608048	0.801788	0.811227	0.794337	0.69846	0.842027	0.754595	0.831595	1	0.789866	0.717337	0.715847	0.700447	0.792846	0.743666	0.767014	0.830601	0.768505	0.784898	0.785892	0.689518	0.803775	0.747144	0.743169	0.759066	0.898659	0.795827	0.745156	0.794337	0.857427	0.719821	0.714853	0.769995	0.725286	0.724789	0.862891	0.759066	0.751615	0.785395	0.64928	0.762543	0.790363	0.706408	0.724292	0.857923	0.751615	0.871833	0.751118	0.858917	0.772479	0.817188	0.698957	0.689021	0.787879	0.788376	0.803279	0.794834	0.772976	0.795827	0.852459	0.763537	0.756085	0.812717	0.758569	0.792846	0.881272	0.888227	0.807253	0.835072	0.703924	0.738202	0.704421	0.604074	0.850969	0.852459	0.717337	0.702434	0.818679
-IRAT362	0.902136	0.892697	0.92002	0.754098	0.874317	0.782414	0.885246	0.881272	0.852956	0.77993	0.774963	0.87382	0.794834	0.820169	0.820169	0.602583	0.944362	0.87531	0.942871	0.704918	0.802782	0.736215	0.915549	0.789866	1	0.710879	0.846498	0.848982	0.941381	0.706408	0.80924	0.813214	0.714357	0.836066	0.915549	0.82315	0.940387	0.676105	0.876801	0.711873	0.828614	0.80924	0.738698	0.942871	0.864878	0.728266	0.722305	0.814208	0.736711	0.759066	0.802782	0.87084	0.695479	0.744163	0.659712	0.917039	0.885246	0.684054	0.808246	0.887233	0.925981	0.905117	0.888723	0.727273	0.868356	0.803775	0.68157	0.660705	0.827124	0.863388	0.881272	0.943368	0.833085	0.88773	0.776453	0.702434	0.738698	0.794337	0.704421	0.941381	0.771485	0.886736	0.812717	0.919026	0.817685	0.731744	0.851962	0.602583	0.703428	0.776453	0.811227	0.835072	0.934426
-GIZA171	0.692499	0.693989	0.688525	0.817685	0.688525	0.697963	0.701441	0.713363	0.712866	0.736215	0.66766	0.692002	0.731247	0.728763	0.743666	0.702931	0.694983	0.687531	0.713363	0.741679	0.725286	0.660705	0.689021	0.717337	0.710879	1	0.696473	0.684054	0.712866	0.757079	0.798311	0.714853	0.735221	0.714853	0.723795	0.675112	0.716841	0.677099	0.682067	0.716841	0.720318	0.738698	0.74466	0.713363	0.724789	0.947839	0.795827	0.708892	0.822156	0.659712	0.737208	0.676105	0.693492	0.679583	0.735221	0.691505	0.688525	0.857923	0.692002	0.723299	0.723299	0.702434	0.677099	0.679583	0.759066	0.742176	0.745156	0.738202	0.686041	0.724292	0.705415	0.712866	0.735718	0.668157	0.692996	0.755092	0.764531	0.717834	0.694486	0.711873	0.690015	0.732737	0.693492	0.691505	0.686538	0.783408	0.687034	0.638351	0.672628	0.693989	0.834078	0.700944	0.704918
-IDSA77	0.817188	0.819672	0.834078	0.715847	0.79533	0.705415	0.783408	0.783408	0.741182	0.717834	0.863885	0.93691	0.74764	0.730253	0.727273	0.597119	0.814704	0.79533	0.830104	0.695479	0.728763	0.628415	0.823646	0.715847	0.846498	0.696473	1	0.960755	0.830601	0.684054	0.762047	0.71535	0.708892	0.731247	0.804769	0.887233	0.832588	0.612022	0.853453	0.682563	0.777447	0.703428	0.689518	0.830104	0.775956	0.710879	0.659215	0.747144	0.696473	0.677099	0.725782	0.786885	0.608544	0.673125	0.629409	0.85693	0.79235	0.670641	0.92002	0.756582	0.829111	0.788376	0.794834	0.660209	0.812221	0.731744	0.64928	0.660209	0.74615	0.76155	0.788376	0.830601	0.742176	0.84153	0.669647	0.655241	0.716344	0.693492	0.620467	0.830601	0.680576	0.736215	0.725782	0.832091	0.962245	0.697466	0.961749	0.583209	0.654247	0.669647	0.755092	0.945852	0.801788
-IRAT216	0.796821	0.784401	0.794834	0.721311	0.773969	0.709886	0.764034	0.795827	0.733731	0.703428	0.87531	0.958271	0.73224	0.714853	0.715847	0.597615	0.79533	0.774963	0.848485	0.694983	0.714357	0.648783	0.79235	0.700447	0.848982	0.684054	0.960755	1	0.848982	0.686538	0.749627	0.725782	0.707402	0.728763	0.821162	0.919523	0.813214	0.60457	0.860904	0.685047	0.76304	0.726776	0.706905	0.849478	0.758569	0.69846	0.668654	0.74764	0.694983	0.695479	0.704421	0.784401	0.602086	0.682563	0.625931	0.870343	0.772976	0.676105	0.949329	0.781918	0.863388	0.771982	0.815201	0.659712	0.823646	0.735221	0.648783	0.659712	0.741679	0.777943	0.759066	0.848982	0.746647	0.807253	0.672131	0.673621	0.704918	0.689021	0.613015	0.848982	0.667163	0.760556	0.727273	0.794834	0.944858	0.69697	0.995032	0.586687	0.640835	0.673125	0.759563	0.981123	0.82613
-IRAT177	0.943865	0.902633	0.921013	0.769001	0.88922	0.828117	0.882265	0.892201	0.859911	0.815698	0.730253	0.88773	0.817685	0.846001	0.822156	0.623448	0.944362	0.890214	0.997516	0.717834	0.804769	0.761053	0.914555	0.792846	0.941381	0.712866	0.830601	0.848982	1	0.72926	0.802285	0.820169	0.736215	0.85693	0.970194	0.821162	0.957278	0.682067	0.839046	0.727769	0.87531	0.84004	0.758569	0.99851	0.877794	0.723299	0.726279	0.857923	0.727769	0.750124	0.820666	0.865872	0.700447	0.768008	0.676602	0.877298	0.90611	0.688028	0.807253	0.909091	0.910084	0.917039	0.944362	0.750124	0.856433	0.814704	0.673621	0.670641	0.872827	0.90611	0.902136	0.998013	0.801292	0.89071	0.781421	0.723299	0.759563	0.791356	0.710383	0.998013	0.777447	0.90462	0.856433	0.915052	0.814704	0.754595	0.851962	0.622454	0.722305	0.782414	0.803279	0.835072	0.946349
-CHAPHUMA	0.697963	0.677596	0.685047	0.837059	0.684054	0.819672	0.719821	0.727769	0.71535	0.770492	0.665176	0.69846	0.760556	0.745156	0.780924	0.627919	0.705415	0.685047	0.729757	0.820666	0.728763	0.66617	0.691505	0.743666	0.706408	0.757079	0.684054	0.686538	0.72926	1	0.747144	0.724292	0.854943	0.718331	0.739195	0.655738	0.719324	0.637854	0.683557	0.880278	0.771485	0.735221	0.919026	0.73075	0.739195	0.756582	0.689021	0.748137	0.719324	0.638351	0.719821	0.679583	0.661202	0.708892	0.668157	0.692996	0.689021	0.733234	0.708395	0.742673	0.703924	0.721808	0.696473	0.701937	0.787382	0.749627	0.777447	0.788376	0.737208	0.793343	0.690015	0.730253	0.697466	0.662692	0.71535	0.912568	0.831595	0.748137	0.669151	0.72926	0.728266	0.744163	0.731744	0.692996	0.674118	0.914059	0.690512	0.611028	0.694983	0.71535	0.692499	0.700447	0.722305
-CIRAD392	0.790859	0.806259	0.805763	0.777943	0.795827	0.781421	0.809737	0.755092	0.764531	0.752111	0.728266	0.742673	0.745156	0.77844	0.789369	0.669151	0.785395	0.796821	0.802782	0.745653	0.777943	0.745156	0.800298	0.767014	0.80924	0.798311	0.762047	0.749627	0.802285	0.747144	1	0.763537	0.718331	0.785395	0.813214	0.777447	0.806259	0.684054	0.743666	0.710879	0.783905	0.827124	0.733731	0.803775	0.830104	0.802782	0.759066	0.772479	0.729757	0.814704	0.785892	0.781421	0.687531	0.747144	0.728266	0.787879	0.795827	0.756582	0.769498	0.782911	0.81073	0.809737	0.763537	0.737208	0.806756	0.829608	0.728266	0.713363	0.765524	0.784898	0.792846	0.803279	0.920517	0.783408	0.716841	0.704421	0.758569	0.727769	0.691505	0.803279	0.723795	0.781421	0.770989	0.803775	0.749131	0.743666	0.752608	0.655241	0.726279	0.717834	0.865872	0.763537	0.799305
-ARROZCEBADA	0.787879	0.812221	0.823646	0.775956	0.823646	0.789369	0.856433	0.838549	0.897665	0.861401	0.66468	0.745653	0.817685	0.821162	0.853949	0.629409	0.80924	0.82464	0.820666	0.695976	0.957774	0.657725	0.837059	0.830601	0.813214	0.714853	0.71535	0.725782	0.820169	0.724292	0.763537	1	0.742176	0.815201	0.841033	0.764531	0.80924	0.74466	0.738698	0.698957	0.81073	0.738698	0.750621	0.821659	0.861898	0.717337	0.704421	0.765524	0.714853	0.679583	0.798808	0.742673	0.748137	0.87531	0.658718	0.773969	0.788872	0.731744	0.723795	0.828614	0.770989	0.814704	0.769498	0.785892	0.773969	0.804769	0.672628	0.652757	0.820169	0.777943	0.811724	0.821162	0.787382	0.799305	0.794337	0.726279	0.748634	0.855936	0.758073	0.820169	0.87382	0.84302	0.77695	0.836562	0.706408	0.74764	0.728763	0.593641	0.74615	0.79533	0.736711	0.741679	0.812221
-INDANE	0.704918	0.717337	0.717834	0.827124	0.724789	0.800795	0.742673	0.73075	0.720318	0.737705	0.650273	0.707402	0.763537	0.739195	0.765027	0.613015	0.71237	0.725782	0.736711	0.767014	0.749627	0.625435	0.725286	0.768505	0.714357	0.735221	0.708892	0.707402	0.736215	0.854943	0.718331	0.742176	1	0.743169	0.736215	0.668654	0.726279	0.66468	0.682563	0.842524	0.76155	0.702434	0.849478	0.737705	0.761053	0.736711	0.678092	0.758073	0.720318	0.665176	0.728763	0.690512	0.66617	0.735718	0.642325	0.702931	0.69697	0.752111	0.701441	0.729757	0.705912	0.715847	0.697466	0.736711	0.77844	0.763537	0.697963	0.712866	0.738202	0.758569	0.69995	0.737208	0.700447	0.694486	0.730253	0.832091	0.796821	0.753105	0.679086	0.736215	0.71535	0.740189	0.751615	0.725782	0.69995	0.842524	0.710383	0.580229	0.727769	0.730253	0.685544	0.710383	0.714357
-DINORADO	0.833582	0.813214	0.826627	0.740189	0.802782	0.770492	0.838549	0.816692	0.863885	0.774963	0.68455	0.762543	0.860407	0.879781	0.802285	0.633383	0.850969	0.804769	0.857427	0.722802	0.801788	0.704421	0.824143	0.784898	0.836066	0.714853	0.731247	0.728763	0.85693	0.718331	0.785395	0.815201	0.743169	1	0.882762	0.753602	0.869846	0.712866	0.774466	0.723795	0.799801	0.784401	0.729757	0.85842	0.827124	0.725286	0.722305	0.825137	0.715847	0.69846	0.836562	0.797317	0.73224	0.831595	0.696473	0.794834	0.822653	0.721808	0.715847	0.802782	0.811724	0.837556	0.812221	0.74615	0.821659	0.802782	0.683557	0.687531	0.863885	0.814704	0.85842	0.857923	0.774466	0.799305	0.753602	0.69846	0.742673	0.788376	0.739195	0.857923	0.762543	0.815201	0.861401	0.82464	0.719324	0.719821	0.732737	0.63537	0.724292	0.754595	0.76155	0.74466	0.837059
-63-104	0.917039	0.876801	0.895181	0.778937	0.862394	0.82613	0.886239	0.884252	0.888723	0.795827	0.723299	0.859911	0.844511	0.87382	0.814208	0.627422	0.916542	0.863388	0.970691	0.734724	0.808743	0.753105	0.885743	0.785892	0.915549	0.723795	0.804769	0.821162	0.970194	0.739195	0.813214	0.841033	0.736215	0.882762	1	0.833085	0.932439	0.692996	0.812221	0.737705	0.856433	0.832091	0.768505	0.970691	0.882762	0.734228	0.742176	0.841033	0.737705	0.742176	0.831595	0.84004	0.711376	0.795827	0.68157	0.852459	0.879285	0.715847	0.808246	0.882265	0.883259	0.892201	0.917536	0.743169	0.866369	0.821659	0.689518	0.687531	0.866865	0.879285	0.886239	0.971187	0.811227	0.863885	0.77546	0.733234	0.767511	0.783408	0.721311	0.971187	0.769498	0.876801	0.850472	0.88922	0.796821	0.763537	0.825137	0.626428	0.71535	0.77546	0.813214	0.836066	0.919523
-IR63380-16	0.769001	0.757576	0.769995	0.707402	0.74615	0.708892	0.769001	0.785892	0.777447	0.71237	0.822653	0.881769	0.740189	0.756582	0.69697	0.623448	0.769498	0.747144	0.821659	0.675112	0.750124	0.647789	0.765524	0.689518	0.82315	0.675112	0.887233	0.919523	0.821162	0.655738	0.777447	0.764531	0.668654	0.753602	0.833085	1	0.788376	0.664183	0.804272	0.654247	0.736215	0.726776	0.676105	0.821659	0.764531	0.687531	0.695479	0.718828	0.677099	0.694486	0.713363	0.756582	0.661699	0.735221	0.672628	0.844511	0.737208	0.655241	0.900646	0.753105	0.839543	0.747144	0.785395	0.68455	0.792846	0.742176	0.629906	0.63686	0.787382	0.752111	0.757079	0.822156	0.774466	0.779434	0.685047	0.643815	0.678092	0.706905	0.672628	0.821162	0.687034	0.732737	0.728266	0.768008	0.878291	0.667163	0.920517	0.616493	0.653751	0.685047	0.787382	0.93542	0.797317
-CANAROXA	0.938897	0.923497	0.945852	0.743169	0.898162	0.819175	0.901143	0.88922	0.880775	0.805763	0.740189	0.847988	0.835569	0.863885	0.834078	0.61848	0.963239	0.899155	0.958768	0.707899	0.815698	0.74615	0.93542	0.803775	0.940387	0.716841	0.832588	0.813214	0.957278	0.719324	0.806259	0.80924	0.726279	0.869846	0.932439	0.788376	1	0.692996	0.846995	0.717834	0.864382	0.82315	0.728763	0.958768	0.88773	0.725286	0.721311	0.850969	0.731744	0.738202	0.836562	0.878788	0.71237	0.769995	0.674615	0.867362	0.918033	0.674118	0.770492	0.891207	0.895181	0.923	0.906607	0.76304	0.864382	0.826627	0.685544	0.671634	0.861898	0.874317	0.932936	0.959265	0.790363	0.917536	0.790363	0.695479	0.76155	0.808246	0.720318	0.958271	0.785395	0.889717	0.852459	0.93691	0.798808	0.742673	0.816195	0.619473	0.740189	0.790363	0.784401	0.798311	0.925484
-CICIHBETON	0.682563	0.706905	0.688525	0.675609	0.702434	0.700944	0.721311	0.68455	0.743666	0.71535	0.570293	0.609538	0.704421	0.742673	0.720815	0.610532	0.691008	0.702434	0.683557	0.642325	0.757079	0.608048	0.691008	0.747144	0.676105	0.677099	0.612022	0.60457	0.682067	0.637854	0.684054	0.74466	0.66468	0.712866	0.692996	0.664183	0.692996	1	0.620467	0.645306	0.703428	0.686041	0.638351	0.683557	0.724789	0.673621	0.651764	0.661202	0.697963	0.613015	0.745156	0.630402	0.961749	0.707402	0.655738	0.651764	0.687531	0.633383	0.616493	0.718331	0.661699	0.704421	0.646299	0.772976	0.66766	0.73224	0.640835	0.631893	0.708892	0.669647	0.690512	0.68306	0.698957	0.667163	0.746647	0.648783	0.646299	0.754595	0.926975	0.682067	0.728763	0.754595	0.694486	0.691505	0.600099	0.634377	0.607551	0.58768	0.724292	0.748634	0.674118	0.619473	0.702931
-IR68704-145-1-1-B	0.814704	0.806259	0.825633	0.704421	0.792846	0.715847	0.801788	0.817685	0.787382	0.723299	0.822653	0.871833	0.749131	0.755589	0.773472	0.60457	0.847988	0.79384	0.839543	0.706905	0.74615	0.672628	0.82315	0.743169	0.876801	0.682067	0.853453	0.860904	0.839046	0.683557	0.743666	0.738698	0.682563	0.774466	0.812221	0.804272	0.846995	0.620467	1	0.684054	0.767014	0.73075	0.692002	0.840537	0.790363	0.69846	0.670641	0.777447	0.733731	0.690512	0.751118	0.82315	0.637854	0.693492	0.644809	0.877298	0.801788	0.637357	0.818182	0.800795	0.859414	0.828614	0.818182	0.669647	0.825633	0.74615	0.673621	0.675609	0.763537	0.781918	0.792846	0.84004	0.754595	0.837059	0.705912	0.657725	0.724789	0.737705	0.649776	0.839046	0.714853	0.793343	0.748137	0.825633	0.828614	0.691008	0.861898	0.631396	0.656731	0.706905	0.73075	0.846001	0.846001
-HAWMOM	0.707402	0.69995	0.694486	0.80775	0.707402	0.804272	0.730253	0.725286	0.723795	0.720318	0.628912	0.69697	0.77695	0.738698	0.758569	0.630402	0.714853	0.708395	0.728266	0.76155	0.706408	0.661699	0.703924	0.759066	0.711873	0.716841	0.682563	0.685047	0.727769	0.880278	0.710879	0.698957	0.842524	0.723795	0.737705	0.654247	0.717834	0.645306	0.684054	1	0.740189	0.735718	0.88773	0.72926	0.724789	0.720318	0.71535	0.749627	0.749627	0.689518	0.768008	0.689021	0.66766	0.677596	0.652757	0.695479	0.702434	0.684054	0.702931	0.711376	0.705415	0.720318	0.687034	0.71535	0.806756	0.745156	0.76304	0.76304	0.737705	0.757079	0.701441	0.728763	0.705912	0.671138	0.729757	0.90611	0.797317	0.742673	0.671634	0.727769	0.711873	0.754595	0.749131	0.704421	0.686538	0.842027	0.689021	0.582712	0.687531	0.729757	0.680079	0.698957	0.725782
-IRAT364	0.859911	0.833582	0.846001	0.780427	0.832091	0.829608	0.824143	0.802285	0.785892	0.848982	0.672131	0.790859	0.770492	0.816692	0.859414	0.613015	0.845504	0.832091	0.875807	0.721311	0.821162	0.741679	0.844511	0.898659	0.828614	0.720318	0.777447	0.76304	0.87531	0.771485	0.783905	0.81073	0.76155	0.799801	0.856433	0.736215	0.864382	0.703428	0.767014	0.740189	1	0.783905	0.761053	0.876801	0.842524	0.728763	0.718828	0.821659	0.727273	0.69697	0.828117	0.803775	0.720815	0.767511	0.661202	0.785395	0.847988	0.693492	0.778937	0.906607	0.803279	0.891704	0.832588	0.790363	0.770492	0.794337	0.678092	0.681073	0.814704	0.82315	0.853949	0.876304	0.766021	0.821659	0.794834	0.746647	0.762047	0.797814	0.732737	0.87531	0.851465	0.87531	0.844014	0.846995	0.768505	0.767014	0.766021	0.613015	0.811227	0.795827	0.723299	0.757079	0.861401
-IRAT212	0.787879	0.777447	0.77993	0.748137	0.76304	0.791356	0.773969	0.775956	0.762543	0.769001	0.716344	0.756582	0.751118	0.777447	0.785395	0.654247	0.802285	0.764034	0.840537	0.710879	0.72926	0.898162	0.773472	0.795827	0.80924	0.738698	0.703428	0.726776	0.84004	0.735221	0.827124	0.738698	0.702434	0.784401	0.832091	0.726776	0.82315	0.686041	0.73075	0.735718	0.783905	1	0.740686	0.840537	0.791356	0.735221	0.71237	0.784401	0.714853	0.834575	0.82762	0.765524	0.704421	0.717337	0.710383	0.778937	0.796821	0.708892	0.719821	0.823646	0.798808	0.81073	0.811227	0.769995	0.796821	0.788872	0.71237	0.711376	0.786388	0.837556	0.778937	0.841033	0.789369	0.756582	0.766518	0.750124	0.74764	0.759563	0.711376	0.84004	0.73075	0.864878	0.79384	0.775956	0.689518	0.729757	0.728763	0.642325	0.726279	0.765524	0.794337	0.721808	0.84302
-KHAODAM	0.709389	0.693989	0.697466	0.879285	0.700447	0.818182	0.73224	0.753105	0.726776	0.774963	0.658718	0.722802	0.771982	0.753602	0.77546	0.608544	0.717834	0.701441	0.759066	0.813214	0.736215	0.672628	0.705912	0.745156	0.738698	0.74466	0.689518	0.706905	0.758569	0.919026	0.733731	0.750621	0.849478	0.729757	0.768505	0.676105	0.728763	0.638351	0.692002	0.88773	0.761053	0.740686	1	0.76006	0.752608	0.757079	0.688525	0.741679	0.718828	0.655738	0.743169	0.692002	0.660705	0.719324	0.645802	0.720318	0.69846	0.728763	0.718828	0.750124	0.731247	0.726279	0.717834	0.702434	0.796821	0.76006	0.77695	0.771982	0.752608	0.811724	0.702434	0.759563	0.71386	0.672131	0.725782	0.943865	0.849975	0.763537	0.668654	0.758569	0.718828	0.760556	0.737208	0.706408	0.68157	0.917536	0.710879	0.595628	0.688525	0.725782	0.706905	0.720815	0.742673
-62667	0.945355	0.904123	0.920517	0.770492	0.89071	0.828614	0.883756	0.892697	0.861401	0.817188	0.73075	0.888227	0.819175	0.846498	0.823646	0.624938	0.944858	0.891704	0.999006	0.717337	0.806259	0.762543	0.914059	0.794337	0.942871	0.713363	0.830104	0.849478	0.99851	0.73075	0.803775	0.821659	0.737705	0.85842	0.970691	0.821659	0.958768	0.683557	0.840537	0.72926	0.876801	0.840537	0.76006	1	0.879285	0.724789	0.726776	0.85842	0.727273	0.751615	0.822156	0.867362	0.701937	0.769498	0.678092	0.878788	0.907601	0.689518	0.80775	0.910581	0.910581	0.91853	0.944858	0.751615	0.857923	0.816195	0.674118	0.671138	0.874317	0.907601	0.902633	0.999503	0.802782	0.891207	0.782911	0.724789	0.76006	0.792846	0.711873	0.99851	0.778937	0.90611	0.857923	0.915549	0.814208	0.755092	0.853453	0.621957	0.723795	0.783905	0.804769	0.835569	0.947839
-IRAT234	0.883259	0.896672	0.90611	0.759066	0.895181	0.853949	0.902136	0.850472	0.853949	0.783905	0.73224	0.783408	0.791853	0.839046	0.874814	0.631396	0.882762	0.895181	0.878291	0.693989	0.881272	0.710383	0.898659	0.857427	0.864878	0.724789	0.775956	0.758569	0.877794	0.739195	0.830104	0.861898	0.761053	0.827124	0.882762	0.764531	0.88773	0.724789	0.790363	0.724789	0.842524	0.791356	0.752608	0.879285	1	0.730253	0.708395	0.810233	0.728763	0.737208	0.836562	0.828117	0.728266	0.803775	0.663686	0.819672	0.877298	0.698957	0.748634	0.857427	0.821659	0.884252	0.828117	0.795827	0.845504	0.879285	0.672628	0.651764	0.847988	0.811724	0.865375	0.878788	0.830104	0.883756	0.815201	0.718331	0.770492	0.827124	0.740189	0.878788	0.810233	0.863885	0.832588	0.90313	0.773969	0.764531	0.76155	0.61848	0.800795	0.815201	0.793343	0.773472	0.865872
-NIPPONBARE_D	0.703924	0.703428	0.694983	0.828117	0.69697	0.705415	0.707899	0.719821	0.720318	0.750621	0.667163	0.707402	0.734724	0.734228	0.749131	0.68455	0.703428	0.69697	0.723795	0.758073	0.729757	0.656234	0.695479	0.719821	0.728266	0.947839	0.710879	0.69846	0.723299	0.756582	0.802782	0.717337	0.736711	0.725286	0.734228	0.687531	0.725286	0.673621	0.69846	0.720318	0.728763	0.735221	0.757079	0.724789	0.730253	1	0.800298	0.717337	0.828614	0.670144	0.739692	0.689518	0.691008	0.681073	0.73075	0.709886	0.69995	0.826627	0.704421	0.728763	0.742673	0.71386	0.686538	0.682067	0.772479	0.74764	0.758569	0.752608	0.695479	0.722802	0.711873	0.724292	0.751118	0.672628	0.696473	0.764531	0.777943	0.724292	0.698957	0.723299	0.69846	0.737208	0.703924	0.698957	0.69995	0.800795	0.702434	0.631893	0.680079	0.697466	0.838549	0.71237	0.711376
-JUMULA2	0.697963	0.694486	0.689021	0.731744	0.698957	0.708395	0.718828	0.694983	0.707402	0.680079	0.599603	0.685544	0.695976	0.736215	0.736215	0.737208	0.708395	0.69995	0.725782	0.68455	0.697963	0.642325	0.695479	0.714853	0.722305	0.795827	0.659215	0.668654	0.726279	0.689021	0.759066	0.704421	0.678092	0.722305	0.742176	0.695479	0.721311	0.651764	0.670641	0.71535	0.718828	0.71237	0.688525	0.726776	0.708395	0.800298	1	0.705415	0.751118	0.692996	0.731744	0.677596	0.675112	0.681073	0.786388	0.714853	0.69697	0.739195	0.686538	0.729757	0.718828	0.700944	0.689518	0.675112	0.708892	0.741679	0.693989	0.688028	0.68157	0.708892	0.712866	0.726279	0.751118	0.683557	0.688525	0.700944	0.697466	0.703428	0.689021	0.726279	0.685544	0.740189	0.69995	0.69697	0.659215	0.702434	0.670641	0.657725	0.663189	0.689518	0.783905	0.683557	0.719324
-CUBA65	0.843517	0.813214	0.809737	0.743169	0.816692	0.801292	0.811724	0.813711	0.818182	0.794834	0.674615	0.774466	0.795827	0.797317	0.827124	0.645306	0.832091	0.817685	0.857427	0.728763	0.786885	0.714357	0.803279	0.769995	0.814208	0.708892	0.747144	0.74764	0.857923	0.748137	0.772479	0.765524	0.758073	0.825137	0.841033	0.718828	0.850969	0.661202	0.777447	0.749627	0.821659	0.784401	0.741679	0.85842	0.810233	0.717337	0.705415	1	0.71386	0.708395	0.80775	0.781421	0.680576	0.775956	0.683557	0.769001	0.829608	0.68306	0.748634	0.813711	0.818679	0.844511	0.808246	0.725286	0.791853	0.816692	0.689518	0.685544	0.839046	0.826627	0.816692	0.857923	0.763537	0.782414	0.728763	0.728266	0.735718	0.791356	0.682563	0.85693	0.765524	0.82613	0.891207	0.803775	0.745156	0.752608	0.751615	0.619473	0.748137	0.729757	0.729757	0.742673	0.835072
-BABER	0.725286	0.728763	0.723299	0.761053	0.721311	0.724789	0.736215	0.741182	0.729757	0.706408	0.659712	0.701937	0.739195	0.737705	0.732737	0.627422	0.742673	0.721311	0.726279	0.723795	0.727273	0.631893	0.717834	0.725286	0.736711	0.822156	0.696473	0.694983	0.727769	0.719324	0.729757	0.714853	0.720318	0.715847	0.737705	0.677099	0.731744	0.697963	0.733731	0.749627	0.727273	0.714853	0.718828	0.727273	0.728763	0.828614	0.751118	0.71386	1	0.689518	0.74615	0.694983	0.719324	0.661699	0.644809	0.703428	0.736215	0.733731	0.692996	0.74615	0.761053	0.701441	0.691008	0.692499	0.783905	0.751118	0.741182	0.736215	0.682067	0.69846	0.727273	0.726776	0.755589	0.704918	0.729757	0.737208	0.737705	0.745653	0.713363	0.725782	0.708892	0.762543	0.691505	0.720318	0.708395	0.749627	0.695976	0.602583	0.658718	0.73075	0.722802	0.707899	0.725782
-CIRAD488	0.725782	0.747144	0.745653	0.669151	0.733731	0.754098	0.745653	0.69697	0.679583	0.647293	0.689021	0.688525	0.669151	0.696473	0.706408	0.642822	0.741182	0.734724	0.750621	0.629906	0.670144	0.867859	0.741182	0.724789	0.759066	0.659712	0.677099	0.695479	0.750124	0.638351	0.814704	0.679583	0.665176	0.69846	0.742176	0.694486	0.738202	0.613015	0.690512	0.689518	0.69697	0.834575	0.655738	0.751615	0.737208	0.670144	0.692996	0.708395	0.689518	1	0.733731	0.757079	0.617486	0.672131	0.623448	0.732737	0.732737	0.646796	0.697466	0.727769	0.755589	0.725782	0.788872	0.725782	0.755589	0.751615	0.641331	0.631396	0.704421	0.709886	0.723795	0.751118	0.839543	0.723299	0.693492	0.661202	0.666667	0.696473	0.624441	0.751118	0.663686	0.768008	0.708892	0.741679	0.685047	0.646796	0.697466	0.637854	0.663189	0.693492	0.748137	0.690512	0.741182
-BENGALYVAKARINA	0.84302	0.82464	0.810233	0.764531	0.841033	0.767014	0.847988	0.77546	0.81073	0.786388	0.661202	0.738202	0.82613	0.847491	0.833582	0.630899	0.817685	0.841033	0.821162	0.719324	0.824143	0.746647	0.820666	0.862891	0.802782	0.737208	0.725782	0.704421	0.820666	0.719821	0.785892	0.798808	0.728763	0.836562	0.831595	0.713363	0.836562	0.745156	0.751118	0.768008	0.828117	0.82762	0.743169	0.822156	0.836562	0.739692	0.731744	0.80775	0.74615	0.733731	1	0.79384	0.764531	0.780427	0.68306	0.772479	0.853949	0.696473	0.704421	0.793343	0.785395	0.819175	0.780924	0.803279	0.800298	0.827124	0.714853	0.718828	0.815698	0.82315	0.82315	0.821659	0.788872	0.782911	0.794834	0.743666	0.76006	0.785892	0.763537	0.820666	0.789866	0.837556	0.805266	0.82315	0.721808	0.733234	0.708395	0.61699	0.791356	0.795827	0.752111	0.719324	0.80775
-ESPERANZA	0.876304	0.864878	0.87233	0.71237	0.864382	0.759563	0.843517	0.796821	0.782414	0.733234	0.781918	0.810233	0.758073	0.781421	0.752608	0.619473	0.875807	0.865375	0.866369	0.661202	0.761053	0.733234	0.868852	0.759066	0.87084	0.676105	0.786885	0.784401	0.865872	0.679583	0.781421	0.742673	0.690512	0.797317	0.84004	0.756582	0.878788	0.630402	0.82315	0.689021	0.803775	0.765524	0.692002	0.867362	0.828117	0.689518	0.677596	0.781421	0.694983	0.757079	0.79384	1	0.643815	0.723299	0.630899	0.834575	0.856433	0.650273	0.740686	0.81073	0.843517	0.829608	0.868852	0.706408	0.805763	0.781918	0.628912	0.628912	0.794337	0.828614	0.84153	0.866865	0.771485	0.846001	0.714853	0.656731	0.716841	0.725782	0.651764	0.866865	0.719821	0.796324	0.768008	0.871336	0.798808	0.693989	0.786388	0.610532	0.721311	0.715847	0.770492	0.769498	0.858917
-BULUPANDAK	0.69995	0.710383	0.692002	0.693989	0.705912	0.704421	0.725782	0.707899	0.762047	0.732737	0.567809	0.620964	0.722802	0.766021	0.739195	0.625931	0.710383	0.705912	0.701937	0.660705	0.76155	0.627422	0.694486	0.751615	0.695479	0.693492	0.608544	0.602086	0.700447	0.661202	0.687531	0.748137	0.66617	0.73224	0.711376	0.661699	0.71237	0.961749	0.637854	0.66766	0.720815	0.704421	0.660705	0.701937	0.728266	0.691008	0.675112	0.680576	0.719324	0.617486	0.764531	0.643815	1	0.720815	0.678092	0.671138	0.704918	0.635867	0.614009	0.737705	0.678092	0.721808	0.66468	0.787382	0.686041	0.735718	0.658222	0.64928	0.728266	0.693989	0.708892	0.701441	0.703428	0.669647	0.775956	0.671138	0.661699	0.77695	0.958271	0.700447	0.74615	0.772976	0.712866	0.694983	0.596622	0.655738	0.605067	0.60308	0.737705	0.777943	0.676602	0.61699	0.721311
-ARIAS	0.74466	0.758073	0.76155	0.737705	0.764531	0.754098	0.783408	0.785395	0.831595	0.788376	0.629409	0.695479	0.810233	0.82762	0.797814	0.627919	0.747144	0.765524	0.768505	0.689518	0.857923	0.655241	0.771982	0.785395	0.744163	0.679583	0.673125	0.682563	0.768008	0.708892	0.747144	0.87531	0.735718	0.831595	0.795827	0.735221	0.769995	0.707402	0.693492	0.677596	0.767511	0.717337	0.719324	0.769498	0.803775	0.681073	0.681073	0.775956	0.661699	0.672131	0.780427	0.723299	0.720815	1	0.648286	0.717834	0.737705	0.716344	0.690512	0.766518	0.727769	0.768505	0.723299	0.769498	0.74466	0.782414	0.656234	0.65226	0.81073	0.745653	0.762543	0.769001	0.756085	0.736215	0.737208	0.688028	0.71237	0.781918	0.726776	0.768008	0.790859	0.773969	0.782414	0.772479	0.669151	0.69846	0.685544	0.580229	0.759563	0.738202	0.714357	0.697466	0.762047
-GOMPA2	0.651267	0.643815	0.636364	0.668157	0.634377	0.644809	0.651267	0.665176	0.702434	0.682067	0.609538	0.651764	0.658222	0.679583	0.68455	0.894188	0.656731	0.63537	0.677099	0.647789	0.675112	0.644312	0.629906	0.64928	0.659712	0.735221	0.629409	0.625931	0.676602	0.668157	0.728266	0.658718	0.642325	0.696473	0.68157	0.672628	0.674615	0.655738	0.644809	0.652757	0.661202	0.710383	0.645802	0.678092	0.663686	0.73075	0.786388	0.683557	0.644809	0.623448	0.68306	0.630899	0.678092	0.648286	1	0.686041	0.646299	0.671634	0.640835	0.651267	0.650273	0.669151	0.635867	0.654247	0.663189	0.678092	0.622454	0.636364	0.707402	0.69995	0.66617	0.677596	0.663686	0.651764	0.645802	0.648286	0.654744	0.695479	0.694983	0.676602	0.652757	0.661699	0.691008	0.633383	0.616493	0.656731	0.627919	0.81073	0.631396	0.645802	0.733234	0.634873	0.672628
-CT13582-15-5-M	0.836066	0.834575	0.849975	0.735718	0.825137	0.742176	0.838053	0.817188	0.80775	0.723795	0.79533	0.881272	0.759563	0.787879	0.775956	0.63388	0.869349	0.82613	0.877794	0.707402	0.762543	0.700944	0.847491	0.762543	0.917039	0.691505	0.85693	0.870343	0.877298	0.692996	0.787879	0.773969	0.702931	0.794834	0.852459	0.844511	0.867362	0.651764	0.877298	0.695479	0.785395	0.778937	0.720318	0.878788	0.819672	0.709886	0.714853	0.769001	0.703428	0.732737	0.772479	0.834575	0.671138	0.717834	0.686041	1	0.819175	0.671634	0.826627	0.84302	0.876801	0.855936	0.840537	0.69995	0.827124	0.777447	0.671138	0.671138	0.790859	0.831098	0.814208	0.878291	0.808743	0.87233	0.728266	0.687034	0.714357	0.755092	0.680079	0.878291	0.723299	0.840537	0.76155	0.848982	0.837059	0.704421	0.871336	0.630899	0.682067	0.72926	0.783905	0.85544	0.882265
-IRAT335	0.958271	0.925981	0.91853	0.723795	0.929459	0.800795	0.89071	0.842027	0.831595	0.787382	0.714853	0.809737	0.791356	0.817685	0.815698	0.606061	0.927968	0.929459	0.907601	0.68455	0.80924	0.703924	0.911078	0.790363	0.885246	0.688525	0.79235	0.772976	0.90611	0.689021	0.795827	0.788872	0.69697	0.822653	0.879285	0.737208	0.918033	0.687531	0.801788	0.702434	0.847988	0.796821	0.69846	0.907601	0.877298	0.69995	0.69697	0.829608	0.736215	0.732737	0.853949	0.856433	0.704918	0.737705	0.646299	0.819175	1	0.649776	0.73224	0.853949	0.851962	0.88773	0.854446	0.743666	0.808246	0.817188	0.657228	0.647293	0.828614	0.832091	0.906607	0.908097	0.825633	0.892201	0.762047	0.663189	0.73224	0.789866	0.704918	0.90611	0.81073	0.853453	0.819175	0.912568	0.807253	0.709389	0.77695	0.582216	0.741679	0.762047	0.742176	0.759066	0.880278
-M202	0.651764	0.674118	0.66766	0.781918	0.671634	0.676105	0.679583	0.673621	0.692002	0.689518	0.637854	0.670144	0.718331	0.710879	0.68306	0.655241	0.651267	0.670641	0.690512	0.707899	0.701441	0.624938	0.668157	0.706408	0.684054	0.857923	0.670641	0.676105	0.688028	0.733234	0.756582	0.731744	0.752111	0.721808	0.715847	0.655241	0.674118	0.633383	0.637357	0.684054	0.693492	0.708892	0.728763	0.689518	0.698957	0.826627	0.739195	0.68306	0.733731	0.646796	0.696473	0.650273	0.635867	0.716344	0.671634	0.671634	0.649776	1	0.679086	0.694486	0.677596	0.662692	0.654247	0.646796	0.717337	0.705415	0.691505	0.703428	0.650273	0.707402	0.653751	0.690015	0.706905	0.646299	0.643318	0.741182	0.716841	0.665176	0.635867	0.689021	0.645306	0.708892	0.66766	0.668654	0.660705	0.736711	0.680079	0.610532	0.647789	0.643318	0.79235	0.690015	0.680079
-IR65907-188-1-B	0.755092	0.745653	0.755092	0.728266	0.733234	0.71386	0.754098	0.769001	0.718828	0.704421	0.836562	0.916542	0.718331	0.700944	0.751615	0.610532	0.754595	0.734228	0.806756	0.707899	0.71535	0.668654	0.749627	0.724292	0.808246	0.692002	0.92002	0.949329	0.807253	0.708395	0.769498	0.723795	0.701441	0.715847	0.808246	0.900646	0.770492	0.616493	0.818182	0.702931	0.778937	0.719821	0.718828	0.80775	0.748634	0.704421	0.686538	0.748634	0.692996	0.697466	0.704421	0.740686	0.614009	0.690512	0.640835	0.826627	0.73224	0.679086	1	0.786885	0.817685	0.768008	0.771485	0.673621	0.809737	0.744163	0.66766	0.674615	0.727769	0.737208	0.744163	0.807253	0.768505	0.766518	0.673125	0.695479	0.705912	0.689021	0.623944	0.807253	0.690015	0.751615	0.73224	0.755092	0.912072	0.700944	0.948336	0.590661	0.671634	0.674118	0.745653	0.963239	0.806259
-IR71525-19-1-1	0.859911	0.839543	0.866865	0.764531	0.82613	0.834575	0.831098	0.847988	0.811724	0.827124	0.692996	0.814704	0.754595	0.806756	0.861401	0.604074	0.887233	0.827124	0.909588	0.703428	0.813214	0.757576	0.859414	0.857923	0.887233	0.723299	0.756582	0.781918	0.909091	0.742673	0.782911	0.828614	0.729757	0.802782	0.882265	0.753105	0.891207	0.718331	0.800795	0.711376	0.906607	0.823646	0.750124	0.910581	0.857427	0.728763	0.729757	0.813711	0.74615	0.727769	0.793343	0.81073	0.737705	0.766518	0.651267	0.84302	0.853949	0.694486	0.786885	1	0.84302	0.898659	0.867362	0.772479	0.788376	0.808246	0.679086	0.669151	0.802782	0.839046	0.851962	0.910084	0.795827	0.84153	0.812717	0.734724	0.741182	0.813711	0.739692	0.910084	0.825633	0.940884	0.818182	0.862891	0.740686	0.74615	0.782911	0.597119	0.77844	0.813711	0.735221	0.767014	0.942871
-CNA-7_BO_1_1_33-13-6-1	0.861898	0.845504	0.855936	0.750621	0.834078	0.76304	0.827124	0.84302	0.802782	0.752608	0.782414	0.843517	0.767511	0.788872	0.786885	0.590164	0.878291	0.835072	0.909588	0.714357	0.760556	0.720815	0.854446	0.751615	0.925981	0.723299	0.829111	0.863388	0.910084	0.703924	0.81073	0.770989	0.705912	0.811724	0.883259	0.839543	0.895181	0.661699	0.859414	0.705415	0.803279	0.798808	0.731247	0.910581	0.821659	0.742673	0.718828	0.818679	0.761053	0.755589	0.785395	0.843517	0.678092	0.727769	0.650273	0.876801	0.851962	0.677596	0.817685	0.84302	1	0.85693	0.85544	0.719821	0.87382	0.79235	0.693989	0.682067	0.804769	0.835072	0.852956	0.910084	0.821659	0.82464	0.750124	0.697963	0.736215	0.76304	0.689021	0.909091	0.736215	0.844511	0.796324	0.854943	0.814208	0.725286	0.865375	0.614009	0.689021	0.751118	0.813711	0.849478	0.891207
-IRAT257	0.905614	0.900149	0.916542	0.741679	0.880775	0.817685	0.885743	0.860904	0.864382	0.816195	0.71386	0.80775	0.796324	0.82464	0.878291	0.610035	0.925981	0.881769	0.917536	0.708395	0.820169	0.776453	0.90611	0.871833	0.905117	0.702434	0.788376	0.771982	0.917039	0.721808	0.809737	0.814704	0.715847	0.837556	0.892201	0.747144	0.923	0.704421	0.828614	0.720318	0.891704	0.81073	0.726279	0.91853	0.884252	0.71386	0.700944	0.844511	0.701441	0.725782	0.819175	0.829608	0.721808	0.768505	0.669151	0.855936	0.88773	0.662692	0.768008	0.898659	0.85693	1	0.864382	0.782414	0.832091	0.817188	0.686041	0.66617	0.848485	0.852956	0.902633	0.918033	0.813711	0.886239	0.781918	0.698957	0.756085	0.808743	0.73075	0.917039	0.85544	0.902136	0.865872	0.912568	0.767511	0.731247	0.774963	0.609041	0.774466	0.782911	0.766021	0.757079	0.923
-IRAT109	0.892201	0.851962	0.868356	0.731247	0.838549	0.780427	0.831595	0.843517	0.808246	0.76304	0.736215	0.850969	0.770989	0.801292	0.773472	0.628415	0.893691	0.839543	0.943865	0.688028	0.756085	0.81073	0.859911	0.751118	0.888723	0.677099	0.794834	0.815201	0.944362	0.696473	0.763537	0.769498	0.697466	0.812221	0.917536	0.785395	0.906607	0.646299	0.818182	0.687034	0.832588	0.811227	0.717834	0.944858	0.828117	0.686538	0.689518	0.808246	0.691008	0.788872	0.780924	0.868852	0.66468	0.723299	0.635867	0.840537	0.854446	0.654247	0.771485	0.867362	0.85544	0.864382	1	0.706408	0.804769	0.774963	0.638847	0.641828	0.827124	0.864382	0.851465	0.944362	0.76155	0.846001	0.732737	0.68157	0.719821	0.741679	0.675609	0.944362	0.724789	0.850969	0.808743	0.862394	0.778937	0.710879	0.814208	0.643318	0.682563	0.733731	0.764531	0.798311	0.903626
-KANIRANGA	0.739692	0.764034	0.746647	0.689021	0.754595	0.79384	0.776453	0.73075	0.752111	0.76155	0.608544	0.669647	0.749627	0.79384	0.805763	0.618977	0.740189	0.755589	0.751615	0.659712	0.797317	0.728763	0.749131	0.858917	0.727273	0.679583	0.660209	0.659712	0.750124	0.701937	0.737208	0.785892	0.736711	0.74615	0.743169	0.68455	0.76304	0.772976	0.669647	0.71535	0.790363	0.769995	0.702434	0.751615	0.795827	0.682067	0.675112	0.725286	0.692499	0.725782	0.803279	0.706408	0.787382	0.769498	0.654247	0.69995	0.743666	0.646796	0.673621	0.772479	0.719821	0.782414	0.706408	1	0.754595	0.800298	0.670144	0.667163	0.794834	0.729757	0.759563	0.752111	0.744163	0.723299	0.840537	0.718828	0.686538	0.825633	0.783408	0.750124	0.812717	0.809737	0.783408	0.751615	0.650273	0.700447	0.662692	0.614009	0.865872	0.840537	0.699454	0.660705	0.743169
-IR66421-096-2-1-1	0.828117	0.817685	0.822156	0.768505	0.806259	0.802782	0.832091	0.84302	0.825633	0.743666	0.777447	0.820666	0.842027	0.820666	0.806756	0.628912	0.845504	0.807253	0.85693	0.76006	0.773472	0.720815	0.816692	0.772479	0.868356	0.759066	0.812221	0.823646	0.856433	0.787382	0.806756	0.773969	0.77844	0.821659	0.866369	0.792846	0.864382	0.66766	0.825633	0.806756	0.770492	0.796821	0.796821	0.857923	0.845504	0.772479	0.708892	0.791853	0.783905	0.755589	0.800298	0.805763	0.686041	0.74466	0.663189	0.827124	0.808246	0.717337	0.809737	0.788376	0.87382	0.832091	0.804769	0.754595	1	0.815201	0.749627	0.741679	0.815698	0.799305	0.818182	0.857427	0.794834	0.789866	0.772976	0.779434	0.796821	0.788872	0.695976	0.856433	0.748137	0.822653	0.799305	0.820169	0.804272	0.800795	0.826627	0.61699	0.707899	0.772976	0.790859	0.837556	0.832588
-GOGO	0.80924	0.814704	0.813214	0.751615	0.816195	0.820666	0.839046	0.796324	0.799801	0.759563	0.701937	0.734228	0.776453	0.805763	0.84153	0.644809	0.81073	0.817188	0.815201	0.721311	0.831098	0.712866	0.80775	0.817188	0.803775	0.742176	0.731744	0.735221	0.814704	0.749627	0.829608	0.804769	0.763537	0.802782	0.821659	0.742176	0.826627	0.73224	0.74615	0.745156	0.794337	0.788872	0.76006	0.816195	0.879285	0.74764	0.741679	0.816692	0.751118	0.751615	0.827124	0.781918	0.735718	0.782414	0.678092	0.777447	0.817188	0.705415	0.744163	0.808246	0.79235	0.817188	0.774963	0.800298	0.815201	1	0.698957	0.682067	0.812717	0.797317	0.798311	0.815698	0.82464	0.791853	0.789866	0.724789	0.777943	0.826627	0.737705	0.814704	0.768008	0.821659	0.811227	0.810233	0.731744	0.76006	0.739195	0.631893	0.814208	0.789866	0.761053	0.750124	0.813711
-GEMJYAJYANAM	0.650273	0.655738	0.651267	0.760556	0.664183	0.711376	0.686041	0.669151	0.693492	0.702931	0.634377	0.654744	0.710879	0.704421	0.714357	0.587183	0.671634	0.665176	0.673125	0.898162	0.678092	0.646299	0.659712	0.698957	0.68157	0.745156	0.64928	0.648783	0.673621	0.777447	0.728266	0.672628	0.697963	0.683557	0.689518	0.629906	0.685544	0.640835	0.673621	0.76304	0.678092	0.71237	0.77695	0.674118	0.672628	0.758569	0.693989	0.689518	0.741182	0.641331	0.714853	0.628912	0.658222	0.656234	0.622454	0.671138	0.657228	0.691505	0.66766	0.679086	0.693989	0.686041	0.638847	0.670144	0.749627	0.698957	1	0.937407	0.649776	0.692002	0.659215	0.673621	0.695479	0.635867	0.731247	0.796324	0.768008	0.690512	0.662196	0.673621	0.657725	0.719324	0.678092	0.662196	0.639344	0.796821	0.651764	0.591157	0.616493	0.73224	0.690512	0.663686	0.674615
-DANGREY	0.644312	0.644809	0.632389	0.754595	0.653254	0.700447	0.670144	0.655241	0.675609	0.688028	0.629409	0.666667	0.712866	0.697466	0.685544	0.602086	0.652757	0.653254	0.670144	0.914059	0.659215	0.645306	0.638847	0.689021	0.660705	0.738202	0.660209	0.659712	0.670641	0.788376	0.713363	0.652757	0.712866	0.687531	0.687531	0.63686	0.671634	0.631893	0.675609	0.76304	0.681073	0.711376	0.771982	0.671138	0.651764	0.752608	0.688028	0.685544	0.736215	0.631396	0.718828	0.628912	0.64928	0.65226	0.636364	0.671138	0.647293	0.703428	0.674615	0.669151	0.682067	0.66617	0.641828	0.667163	0.741679	0.682067	0.937407	1	0.658718	0.689021	0.646299	0.670641	0.660705	0.626925	0.717337	0.794337	0.752111	0.671634	0.656234	0.670641	0.63388	0.701441	0.670144	0.641331	0.64928	0.784898	0.661699	0.607054	0.60457	0.718331	0.685544	0.672628	0.66468
-BINULAWAN	0.860407	0.819175	0.82464	0.731247	0.821659	0.802285	0.832588	0.835569	0.867859	0.820666	0.686538	0.774466	0.848485	0.852956	0.82315	0.659215	0.847988	0.822653	0.873323	0.703924	0.837556	0.719324	0.821162	0.787879	0.827124	0.686041	0.74615	0.741679	0.872827	0.737208	0.765524	0.820169	0.738202	0.863885	0.866865	0.787382	0.861898	0.708892	0.763537	0.737705	0.814704	0.786388	0.752608	0.874317	0.847988	0.695479	0.68157	0.839046	0.682067	0.704421	0.815698	0.794337	0.728266	0.81073	0.707402	0.790859	0.828614	0.650273	0.727769	0.802782	0.804769	0.848485	0.827124	0.794834	0.815698	0.812717	0.649776	0.658718	1	0.829608	0.857427	0.87382	0.750621	0.794337	0.780427	0.716344	0.736711	0.849975	0.736215	0.87382	0.817188	0.808246	0.87531	0.820666	0.74615	0.739692	0.74466	0.626428	0.774963	0.780427	0.738698	0.745653	0.842027
-CAIAPO	0.853949	0.834575	0.844014	0.806259	0.820169	0.806756	0.827124	0.825137	0.818679	0.817188	0.707899	0.814704	0.801292	0.825633	0.795827	0.640835	0.865375	0.821162	0.906607	0.74615	0.768505	0.763537	0.835569	0.788376	0.863388	0.724292	0.76155	0.777943	0.90611	0.793343	0.784898	0.777943	0.758569	0.814704	0.879285	0.752111	0.874317	0.669647	0.781918	0.757079	0.82315	0.837556	0.811724	0.907601	0.811724	0.722802	0.708892	0.826627	0.69846	0.709886	0.82315	0.828614	0.693989	0.745653	0.69995	0.831098	0.832091	0.707402	0.737208	0.839046	0.835072	0.852956	0.864382	0.729757	0.799305	0.797317	0.692002	0.689021	0.829608	1	0.830104	0.907104	0.751118	0.814704	0.742176	0.781421	0.782911	0.768008	0.69995	0.90611	0.739195	0.854446	0.801292	0.838053	0.742673	0.79384	0.781918	0.629906	0.726776	0.743169	0.789866	0.764034	0.871336
-IGUAPECATETO	0.922504	0.90313	0.927471	0.736711	0.882762	0.80775	0.879781	0.858917	0.862394	0.802285	0.701937	0.794834	0.811227	0.825633	0.834575	0.617983	0.928962	0.882762	0.902633	0.68455	0.822156	0.718828	0.917039	0.803279	0.881272	0.705415	0.788376	0.759066	0.902136	0.690015	0.792846	0.811724	0.69995	0.85842	0.886239	0.757079	0.932936	0.690512	0.792846	0.701441	0.853949	0.778937	0.702434	0.902633	0.865375	0.711873	0.712866	0.816692	0.727273	0.723795	0.82315	0.84153	0.708892	0.762543	0.66617	0.814208	0.906607	0.653751	0.744163	0.851962	0.852956	0.902633	0.851465	0.759563	0.818182	0.798311	0.659215	0.646299	0.857427	0.830104	1	0.90313	0.798808	0.899155	0.761053	0.670144	0.740189	0.808743	0.718828	0.901143	0.822653	0.836562	0.846995	0.915549	0.79235	0.713363	0.762047	0.609041	0.736711	0.761053	0.76304	0.753105	0.87233
-IRAT170	0.944858	0.90462	0.921013	0.769995	0.890214	0.828117	0.883259	0.893194	0.860904	0.816692	0.730253	0.88773	0.819672	0.846001	0.82315	0.624441	0.944362	0.891207	0.999503	0.716841	0.805763	0.76304	0.913562	0.794834	0.943368	0.712866	0.830601	0.848982	0.998013	0.730253	0.803279	0.821162	0.737208	0.857923	0.971187	0.822156	0.959265	0.68306	0.84004	0.728763	0.876304	0.841033	0.759563	0.999503	0.878788	0.724292	0.726279	0.857923	0.726776	0.751118	0.821659	0.866865	0.701441	0.769001	0.677596	0.878291	0.908097	0.690015	0.807253	0.910084	0.910084	0.918033	0.944362	0.752111	0.857427	0.815698	0.673621	0.670641	0.87382	0.907104	0.90313	1	0.802285	0.89071	0.783408	0.724292	0.759563	0.79235	0.711376	0.998013	0.77844	0.905614	0.85842	0.915052	0.814704	0.754595	0.853949	0.621461	0.724292	0.783408	0.804272	0.835072	0.947342
-IRAT380	0.81073	0.838053	0.832588	0.758073	0.82464	0.793343	0.850472	0.772976	0.768505	0.711376	0.694486	0.740686	0.726279	0.757576	0.796324	0.61848	0.812221	0.82464	0.801788	0.707899	0.77695	0.709389	0.827124	0.772976	0.833085	0.735718	0.742176	0.746647	0.801292	0.697466	0.920517	0.787382	0.700447	0.774466	0.811227	0.774466	0.790363	0.698957	0.754595	0.705912	0.766021	0.789369	0.71386	0.802782	0.830104	0.751118	0.751118	0.763537	0.755589	0.839543	0.788872	0.771485	0.703428	0.756085	0.663686	0.808743	0.825633	0.706905	0.768505	0.795827	0.821659	0.813711	0.76155	0.744163	0.794834	0.82464	0.695479	0.660705	0.750621	0.751118	0.798808	0.802285	1	0.80924	0.721808	0.682563	0.725782	0.752608	0.700447	0.801292	0.766518	0.804272	0.755092	0.830601	0.752111	0.704918	0.750621	0.595628	0.733234	0.722802	0.824143	0.760556	0.812221
-ARAGUAIA	0.908097	0.928465	0.963736	0.699454	0.901143	0.812221	0.902136	0.837556	0.828117	0.762047	0.751118	0.829111	0.76304	0.791356	0.796324	0.611525	0.936413	0.901143	0.890214	0.663189	0.806756	0.678589	0.950323	0.795827	0.88773	0.668157	0.84153	0.807253	0.89071	0.662692	0.783408	0.799305	0.694486	0.799305	0.863885	0.779434	0.917536	0.667163	0.837059	0.671138	0.821659	0.756582	0.672131	0.891207	0.883756	0.672628	0.683557	0.782414	0.704918	0.723299	0.782911	0.846001	0.669647	0.736215	0.651764	0.87233	0.892201	0.646299	0.766518	0.84153	0.82464	0.886239	0.846001	0.723299	0.789866	0.791853	0.635867	0.626925	0.794337	0.814704	0.899155	0.89071	0.80924	1	0.748634	0.635867	0.720815	0.771485	0.682563	0.89071	0.774466	0.839046	0.781918	0.952807	0.830601	0.684054	0.808246	0.60159	0.709389	0.749627	0.758569	0.79235	0.871833
-GOGOLEMPAK	0.756085	0.751615	0.774963	0.709389	0.755092	0.791356	0.782911	0.780924	0.770492	0.800795	0.635867	0.698957	0.750124	0.793343	0.835072	0.597615	0.788376	0.755092	0.782911	0.726776	0.801788	0.686538	0.786388	0.852459	0.776453	0.692996	0.669647	0.672131	0.781421	0.71535	0.716841	0.794337	0.730253	0.753602	0.77546	0.685047	0.790363	0.746647	0.705912	0.729757	0.794834	0.766518	0.725782	0.782911	0.815201	0.696473	0.688525	0.728763	0.729757	0.693492	0.794834	0.714853	0.775956	0.737208	0.645802	0.728266	0.762047	0.643318	0.673125	0.812717	0.750124	0.781918	0.732737	0.840537	0.772976	0.789866	0.731247	0.717337	0.780427	0.742176	0.761053	0.783408	0.721808	0.748634	1	0.734228	0.721808	0.838053	0.783905	0.782414	0.807253	0.852956	0.76006	0.786885	0.660705	0.728763	0.675112	0.577745	0.77993	0.998013	0.676105	0.674118	0.790363
-JAOHAW	0.674118	0.666667	0.661202	0.858917	0.674118	0.801788	0.69697	0.717834	0.702434	0.762543	0.624441	0.688525	0.76155	0.741182	0.758073	0.61699	0.68157	0.675112	0.723795	0.79384	0.709886	0.682067	0.670641	0.763537	0.702434	0.755092	0.655241	0.673621	0.723299	0.912568	0.704421	0.726279	0.832091	0.69846	0.733234	0.643815	0.695479	0.648783	0.657725	0.90611	0.746647	0.750124	0.943865	0.724789	0.718331	0.764531	0.700944	0.728266	0.737208	0.661202	0.743666	0.656731	0.671138	0.688028	0.648286	0.687034	0.663189	0.741182	0.695479	0.734724	0.697963	0.698957	0.68157	0.718828	0.779434	0.724789	0.796324	0.794337	0.716344	0.781421	0.670144	0.724292	0.682563	0.635867	0.734228	1	0.813711	0.748137	0.674118	0.723299	0.705415	0.777943	0.718828	0.671138	0.647293	0.898162	0.677596	0.595132	0.691008	0.734228	0.69846	0.687531	0.718331
-CHALOYOE	0.744163	0.733731	0.743169	0.825633	0.736215	0.773472	0.750124	0.768008	0.74466	0.77993	0.692499	0.718828	0.77695	0.740686	0.779434	0.620467	0.746647	0.736215	0.759066	0.789369	0.750124	0.672628	0.751615	0.756085	0.738698	0.764531	0.716344	0.704918	0.759563	0.831595	0.758569	0.748634	0.796821	0.742673	0.767511	0.678092	0.76155	0.646299	0.724789	0.797317	0.762047	0.74764	0.849975	0.76006	0.770492	0.777943	0.697466	0.735718	0.737705	0.666667	0.76006	0.716841	0.661699	0.71237	0.654744	0.714357	0.73224	0.716841	0.705912	0.741182	0.736215	0.756085	0.719821	0.686538	0.796821	0.777943	0.768008	0.752111	0.736711	0.782911	0.740189	0.759563	0.725782	0.720815	0.721808	0.813711	1	0.741679	0.673621	0.758569	0.735718	0.750621	0.727273	0.752111	0.704421	0.854943	0.707899	0.621461	0.679583	0.721808	0.723795	0.711873	0.743666
-GANIGI	0.785892	0.800298	0.796821	0.753105	0.783905	0.820169	0.805763	0.82464	0.868852	0.846498	0.661699	0.711873	0.787879	0.806259	0.860904	0.657228	0.821162	0.785892	0.791853	0.701937	0.864382	0.68455	0.793343	0.812717	0.794337	0.717834	0.693492	0.689021	0.791356	0.748137	0.727769	0.855936	0.753105	0.788376	0.783408	0.706905	0.808246	0.754595	0.737705	0.742673	0.797814	0.759563	0.763537	0.792846	0.827124	0.724292	0.703428	0.791356	0.745653	0.696473	0.785892	0.725782	0.77695	0.781918	0.695479	0.755092	0.789866	0.665176	0.689021	0.813711	0.76304	0.808743	0.741679	0.825633	0.788872	0.826627	0.690512	0.671634	0.849975	0.768008	0.808743	0.79235	0.752608	0.771485	0.838053	0.748137	0.741679	1	0.781918	0.791356	0.877794	0.838053	0.82464	0.795827	0.695479	0.764531	0.692002	0.610532	0.775956	0.838053	0.693989	0.691008	0.798311
-GUNDILKUNING	0.698957	0.707402	0.702931	0.701937	0.701937	0.71237	0.721808	0.717834	0.765027	0.741679	0.578738	0.630899	0.728763	0.771982	0.748137	0.643815	0.719324	0.701937	0.711873	0.66766	0.768505	0.634377	0.705415	0.758569	0.704421	0.694486	0.620467	0.613015	0.710383	0.669151	0.691505	0.758073	0.679086	0.739195	0.721311	0.672628	0.720318	0.926975	0.649776	0.671634	0.732737	0.711376	0.668654	0.711873	0.740189	0.698957	0.689021	0.682563	0.713363	0.624441	0.763537	0.651764	0.958271	0.726776	0.694983	0.680079	0.704918	0.635867	0.623944	0.739692	0.689021	0.73075	0.675609	0.783408	0.695976	0.737705	0.662196	0.656234	0.736215	0.69995	0.718828	0.711376	0.700447	0.682563	0.783905	0.674118	0.673621	0.781918	1	0.710383	0.74615	0.777943	0.719821	0.705912	0.609538	0.665673	0.615002	0.627919	0.727769	0.785892	0.680576	0.627919	0.722305
-IRAT2	0.944858	0.902633	0.921013	0.769001	0.890214	0.827124	0.882265	0.891207	0.860904	0.815698	0.72926	0.88773	0.817685	0.846995	0.822156	0.623448	0.943368	0.891207	0.997516	0.717834	0.804769	0.761053	0.913562	0.792846	0.941381	0.711873	0.830601	0.848982	0.998013	0.72926	0.803279	0.820169	0.736215	0.857923	0.971187	0.821162	0.958271	0.682067	0.839046	0.727769	0.87531	0.84004	0.758569	0.99851	0.878788	0.723299	0.726279	0.85693	0.725782	0.751118	0.820666	0.866865	0.700447	0.768008	0.676602	0.878291	0.90611	0.689021	0.807253	0.910084	0.909091	0.917039	0.944362	0.750124	0.856433	0.814704	0.673621	0.670641	0.87382	0.90611	0.901143	0.998013	0.801292	0.89071	0.782414	0.723299	0.758569	0.791356	0.710383	1	0.777447	0.90462	0.857427	0.916046	0.814704	0.753602	0.851962	0.623448	0.723299	0.783408	0.803279	0.835072	0.947342
-IRAT366	0.80775	0.805266	0.800795	0.733234	0.804769	0.800298	0.82464	0.796821	0.841033	0.895181	0.622951	0.69995	0.769995	0.779434	0.891704	0.624441	0.808246	0.804769	0.777943	0.673125	0.879285	0.688525	0.811227	0.881272	0.771485	0.690015	0.680576	0.667163	0.777447	0.728266	0.723795	0.87382	0.71535	0.762543	0.769498	0.687034	0.785395	0.728763	0.714853	0.711873	0.851465	0.73075	0.718828	0.778937	0.810233	0.69846	0.685544	0.765524	0.708892	0.663686	0.789866	0.719821	0.74615	0.790859	0.652757	0.723299	0.81073	0.645306	0.690015	0.825633	0.736215	0.85544	0.724789	0.812717	0.748137	0.768008	0.657725	0.63388	0.817188	0.739195	0.822653	0.77844	0.766518	0.774466	0.807253	0.705415	0.735718	0.877794	0.74615	0.777447	1	0.830104	0.803775	0.813711	0.691505	0.731744	0.669151	0.577745	0.796821	0.808246	0.655241	0.670144	0.79533
-IRAT104	0.857427	0.846995	0.864382	0.769001	0.833582	0.853949	0.845504	0.847491	0.831098	0.842524	0.679583	0.794337	0.789866	0.836066	0.862891	0.61848	0.888723	0.834575	0.905117	0.706905	0.82762	0.782911	0.857923	0.888227	0.886736	0.732737	0.736215	0.760556	0.90462	0.744163	0.781421	0.84302	0.740189	0.815201	0.876801	0.732737	0.889717	0.754595	0.793343	0.754595	0.87531	0.864878	0.760556	0.90611	0.863885	0.737208	0.740189	0.82613	0.762543	0.768008	0.837556	0.796324	0.772976	0.773969	0.661699	0.840537	0.853453	0.708892	0.751615	0.940884	0.844511	0.902136	0.850969	0.809737	0.822653	0.821659	0.719324	0.701441	0.808246	0.854446	0.836562	0.905614	0.804272	0.839046	0.852956	0.777943	0.750621	0.838053	0.777943	0.90462	0.830104	1	0.821659	0.859414	0.721311	0.753602	0.764531	0.60159	0.777943	0.853949	0.752608	0.746647	0.910581
-DAVAO	0.838053	0.822653	0.80924	0.735718	0.818182	0.809737	0.808246	0.799305	0.832588	0.791356	0.660209	0.753105	0.782414	0.803775	0.82762	0.637854	0.830601	0.820169	0.857923	0.709389	0.790363	0.742673	0.805763	0.807253	0.812717	0.693492	0.725782	0.727273	0.856433	0.731744	0.770989	0.77695	0.751615	0.861401	0.850472	0.728266	0.852459	0.694486	0.748137	0.749131	0.844014	0.79384	0.737208	0.857923	0.832588	0.703924	0.69995	0.891207	0.691505	0.708892	0.805266	0.768008	0.712866	0.782414	0.691008	0.76155	0.819175	0.66766	0.73224	0.818182	0.796324	0.865872	0.808743	0.783408	0.799305	0.811227	0.678092	0.670144	0.87531	0.801292	0.846995	0.85842	0.755092	0.781918	0.76006	0.718828	0.727273	0.82464	0.719821	0.857427	0.803775	0.821659	1	0.806259	0.721808	0.737208	0.730253	0.630899	0.763537	0.759066	0.728266	0.72926	0.837556
-HD1-4	0.931446	0.955787	0.98609	0.731744	0.941381	0.826627	0.942375	0.855936	0.846498	0.797317	0.738698	0.816692	0.800298	0.821659	0.836562	0.593145	0.961749	0.941381	0.914555	0.688525	0.84302	0.702931	0.989568	0.835072	0.919026	0.691505	0.832091	0.794834	0.915052	0.692996	0.803775	0.836562	0.725782	0.82464	0.88922	0.768008	0.93691	0.691505	0.825633	0.704421	0.846995	0.775956	0.706408	0.915549	0.90313	0.698957	0.69697	0.803775	0.720318	0.741679	0.82315	0.871336	0.694983	0.772479	0.633383	0.848982	0.912568	0.668654	0.755092	0.862891	0.854943	0.912568	0.862394	0.751615	0.820169	0.810233	0.662196	0.641331	0.820666	0.838053	0.915549	0.915052	0.830601	0.952807	0.786885	0.671138	0.752111	0.795827	0.705912	0.916046	0.813711	0.859414	0.806259	1	0.820169	0.716344	0.796821	0.58619	0.734724	0.787879	0.781918	0.77993	0.901143
-CURINCA	0.831098	0.809737	0.821162	0.710879	0.810233	0.720318	0.782414	0.769498	0.72926	0.703924	0.864878	0.921013	0.728763	0.711376	0.71535	0.604074	0.805763	0.80924	0.814208	0.68455	0.722802	0.616493	0.814704	0.703924	0.817685	0.686538	0.962245	0.944858	0.814704	0.674118	0.749131	0.706408	0.69995	0.719324	0.796821	0.878291	0.798808	0.600099	0.828614	0.686538	0.768505	0.689518	0.68157	0.814208	0.773969	0.69995	0.659215	0.745156	0.708395	0.685047	0.721808	0.798808	0.596622	0.669151	0.616493	0.837059	0.807253	0.660705	0.912072	0.740686	0.814208	0.767511	0.778937	0.650273	0.804272	0.731744	0.639344	0.64928	0.74615	0.742673	0.79235	0.814704	0.752111	0.830601	0.660705	0.647293	0.704421	0.695479	0.609538	0.814704	0.691505	0.721311	0.721808	0.820169	1	0.687531	0.946846	0.568306	0.651267	0.660705	0.745156	0.938897	0.785892
-DAM	0.721311	0.700944	0.709389	0.874317	0.705415	0.825137	0.743169	0.751118	0.740686	0.783905	0.666667	0.711873	0.762047	0.752608	0.783408	0.617486	0.729757	0.706408	0.754098	0.806259	0.755092	0.656731	0.71386	0.738202	0.731744	0.783408	0.697466	0.69697	0.754595	0.914059	0.743666	0.74764	0.842524	0.719821	0.763537	0.667163	0.742673	0.634377	0.691008	0.842027	0.767014	0.729757	0.917536	0.755092	0.764531	0.800795	0.702434	0.752608	0.749627	0.646796	0.733234	0.693989	0.655738	0.69846	0.656731	0.704421	0.709389	0.736711	0.700944	0.74615	0.725286	0.731247	0.710879	0.700447	0.800795	0.76006	0.796821	0.784898	0.739692	0.79384	0.713363	0.754595	0.704918	0.684054	0.728763	0.898162	0.854943	0.764531	0.665673	0.753602	0.731744	0.753602	0.737208	0.716344	0.687531	1	0.69995	0.60159	0.678589	0.728763	0.702931	0.709886	0.726776
-CIRAD403	0.798808	0.788376	0.797814	0.725286	0.77695	0.712866	0.768008	0.797814	0.735718	0.706408	0.87531	0.959265	0.736215	0.716841	0.718828	0.597615	0.798311	0.777943	0.853453	0.69697	0.717337	0.651764	0.79533	0.704421	0.851962	0.687034	0.961749	0.995032	0.851962	0.690512	0.752608	0.728763	0.710383	0.732737	0.825137	0.920517	0.816195	0.607551	0.861898	0.689021	0.766021	0.728763	0.710879	0.853453	0.76155	0.702434	0.670641	0.751615	0.695976	0.697466	0.708395	0.786388	0.605067	0.685544	0.627919	0.871336	0.77695	0.680079	0.948336	0.782911	0.865375	0.774963	0.814208	0.662692	0.826627	0.739195	0.651764	0.661699	0.74466	0.781918	0.762047	0.853949	0.750621	0.808246	0.675112	0.677596	0.707899	0.692002	0.615002	0.851962	0.669151	0.764531	0.730253	0.796821	0.946846	0.69995	1	0.584699	0.643815	0.675112	0.763537	0.981123	0.828117
-JUMALI	0.592151	0.591654	0.588177	0.598112	0.582216	0.605564	0.598112	0.591157	0.617486	0.598112	0.594138	0.598609	0.591157	0.621461	0.613512	0.845007	0.603577	0.582216	0.621957	0.605564	0.608048	0.668654	0.582712	0.604074	0.602583	0.638351	0.583209	0.586687	0.622454	0.611028	0.655241	0.593641	0.580229	0.63537	0.626428	0.616493	0.619473	0.58768	0.631396	0.582712	0.613015	0.642325	0.595628	0.621957	0.61848	0.631893	0.657725	0.619473	0.602583	0.637854	0.61699	0.610532	0.60308	0.580229	0.81073	0.630899	0.582216	0.610532	0.590661	0.597119	0.614009	0.609041	0.643318	0.614009	0.61699	0.631893	0.591157	0.607054	0.626428	0.629906	0.609041	0.621461	0.595628	0.60159	0.577745	0.595132	0.621461	0.610532	0.627919	0.623448	0.577745	0.60159	0.630899	0.58619	0.568306	0.60159	0.584699	1	0.600099	0.577745	0.645306	0.592648	0.603577
-JIMBRUKJOLOWORO	0.739692	0.750124	0.735718	0.688028	0.74764	0.771982	0.74764	0.715847	0.707402	0.739692	0.60159	0.655738	0.728763	0.766021	0.812717	0.595132	0.716344	0.74764	0.723795	0.61997	0.77546	0.692002	0.730253	0.850969	0.703428	0.672628	0.654247	0.640835	0.722305	0.694983	0.726279	0.74615	0.727769	0.724292	0.71535	0.653751	0.740189	0.724292	0.656731	0.687531	0.811227	0.726279	0.688525	0.723795	0.800795	0.680079	0.663189	0.748137	0.658718	0.663189	0.791356	0.721311	0.737705	0.759563	0.631396	0.682067	0.741679	0.647789	0.671634	0.77844	0.689021	0.774466	0.682563	0.865872	0.707899	0.814208	0.616493	0.60457	0.774963	0.726776	0.736711	0.724292	0.733234	0.709389	0.77993	0.691008	0.679583	0.775956	0.727769	0.723299	0.796821	0.777943	0.763537	0.734724	0.651267	0.678589	0.643815	0.600099	1	0.77993	0.680576	0.641828	0.739195
-GOGOLEMPUK	0.757079	0.751615	0.774963	0.710383	0.756085	0.791356	0.783905	0.780924	0.771485	0.801788	0.63686	0.69995	0.750124	0.79533	0.835072	0.597615	0.789369	0.756085	0.782911	0.727769	0.801788	0.685544	0.787382	0.852459	0.776453	0.693989	0.669647	0.673125	0.782414	0.71535	0.717834	0.79533	0.730253	0.754595	0.77546	0.685047	0.790363	0.748634	0.706905	0.729757	0.795827	0.765524	0.725782	0.783905	0.815201	0.697466	0.689518	0.729757	0.73075	0.693492	0.795827	0.715847	0.777943	0.738202	0.645802	0.72926	0.762047	0.643318	0.674118	0.813711	0.751118	0.782911	0.733731	0.840537	0.772976	0.789866	0.73224	0.718331	0.780427	0.743169	0.761053	0.783408	0.722802	0.749627	0.998013	0.734228	0.721808	0.838053	0.785892	0.783408	0.808246	0.853949	0.759066	0.787879	0.660705	0.728763	0.675112	0.577745	0.77993	1	0.677099	0.675112	0.791356
-CIRAD394	0.767014	0.790363	0.783905	0.761053	0.778937	0.725782	0.783905	0.742176	0.750621	0.693492	0.725286	0.755589	0.71535	0.742673	0.705912	0.677099	0.764531	0.778937	0.803775	0.700944	0.727273	0.718331	0.781421	0.717337	0.811227	0.834078	0.755092	0.759563	0.803279	0.692499	0.865872	0.736711	0.685544	0.76155	0.813214	0.787382	0.784401	0.674118	0.73075	0.680079	0.723299	0.794337	0.706905	0.804769	0.793343	0.838549	0.783905	0.729757	0.722802	0.748137	0.752111	0.770492	0.676602	0.714357	0.733234	0.783905	0.742176	0.79235	0.745653	0.735221	0.813711	0.766021	0.764531	0.699454	0.790859	0.761053	0.690512	0.685544	0.738698	0.789866	0.76304	0.804272	0.824143	0.758569	0.676105	0.69846	0.723795	0.693989	0.680576	0.803279	0.655241	0.752608	0.728266	0.781918	0.745156	0.702931	0.763537	0.645306	0.680576	0.677099	1	0.773472	0.781421
-IR63372-08	0.781918	0.769498	0.780924	0.735221	0.76006	0.712866	0.778937	0.796821	0.74764	0.697466	0.868356	0.944362	0.747144	0.729757	0.717834	0.605564	0.781421	0.761053	0.834575	0.707899	0.728266	0.642822	0.77844	0.702434	0.835072	0.700944	0.945852	0.981123	0.835072	0.700447	0.763537	0.741679	0.710383	0.74466	0.836066	0.93542	0.798311	0.619473	0.846001	0.698957	0.757079	0.721808	0.720815	0.835569	0.773472	0.71237	0.683557	0.742673	0.707899	0.690512	0.719324	0.769498	0.61699	0.697466	0.634873	0.85544	0.759066	0.690015	0.963239	0.767014	0.849478	0.757079	0.798311	0.660705	0.837556	0.750124	0.663686	0.672628	0.745653	0.764034	0.753105	0.835072	0.760556	0.79235	0.674118	0.687531	0.711873	0.691008	0.627919	0.835072	0.670144	0.746647	0.72926	0.77993	0.938897	0.709886	0.981123	0.592648	0.641828	0.675112	0.773472	1	0.812221
-IR60080-46A	0.899155	0.879781	0.901143	0.753105	0.867362	0.807253	0.869349	0.878291	0.845007	0.808743	0.738202	0.861898	0.787879	0.817188	0.84004	0.617486	0.924491	0.868356	0.946846	0.702931	0.799801	0.769001	0.898659	0.818679	0.934426	0.704918	0.801788	0.82613	0.946349	0.722305	0.799305	0.812221	0.714357	0.837059	0.919523	0.797317	0.925484	0.702931	0.846001	0.725782	0.861401	0.84302	0.742673	0.947839	0.865872	0.711376	0.719324	0.835072	0.725782	0.741182	0.80775	0.858917	0.721311	0.762047	0.672628	0.882265	0.880278	0.680079	0.806259	0.942871	0.891207	0.923	0.903626	0.743169	0.832588	0.813711	0.674615	0.66468	0.842027	0.871336	0.87233	0.947342	0.812221	0.871833	0.790363	0.718331	0.743666	0.798311	0.722305	0.947342	0.79533	0.910581	0.837556	0.901143	0.785892	0.726776	0.828117	0.603577	0.739195	0.791356	0.781421	0.812221	1
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/test-data/analyse.log
--- a/MDSplot/test-data/analyse.log	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-
-@----------------------------------------------------------@
-|        PLINK!       |     v1.07      |   10/Aug/2009     |
-|----------------------------------------------------------|
-|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
-|----------------------------------------------------------|
-|  For documentation, citation & bug-report instructions:  |
-|        http://pngu.mgh.harvard.edu/purcell/plink/        |
-@----------------------------------------------------------@
-
-Skipping web check... [ --noweb ] 
-Writing this text to log file [ analyse.log ]
-Analysis started: Tue Jan 20 09:30:56 2015
-
-Options in effect:
-	--file input
-	--noweb
-	--cluster
-	--matrix
-	--mds-plot 2
-	--out analyse
-
-2013 (of 2013) markers to be included from [ input.map ]
-93 individuals read from [ input.ped ] 
-93 individuals with nonmissing phenotypes
-Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
-Missing phenotype value is also -9
-0 cases, 93 controls and 0 missing
-93 males, 0 females, and 0 of unspecified sex
-Before frequency and genotyping pruning, there are 2013 SNPs
-Converting data to SNP-major format
-93 founders and 0 non-founders found
-Total genotyping rate in remaining individuals is 1
-0 SNPs failed missingness test ( GENO > 1 )
-0 SNPs failed frequency test ( MAF < 0 )
-Converting data to Individual-major format
-After frequency and genotyping pruning, there are 2013 SNPs
-After filtering, 0 cases, 93 controls and 0 missing
-After filtering, 93 males, 0 females, and 0 of unspecified sex
-
- **Warning** this analysis typically requires whole-genome level data
-             to give accurate results 
-
-Clustering individuals based on genome-wide IBS
-Merge distance p-value constraint = 0
-IBS(g) calculation: 0 of 4278         
IBS(g) calculation: 100 of 4278         
IBS(g) calculation: 200 of 4278         
IBS(g) calculation: 300 of 4278         
IBS(g) calculation: 400 of 4278         
IBS(g) calculation: 500 of 4278         
IBS(g) calculation: 600 of 4278         
IBS(g) calculation: 700 of 4278         
IBS(g) calculation: 800 of 4278         
IBS(g) calculation: 900 of 4278         
IBS(g) calculation: 1000 of 4278         
IBS(g) calculation: 1100 of 4278         
IBS(g) calculation: 1200 of 4278         
IBS(g) calculation: 1300 of 4278         
IBS(g) calculation: 1400 of 4278         
IBS(g) calculation: 1500 of 4278         
IBS(g) calculation: 1600 of 4278         
IBS(g) calculation: 1700 of 4278         
IBS(g) calculation: 1800 of 4278         
IBS(g) calculation: 1900 of 4278         
IBS(g) calculation: 2000 of 4278         
IBS(g) calculation: 2100 of 4278         
IBS(g) calculation: 2200 of 4278         
IBS(g) calculation: 2300 of 4278         
IBS(g) calculation: 2400 of 4278         
IBS(g) calculation: 2500 of 4278         
IBS(g) calculation: 2600 of 4278         
IBS(g) calculation: 2700 of 4278         
IBS(g) calculation: 2800 of 4278         
IBS(g) calculation: 2900 of 4278         
IBS(g) calculation: 3000 of 4278         
IBS(g) calculation: 3100 of 4278         
IBS(g) calculation: 3200 of 4278         
IBS(g) calculation: 3300 of 4278         
IBS(g) calculation: 3400 of 4278         
IBS(g) calculation: 3500 of 4278         
IBS(g) calculation: 3600 of 4278         
IBS(g) calculation: 3700 of 4278         
IBS(g) calculation: 3800 of 4278         
IBS(g) calculation: 3900 of 4278         
IBS(g) calculation: 4000 of 4278         
IBS(g) calculation: 4100 of 4278         
IBS(g) calculation: 4200 of 4278         
Writing IBS similarity matrix to [ analyse.mibs ]
-Of these, 4278 are pairable based on constraints
-Writing cluster progress to [ analyse.cluster0 ]
-Writing cluster solution (1) [ analyse.cluster1 ]
-Writing cluster solution (2) [ analyse.cluster2 ]
-Writing cluster solution (3) [ analyse.cluster3 ]
-Writing MDS solution to [ analyse.mds ] 
-MDS plot of individuals (not clusters)
-
-Analysis finished: Tue Jan 20 09:30:57 2015
-
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/test-data/analyse.mds_plot.txt
--- a/MDSplot/test-data/analyse.mds_plot.txt	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-IRAT112	-0.0969382	0.0376036
-IAC25	-0.0918126	0.0501177
-IAC165	-0.104815	0.0453876
-KARASUKARASURANKASU	0.107782	-0.0683546
-DOURADOPRECOCE	-0.0831697	0.0516412
-CUIABANA	0.0327877	0.0497752
-BICOBRANCO	-0.0554177	0.0501857
-CAAWA/FORTUNA6	-0.052355	0.0170584
-CANELADEFERRO	-0.0142283	0.0598394
-CIRAD358	0.0497841	0.0645487
-COLOMBIA1	-0.110347	-0.172742
-CIRAD409	-0.113614	-0.105898
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-BAKUNGH	0.0199022	0.0613692
-FOHISOMOTRA	0.0344309	0.0697592
-KAKANI2	0.147713	-0.0780455
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-IAC47	-0.0968934	0.0477667
-MOROBEREKAN	0.0395544	0.0952695
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-ESPERANZA	-0.108888	-0.00812147
-BULUPANDAK	0.119762	0.143912
-ARIAS	0.0327948	0.0827878
-GOMPA2	0.133341	-0.0543414
-CT13582-15-5-M	-0.0922561	-0.0543988
-IRAT335	-0.0886849	0.0522465
-M202	0.13463	-0.106462
-IR65907-188-1-B	-0.0755893	-0.136821
-IR71525-19-1-1	-0.0353444	0.0478985
-CNA-7_BO_1_1_33-13-6-1	-0.0823478	-0.0435581
-IRAT257	-0.0606191	0.0564989
-IRAT109	-0.1006	-0.00959445
-KANIRANGA	0.0705459	0.129888
-IR66421-096-2-1-1	-0.00859728	-0.0570793
-GOGO	0.0232414	0.0351889
-GEMJYAJYANAM	0.170032	-0.0857315
-DANGREY	0.175792	-0.113683
-BINULAWAN	-0.0208225	0.0611919
-CAIAPO	-0.0149329	-0.0122987
-IGUAPECATETO	-0.0740464	0.0552386
-IRAT170	-0.0756928	0.00297643
-IRAT380	-0.0210318	-0.00092536
-ARAGUAIA	-0.123443	0.0273298
-GOGOLEMPAK	0.0598291	0.107462
-JAOHAW	0.17563	-0.0587865
-CHALOYOE	0.0904761	-0.0565325
-GANIGI	0.0526286	0.0960475
-GUNDILKUNING	0.116788	0.130234
-IRAT2	-0.0762849	0.00262428
-IRAT366	0.0273652	0.13551
-IRAT104	-0.00310702	0.0636479
-DAVAO	-0.00538403	0.0564886
-HD1-4	-0.0960109	0.0459137
-CURINCA	-0.128876	-0.121141
-DAM	0.129029	-0.0660183
-CIRAD403	-0.117849	-0.134651
-JUMALI	0.123992	-0.0843623
-JIMBRUKJOLOWORO	0.0549906	0.135017
-GOGOLEMPUK	0.0597267	0.10733
-CIRAD394	0.0040454	-0.0885135
-IR63372-08	-0.0951857	-0.140804
-IR60080-46A	-0.0732581	0.0197832
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/test-data/input.map
--- a/MDSplot/test-data/input.map	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-Chr1 Chr1:4832810 0 4832810
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-Chr1 Chr1:4896826 0 4896826
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-Chr1 Chr1:4988653 0 4988653
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-Chr1 Chr1:5009291 0 5009291
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-Chr1 Chr1:5027851 0 5027851
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-Chr1 Chr1:5244943 0 5244943
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-Chr1 Chr1:5762097 0 5762097
-Chr1 Chr1:5763894 0 5763894
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-Chr1 Chr1:5811759 0 5811759
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-Chr1 Chr1:5837668 0 5837668
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-Chr1 Chr1:6274026 0 6274026
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-Chr1 Chr1:6492918 0 6492918
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-Chr1 Chr1:6500649 0 6500649
-Chr1 Chr1:6501316 0 6501316
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-Chr1 Chr1:6507753 0 6507753
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-Chr1 Chr1:6560309 0 6560309
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-Chr1 Chr1:6571552 0 6571552
-Chr1 Chr1:6574768 0 6574768
-Chr1 Chr1:6578214 0 6578214
-Chr1 Chr1:6585909 0 6585909
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-Chr1 Chr1:6641644 0 6641644
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-Chr1 Chr1:6712989 0 6712989
-Chr1 Chr1:6796366 0 6796366
-Chr1 Chr1:6811072 0 6811072
-Chr1 Chr1:6811076 0 6811076
-Chr1 Chr1:6811091 0 6811091
-Chr1 Chr1:6811121 0 6811121
-Chr1 Chr1:6847337 0 6847337
-Chr1 Chr1:6847349 0 6847349
-Chr1 Chr1:6849645 0 6849645
-Chr1 Chr1:6849893 0 6849893
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-Chr1 Chr1:6873205 0 6873205
-Chr1 Chr1:6891098 0 6891098
-Chr1 Chr1:6900133 0 6900133
-Chr1 Chr1:6902826 0 6902826
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-Chr1 Chr1:6975467 0 6975467
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-Chr1 Chr1:7005674 0 7005674
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-Chr1 Chr1:7015263 0 7015263
-Chr1 Chr1:7035291 0 7035291
-Chr1 Chr1:7059462 0 7059462
-Chr1 Chr1:7101706 0 7101706
-Chr1 Chr1:7119061 0 7119061
-Chr1 Chr1:7125222 0 7125222
-Chr1 Chr1:7125225 0 7125225
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-Chr1 Chr1:7125735 0 7125735
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-Chr1 Chr1:7127013 0 7127013
-Chr1 Chr1:7127054 0 7127054
-Chr1 Chr1:7175375 0 7175375
-Chr1 Chr1:7224154 0 7224154
-Chr1 Chr1:7228825 0 7228825
-Chr1 Chr1:7233690 0 7233690
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-Chr1 Chr1:7258509 0 7258509
-Chr1 Chr1:7276068 0 7276068
-Chr1 Chr1:7298968 0 7298968
-Chr1 Chr1:7312405 0 7312405
-Chr1 Chr1:7326667 0 7326667
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-Chr1 Chr1:7343462 0 7343462
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-Chr1 Chr1:7370299 0 7370299
-Chr1 Chr1:7389877 0 7389877
-Chr1 Chr1:7412734 0 7412734
-Chr1 Chr1:7412745 0 7412745
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-Chr1 Chr1:7420788 0 7420788
-Chr1 Chr1:7436962 0 7436962
-Chr1 Chr1:7438755 0 7438755
-Chr1 Chr1:7442314 0 7442314
-Chr1 Chr1:7447389 0 7447389
-Chr1 Chr1:7455402 0 7455402
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-Chr1 Chr1:7465212 0 7465212
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-Chr1 Chr1:7566207 0 7566207
-Chr1 Chr1:7618541 0 7618541
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-Chr1 Chr1:7764482 0 7764482
-Chr1 Chr1:7766950 0 7766950
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-Chr1 Chr1:7778309 0 7778309
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-Chr1 Chr1:8289727 0 8289727
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-Chr1 Chr1:8813546 0 8813546
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-Chr1 Chr1:8908924 0 8908924
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-Chr1 Chr1:9056785 0 9056785
-Chr1 Chr1:9057140 0 9057140
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-Chr1 Chr1:9646665 0 9646665
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-Chr1 Chr1:9671547 0 9671547
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-Chr1 Chr1:9931813 0 9931813
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-Chr1 Chr1:10146542 0 10146542
-Chr1 Chr1:10149878 0 10149878
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-Chr1 Chr1:10245252 0 10245252
-Chr1 Chr1:10246598 0 10246598
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-Chr1 Chr1:10267431 0 10267431
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-Chr1 Chr1:10285499 0 10285499
-Chr1 Chr1:10299032 0 10299032
-Chr1 Chr1:10299079 0 10299079
-Chr1 Chr1:10330001 0 10330001
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-Chr1 Chr1:10438894 0 10438894
-Chr1 Chr1:10471259 0 10471259
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-Chr1 Chr1:11078438 0 11078438
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-Chr1 Chr1:11158380 0 11158380
-Chr1 Chr1:11166945 0 11166945
-Chr1 Chr1:11166963 0 11166963
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-Chr1 Chr1:11226698 0 11226698
-Chr1 Chr1:11232299 0 11232299
-Chr1 Chr1:11276184 0 11276184
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-Chr1 Chr1:11451409 0 11451409
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-Chr1 Chr1:11611190 0 11611190
-Chr1 Chr1:11611212 0 11611212
-Chr1 Chr1:11631478 0 11631478
-Chr1 Chr1:11665440 0 11665440
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-Chr1 Chr1:11777126 0 11777126
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-Chr1 Chr1:12193809 0 12193809
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-Chr1 Chr1:12640384 0 12640384
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-Chr1 Chr1:13193179 0 13193179
-Chr1 Chr1:13240036 0 13240036
-Chr1 Chr1:13240087 0 13240087
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-Chr1 Chr1:13266147 0 13266147
-Chr1 Chr1:13274557 0 13274557
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-Chr1 Chr1:13293946 0 13293946
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-Chr1 Chr1:13294538 0 13294538
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-Chr1 Chr1:13295419 0 13295419
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-Chr1 Chr1:13549673 0 13549673
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-Chr1 Chr1:13583363 0 13583363
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-Chr1 Chr1:15640039 0 15640039
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-Chr1 Chr1:18663992 0 18663992
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-Chr1 Chr1:18828386 0 18828386
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-Chr1 Chr1:19012605 0 19012605
-Chr1 Chr1:19031487 0 19031487
-Chr1 Chr1:19058808 0 19058808
-Chr1 Chr1:19080444 0 19080444
-Chr1 Chr1:19286858 0 19286858
-Chr1 Chr1:19286869 0 19286869
-Chr1 Chr1:19333051 0 19333051
-Chr1 Chr1:19355961 0 19355961
-Chr1 Chr1:19457517 0 19457517
-Chr1 Chr1:19463824 0 19463824
-Chr1 Chr1:19546252 0 19546252
-Chr1 Chr1:19548751 0 19548751
-Chr1 Chr1:19600679 0 19600679
-Chr1 Chr1:19616107 0 19616107
-Chr1 Chr1:19682153 0 19682153
-Chr1 Chr1:19682333 0 19682333
-Chr1 Chr1:19683507 0 19683507
-Chr1 Chr1:19692522 0 19692522
-Chr1 Chr1:19844645 0 19844645
-Chr1 Chr1:19875492 0 19875492
-Chr1 Chr1:19884303 0 19884303
-Chr1 Chr1:19890812 0 19890812
-Chr1 Chr1:19918575 0 19918575
-Chr1 Chr1:19960915 0 19960915
-Chr1 Chr1:20043559 0 20043559
-Chr1 Chr1:20043762 0 20043762
-Chr1 Chr1:20200430 0 20200430
-Chr1 Chr1:20244907 0 20244907
-Chr1 Chr1:20283003 0 20283003
-Chr1 Chr1:20297936 0 20297936
-Chr1 Chr1:20307459 0 20307459
-Chr1 Chr1:20414880 0 20414880
-Chr1 Chr1:20418207 0 20418207
-Chr1 Chr1:20453895 0 20453895
-Chr1 Chr1:20457891 0 20457891
-Chr1 Chr1:20480254 0 20480254
-Chr1 Chr1:20484206 0 20484206
-Chr1 Chr1:20502469 0 20502469
-Chr1 Chr1:20502498 0 20502498
-Chr1 Chr1:20527190 0 20527190
-Chr1 Chr1:20536861 0 20536861
-Chr1 Chr1:20583778 0 20583778
-Chr1 Chr1:20603211 0 20603211
-Chr1 Chr1:20628363 0 20628363
-Chr1 Chr1:20749512 0 20749512
-Chr1 Chr1:20808148 0 20808148
-Chr1 Chr1:20808185 0 20808185
-Chr1 Chr1:20808188 0 20808188
-Chr1 Chr1:20941827 0 20941827
-Chr1 Chr1:20985001 0 20985001
-Chr1 Chr1:21014787 0 21014787
-Chr1 Chr1:21044771 0 21044771
-Chr1 Chr1:21082093 0 21082093
-Chr1 Chr1:21126090 0 21126090
-Chr1 Chr1:21160401 0 21160401
-Chr1 Chr1:21160870 0 21160870
-Chr1 Chr1:21201262 0 21201262
-Chr1 Chr1:21201330 0 21201330
-Chr1 Chr1:21203185 0 21203185
-Chr1 Chr1:21237101 0 21237101
-Chr1 Chr1:21238922 0 21238922
-Chr1 Chr1:21240239 0 21240239
-Chr1 Chr1:21241093 0 21241093
-Chr1 Chr1:21275917 0 21275917
-Chr1 Chr1:21357238 0 21357238
-Chr1 Chr1:21385607 0 21385607
-Chr1 Chr1:21415113 0 21415113
-Chr1 Chr1:21440962 0 21440962
-Chr1 Chr1:21503565 0 21503565
-Chr1 Chr1:21562231 0 21562231
-Chr1 Chr1:21603665 0 21603665
-Chr1 Chr1:21672420 0 21672420
-Chr1 Chr1:21684647 0 21684647
-Chr1 Chr1:21687037 0 21687037
-Chr1 Chr1:21692496 0 21692496
-Chr1 Chr1:21700123 0 21700123
-Chr1 Chr1:21712360 0 21712360
-Chr1 Chr1:21750711 0 21750711
-Chr1 Chr1:21750725 0 21750725
-Chr1 Chr1:21788731 0 21788731
-Chr1 Chr1:21788887 0 21788887
-Chr1 Chr1:21793111 0 21793111
-Chr1 Chr1:21793114 0 21793114
-Chr1 Chr1:21811411 0 21811411
-Chr1 Chr1:22221087 0 22221087
-Chr1 Chr1:22362000 0 22362000
-Chr1 Chr1:22365064 0 22365064
-Chr1 Chr1:22366394 0 22366394
-Chr1 Chr1:22420228 0 22420228
-Chr1 Chr1:22434088 0 22434088
-Chr1 Chr1:22436948 0 22436948
-Chr1 Chr1:22438238 0 22438238
-Chr1 Chr1:22441431 0 22441431
-Chr1 Chr1:22446965 0 22446965
-Chr1 Chr1:22452793 0 22452793
-Chr1 Chr1:22452814 0 22452814
-Chr1 Chr1:22456223 0 22456223
-Chr1 Chr1:22456541 0 22456541
-Chr1 Chr1:22464901 0 22464901
-Chr1 Chr1:22464938 0 22464938
-Chr1 Chr1:22465695 0 22465695
-Chr1 Chr1:22467542 0 22467542
-Chr1 Chr1:22468575 0 22468575
-Chr1 Chr1:22486715 0 22486715
-Chr1 Chr1:22486765 0 22486765
-Chr1 Chr1:22507492 0 22507492
-Chr1 Chr1:22527085 0 22527085
-Chr1 Chr1:22557545 0 22557545
-Chr1 Chr1:22560937 0 22560937
-Chr1 Chr1:22591601 0 22591601
-Chr1 Chr1:22594675 0 22594675
-Chr1 Chr1:22617285 0 22617285
-Chr1 Chr1:22636521 0 22636521
-Chr1 Chr1:22672543 0 22672543
-Chr1 Chr1:22672589 0 22672589
-Chr1 Chr1:22674616 0 22674616
-Chr1 Chr1:22726998 0 22726998
-Chr1 Chr1:22739593 0 22739593
-Chr1 Chr1:22739596 0 22739596
-Chr1 Chr1:22739995 0 22739995
-Chr1 Chr1:22740010 0 22740010
-Chr1 Chr1:22780246 0 22780246
-Chr1 Chr1:22822065 0 22822065
-Chr1 Chr1:22828980 0 22828980
-Chr1 Chr1:22837071 0 22837071
-Chr1 Chr1:22837075 0 22837075
-Chr1 Chr1:22974966 0 22974966
-Chr1 Chr1:22974971 0 22974971
-Chr1 Chr1:22974974 0 22974974
-Chr1 Chr1:22975037 0 22975037
-Chr1 Chr1:22991392 0 22991392
-Chr1 Chr1:22991925 0 22991925
-Chr1 Chr1:23006900 0 23006900
-Chr1 Chr1:23006936 0 23006936
-Chr1 Chr1:23079278 0 23079278
-Chr1 Chr1:23083004 0 23083004
-Chr1 Chr1:23096859 0 23096859
-Chr1 Chr1:23103054 0 23103054
-Chr1 Chr1:23147512 0 23147512
-Chr1 Chr1:23151111 0 23151111
-Chr1 Chr1:23152355 0 23152355
-Chr1 Chr1:23168512 0 23168512
-Chr1 Chr1:23171855 0 23171855
-Chr1 Chr1:23183180 0 23183180
-Chr1 Chr1:23203034 0 23203034
-Chr1 Chr1:23216787 0 23216787
-Chr1 Chr1:23235085 0 23235085
-Chr1 Chr1:23248184 0 23248184
-Chr1 Chr1:23297650 0 23297650
-Chr1 Chr1:23324317 0 23324317
-Chr1 Chr1:23332211 0 23332211
-Chr1 Chr1:23338972 0 23338972
-Chr1 Chr1:23349168 0 23349168
-Chr1 Chr1:23351414 0 23351414
-Chr1 Chr1:23353553 0 23353553
-Chr1 Chr1:23366101 0 23366101
-Chr1 Chr1:23378783 0 23378783
-Chr1 Chr1:23392716 0 23392716
-Chr1 Chr1:23395515 0 23395515
-Chr1 Chr1:23395522 0 23395522
-Chr1 Chr1:23403909 0 23403909
-Chr1 Chr1:23404803 0 23404803
-Chr1 Chr1:23404854 0 23404854
-Chr1 Chr1:23426983 0 23426983
-Chr1 Chr1:23426986 0 23426986
-Chr1 Chr1:23431931 0 23431931
-Chr1 Chr1:23448547 0 23448547
-Chr1 Chr1:23530885 0 23530885
-Chr1 Chr1:23531955 0 23531955
-Chr1 Chr1:23543040 0 23543040
-Chr1 Chr1:23556083 0 23556083
-Chr1 Chr1:23575160 0 23575160
-Chr1 Chr1:23610833 0 23610833
-Chr1 Chr1:23610842 0 23610842
-Chr1 Chr1:23620798 0 23620798
-Chr1 Chr1:23624047 0 23624047
-Chr1 Chr1:23634488 0 23634488
-Chr1 Chr1:23648137 0 23648137
-Chr1 Chr1:23651986 0 23651986
-Chr1 Chr1:23721841 0 23721841
-Chr1 Chr1:23721844 0 23721844
-Chr1 Chr1:23731885 0 23731885
-Chr1 Chr1:23756111 0 23756111
-Chr1 Chr1:23762143 0 23762143
-Chr1 Chr1:23782998 0 23782998
-Chr1 Chr1:23785932 0 23785932
-Chr1 Chr1:23836611 0 23836611
-Chr1 Chr1:23857915 0 23857915
-Chr1 Chr1:23863742 0 23863742
-Chr1 Chr1:23882305 0 23882305
-Chr1 Chr1:23896573 0 23896573
-Chr1 Chr1:23897070 0 23897070
-Chr1 Chr1:23913125 0 23913125
-Chr1 Chr1:23922001 0 23922001
-Chr1 Chr1:23935969 0 23935969
-Chr1 Chr1:23939765 0 23939765
-Chr1 Chr1:23972022 0 23972022
-Chr1 Chr1:23986664 0 23986664
-Chr1 Chr1:24004564 0 24004564
-Chr1 Chr1:24034453 0 24034453
-Chr1 Chr1:24037402 0 24037402
-Chr1 Chr1:24049164 0 24049164
-Chr1 Chr1:24092946 0 24092946
-Chr1 Chr1:24093753 0 24093753
-Chr1 Chr1:24116624 0 24116624
-Chr1 Chr1:24116678 0 24116678
-Chr1 Chr1:24124359 0 24124359
-Chr1 Chr1:24129826 0 24129826
-Chr1 Chr1:24147784 0 24147784
-Chr1 Chr1:24234620 0 24234620
-Chr1 Chr1:24234629 0 24234629
-Chr1 Chr1:24234677 0 24234677
-Chr1 Chr1:24239996 0 24239996
-Chr1 Chr1:24240019 0 24240019
-Chr1 Chr1:24310319 0 24310319
-Chr1 Chr1:24336951 0 24336951
-Chr1 Chr1:24381824 0 24381824
-Chr1 Chr1:24462566 0 24462566
-Chr1 Chr1:24482154 0 24482154
-Chr1 Chr1:24489729 0 24489729
-Chr1 Chr1:24502190 0 24502190
-Chr1 Chr1:24510021 0 24510021
-Chr1 Chr1:24533617 0 24533617
-Chr1 Chr1:24560384 0 24560384
-Chr1 Chr1:24560461 0 24560461
-Chr1 Chr1:24563014 0 24563014
-Chr1 Chr1:24567170 0 24567170
-Chr1 Chr1:24593376 0 24593376
-Chr1 Chr1:24617946 0 24617946
-Chr1 Chr1:24640251 0 24640251
-Chr1 Chr1:24657015 0 24657015
-Chr1 Chr1:24657701 0 24657701
-Chr1 Chr1:24669568 0 24669568
-Chr1 Chr1:24695185 0 24695185
-Chr1 Chr1:24709143 0 24709143
-Chr1 Chr1:24709146 0 24709146
-Chr1 Chr1:24729468 0 24729468
-Chr1 Chr1:24760790 0 24760790
-Chr1 Chr1:24760793 0 24760793
-Chr1 Chr1:24765623 0 24765623
-Chr1 Chr1:24779640 0 24779640
-Chr1 Chr1:24809285 0 24809285
-Chr1 Chr1:24818955 0 24818955
-Chr1 Chr1:24836934 0 24836934
-Chr1 Chr1:24841900 0 24841900
-Chr1 Chr1:24848754 0 24848754
-Chr1 Chr1:24851489 0 24851489
-Chr1 Chr1:24859483 0 24859483
-Chr1 Chr1:24859549 0 24859549
-Chr1 Chr1:24867007 0 24867007
-Chr1 Chr1:24870728 0 24870728
-Chr1 Chr1:24871752 0 24871752
-Chr1 Chr1:24874960 0 24874960
-Chr1 Chr1:24874996 0 24874996
-Chr1 Chr1:24887222 0 24887222
-Chr1 Chr1:24896805 0 24896805
-Chr1 Chr1:24919167 0 24919167
-Chr1 Chr1:24920731 0 24920731
-Chr1 Chr1:24926843 0 24926843
-Chr1 Chr1:24934092 0 24934092
-Chr1 Chr1:24970821 0 24970821
-Chr1 Chr1:24970826 0 24970826
-Chr1 Chr1:24970829 0 24970829
-Chr1 Chr1:24987874 0 24987874
-Chr1 Chr1:25012595 0 25012595
-Chr1 Chr1:25016468 0 25016468
-Chr1 Chr1:25067075 0 25067075
-Chr1 Chr1:25077288 0 25077288
-Chr1 Chr1:25091984 0 25091984
-Chr1 Chr1:25115923 0 25115923
-Chr1 Chr1:25136014 0 25136014
-Chr1 Chr1:25155677 0 25155677
-Chr1 Chr1:25160990 0 25160990
-Chr1 Chr1:25160993 0 25160993
-Chr1 Chr1:25230277 0 25230277
-Chr1 Chr1:25259414 0 25259414
-Chr1 Chr1:25262919 0 25262919
-Chr1 Chr1:25262924 0 25262924
-Chr1 Chr1:25266878 0 25266878
-Chr1 Chr1:25266881 0 25266881
-Chr1 Chr1:25266922 0 25266922
-Chr1 Chr1:25281106 0 25281106
-Chr1 Chr1:25281928 0 25281928
-Chr1 Chr1:25294455 0 25294455
-Chr1 Chr1:25298123 0 25298123
-Chr1 Chr1:25362835 0 25362835
-Chr1 Chr1:25371899 0 25371899
-Chr1 Chr1:25372636 0 25372636
-Chr1 Chr1:25414435 0 25414435
-Chr1 Chr1:25414438 0 25414438
-Chr1 Chr1:25498933 0 25498933
-Chr1 Chr1:25508055 0 25508055
-Chr1 Chr1:25593002 0 25593002
-Chr1 Chr1:25596880 0 25596880
-Chr1 Chr1:25642202 0 25642202
-Chr1 Chr1:25642232 0 25642232
-Chr1 Chr1:25684059 0 25684059
-Chr1 Chr1:25685951 0 25685951
-Chr1 Chr1:25844706 0 25844706
-Chr1 Chr1:25852185 0 25852185
-Chr1 Chr1:26199529 0 26199529
-Chr1 Chr1:26294671 0 26294671
-Chr1 Chr1:26438710 0 26438710
-Chr1 Chr1:26481633 0 26481633
-Chr1 Chr1:26511593 0 26511593
-Chr1 Chr1:26523741 0 26523741
-Chr1 Chr1:26692985 0 26692985
-Chr1 Chr1:26734999 0 26734999
-Chr1 Chr1:26786974 0 26786974
-Chr1 Chr1:26786992 0 26786992
-Chr1 Chr1:26816312 0 26816312
-Chr1 Chr1:26822126 0 26822126
-Chr1 Chr1:26863487 0 26863487
-Chr1 Chr1:26917422 0 26917422
-Chr1 Chr1:27025297 0 27025297
-Chr1 Chr1:27028736 0 27028736
-Chr1 Chr1:27029297 0 27029297
-Chr1 Chr1:27091260 0 27091260
-Chr1 Chr1:27104120 0 27104120
-Chr1 Chr1:27146134 0 27146134
-Chr1 Chr1:27266029 0 27266029
-Chr1 Chr1:27285055 0 27285055
-Chr1 Chr1:27285080 0 27285080
-Chr1 Chr1:27289893 0 27289893
-Chr1 Chr1:27338364 0 27338364
-Chr1 Chr1:27417659 0 27417659
-Chr1 Chr1:27435104 0 27435104
-Chr1 Chr1:27506185 0 27506185
-Chr1 Chr1:27587166 0 27587166
-Chr1 Chr1:27596768 0 27596768
-Chr1 Chr1:27610155 0 27610155
-Chr1 Chr1:27666969 0 27666969
-Chr1 Chr1:27718132 0 27718132
-Chr1 Chr1:27735730 0 27735730
-Chr1 Chr1:27736608 0 27736608
-Chr1 Chr1:27737357 0 27737357
-Chr1 Chr1:27737916 0 27737916
-Chr1 Chr1:27759181 0 27759181
-Chr1 Chr1:27771876 0 27771876
-Chr1 Chr1:27868280 0 27868280
-Chr1 Chr1:27868311 0 27868311
-Chr1 Chr1:27873027 0 27873027
-Chr1 Chr1:27907035 0 27907035
-Chr1 Chr1:27941462 0 27941462
-Chr1 Chr1:27941465 0 27941465
-Chr1 Chr1:27949168 0 27949168
-Chr1 Chr1:27997299 0 27997299
-Chr1 Chr1:28028497 0 28028497
-Chr1 Chr1:28028544 0 28028544
-Chr1 Chr1:28051371 0 28051371
-Chr1 Chr1:28058059 0 28058059
-Chr1 Chr1:28099212 0 28099212
-Chr1 Chr1:28100175 0 28100175
-Chr1 Chr1:28113816 0 28113816
-Chr1 Chr1:28116035 0 28116035
-Chr1 Chr1:28121245 0 28121245
-Chr1 Chr1:28121248 0 28121248
-Chr1 Chr1:28121386 0 28121386
-Chr1 Chr1:28145665 0 28145665
-Chr1 Chr1:28152031 0 28152031
-Chr1 Chr1:28163355 0 28163355
-Chr1 Chr1:28167914 0 28167914
-Chr1 Chr1:28169187 0 28169187
-Chr1 Chr1:28185610 0 28185610
-Chr1 Chr1:28232781 0 28232781
-Chr1 Chr1:28237644 0 28237644
-Chr1 Chr1:28265490 0 28265490
-Chr1 Chr1:28265521 0 28265521
-Chr1 Chr1:28265640 0 28265640
-Chr1 Chr1:28268218 0 28268218
-Chr1 Chr1:28284170 0 28284170
-Chr1 Chr1:28291784 0 28291784
-Chr1 Chr1:28297312 0 28297312
-Chr1 Chr1:28315347 0 28315347
-Chr1 Chr1:28326804 0 28326804
-Chr1 Chr1:28342158 0 28342158
-Chr1 Chr1:28342161 0 28342161
-Chr1 Chr1:28350843 0 28350843
-Chr1 Chr1:28372588 0 28372588
-Chr1 Chr1:28376571 0 28376571
-Chr1 Chr1:28390748 0 28390748
-Chr1 Chr1:28429525 0 28429525
-Chr1 Chr1:28454740 0 28454740
-Chr1 Chr1:28512339 0 28512339
-Chr1 Chr1:28514788 0 28514788
-Chr1 Chr1:28519768 0 28519768
-Chr1 Chr1:28537829 0 28537829
-Chr1 Chr1:28537832 0 28537832
-Chr1 Chr1:28552455 0 28552455
-Chr1 Chr1:28555605 0 28555605
-Chr1 Chr1:28568271 0 28568271
-Chr1 Chr1:28579083 0 28579083
-Chr1 Chr1:28624282 0 28624282
-Chr1 Chr1:28624318 0 28624318
-Chr1 Chr1:28629177 0 28629177
-Chr1 Chr1:28657314 0 28657314
-Chr1 Chr1:28657913 0 28657913
-Chr1 Chr1:28661347 0 28661347
-Chr1 Chr1:28661378 0 28661378
-Chr1 Chr1:28661381 0 28661381
-Chr1 Chr1:28662072 0 28662072
-Chr1 Chr1:28662082 0 28662082
-Chr1 Chr1:28669462 0 28669462
-Chr1 Chr1:28671486 0 28671486
-Chr1 Chr1:28671984 0 28671984
-Chr1 Chr1:28707366 0 28707366
-Chr1 Chr1:28707974 0 28707974
-Chr1 Chr1:28709069 0 28709069
-Chr1 Chr1:28709128 0 28709128
-Chr1 Chr1:28709131 0 28709131
-Chr1 Chr1:28739760 0 28739760
-Chr1 Chr1:28752523 0 28752523
-Chr1 Chr1:28776300 0 28776300
-Chr1 Chr1:28790241 0 28790241
-Chr1 Chr1:28797680 0 28797680
-Chr1 Chr1:28810134 0 28810134
-Chr1 Chr1:28818609 0 28818609
-Chr1 Chr1:28818659 0 28818659
-Chr1 Chr1:28839003 0 28839003
-Chr1 Chr1:28893652 0 28893652
-Chr1 Chr1:28911097 0 28911097
-Chr1 Chr1:28912479 0 28912479
-Chr1 Chr1:28920030 0 28920030
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-Chr1 Chr1:28937099 0 28937099
-Chr1 Chr1:28937110 0 28937110
-Chr1 Chr1:28950372 0 28950372
-Chr1 Chr1:28953029 0 28953029
-Chr1 Chr1:28975242 0 28975242
-Chr1 Chr1:28976173 0 28976173
-Chr1 Chr1:28976215 0 28976215
-Chr1 Chr1:28980467 0 28980467
-Chr1 Chr1:28985758 0 28985758
-Chr1 Chr1:28985794 0 28985794
-Chr1 Chr1:28992324 0 28992324
-Chr1 Chr1:28993573 0 28993573
-Chr1 Chr1:29062709 0 29062709
-Chr1 Chr1:29062777 0 29062777
-Chr1 Chr1:29069259 0 29069259
-Chr1 Chr1:29104165 0 29104165
-Chr1 Chr1:29110315 0 29110315
-Chr1 Chr1:29116135 0 29116135
-Chr1 Chr1:29143205 0 29143205
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-Chr1 Chr1:29221871 0 29221871
-Chr1 Chr1:29221916 0 29221916
-Chr1 Chr1:29240567 0 29240567
-Chr1 Chr1:29275468 0 29275468
-Chr1 Chr1:29290850 0 29290850
-Chr1 Chr1:29291614 0 29291614
-Chr1 Chr1:29294897 0 29294897
-Chr1 Chr1:29323260 0 29323260
-Chr1 Chr1:29338674 0 29338674
-Chr1 Chr1:29342748 0 29342748
-Chr1 Chr1:29368312 0 29368312
-Chr1 Chr1:29368316 0 29368316
-Chr1 Chr1:29381840 0 29381840
-Chr1 Chr1:29388895 0 29388895
-Chr1 Chr1:29426085 0 29426085
-Chr1 Chr1:29442134 0 29442134
-Chr1 Chr1:29442212 0 29442212
-Chr1 Chr1:29444106 0 29444106
-Chr1 Chr1:29445837 0 29445837
-Chr1 Chr1:29459338 0 29459338
-Chr1 Chr1:29462209 0 29462209
-Chr1 Chr1:29464821 0 29464821
-Chr1 Chr1:29520268 0 29520268
-Chr1 Chr1:29529194 0 29529194
-Chr1 Chr1:29529520 0 29529520
-Chr1 Chr1:29529573 0 29529573
-Chr1 Chr1:29540540 0 29540540
-Chr1 Chr1:29556065 0 29556065
-Chr1 Chr1:29556067 0 29556067
-Chr1 Chr1:29556722 0 29556722
-Chr1 Chr1:29556725 0 29556725
-Chr1 Chr1:29569341 0 29569341
-Chr1 Chr1:29615657 0 29615657
-Chr1 Chr1:29665399 0 29665399
-Chr1 Chr1:29676504 0 29676504
-Chr1 Chr1:29707926 0 29707926
-Chr1 Chr1:29732730 0 29732730
-Chr1 Chr1:29734245 0 29734245
-Chr1 Chr1:29736117 0 29736117
-Chr1 Chr1:29741984 0 29741984
-Chr1 Chr1:29741987 0 29741987
-Chr1 Chr1:29755512 0 29755512
-Chr1 Chr1:29758534 0 29758534
-Chr1 Chr1:29770060 0 29770060
-Chr1 Chr1:29770066 0 29770066
-Chr1 Chr1:29780222 0 29780222
-Chr1 Chr1:29805304 0 29805304
-Chr1 Chr1:29805469 0 29805469
-Chr1 Chr1:29810581 0 29810581
-Chr1 Chr1:29871968 0 29871968
-Chr1 Chr1:29894876 0 29894876
-Chr1 Chr1:29912009 0 29912009
-Chr1 Chr1:29934876 0 29934876
-Chr1 Chr1:29934926 0 29934926
-Chr1 Chr1:29956787 0 29956787
-Chr1 Chr1:29976618 0 29976618
-Chr1 Chr1:29976945 0 29976945
-Chr1 Chr1:29977025 0 29977025
-Chr1 Chr1:29981185 0 29981185
-Chr1 Chr1:29981189 0 29981189
-Chr1 Chr1:29988911 0 29988911
-Chr1 Chr1:29989242 0 29989242
-Chr1 Chr1:29993665 0 29993665
-Chr1 Chr1:29994545 0 29994545
-Chr1 Chr1:29994671 0 29994671
-Chr1 Chr1:30033870 0 30033870
-Chr1 Chr1:30037897 0 30037897
-Chr1 Chr1:30048246 0 30048246
-Chr1 Chr1:30048276 0 30048276
-Chr1 Chr1:30096375 0 30096375
-Chr1 Chr1:30157657 0 30157657
-Chr1 Chr1:30167454 0 30167454
-Chr1 Chr1:30183413 0 30183413
-Chr1 Chr1:30197987 0 30197987
-Chr1 Chr1:30244448 0 30244448
-Chr1 Chr1:30244449 0 30244449
-Chr1 Chr1:30265177 0 30265177
-Chr1 Chr1:30500836 0 30500836
-Chr1 Chr1:30557638 0 30557638
-Chr1 Chr1:30617594 0 30617594
-Chr1 Chr1:30632340 0 30632340
-Chr1 Chr1:30645778 0 30645778
-Chr1 Chr1:30666725 0 30666725
-Chr1 Chr1:30679434 0 30679434
-Chr1 Chr1:30715119 0 30715119
-Chr1 Chr1:30862865 0 30862865
-Chr1 Chr1:30875285 0 30875285
-Chr1 Chr1:30988314 0 30988314
-Chr1 Chr1:31252146 0 31252146
-Chr1 Chr1:31252678 0 31252678
-Chr1 Chr1:31252704 0 31252704
-Chr1 Chr1:31305056 0 31305056
-Chr1 Chr1:31353236 0 31353236
-Chr1 Chr1:31396730 0 31396730
-Chr1 Chr1:31421361 0 31421361
-Chr1 Chr1:31431656 0 31431656
-Chr1 Chr1:31453373 0 31453373
-Chr1 Chr1:31485589 0 31485589
-Chr1 Chr1:31509969 0 31509969
-Chr1 Chr1:31509971 0 31509971
-Chr1 Chr1:31510049 0 31510049
-Chr1 Chr1:31524422 0 31524422
-Chr1 Chr1:31557933 0 31557933
-Chr1 Chr1:31557936 0 31557936
-Chr1 Chr1:31557986 0 31557986
-Chr1 Chr1:31559810 0 31559810
-Chr1 Chr1:31559895 0 31559895
-Chr1 Chr1:31566399 0 31566399
-Chr1 Chr1:31569296 0 31569296
-Chr1 Chr1:31571201 0 31571201
-Chr1 Chr1:31571975 0 31571975
-Chr1 Chr1:31571987 0 31571987
-Chr1 Chr1:31577334 0 31577334
-Chr1 Chr1:31602416 0 31602416
-Chr1 Chr1:31608861 0 31608861
-Chr1 Chr1:31630945 0 31630945
-Chr1 Chr1:31656589 0 31656589
-Chr1 Chr1:31677735 0 31677735
-Chr1 Chr1:31684486 0 31684486
-Chr1 Chr1:31695659 0 31695659
-Chr1 Chr1:31779847 0 31779847
-Chr1 Chr1:31779850 0 31779850
-Chr1 Chr1:31779865 0 31779865
-Chr1 Chr1:31811093 0 31811093
-Chr1 Chr1:31811659 0 31811659
-Chr1 Chr1:31826446 0 31826446
-Chr1 Chr1:31850290 0 31850290
-Chr1 Chr1:31857928 0 31857928
-Chr1 Chr1:31857929 0 31857929
-Chr1 Chr1:31862466 0 31862466
-Chr1 Chr1:31862528 0 31862528
-Chr1 Chr1:31867111 0 31867111
-Chr1 Chr1:31876051 0 31876051
-Chr1 Chr1:31889377 0 31889377
-Chr1 Chr1:31889485 0 31889485
-Chr1 Chr1:31907055 0 31907055
-Chr1 Chr1:31927140 0 31927140
-Chr1 Chr1:31995350 0 31995350
-Chr1 Chr1:32015975 0 32015975
-Chr1 Chr1:32020723 0 32020723
-Chr1 Chr1:32043018 0 32043018
-Chr1 Chr1:32077755 0 32077755
-Chr1 Chr1:32084837 0 32084837
-Chr1 Chr1:32099526 0 32099526
-Chr1 Chr1:32109172 0 32109172
-Chr1 Chr1:32111760 0 32111760
-Chr1 Chr1:32112621 0 32112621
-Chr1 Chr1:32112622 0 32112622
-Chr1 Chr1:32119131 0 32119131
-Chr1 Chr1:32133860 0 32133860
-Chr1 Chr1:32139702 0 32139702
-Chr1 Chr1:32139722 0 32139722
-Chr1 Chr1:32153707 0 32153707
-Chr1 Chr1:32165197 0 32165197
-Chr1 Chr1:32217903 0 32217903
-Chr1 Chr1:32331774 0 32331774
-Chr1 Chr1:32360773 0 32360773
-Chr1 Chr1:32449071 0 32449071
-Chr1 Chr1:32499753 0 32499753
-Chr1 Chr1:32510853 0 32510853
-Chr1 Chr1:32527882 0 32527882
-Chr1 Chr1:32527981 0 32527981
-Chr1 Chr1:32587107 0 32587107
-Chr1 Chr1:32598032 0 32598032
-Chr1 Chr1:32610324 0 32610324
-Chr1 Chr1:32632614 0 32632614
-Chr1 Chr1:32654599 0 32654599
-Chr1 Chr1:32734148 0 32734148
-Chr1 Chr1:32735557 0 32735557
-Chr1 Chr1:32738743 0 32738743
-Chr1 Chr1:32741911 0 32741911
-Chr1 Chr1:32999294 0 32999294
-Chr1 Chr1:33076887 0 33076887
-Chr1 Chr1:33081781 0 33081781
-Chr1 Chr1:33091343 0 33091343
-Chr1 Chr1:33091346 0 33091346
-Chr1 Chr1:33093016 0 33093016
-Chr1 Chr1:33099125 0 33099125
-Chr1 Chr1:33101161 0 33101161
-Chr1 Chr1:33284722 0 33284722
-Chr1 Chr1:33293797 0 33293797
-Chr1 Chr1:33327786 0 33327786
-Chr1 Chr1:33327839 0 33327839
-Chr1 Chr1:33336223 0 33336223
-Chr1 Chr1:33336318 0 33336318
-Chr1 Chr1:33364796 0 33364796
-Chr1 Chr1:33496512 0 33496512
-Chr1 Chr1:33783168 0 33783168
-Chr1 Chr1:33783179 0 33783179
-Chr1 Chr1:33783182 0 33783182
-Chr1 Chr1:33871635 0 33871635
-Chr1 Chr1:33920570 0 33920570
-Chr1 Chr1:33921227 0 33921227
-Chr1 Chr1:33930751 0 33930751
-Chr1 Chr1:33973542 0 33973542
-Chr1 Chr1:33974278 0 33974278
-Chr1 Chr1:33974856 0 33974856
-Chr1 Chr1:34039707 0 34039707
-Chr1 Chr1:34109518 0 34109518
-Chr1 Chr1:34167104 0 34167104
-Chr1 Chr1:34187435 0 34187435
-Chr1 Chr1:34203919 0 34203919
-Chr1 Chr1:34225494 0 34225494
-Chr1 Chr1:34226293 0 34226293
-Chr1 Chr1:34237359 0 34237359
-Chr1 Chr1:34290046 0 34290046
-Chr1 Chr1:34290097 0 34290097
-Chr1 Chr1:34307022 0 34307022
-Chr1 Chr1:34307825 0 34307825
-Chr1 Chr1:34327301 0 34327301
-Chr1 Chr1:34335058 0 34335058
-Chr1 Chr1:34422874 0 34422874
-Chr1 Chr1:34429355 0 34429355
-Chr1 Chr1:34435745 0 34435745
-Chr1 Chr1:34446335 0 34446335
-Chr1 Chr1:34461102 0 34461102
-Chr1 Chr1:34511690 0 34511690
-Chr1 Chr1:34512803 0 34512803
-Chr1 Chr1:34514240 0 34514240
-Chr1 Chr1:34546434 0 34546434
-Chr1 Chr1:34546490 0 34546490
-Chr1 Chr1:34550321 0 34550321
-Chr1 Chr1:34551808 0 34551808
-Chr1 Chr1:34568945 0 34568945
-Chr1 Chr1:34571150 0 34571150
-Chr1 Chr1:34588553 0 34588553
-Chr1 Chr1:34600584 0 34600584
-Chr1 Chr1:34680506 0 34680506
-Chr1 Chr1:34707422 0 34707422
-Chr1 Chr1:34712326 0 34712326
-Chr1 Chr1:34729316 0 34729316
-Chr1 Chr1:34731317 0 34731317
-Chr1 Chr1:34739250 0 34739250
-Chr1 Chr1:34745122 0 34745122
-Chr1 Chr1:34745238 0 34745238
-Chr1 Chr1:34762181 0 34762181
-Chr1 Chr1:34762285 0 34762285
-Chr1 Chr1:34815236 0 34815236
-Chr1 Chr1:34815295 0 34815295
-Chr1 Chr1:34819411 0 34819411
-Chr1 Chr1:34846870 0 34846870
-Chr1 Chr1:34890450 0 34890450
-Chr1 Chr1:34896321 0 34896321
-Chr1 Chr1:34939106 0 34939106
-Chr1 Chr1:34965744 0 34965744
-Chr1 Chr1:34983193 0 34983193
-Chr1 Chr1:35001790 0 35001790
-Chr1 Chr1:35007259 0 35007259
-Chr1 Chr1:35008760 0 35008760
-Chr1 Chr1:35061621 0 35061621
-Chr1 Chr1:35086602 0 35086602
-Chr1 Chr1:35094231 0 35094231
-Chr1 Chr1:35108977 0 35108977
-Chr1 Chr1:35128150 0 35128150
-Chr1 Chr1:35144020 0 35144020
-Chr1 Chr1:35149305 0 35149305
-Chr1 Chr1:35180600 0 35180600
-Chr1 Chr1:35193967 0 35193967
-Chr1 Chr1:35200915 0 35200915
-Chr1 Chr1:35307114 0 35307114
-Chr1 Chr1:35347362 0 35347362
-Chr1 Chr1:35400756 0 35400756
-Chr1 Chr1:35596032 0 35596032
-Chr1 Chr1:35608865 0 35608865
-Chr1 Chr1:35638872 0 35638872
-Chr1 Chr1:35638984 0 35638984
-Chr1 Chr1:35742358 0 35742358
-Chr1 Chr1:35747789 0 35747789
-Chr1 Chr1:35958247 0 35958247
-Chr1 Chr1:35963677 0 35963677
-Chr1 Chr1:35967289 0 35967289
-Chr1 Chr1:36013936 0 36013936
-Chr1 Chr1:36029152 0 36029152
-Chr1 Chr1:36131798 0 36131798
-Chr1 Chr1:36132244 0 36132244
-Chr1 Chr1:36132263 0 36132263
-Chr1 Chr1:36135270 0 36135270
-Chr1 Chr1:36143155 0 36143155
-Chr1 Chr1:36231871 0 36231871
-Chr1 Chr1:36300575 0 36300575
-Chr1 Chr1:36370973 0 36370973
-Chr1 Chr1:36621359 0 36621359
-Chr1 Chr1:36696208 0 36696208
-Chr1 Chr1:36718312 0 36718312
-Chr1 Chr1:36718341 0 36718341
-Chr1 Chr1:36720865 0 36720865
-Chr1 Chr1:36740809 0 36740809
-Chr1 Chr1:36882749 0 36882749
-Chr1 Chr1:36882752 0 36882752
-Chr1 Chr1:36956337 0 36956337
-Chr1 Chr1:37046646 0 37046646
-Chr1 Chr1:37064309 0 37064309
-Chr1 Chr1:37137468 0 37137468
-Chr1 Chr1:37146622 0 37146622
-Chr1 Chr1:37189534 0 37189534
-Chr1 Chr1:37233741 0 37233741
-Chr1 Chr1:37583011 0 37583011
-Chr1 Chr1:37677255 0 37677255
-Chr1 Chr1:37712681 0 37712681
-Chr1 Chr1:37719614 0 37719614
-Chr1 Chr1:37723312 0 37723312
-Chr1 Chr1:37733048 0 37733048
-Chr1 Chr1:37764798 0 37764798
-Chr1 Chr1:37879500 0 37879500
-Chr1 Chr1:37975727 0 37975727
-Chr1 Chr1:38176391 0 38176391
-Chr1 Chr1:38233881 0 38233881
-Chr1 Chr1:38434703 0 38434703
-Chr1 Chr1:38434765 0 38434765
-Chr1 Chr1:38501100 0 38501100
-Chr1 Chr1:38515009 0 38515009
-Chr1 Chr1:38515041 0 38515041
-Chr1 Chr1:38515044 0 38515044
-Chr1 Chr1:38560569 0 38560569
-Chr1 Chr1:38654332 0 38654332
-Chr1 Chr1:38804627 0 38804627
-Chr1 Chr1:38808462 0 38808462
-Chr1 Chr1:38808537 0 38808537
-Chr1 Chr1:38836845 0 38836845
-Chr1 Chr1:38836848 0 38836848
-Chr1 Chr1:38853248 0 38853248
-Chr1 Chr1:38897705 0 38897705
-Chr1 Chr1:38904917 0 38904917
-Chr1 Chr1:38946119 0 38946119
-Chr1 Chr1:38960837 0 38960837
-Chr1 Chr1:38968039 0 38968039
-Chr1 Chr1:38970709 0 38970709
-Chr1 Chr1:38970729 0 38970729
-Chr1 Chr1:38996984 0 38996984
-Chr1 Chr1:39006552 0 39006552
-Chr1 Chr1:39021617 0 39021617
-Chr1 Chr1:39021775 0 39021775
-Chr1 Chr1:39021790 0 39021790
-Chr1 Chr1:39022928 0 39022928
-Chr1 Chr1:39029042 0 39029042
-Chr1 Chr1:39041227 0 39041227
-Chr1 Chr1:39069588 0 39069588
-Chr1 Chr1:39073687 0 39073687
-Chr1 Chr1:39073738 0 39073738
-Chr1 Chr1:39097844 0 39097844
-Chr1 Chr1:39101078 0 39101078
-Chr1 Chr1:39102140 0 39102140
-Chr1 Chr1:39102194 0 39102194
-Chr1 Chr1:39102232 0 39102232
-Chr1 Chr1:39102838 0 39102838
-Chr1 Chr1:39102892 0 39102892
-Chr1 Chr1:39108593 0 39108593
-Chr1 Chr1:39128415 0 39128415
-Chr1 Chr1:39133282 0 39133282
-Chr1 Chr1:39133285 0 39133285
-Chr1 Chr1:39134928 0 39134928
-Chr1 Chr1:39137464 0 39137464
-Chr1 Chr1:39140488 0 39140488
-Chr1 Chr1:39140501 0 39140501
-Chr1 Chr1:39140562 0 39140562
-Chr1 Chr1:39143929 0 39143929
-Chr1 Chr1:39143942 0 39143942
-Chr1 Chr1:39163136 0 39163136
-Chr1 Chr1:39168222 0 39168222
-Chr1 Chr1:39168248 0 39168248
-Chr1 Chr1:39176048 0 39176048
-Chr1 Chr1:39176083 0 39176083
-Chr1 Chr1:39176096 0 39176096
-Chr1 Chr1:39191305 0 39191305
-Chr1 Chr1:39200362 0 39200362
-Chr1 Chr1:39209686 0 39209686
-Chr1 Chr1:39245265 0 39245265
-Chr1 Chr1:39254110 0 39254110
-Chr1 Chr1:39256552 0 39256552
-Chr1 Chr1:39257845 0 39257845
-Chr1 Chr1:39260372 0 39260372
-Chr1 Chr1:39276276 0 39276276
-Chr1 Chr1:39282424 0 39282424
-Chr1 Chr1:39292491 0 39292491
-Chr1 Chr1:39300391 0 39300391
-Chr1 Chr1:39305750 0 39305750
-Chr1 Chr1:39305832 0 39305832
-Chr1 Chr1:39305833 0 39305833
-Chr1 Chr1:39416338 0 39416338
-Chr1 Chr1:39422113 0 39422113
-Chr1 Chr1:39422116 0 39422116
-Chr1 Chr1:39447228 0 39447228
-Chr1 Chr1:39448870 0 39448870
-Chr1 Chr1:39449861 0 39449861
-Chr1 Chr1:39466839 0 39466839
-Chr1 Chr1:39468037 0 39468037
-Chr1 Chr1:39470931 0 39470931
-Chr1 Chr1:39470949 0 39470949
-Chr1 Chr1:39472460 0 39472460
-Chr1 Chr1:39491532 0 39491532
-Chr1 Chr1:39506634 0 39506634
-Chr1 Chr1:39506654 0 39506654
-Chr1 Chr1:39511185 0 39511185
-Chr1 Chr1:39537504 0 39537504
-Chr1 Chr1:39553116 0 39553116
-Chr1 Chr1:39553118 0 39553118
-Chr1 Chr1:39554204 0 39554204
-Chr1 Chr1:39562746 0 39562746
-Chr1 Chr1:39562839 0 39562839
-Chr1 Chr1:39563425 0 39563425
-Chr1 Chr1:39563606 0 39563606
-Chr1 Chr1:39589518 0 39589518
-Chr1 Chr1:39605046 0 39605046
-Chr1 Chr1:39614442 0 39614442
-Chr1 Chr1:39614444 0 39614444
-Chr1 Chr1:39656022 0 39656022
-Chr1 Chr1:39663360 0 39663360
-Chr1 Chr1:39673624 0 39673624
-Chr1 Chr1:39681600 0 39681600
-Chr1 Chr1:39681665 0 39681665
-Chr1 Chr1:39700372 0 39700372
-Chr1 Chr1:39734217 0 39734217
-Chr1 Chr1:39734228 0 39734228
-Chr1 Chr1:39740660 0 39740660
-Chr1 Chr1:39780551 0 39780551
-Chr1 Chr1:39783176 0 39783176
-Chr1 Chr1:39791872 0 39791872
-Chr1 Chr1:39791875 0 39791875
-Chr1 Chr1:39818103 0 39818103
-Chr1 Chr1:39839114 0 39839114
-Chr1 Chr1:39839354 0 39839354
-Chr1 Chr1:39880825 0 39880825
-Chr1 Chr1:39912134 0 39912134
-Chr1 Chr1:39914173 0 39914173
-Chr1 Chr1:40019475 0 40019475
-Chr1 Chr1:40020184 0 40020184
-Chr1 Chr1:40047201 0 40047201
-Chr1 Chr1:40070589 0 40070589
-Chr1 Chr1:40070640 0 40070640
-Chr1 Chr1:40097004 0 40097004
-Chr1 Chr1:40102224 0 40102224
-Chr1 Chr1:40124493 0 40124493
-Chr1 Chr1:40162664 0 40162664
-Chr1 Chr1:40169490 0 40169490
-Chr1 Chr1:40169725 0 40169725
-Chr1 Chr1:40229425 0 40229425
-Chr1 Chr1:40256509 0 40256509
-Chr1 Chr1:40264576 0 40264576
-Chr1 Chr1:40278864 0 40278864
-Chr1 Chr1:40279140 0 40279140
-Chr1 Chr1:40328142 0 40328142
-Chr1 Chr1:40331205 0 40331205
-Chr1 Chr1:40331613 0 40331613
-Chr1 Chr1:40383282 0 40383282
-Chr1 Chr1:40411351 0 40411351
-Chr1 Chr1:40412326 0 40412326
-Chr1 Chr1:40412384 0 40412384
-Chr1 Chr1:40425786 0 40425786
-Chr1 Chr1:40425980 0 40425980
-Chr1 Chr1:40430300 0 40430300
-Chr1 Chr1:40431468 0 40431468
-Chr1 Chr1:40443092 0 40443092
-Chr1 Chr1:40466784 0 40466784
-Chr1 Chr1:40466808 0 40466808
-Chr1 Chr1:40467144 0 40467144
-Chr1 Chr1:40490613 0 40490613
-Chr1 Chr1:40497209 0 40497209
-Chr1 Chr1:40527519 0 40527519
-Chr1 Chr1:40541490 0 40541490
-Chr1 Chr1:40566515 0 40566515
-Chr1 Chr1:40566534 0 40566534
-Chr1 Chr1:40566620 0 40566620
-Chr1 Chr1:40567925 0 40567925
-Chr1 Chr1:40567928 0 40567928
-Chr1 Chr1:40567983 0 40567983
-Chr1 Chr1:40584846 0 40584846
-Chr1 Chr1:40587621 0 40587621
-Chr1 Chr1:40610397 0 40610397
-Chr1 Chr1:40618489 0 40618489
-Chr1 Chr1:40663740 0 40663740
-Chr1 Chr1:40670043 0 40670043
-Chr1 Chr1:40671084 0 40671084
-Chr1 Chr1:40696256 0 40696256
-Chr1 Chr1:40701640 0 40701640
-Chr1 Chr1:40715751 0 40715751
-Chr1 Chr1:40720697 0 40720697
-Chr1 Chr1:40732591 0 40732591
-Chr1 Chr1:40734965 0 40734965
-Chr1 Chr1:40737721 0 40737721
-Chr1 Chr1:40754319 0 40754319
-Chr1 Chr1:40758533 0 40758533
-Chr1 Chr1:40763346 0 40763346
-Chr1 Chr1:40779806 0 40779806
-Chr1 Chr1:40788831 0 40788831
-Chr1 Chr1:40799111 0 40799111
-Chr1 Chr1:40799114 0 40799114
-Chr1 Chr1:40817991 0 40817991
-Chr1 Chr1:40822307 0 40822307
-Chr1 Chr1:40839200 0 40839200
-Chr1 Chr1:40839223 0 40839223
-Chr1 Chr1:40840213 0 40840213
-Chr1 Chr1:40858290 0 40858290
-Chr1 Chr1:40858295 0 40858295
-Chr1 Chr1:40894634 0 40894634
-Chr1 Chr1:40898694 0 40898694
-Chr1 Chr1:40925279 0 40925279
-Chr1 Chr1:40929959 0 40929959
-Chr1 Chr1:40960080 0 40960080
-Chr1 Chr1:40960462 0 40960462
-Chr1 Chr1:41004912 0 41004912
-Chr1 Chr1:41011386 0 41011386
-Chr1 Chr1:41019437 0 41019437
-Chr1 Chr1:41019737 0 41019737
-Chr1 Chr1:41067201 0 41067201
-Chr1 Chr1:41083723 0 41083723
-Chr1 Chr1:41090716 0 41090716
-Chr1 Chr1:41100340 0 41100340
-Chr1 Chr1:41108816 0 41108816
-Chr1 Chr1:41108887 0 41108887
-Chr1 Chr1:41109440 0 41109440
-Chr1 Chr1:41111944 0 41111944
-Chr1 Chr1:41111947 0 41111947
-Chr1 Chr1:41118560 0 41118560
-Chr1 Chr1:41143869 0 41143869
-Chr1 Chr1:41147615 0 41147615
-Chr1 Chr1:41177801 0 41177801
-Chr1 Chr1:41184713 0 41184713
-Chr1 Chr1:41190745 0 41190745
-Chr1 Chr1:41190886 0 41190886
-Chr1 Chr1:41198840 0 41198840
-Chr1 Chr1:41203547 0 41203547
-Chr1 Chr1:41203607 0 41203607
-Chr1 Chr1:41207247 0 41207247
-Chr1 Chr1:41212475 0 41212475
-Chr1 Chr1:41212487 0 41212487
-Chr1 Chr1:41212533 0 41212533
-Chr1 Chr1:41230880 0 41230880
-Chr1 Chr1:41232475 0 41232475
-Chr1 Chr1:41244079 0 41244079
-Chr1 Chr1:41244197 0 41244197
-Chr1 Chr1:41244212 0 41244212
-Chr1 Chr1:41244216 0 41244216
-Chr1 Chr1:41249220 0 41249220
-Chr1 Chr1:41252326 0 41252326
-Chr1 Chr1:41273858 0 41273858
-Chr1 Chr1:41304331 0 41304331
-Chr1 Chr1:41310422 0 41310422
-Chr1 Chr1:41310467 0 41310467
-Chr1 Chr1:41340158 0 41340158
-Chr1 Chr1:41340177 0 41340177
-Chr1 Chr1:41349818 0 41349818
-Chr1 Chr1:41349829 0 41349829
-Chr1 Chr1:41385420 0 41385420
-Chr1 Chr1:41400248 0 41400248
-Chr1 Chr1:41400271 0 41400271
-Chr1 Chr1:41490826 0 41490826
-Chr1 Chr1:41512212 0 41512212
-Chr1 Chr1:41512215 0 41512215
-Chr1 Chr1:41512261 0 41512261
-Chr1 Chr1:41637415 0 41637415
-Chr1 Chr1:41670025 0 41670025
-Chr1 Chr1:41693420 0 41693420
-Chr1 Chr1:41696631 0 41696631
-Chr1 Chr1:41710111 0 41710111
-Chr1 Chr1:41714865 0 41714865
-Chr1 Chr1:41714920 0 41714920
-Chr1 Chr1:41733418 0 41733418
-Chr1 Chr1:41742929 0 41742929
-Chr1 Chr1:41742940 0 41742940
-Chr1 Chr1:41743485 0 41743485
-Chr1 Chr1:41768676 0 41768676
-Chr1 Chr1:41828250 0 41828250
-Chr1 Chr1:41839769 0 41839769
-Chr1 Chr1:41851283 0 41851283
-Chr1 Chr1:41870526 0 41870526
-Chr1 Chr1:41895414 0 41895414
-Chr1 Chr1:41914765 0 41914765
-Chr1 Chr1:41921319 0 41921319
-Chr1 Chr1:41939834 0 41939834
-Chr1 Chr1:41940779 0 41940779
-Chr1 Chr1:41942046 0 41942046
-Chr1 Chr1:41945638 0 41945638
-Chr1 Chr1:41954934 0 41954934
-Chr1 Chr1:41958052 0 41958052
-Chr1 Chr1:41961218 0 41961218
-Chr1 Chr1:41961221 0 41961221
-Chr1 Chr1:41965592 0 41965592
-Chr1 Chr1:41965659 0 41965659
-Chr1 Chr1:41968928 0 41968928
-Chr1 Chr1:41968936 0 41968936
-Chr1 Chr1:41970211 0 41970211
-Chr1 Chr1:41998459 0 41998459
-Chr1 Chr1:42001355 0 42001355
-Chr1 Chr1:42047135 0 42047135
-Chr1 Chr1:42047157 0 42047157
-Chr1 Chr1:42061862 0 42061862
-Chr1 Chr1:42063149 0 42063149
-Chr1 Chr1:42081350 0 42081350
-Chr1 Chr1:42081405 0 42081405
-Chr1 Chr1:42088625 0 42088625
-Chr1 Chr1:42089983 0 42089983
-Chr1 Chr1:42097607 0 42097607
-Chr1 Chr1:42106144 0 42106144
-Chr1 Chr1:42138453 0 42138453
-Chr1 Chr1:42150639 0 42150639
-Chr1 Chr1:42155417 0 42155417
-Chr1 Chr1:42156013 0 42156013
-Chr1 Chr1:42164107 0 42164107
-Chr1 Chr1:42165734 0 42165734
-Chr1 Chr1:42169797 0 42169797
-Chr1 Chr1:42169819 0 42169819
-Chr1 Chr1:42187340 0 42187340
-Chr1 Chr1:42192288 0 42192288
-Chr1 Chr1:42196386 0 42196386
-Chr1 Chr1:42227135 0 42227135
-Chr1 Chr1:42229251 0 42229251
-Chr1 Chr1:42231379 0 42231379
-Chr1 Chr1:42242069 0 42242069
-Chr1 Chr1:42244104 0 42244104
-Chr1 Chr1:42276315 0 42276315
-Chr1 Chr1:42301791 0 42301791
-Chr1 Chr1:42302347 0 42302347
-Chr1 Chr1:42324275 0 42324275
-Chr1 Chr1:42332621 0 42332621
-Chr1 Chr1:42352040 0 42352040
-Chr1 Chr1:42352085 0 42352085
-Chr1 Chr1:42352093 0 42352093
-Chr1 Chr1:42352397 0 42352397
-Chr1 Chr1:42354188 0 42354188
-Chr1 Chr1:42354191 0 42354191
-Chr1 Chr1:42357534 0 42357534
-Chr1 Chr1:42357591 0 42357591
-Chr1 Chr1:42367404 0 42367404
-Chr1 Chr1:42367442 0 42367442
-Chr1 Chr1:42419046 0 42419046
-Chr1 Chr1:42419769 0 42419769
-Chr1 Chr1:42421769 0 42421769
-Chr1 Chr1:42423110 0 42423110
-Chr1 Chr1:42427556 0 42427556
-Chr1 Chr1:42460597 0 42460597
-Chr1 Chr1:42460615 0 42460615
-Chr1 Chr1:42469025 0 42469025
-Chr1 Chr1:42471750 0 42471750
-Chr1 Chr1:42479925 0 42479925
-Chr1 Chr1:42487487 0 42487487
-Chr1 Chr1:42487514 0 42487514
-Chr1 Chr1:42548763 0 42548763
-Chr1 Chr1:42583428 0 42583428
-Chr1 Chr1:42586452 0 42586452
-Chr1 Chr1:42594255 0 42594255
-Chr1 Chr1:42596478 0 42596478
-Chr1 Chr1:42602822 0 42602822
-Chr1 Chr1:42602885 0 42602885
-Chr1 Chr1:42610308 0 42610308
-Chr1 Chr1:42612885 0 42612885
-Chr1 Chr1:42616231 0 42616231
-Chr1 Chr1:42620187 0 42620187
-Chr1 Chr1:42620190 0 42620190
-Chr1 Chr1:42620878 0 42620878
-Chr1 Chr1:42620881 0 42620881
-Chr1 Chr1:42631741 0 42631741
-Chr1 Chr1:42634538 0 42634538
-Chr1 Chr1:42664013 0 42664013
-Chr1 Chr1:42665624 0 42665624
-Chr1 Chr1:42666354 0 42666354
-Chr1 Chr1:42669650 0 42669650
-Chr1 Chr1:42669653 0 42669653
-Chr1 Chr1:42673304 0 42673304
-Chr1 Chr1:42674707 0 42674707
-Chr1 Chr1:42682058 0 42682058
-Chr1 Chr1:42682061 0 42682061
-Chr1 Chr1:42690508 0 42690508
-Chr1 Chr1:42706257 0 42706257
-Chr1 Chr1:42711112 0 42711112
-Chr1 Chr1:42762398 0 42762398
-Chr1 Chr1:42763941 0 42763941
-Chr1 Chr1:42763944 0 42763944
-Chr1 Chr1:42766241 0 42766241
-Chr1 Chr1:42777810 0 42777810
-Chr1 Chr1:42780446 0 42780446
-Chr1 Chr1:42825046 0 42825046
-Chr1 Chr1:42826857 0 42826857
-Chr1 Chr1:42880271 0 42880271
-Chr1 Chr1:42916070 0 42916070
-Chr1 Chr1:42916090 0 42916090
-Chr1 Chr1:42920553 0 42920553
-Chr1 Chr1:42928342 0 42928342
-Chr1 Chr1:42959997 0 42959997
-Chr1 Chr1:42968423 0 42968423
-Chr1 Chr1:43046967 0 43046967
-Chr1 Chr1:43048104 0 43048104
-Chr1 Chr1:43065469 0 43065469
-Chr1 Chr1:43068624 0 43068624
-Chr1 Chr1:43072051 0 43072051
-Chr1 Chr1:43073361 0 43073361
-Chr1 Chr1:43079457 0 43079457
-Chr1 Chr1:43079480 0 43079480
-Chr1 Chr1:43093204 0 43093204
-Chr1 Chr1:43100601 0 43100601
-Chr1 Chr1:43123958 0 43123958
-Chr1 Chr1:43132577 0 43132577
-Chr1 Chr1:43141118 0 43141118
-Chr1 Chr1:43141179 0 43141179
-Chr1 Chr1:43154143 0 43154143
-Chr1 Chr1:43158899 0 43158899
-Chr1 Chr1:43179527 0 43179527
-Chr1 Chr1:43214669 0 43214669
-Chr1 Chr1:43229591 0 43229591
-Chr1 Chr1:43249859 0 43249859
-Chr1 Chr1:43269458 0 43269458
diff -r 420b57c3c185 -r feb40a9a8eae MDSplot/test-data/input.ped
--- a/MDSplot/test-data/input.ped	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-IRAT112	1	0	0	1	1	1 1	4 4	2 2	1 1	4 4	2 2	1 1	1 1	4 4	4 4	1 1	1 1	4 4	1 1	1 1	1 1	4 4	4 4	3 3	4 4	2 2	1 1	3 3	1 1	1 1	4 4	1 1	1 1	2 2	1 1	4 4	1 1	1 1	4 4	2 2	4 4	1 1	1 1	4 4	3 3	1 1	1 1	1 1	1 1	4 4	2 2	1 1	4 4	4 4	4 4	4 4	1 1	4 4	4 4	4 4	4 4	4 4	1 1	1 1	4 4	4 4	3 3	4 4	1 1	1 1	4 4	1 1	1 1	4 4	1 1	4 4	1 1	3 3	4 4	4 4	2 2	1 1	4 4	1 1	4 4	1 1	4 4	1 1	1 1	4 4	1 1	4 4	1 1	4 4	4 4	1 1	4 4	2 2	2 2	4 4	2 2	1 1	1 1	3 3	3 3	4 4	4 4	3 3	3 3	2 2	1 1	2 2	4 4	1 1	1 1	4 4	1 1	4 4	1 1	4 4	4 4	4 4	4 4	3 3	1 1	4 4	4 4	4 4	1 1	1 1	4 4	4 4	1 1	4 4	1 1	1 1	3 3	4 4	4 4	3 3	4 4	1 1	3 3	3 3	3 3	1 1	2 2	4 4	1 1	1 1	1 1	4 4	4 4	1 1	4 4	1 1	1 1	4 4	4 4	3 3	2 2	4 4	4 4	1 1	3 3	2 2	3 3	4 4	1 1	4 4	4 4	4 4	2 2	3 3	1 1	1 1	1 1	1 1	4 4	1 1	1 1	4 4	1 1	1 1	1 1	1 1	4 4	4 4	4 4	1 1	2 2	4 4	4 4	1 1	4 4	2 2	3 3	3 3	1 1	3 3	4 4	1 1	3 3	4 4	1 1	4 4	2 2	2 2	1 1	1 1	4 4	4 4	4 4	2 2	1 1	1 1	4 4	1 1	4 4	1 1	4 4	4 4	1 1	4 4	4 4	4 4	4 4	4 4	4 4	1 1	1 1	1 1	1 1	1 1	2 2	2 2	4 4	1 1	4 4	1 1	4 4	1 1	3 3	3 3	1 1	4 4	1 1	2 2	4 4	4 4	1 1	4 4	1 1	4 4	4 4	1 1	1 1	4 4	4 4	1 1	3 3	4 4	2 2	1 1	4 4	4 4	1 1	1 1	4 4	4 4	1 1	1 1	1 1	1 1	4 4	1 1	2 2	1 1	2 2	4 4	2 2	3 3	4 4	1 1	4 4	2 2	4 4	4 4	1 1	4 4	1 1	4 4	4 4	4 4	1 1	4 4	4 4	1 1	1 1	1 1	4 4	1 1	3 3	4 4	4 4	1 1	2 2	1 1	4 4	4 4	1 1	1 1	1 1	4 4	4 4	1 1	4 4	2 2	4 4	3 3	4 4	1 1	4 4	1 1	4 4	1 1	1 1	1 1	2 2	4 4	1 1	3 3	2 2	2 2	3 3	3 3	1 1	2 2	1 1	3 3	1 1	4 4	4 4	4 4	1 1	4 4	2 2	2 2	1 1	4 4	4 4	1 1	2 2	4 4	1 1	4 4	1 1	2 2	1 1	2 2	1 1	4 4	1 1	1 1	4 4	1 1	1 1	1 1	4 4	3 3	4 4	2 2	1 1	1 1	4 4	1 1	4 4	4 4	1 1	1 1	1 1	4 4	1 1	4 4	1 1	1 1	3 3	1 1	4 4	3 3	2 2	1 1	4 4	4 4	3 3	1 1	2 2	2 2	1 1	3 3	4 4	1 1	1 1	3 3	1 1	4 4	4 4	1 1	1 1	4 4	1 1	1 1	1 1	4 4	1 1	1 1	4 4	1 1	1 1	4 4	2 2	4 4	4 4	3 3	4 4	1 1	1 1	4 4	1 1	1 1	2 2	4 4	2 2	2 2	3 3	4 4	3 3	2 2	1 1	1 1	2 2	1 1	4 4	3 3	2 2	4 4	1 1	1 1	1 1	4 4	4 4	1 1	4 4	1 1	4 4	4 4	2 2	1 1	4 4	4 4	1 1	1 1	1 1	3 3	1 1	2 2	1 1	1 1	2 2	1 1	1 1	2 2	1 1	2 2	3 3	4 4	1 1	2 2	1 1	2 2	4 4	4 4	1 1	1 1	4 4	3 3	1 1	4 4	1 1	4 4	1 1	4 4	4 4	3 3	4 4	3 3	4 4	3 3	1 1	4 4	1 1	1 1	4 4	1 1	4 4	4 4	4 4	1 1	4 4	4 4	1 1	4 4	1 1	1 1	1 1	1 1	4 4	3 3	4 4	1 1	4 4	3 3	4 4	4 4	4 4	1 1	4 4	4 4	3 3	4 4	3 3	4 4	1 1	1 1	4 4	1 1	1 1	4 4	1 1	1 1	1 1	4 4	4 4	1 1	1 1	4 4	2 2	4 4	2 2	1 1	3 3	1 1	4 4	1 1	2 2	1 1	3 3	2 2	4 4	4 4	1 1	4 4	3 3	4 4	4 4	4 4	1 1	3 3	4 4	4 4	4 4	3 3	4 4	4 4	1 1	2 2	1 1	4 4	4 4	2 2	1 1	1 1	4 4	4 4	1 1	4 4	2 2	3 3	2 2	1 1	1 1	1 1	1 1	4 4	1 1	4 4	1 1	3 3	2 2	1 1	3 3	4 4	2 2	2 2	4 4	2 2	2 2	4 4	1 1	1 1	1 1	1 1	1 1	1 1	1 1	3 3	4 4	1 1	1 1	1 1	3 3	1 1	4 4	4 4	1 1	4 4	1 1	4 4	1 1	4 4	3 3	1 1	4 4	3 3	4 4	1 1	4 4	4 4	4 4	2 2	4 4	1 1	4 4	4 4	1 1	4 4	4 4	2 2	1 1	4 4	3 3	4 4	1 1	3 3	1 1	4 4	4 4	1 1	1 1	4 4	4 4	1 1	3 3	1 1	4 4	1 1	2 2	4 4	1 1	4 4	4 4	4 4	1 1	2 2	4 4	1 1	3 3	1 1	4 4	4 4	1 1	4 4	1 1	4 4	4 4	4 4	1 1	4 4	1 1	4 4	1 1	1 1	2 2	4 4	1 1	4 4	4 4	1 1	1 1	3 3	1 1	1 1	1 1	4 4	1 1	3 3	2 2	2 2	2 2	3 3	1 1	1 1	1 1	1 1	1 1	4 4	4 4	1 1	1 1	1 1	1 1	1 1	1 1	4 4	1 1	4 4	1 1	4 4	1 1	4 4	4 4	1 1	3 3	4 4	3 3	2 2	1 1	1 1	1 1	4 4	1 1	4 4	1 1	4 4	1 1	1 1	3 3	4 4	4 4	3 3	4 4	3 3	3 3	3 3	1 1	1 1	1 1	1 1	4 4	4 4	4 4	2 2	1 1	4 4	1 1	4 4	3 3	3 3	3 3	4 4	3 3	4 4	4 4	4 4	4 4	4 4	1 1	4 4	4 4	1 1	4 4	4 4	1 1	1 1	3 3	1 1	3 3	4 4	4 4	1 1	1 1	1 1	1 1	1 1	1 1	4 4	4 4	4 4	4 4	4 4	2 2	1 1	4 4	3 3	4 4	1 1	4 4	1 1	1 1	4 4	4 4	1 1	4 4	2 2	1 1	3 3	1 1	4 4	1 1	1 1	4 4	4 4	1 1	4 4	1 1	1 1	1 1	1 1	2 2	4 4	1 1	4 4	1 1	4 4	1 1	4 4	4 4	1 1	1 1	4 4	4 4	4 4	4 4	4 4	1 1	3 3	1 1	1 1	1 1	1 1	4 4	1 1	4 4	1 1	4 4	3 3	1 1	1 1	1 1	4 4	4 4	1 1	1 1	1 1	4 4	1 1	4 4	4 4	4 4	1 1	1 1	1 1	1 1	4 4	1 1	4 4	4 4	3 3	1 1	1 1	4 4	3 3	1 1	1 1	1 1	1 1	1 1	4 4	1 1	1 1	4 4	1 1	1 1	1 1	4 4	4 4	1 1	2 2	1 1	4 4	4 4	4 4	3 3	1 1	2 2	1 1	1 1	4 4	4 4	2 2	1 1	1 1	2 2	4 4	1 1	3 3	4 4	1 1	1 1	4 4	1 1	4 4	1 1	4 4	3 3	3 3	2 2	3 3	4 4	1 1	1 1	4 4	1 1	4 4	1 1	4 4	4 4	4 4	1 1	3 3	1 1	4 4	4 4	1 1	4 4	1 1	4 4	1 1	4 4	1 1	4 4	1 1	1 1	4 4	2 2	1 1	4 4	4 4	4 4	1 1	4 4	4 4	4 4	1 1	4 4	4 4	2 2	4 4	1 1	3 3	3 3	4 4	1 1	1 1	1 1	1 1	4 4	2 2	3 3	1 1	3 3	1 1	4 4	4 4	2 2	4 4	4 4	1 1	3 3	1 1	4 4	1 1	4 4	1 1	4 4	3 3	4 4	3 3	1 1	4 4	1 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4	1 1	4 4	4 4	2 2	3 3	1 1	1 1	4 4	4 4	3 3	2 2	1 1	2 2	2 2	1 1	3 3	2 2	1 1	1 1	4 4	1 1	1 1	4 4	4 4	4 4	1 1	1 1	4 4	1 1	3 3	1 1	3 3	4 4	1 1	4 4	1 1	4 4	1 1	4 4	1 1	4 4	3 3	2 2	4 4	1 1	4 4	1 1	4 4	2 2	3 3	4 4	1 1	4 4	1 1	4 4	2 2	4 4	4 4	1 1	4 4	4 4	4 4	4 4	2 2	1 1	4 4	4 4	4 4	1 1	1 1	1 1	4 4	4 4	1 1	1 1	4 4	1 1	1 1	1 1	4 4	1 1	4 4	2 2	1 1	1 1	4 4	1 1	4 4	3 3	1 1	4 4	1 1	4 4	1 1	1 1	4 4	1 1	1 1	3 3	2 2	4 4	4 4	4 4	4 4	1 1	4 4	2 2	1 1	4 4	1 1	2 2	4 4	1 1	3 3	1 1	1 1	3 3	1 1	1 1	1 1	4 4	1 1	1 1	4 4	3 3	3 3	2 2	4 4	4 4	4 4	1 1	4 4	4 4	4 4	2 2	4 4	4 4	1 1	4 4	4 4	3 3	1 1	3 3	4 4	3 3	1 1	1 1	4 4	4 4	1 1	4 4	4 4	1 1	1 1	2 2	4 4	2 2	2 2	1 1	4 4	4 4	2 2	4 4	4 4	4 4	3 3	1 1	3 3	3 3	3 3	4 4	4 4	2 2	1 1	2 2	4 4	1 1	4 4	2 2	1 1	1 1	4 4	1 1	1 1	2 2	1 1	3 3	1 1	4 4	1 1	4 4	1 1	2 2	3 3	4 4	1 1	3 3	4 4	1 1	4 4	1 1	1 1	1 1	2 2	1 1	3 3	3 3	1 1	4 4	1 1	1 1	1 1	4 4	1 1	2 2	4 4	2 2	4 4	1 1	2 2	4 4	1 1	4 4	4 4	4 4	2 2	1 1	4 4	4 4	1 1	4 4	1 1	4 4	1 1	3 3	1 1	4 4	4 4	3 3	3 3	1 1	1 1	1 1	4 4	4 4	4 4	2 2	1 1	1 1	4 4	1 1	3 3	3 3	2 2	1 1	4 4	3 3	4 4	4 4	1 1	4 4	1 1	4 4	4 4	4 4	2 2	1 1	4 4	1 1	4 4	4 4	1 1	4 4	4 4	1 1	1 1	4 4	1 1	2 2	4 4	4 4	4 4	1 1	4 4	4 4	4 4	2 2	3 3	4 4	4 4	1 1	3 3	2 2	2 2	1 1	1 1	1 1	4 4	2 2	1 1	1 1	4 4	1 1	2 2	1 1	3 3	1 1	1 1	4 4	4 4	2 2	4 4	3 3	3 3	1 1	2 2	2 2	4 4	2 2	3 3	1 1	1 1	3 3	3 3	1 1	4 4	1 1	1 1	3 3	4 4	2 2	4 4	4 4	3 3	2 2	3 3	3 3	4 4	4 4	2 2	2 2	4 4	2 2	4 4	4 4	4 4	2 2	4 4	4 4	1 1	4 4	4 4	3 3	1 1	1 1	4 4	1 1	4 4	1 1	4 4	4 4	4 4	1 1	1 1	1 1	4 4	1 1	1 1	3 3	1 1	1 1	3 3	1 1	4 4	3 3	3 3	1 1	4 4	1 1	3 3	3 3	3 3	1 1	4 4	4 4	1 1	4 4	3 3	4 4	4 4	3 3	4 4	4 4	1 1	4 4	4 4	4 4	1 1	4 4	3 3	4 4	4 4	1 1	3 3	4 4	1 1	1 1	2 2	4 4	3 3	2 2	3 3	1 1	1 1	4 4	4 4	4 4	3 3	2 2	4 4	1 1	1 1	4 4	4 4	1 1	1 1	2 2	1 1	1 1	4 4	1 1	3 3	1 1	3 3	1 1	1 1	1 1	4 4	1 1	4 4	1 1	1 1	4 4	4 4	1 1	1 1	4 4	4 4	4 4	4 4	1 1	4 4	3 3	1 1	3 3	3 3	1 1	3 3	4 4	4 4	4 4	1 1	4 4	4 4	4 4	1 1	1 1	4 4	4 4	4 4	4 4	2 2	4 4	2 2	4 4	2 2	1 1	3 3	1 1	1 1	1 1	1 1	1 1	1 1	4 4	4 4	4 4	4 4	4 4	2 2	1 1	2 2	4 4	1 1	1 1	1 1	3 3	1 1	1 1	1 1	1 1	4 4	1 1	2 2	3 3	4 4	1 1	4 4	3 3	3 3	3 3	1 1	4 4	3 3	3 3	4 4	1 1	1 1	1 1	1 1	1 1	4 4	4 4	2 2	4 4	1 1	4 4	4 4	4 4	1 1	1 1	1 1	4 4	1 1	2 2	4 4	1 1	4 4	1 1	1 1	1 1	1 1	1 1	4 4	4 4	2 2	4 4	4 4	3 3	4 4	4 4	1 1	1 1	4 4	1 1	4 4	4 4	4 4	1 1	1 1	4 4	1 1	2 2	1 1	4 4	4 4	4 4	1 1	2 2	4 4	1 1	1 1	3 3	4 4	1 1	4 4	1 1	4 4	1 1	4 4	1 1	4 4	1 1	1 1	4 4	4 4	2 2	4 4	4 4	3 3	1 1	1 1	4 4	2 2	1 1	3 3	1 1	1 1	4 4	4 4	3 3	4 4	1 1	4 4	1 1	1 1	4 4	4 4	2 2	3 3	4 4	2 2	4 4	4 4	2 2	1 1	2 2	1 1	2 2	1 1	1 1	4 4	1 1	1 1	4 4	3 3	1 1	4 4	1 1	1 1	4 4	4 4	1 1	4 4	2 2	1 1	1 1	4 4	1 1	1 1	1 1	4 4	1 1	4 4	4 4	3 3	4 4	2 2	1 1	2 2	4 4	4 4	1 1	1 1	1 1	4 4	1 1	1 1	1 1	1 1	4 4	2 2	1 1	1 1	4 4	4 4	1 1	4 4	2 2	3 3	1 1	1 1	4 4	4 4	1 1	2 2	4 4	1 1	1 1	2 2	1 1	4 4	4 4	4 4	4 4	3 3	3 3	4 4	4 4	2 2	4 4	1 1	1 1	1 1	4 4	1 1	4 4	4 4	1 1	4 4	3 3	1 1	1 1	1 1	1 1	1 1	1 1	4 4	3 3	4 4	3 3	4 4	4 4	1 1	3 3	4 4	1 1	4 4	1 1	1 1	4 4	4 4	4 4	2 2	4 4	3 3	2 2	4 4	4 4	4 4	4 4	4 4	4 4	4 4	1 1	4 4	3 3	1 1	4 4	1 1	2 2	3 3	2 2	4 4	1 1	1 1	4 4	3 3	2 2	4 4	2 2	1 1	3 3	4 4	1 1	1 1	1 1	3 3	1 1	1 1	4 4	4 4	4 4	1 1	1 1	1 1	1 1	1 1	3 3	4 4	2 2	4 4	1 1	1 1	4 4	2 2	4 4	4 4	4 4	3 3	1 1	1 1	3 3	1 1	2 2	1 1	3 3	2 2	1 1	2 2	1 1	1 1	1 1	2 2	1 1	4 4	3 3	1 1	3 3	1 1	1 1	3 3	4 4	1 1	3 3	4 4	4 4	4 4	1 1	4 4	1 1	1 1	1 1	4 4	4 4	1 1	4 4	4 4	1 1	1 1	2 2	3 3	3 3	4 4	4 4	4 4	1 1	1 1	1 1	4 4	2 2	1 1	4 4	2 2	2 2	4 4	4 4	1 1	2 2	4 4	3 3	4 4	4 4	4 4	1 1	3 3	4 4	2 2	1 1	4 4	3 3	1 1	4 4	2 2	1 1	4 4	3 3	1 1	1 1	4 4	2 2	4 4	4 4	4 4	1 1	4 4	3 3	4 4	4 4	1 1	4 4	4 4	1 1	4 4	4 4	4 4	2 2	1 1	1 1	1 1	3 3	4 4	1 1	1 1	4 4	1 1	4 4	3 3	1 1	1 1	4 4	3 3	1 1	4 4	2 2	4 4	1 1	2 2	1 1	1 1	4 4	4 4	4 4	1 1	1 1	1 1	2 2	4 4	3 3	1 1	2 2	1 1	1 1	1 1	4 4	4 4	4 4	1 1	4 4	1 1	3 3	1 1	2 2	3 3	2 2	3 3	1 1	1 1	1 1	1 1	1 1	4 4	3 3	4 4	2 2	1 1	1 1	4 4	4 4	4 4	2 2	4 4	4 4	4 4	4 4	2 2	1 1	3 3	4 4	4 4	4 4	1 1	1 1	3 3	1 1	3 3	1 1	1 1	4 4	1 1	4 4	1 1	1 1	3 3	1 1	4 4	1 1	4 4	1 1	1 1	1 1	1 1	1 1	1 1	4 4	1 1	4 4	1 1	4 4	1 1	1 1	1 1	4 4	1 1	4 4	4 4	1 1	4 4	1 1	1 1	1 1	4 4	1 1	4 4	4 4	4 4	2 2	3 3	3 3	1 1	1 1	2 2	4 4	1 1	1 1	2 2	4 4	3 3	2 2	4 4	4 4	1 1	4 4	4 4	4 4	1 1	1 1	4 4
diff -r 420b57c3c185 -r feb40a9a8eae PedToFasta/Ped2Fasta.pl
--- a/PedToFasta/Ped2Fasta.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-
-#!/usr/bin/perl
-
-use strict;
-use Getopt::Long;
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-
-where <args> are:
-
-    -i, --in           <PED input>
-    -o, --out          <Fasta output>
-~;
-$usage .= "\n";
-
-my ($input,$out);
-
-
-
-GetOptions(
-	"in=s"          => \$input,
-	"out=s"          => \$out,
-);
-
-
-die $usage
-  if ( !$input || !$out);
-  
-
-my %IUPAC =
-(
-	'00'=> "?",
-	'AA'=> "A",
-	'CC'=> "C",
-	'GG'=> "G",
-	'TT'=> "T",
-        'AG'=> "R",
-        'GA'=> "R",
-        'CT'=> "Y",
-        'TC'=> "Y",
-        'TG'=> "K",
-        'GT'=> "K",
-        'CG'=> "S",
-        'GC'=> "S",
-        'AT'=> "W",
-        'TA'=> "W",
-        'AC'=> "M",
-        'CA'=> "M",
-);
-
-open(my $O,">$out");
-open(my $P,$input) or die "File does not exist";
-while(<$P>)
-{
-	my $line = $_;
-	$line =~s/\r//g;
-	$line =~s/\n//g;
-	my @infos = split("\t",$_);
-	my $ind = $infos[0];
-	print $O ">$ind\n";
-	for (my $i = 6; $i <= $#infos; $i= $i+2)
-	{
-		my $code = $infos[$i].$infos[$i+1];
-		my $letter = $IUPAC{$code};
-		print $O $letter;
-	}
-	print $O "\n";
-}
-close($P);
-close($O);
diff -r 420b57c3c185 -r feb40a9a8eae PedToFasta/pedToFasta.xml
--- a/PedToFasta/pedToFasta.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,171 +0,0 @@
-<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0">
-    
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
-    <description> Convert PED file to Fasta File </description>
-    
-    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
-    <requirements>
-        <requirement type="binary">perl</requirement>
-    </requirements>
-    
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
-    
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="perl">
-	Ped2Fasta.pl --in $filein --out $fileout 
-    </command>
-     
-    <!-- [REQUIRED] Input files and tool parameters -->
-    <inputs>
-	<param name="filein" type="data" format="txt" optional="false" label="PED input" />
-	<param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/>
-    </inputs>
-    
-    <!-- [REQUIRED] Output files -->
-    <outputs>
-	<data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" />
-    </outputs>
-    
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-        <test>
-         <param name="filein" value="sample.ped" />
-         <output name="fileout" file="result.fa" />
-        </test>
-    </tests>
-    
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
-
-.. class:: infomark
-
-**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
-
- | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
-.. class:: infomark
-
-**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. 
-
-.. class:: infomark
-
-**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr 
-
----------------------------------------------------
-
-=========
-Ped2Fasta
-=========
-
------------
-Description
------------
-
-  Convert PED file to Fasta File
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ========================== =======
-Name            output file(s)             format 
-=============== ========================== =======
-VCFtools Filter VCF file  	 	   VCF
-=============== ========================== =======
-
-
-**Downstream tool**
-
-=========== ========================== =======
-Name            input file(s)          format
-=========== ========================== =======
-Readseq     Fasta alignment	       fasta
-=========== ========================== =======
-
-
-----------
-Input file
-----------
-
-PED file
-	PED file usually from VCF tools
-
-----------
-Parameters
-----------
-
-Output file name
-	Prefix for the output fasta file
-
-------------
-Output files
-------------
-
-Fasta file
-	PED file conversion 
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-PED file
----------
-
-::
-
-	CATB1   CATB1   0       0       0       0       C       T       T       A       C       T       A       T       A       T       A       G       G       A
-
-Parameters
-==========
-
-Output name -> pedFile
-
-Output files
-============
-
-pedFile.fa
-----------
-
-::
-
-        YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY
-
-
-    </help>
-
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae PedToFasta/test-data/result.fa
--- a/PedToFasta/test-data/result.fa	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->CATB1
-YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRYYKKYWRMMWKYYSYYWRYSKRWRSRRRYYWYYYKYYKYRMKKRYYRKYKKWWKRYWRMYRSWYWYYWRRRRRYRSRKRWKWRKKYYYKMKYYYSWSSYRRKRMSKMKRRKRWRRRRYWRKKYWRKRYWWWKMRRRYRYYWWRYYRKKWYYRRWYYRKYSRRYWRYWSWYYWWKYYKYWYRMRYRYYRRWYYYSRYRRKRRYMMSSRRYYYSRMWRRRRSWRYYMYYRYWYRRSSYYMYRKKRKYWKRRYYRYRMMWYWRYSSWYYYRYWWWWWRYRRYRYWWMMYRYYYRSYYRRRRRYYYRYYRRKKMYMRRRRSYKYRRRYWYRRYWRYSYYRYRRYSRMMKRKYYYMMRWYKWYMRYRSWRYRYMYMMRRYSRYRRRSRRSRRMKRKYYYRRYMYYRYRRKYRRRRRYYRYYWYYSRRMKRYYYSYRRYYWRMYSRYYYMMRRYYRWKMWWWYRRWYYYSWRRYRYRYRRRYRYRYRYYYYRRRWMYKMWRRYYYYRMYSSRRRWYRWRRRWYRWYRKWYYMKRYRMYRYMRRYRYYYYYRMRRWYYRSYYSYRYYYYSWKYMRYYYYYYYRRKWYYMYRYMWYYYSYYMWYMWSYWWWYRYYYSYRYMMRRRYKYRWRYYRRRKYYYKRYYRYYMYRMRYYYKWYWWYYKYRYWWRYRMSSYYYYYKYRYRRYYRYYRYRKRYYKYYYWYRYRRYYYRMYYRRRYWRRKRYYYYRRRYRYYKYYRRRRWYKWRRRMYWRYRRSWSSYYYYRYYYYYSRYYMRRYSRWMYRYYYRRYRYWYYYMWWRRYMRYYYRRMYRRSKRRYYSRYKRRRMRWYYMWYYMRWYYWWYYYKSYKYYYYYYYWYYSRWSYYYYRRYSRMYYYRRYSWYYYYWRYYSRYYKRRYYYMWYYYRWWYKYMYRRRMYYSRKYMMYYRRRWRYRRRMYKYRKRYRYRSYYRYSRMYWWWWWWYKYRSYYWKMRWWYWSMMSMRKYRSWWMKWYYYWKRRKRWRWYWWWYSYRSYYYYYRRWMMRWYRYYWYKRMWRYRYYRRWWRYMYYYRYYYMRYYYRRYRWRYRYWWKWMRWRYYRRRYWSYWRSRYWYSRYKRRYRRKRYRYWSWWYRWRRRKYKYRYYWYKKRYYYRRYYYYYRKRYKYMYYRWYKRWMYRRKYRRRYRYRWYSYRYKYMSYYRWRMWKSRSYYRWSRRRRYSMSRRWKRRRYYYRRYWWYYRRYMYMRRYWWRYYYRMRKKYKWMYYRMYYKMWMYRWRKYRSRMKSYRSYYRWMMSSKRYMYKYRWRRRRRYYSRKYRYYYYRYRRKRYYYWYYWYYWRYRKMRKRRYRYWWMMRRRYYYYWSWSRMWWYRWYSYYWRYYRRYRRYYRRRWYSSRYRYYSRRKWYSMYSSKYYRMRRRYWMRYRKRRRRKYYWSYRYYYYRRMRRYWRRRRYSYRYYRRWSRMSRYSRWYRSRYRKKWYRYYWRWRRYMKRKRKKRKYMMKYRMRRRYRRYYRMWWRRRYYWWYRKRYYYRYYYYYRYYWRRYYMYSSWRRKYRRYYRRKYSMWMWRYRMRRYRMYRRWRWRKRYSKYSSRYSRYYMRRRRWKYRSRRKKYRRMMYRMRWRRRKRWRRYYKWYRKRRRMKRRSYYWSRKRRRMYWWWWKRYRRYYMWMYRRYRRMYYSWYMMYRYSKWWRYWYRWYWWYRRYRSSMYKMSYRSRRYYYYMKWWMKSRMRYRSRYMRRRYWRYMKYRYSWWMSKYYSWYRYRRRMYYWSRWWYYRYMSSYYYRYYWYYMRYSMWRYRYYRKRRRRMRYRRWYSYYWYYMWYRYYRWRYYYSRRYRRRMMMRSYKRWWKRYYRRKYRYWRRRYWRRRYMYYYWYWYYWRRRYRYRSRWMRRRWYYYKWYRRYSRKMRRRRSKYMWKRYMKKRSMKYYRRRRKRYRKYRYMYYYYRRRMKKMRWYYKWYMWYSWWRYRKYKWWRKYRRYMYRWRYWWRYWMRRRRRRRKRSYMKYRRKRKWRYYWKSSYYWYMSYSYRWRRRMRWMRWSWYSRYYYWWRRYRSWWSKSRYYYYYYMYRYSRWSWYYYMYWYRRYWRYYYWSYRYYRKWRYYRYRWKYMSYRRRKRRWYYWKSKSYMSRRYYYYYYYYRYRWSWMYWRKYMRWYRKYRRMMYYRMYMWYKWYYRWRRRYRYYRYYYRYSYYWWYYYRYRRRSRRYRMYMKYKYRYSYKYWRWRRYSYRWKRYYWRYYYYKYMWYMWRYMWSRKRWYRMRYYRYKRSRRRWRMRRKYRYRYRYRRYRKYYRRYRRMSKRKRWKRWMYMYKRWRSRYYYKRWYRRRKRYRRYWWKYYYRMRYRRMRWSYSYWWRYMWYKRKSYRMYWKSKSRWYYYRRRSRYRYKRYWWWRMWYYSYRRYKYYYSWYKRMYRKRRRYYWSKYSKYYMYYYYKRKYYYSSRRRYRSWYRYRKMSYRRWMRSYKRYKKWYYYYMKRYWYYRYRRMRSMMYSMKYYYSRKYRYMYSRKYKYYYKRKYWYKYYYRYRRKYWRRRYYSRYRWWRRRWYMRWRRRRRYSRWKYRMWYYYRYRYRRRRRYRRRYYYYWYYRRYYYRMKYYYWWMWRRRRYRYRRRWMKRRYWKKRYRYMYMYYRYYWRYRRWRWRMYYSRWRYRYYRMKRMWSRRKRRYYRYRKWWMSYRRRRSWKYSMKYWRSYSYSSYRKRRKSYYYRWRYWYYRYRRRYYYRYRYRRYRWWYYRYRSYRRYRMRKYSYWYMWYRYYRYYYSWYYRMRKRYSYWYRWYRYRYRYYYYRRMYRYWYYYYRYRSMRYKRYRYKMYYYYYRSWSMRRYRSWYYWWYYWYRYRRYSRRYYRYKYRYRYYYRRRSYKRMYRMYWWSRWYYMYKYRRMYWRKYRYRRYYRKRYYWYYWYRRRRSRYSYYRYYRWYRRWKRRYRWSYRRYYRYYRYRRRYRKMYWYMSRYRYYWSWKRWYYMSMRWRRYKYYYRYRKWYYRRKYRRMWMWYRSKKKKYRSKWWMYYSMYRRMWRKMKRYYRRKMRKKYYWRKWKYYRRRRMYRWRRWKSRKKYMRWYRSRRKYKSWRSRRRYKYWYWYYMYRYYRRYSRRRYRYKWRRYYKMWWKYYWMRMYRRRYSYYRWMYYRYSSYYYRSRWWRSKRYRRMKYWRRSRRYYSRYRYYRYRYMSYRRYMRYRYYRMRWYRYMWKWRYKYRRKRRKSYYMRRYYYYYYMYRRRRKYYKRRWYYWMRYYRRRYYYKRYYRYYRYMKRRYRYWWYRRRRYRYYSWMMWYWMYWSYYRWWWYRRRRYWYKSKRYSSYYYWRRRMMRSYYKYRKYYMYKRYYYKRYSMYYWYRSWRRWRYKRYRYYYRYRKYYYRYKYYYYRSYKWYMWSMRRYRMKRMRYSRYSRYYYRMYKRRRWRYYRRRRYYWYYWRRKWKKRYRWRWYSMYRRSMRWWWSMRMSRKYWRRYYYWYRYSYRMWMRSWRYKKRRWSSYYYYYRYYYMYYYYMRYKYYRWYYYRYYYYYYRMYYYRRRYYYYRRYKWRYRRRYWWYKMRKSYYYYYRYWRRRRKSYSYM
diff -r 420b57c3c185 -r feb40a9a8eae PedToFasta/test-data/sample.ped
--- a/PedToFasta/test-data/sample.ped	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
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	A	C	T	C	T	C	T	C	T	C	G	T	G	A	T	G	T	C	C	T	T	C	G	C	G	C	A	G	A	G	A	G	T	C	G	A	C	G	T	A	T	C	A	G	T	C	A	G	G	T	C	A	G	C	C	T	A	G	A	G	T	A	C	A	A	G	G	C	T	C	T	G	G	A	T	C	G	T	G	T	A	T	C	T	C	T	C	T	C	T	A	C	T	G	A	G	C	T	T	A	C	T	T	C	G	A	C	T	A	G	G	A	A	C	G	A	G	C	C	A	C	A	C	T	G	C	A	C	T	G	C	T	C	T	C	T	G	C	G	A	T	G	T	C	G	A	C	T	C	A	C	T	C	G	A	G	G	T	C	T	G	T	C	T	T	C	C	T	G	T	G	A	T	G	T	C	A	T	T	C	T	G	T	C	C	T	T	C	A	G	C	T	A	G	G	A	T	G	C	T	A	T	G	A	A	G	G	A	C	T	C	T	G	C	A	G	C	T	G	A	T	A	T	A	A	G	G	A	A	G	T	A	T	C	A	C	A	G	T	A	G	A	A	G	G	A	A	G	G	A	C	T	C	G	G	A	T	A	G	T	T	C	A	G	A	C	T	A	C	T	C	T	T	C	A	G	T	C	A	G	T	C	G	A	A	G	A	G	A	G	G	A	C	T	A	G	G	A	A	G	C	T	C	T	T	C	C	T	A	T	T	C	C	T	A	G	G	A	C	T	T	C	T	C	G	A	C	A	G	T	T	C	T	C	T	C	T	A	A	T	C	A	A	T	A	G	A	G	A	G	A	G	C	T	A	G	C	T	A	G	A	G	A	G	A	T	A	C	T	G	G	A	A	G	T	C	T	A	G	T	T	G	A	G	T	C	A	G	T	C	C	A	C	T	C	A	T	C	T	C	A	G	C	T	T	C	T	A	A	G	C	T	A	G	G	A	T	A	G	A	A	T	A	G	A	C	T	C	C	T	G	C	G	A	T	A	G	A	C	T	A	G	T	C	C	T	G	A	C	A	G	T	G	A	C	A	A	T	C	G	G	A	A	G	G	T	A	G	G	A	C	T	T	C	G	A	C	T	A	G	G	T	A	T	T	A	A	C	C	G	C	T	G	A	G	A	A	G	A	G	C	G	T	A	G	T	C	T	G	C	A	C	T	G	T	C	T	A	A	G	C	G	C	T	G	C	T	C	C	G	G	C	C	T	G	A	T	G	G	A	A	G	T	G	C	G	C	T	C	T	T	C	A	G	A	T	A	G	T	C	A	T	C	T	C	T	G	A	C	T	G	A	G	A	A	G	C	T	T	C	T	C	A	G	T	C	G	A	T	C	A	G	A	G	C	T	G	A	A	T	A	T	T	C	T	C	G	A	T	C	A	G	G	C	C	T	G	A	A	G	T	C	G	A	A	C	A	G	G	T	T	C	G	C	C	T	T	A	C	T	C	A	A	T	C	T	G	A	C	T	T	C	G	A	T	C	T	C	T	C	C	G	A	T	T	C	C	T	G	A	A	C	G	A	T	G	G	A	T	C	G	C	C	T	A	T	C	T	A	G	A	T	T	C	A	G	C	T	G	A	C	T	G	A	C	T	T	C	C	T	C	T	G	A	G	A	A	C	C	T	G	A	C	T	T	A	C	T	C	T	T	C	T	C	G	A	C	T	G	A	G	C	A	C	G	A	T	C	T	G	G	A	C	T	G	A	T	C	T	G	C	A	C	T	C	T	T	C	C	T	T	C	A	G	C	G	T	A	C	G	A	C	A	G	A	G	C	T	G	A	G	C	A	T	T	C	C	T	T	A	A	T	T	C	C	T	T	A	C	T	G	A	C	T	G	A	A	G	T	C	C	G	G	A	G	A	T	C	T	C	A	G	C	T	T	G	C	T	A	G	C	T	A	G	T	C	T	C	T	C	A	G	G	A	G	A	C	G	C	T	T	G	A	G	C	A	C	T	A	G	C	A	T	C	A	T	T	A	G	C	A	G	T	A	T	C	C	T	C	A	T	C	T	G	T	C	A	G	A	G	C	A	C	T	A	T	A	G	G	T	T	C	G	A	C	T	G	A	G	A	C	T	C	T	G	A	G	T	G	A	T	C	T	C	T	A	C	T	C	T	A	T	C	T	G	A	A	G	G	A	G	A	G	C	A	G	T	C	C	G	C	T	C	T	G	A	C	T	C	T	G	A	A	T	C	T	G	A	A	G	T	A	T	G	G	A	G	A	C	T	G	A	T	A	G	C	C	T	G	A	G	A	T	C	C	T	G	A	T	C	T	C	G	A	C	T	G	A	G	A	G	A	T	C	A	G	T	G	A	C	C	T	T	A	T	C	C	A	G	C	G	A	C	T	G	A	C	T	C	T	T	A	C	G	T	A	T	G	G	A	T	A	C	T	C	T	A	C	G	C	A	C	G	A	A	T	A	G	A	G	T	C	G	T	C	T	C	T	T	C	A	G	T	C	A	G	T	G	A	T	T	C	C	T	G	A	A	G	G	T	T	C	A	G	G	A	A	C	A	T	A	C	T	A	C	T	A	G	G	C	T	G	G	T	G	T	G	T	T	C	A	G	G	C	T	G	T	A	A	T	A	C	T	C	C	T	G	C	C	A	C	T	A	G	A	G	A	C	T	A	A	G	T	G	A	C	T	G	G	A	T	C	T	C	A	G	G	A	T	G	C	A	A	G	G	T	G	T	C	T	C	T	T	A	G	A	T	G	A	T	T	G	C	T	C	T	A	G	G	A	G	A	G	A	A	C	C	T	G	A	T	A	A	G	G	A	A	T	T	G	G	C	A	G	T	G	G	T	T	C	A	C	G	A	T	A	T	C	G	A	C	G	A	G	G	A	G	T	C	T	G	T	C	G	A	T	G	A	G	C	G	A	A	G	G	A	T	C	G	T	C	T	A	T	T	C	A	T	T	C	T	C	A	C	T	C	G	A	T	C	C	T	G	A	G	A	C	T	C	G	G	A	G	A	A	G	C	T	G	A	T	C	T	G	A	T	A	G	A	G	C	T	T	C	G	T	A	C	T	A	T	A	G	T	C	T	C	T	T	A	A	C	G	A	C	A	C	T	A	G	G	A	A	G	C	T	C	G	C	T	C	T	G	A	T	A	C	A	T	C	C	T	A	G	T	C	G	C	C	G	C	T	C	T	C	T	G	A	C	G	G	A	A	T	A	T	G	A	C	G	G	T	A	G	C	T	A	G	A	G	C	A	G	T	C	T	A	T	A	G	A	G	C	G	G	A	A	G	C	T	C	T	G	C	G	A	C	T	A	G	T	C	T	C	A	G	T	C	G	A	C	T	A	C	C	G	C	T	A	G	A	G	C	T	C	A	G	A	T	C	A	G	C	T	T	C	G	A	C	A	A	G	A	T	T	C	A	G	C	T	C	A	T	A	G	T	T	A	G	A	T	C	T	G	C	T	G	A	G	A	G	T	G	A	G	A	G	T	G	C	C	T	C	T	A	C	A	G	G	A	C	T	C	T	C	T	C	T	C	T	T	C	C	A	C	T	G	A	G	A	G	A	G	A	G	T	T	C	T	C	G	T	A	G	G	A	A	T	T	C	T	C	A	T	A	C	A	G	T	C	C	T	G	A	G	A	A	G	C	T	T	C	T	C	G	T	G	A	T	C	C	T	A	G	T	C	T	C	A	G	C	T	A	C	T	G	G	A	A	G	C	T	A	G	C	T	T	A	T	A	C	T	G	A	A	G	A	G	G	A	C	T	G	A	C	T	T	C	C	G	A	T	A	C	C	A	T	A	C	T	T	A	C	A	T	C	A	T	C	G	T	C	T	C	G	A	T	A	T	A	T	A	T	C	G	A	A	G	A	G	G	A	C	T	T	A	C	T	G	T	G	C	T	G	G	A	T	C	G	C	G	C	C	T	C	T	T	C	A	T	G	A	G	A	G	A	A	C	A	C	A	G	C	G	T	C	T	C	T	G	C	T	A	G	G	T	C	T	C	T	C	A	C	T	T	G	A	G	T	C	C	T	T	C	T	G	G	A	C	T	G	C	C	A	T	C	T	C	T	A	T	C	G	A	G	C	A	T	G	A	A	G	T	A	A	G	C	T	G	T	A	G	C	T	A	G	T	C	T	C	T	C	A	G	T	C	A	G	G	T	C	T	T	C	T	C	A	G	C	T	T	G	C	T	C	T	C	T	C	T	G	A	G	C	C	T	G	T	T	A	C	T	A	C	T	A	G	C	A	C	G	A	A	G	C	T	A	G	C	A	T	G	G	A	A	C	A	G	T	C	G	C	G	A	C	T	C	G	A	G	C	T	C	T	T	C	G	A	C	A	T	C	T	G	A	G	G	A	G	A	A	T	A	G	C	T	C	T	G	A	G	A	G	A	A	G	T	C	T	C	A	T	T	C	T	C	A	T	A	G	G	A	T	G	A	T	G	T	T	G	A	G	T	C	A	G	A	T	A	G	A	T	C	T	C	G	C	A	C	T	G	A	G	A	G	C	C	A	G	A	A	T	T	A	A	T	C	G	C	A	A	G	C	A	C	G	G	A	G	T	C	T	T	A	A	G	G	A	C	T	T	C	C	T	A	T	C	T	A	G	T	C	C	G	C	T	A	G	A	C	T	A	A	C	A	G	G	C	A	T	A	G	C	T	T	G	T	G	A	G	A	G	T	A	C	G	G	C	C	T	T	C	T	C	C	T	T	C	G	A	T	C	T	C	T	C	C	A	C	T	C	T	T	C	T	C	A	C	A	G	C	T	G	T	T	C	T	C	A	G	T	A	C	T	T	C	C	T	A	G	C	T	C	T	C	T	C	T	C	T	C	T	G	A	A	C	C	T	C	T	C	T	G	A	G	A	G	A	C	T	T	C	C	T	T	C	A	G	A	G	C	T	T	G	T	A	G	A	C	T	G	A	A	G	G	A	C	T	A	T	A	T	T	C	T	G	A	C	G	A	G	T	C	G	C	T	T	C	T	C	T	C	T	C	G	A	C	T	T	A	G	A	G	A	A	G	A	G	T	G	G	C	T	C	C	G	T	C	C	A	G	A
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/Rooting.pl
--- a/Rooting/Rooting.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-use Bio::SeqIO;
-use Cwd ;
-use FindBin qw ( $Bin $Script );
-
-my $CURRENT_DIR = $Bin;
-
-my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar";
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -i, --input         <newick input>
-    -o, --output        <newick output>
-~;
-$usage .= "\n";
-
-my ($input,$outfile);
-
-
-GetOptions(
-	"input=s"    => \$input,
-	"output=s"   => \$outfile
-);
-
-
-die $usage
-  if ( !$input || !$outfile);
-  
-my $treefile = $input;
-	
-
-# replace negative values by 0
-open(T,$treefile);
-open(T2,">$treefile.2");
-while(<T>)
-{
-	my $line = $_;
-	$line =~s/\-\d+\.*\d*\,/0,/g;
-	$line =~s/\-\d+\.*\d*\)/0\)/g;
-	print T2 $line;
-}
-close(T);
-close(T2);
-	
-my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1";
-system($rooting_command);
-
-unlink("$treefile.all");
-unlink("$treefile.2");
-rename("$treefile.midpoint",$outfile);
-
-	
-	
-
-
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/Rootings_54.jar
Binary file Rooting/Rootings_54.jar has changed
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/rooting.xml
--- a/Rooting/rooting.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,193 +0,0 @@
-<tool id="sniplay_rooting" name="Rooting" version="1.0.2">
-    
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
-    <description> Midpoint rooting of newick tree </description>
-    
-    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
-    <requirements>
-        <requirement type="binary">perl</requirement>
-	<requirement type="package">Rootings_54.jar</requirement>
-    </requirements>
-    
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
-    
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="perl">
-	Rooting.pl -i $filein -o $fileout &amp;&amp; mv ${filein}.rooting.log $fileout_log
-    </command>
-   
-    <!-- [REQUIRED] Input files and tool parameters -->
-    <inputs>
-	<param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" />
-	<param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
-    </inputs> 
-    
-    <!-- [REQUIRED] Output files -->
-    <outputs>
-	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
-	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
-    </outputs>
-    
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-
-        <test>
-         <param name="filein" value="newick" />
-         <output name="fileout" file="out_tree" />
-	 <output name="fileout_log" file="out_tree.log" />
-        </test>
-
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-    
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
-
-
-.. class:: infomark
-
-**Authors** Jean-François Dufayard, CIRAD, South Green platform
-
-
-.. class:: infomark
-
-**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
-
-.. class:: infomark
-
-**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
-
-.. class:: infomark
-
-**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
----------------------------------------------------
-
-
-
-
-=======
-Rooting
-=======
-
------------
-Description
------------
-
-  Compute a midpoint newick rooted tree.
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=========== ========================== =======
-Name            output file(s)         format 
-=========== ========================== =======
-fastme      Newick tree                Newick 
-=========== ========================== =======
-
-
-
-----------
-Input file
-----------
-
-Newick file
-	
-
-----------
-Parameters
-----------
-
-Output name
-        Output base name for the ouput files
-
-
-------------
-Output files
-------------
-
-Output_name
-	Resulting tree rooted in newick format
-
-Output_name.log
-	Log file
-
-------------
-Dependencies
-------------
-Rooting
-	CIRAD tool. Contact jean-francois.dufayard@cirad.fr
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-Newick file
------------
-
-::
-	
-	(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
-
-
-Parameters
-==========
-
-Output name -> out tree
-
-
-Output files
-============
-
-out tree
---------
-
-::
-
-	(ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
-	
-
-    </help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-    
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/rooting.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Rooting/rooting.xml~	Fri Jul 10 10:38:11 2015 -0400
@@ -0,0 +1,193 @@
+<tool id="sniplay_rooting" name="Rooting" version="1.0.2">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description> Midpoint rooting of newick tree </description>
+    
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</requirement>
+	<requirement type="package">Rootings_54.jar</requirement>
+    </requirements>
+    
+    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
+    <version_command>
+<!--
+        tool_binary -v
+-->
+    </version_command>
+    
+    <!-- [REQUIRED] The command to execute -->
+    <command interpreter="perl">
+	Rooting.pl -i $filein -o $fileout &amp;&amp; mv ${filein}.rooting.log $fileout_log
+    </command>
+   
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" />
+	<param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
+    </inputs> 
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
+	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+    </outputs>
+    
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    
+    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
+    <tests>
+        <!-- [HELP] Test files have to be in the ~/test-data directory -->
+
+        <test>
+         <param name="filein" value="newick" />
+         <output name="fileout" file="out_tree" />
+	 <output name="fileout_log" file="out_tree.log" />
+        </test>
+
+        <!-- [HELP] Multiple tests can be defined with different parameters -->
+<!--
+        <test>
+        </test>
+-->
+    </tests>
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help>
+
+
+.. class:: infomark
+
+**Authors** Jean-François Dufayard, CIRAD, South Green platform
+
+
+.. class:: infomark
+
+**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
+
+.. class:: infomark
+
+**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
+
+.. class:: infomark
+
+**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
+
+---------------------------------------------------
+
+
+
+
+=======
+Rooting
+=======
+
+-----------
+Description
+-----------
+
+  Compute a midpoint newick rooted tree.
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tool**
+
+=========== ========================== =======
+Name            output file(s)         format 
+=========== ========================== =======
+fastme      Newick tree                Newick 
+=========== ========================== =======
+
+
+
+----------
+Input file
+----------
+
+Newick file
+	
+
+----------
+Parameters
+----------
+
+Output name
+        Output base name for the ouput files
+
+
+------------
+Output files
+------------
+
+Output_name
+	Resulting tree rooted in newick format
+
+Output_name.log
+	Log file
+
+------------
+Dependencies
+------------
+Rooting
+	CIRAD tool. Contact jean-francois.dufayard@cirad.fr
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+Newick file
+-----------
+
+::
+	
+	(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
+
+
+Parameters
+==========
+
+Output name -> out tree
+
+
+Output files
+============
+
+out tree
+--------
+
+::
+
+	(ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
+	
+
+    </help>
+    <citations>
+        <!-- [HELP] As DOI or BibTex entry -->
+    	<citation type="bibtex">@article{Dereeper03062015,
+author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
+title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
+year = {2015}, 
+doi = {10.1093/nar/gkv351}, 
+abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
+URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
+eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
+journal = {Nucleic Acids Research} 
+}
+
+    	</citation>
+
+    </citations>
+    
+</tool>
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/test-data/newick
--- a/Rooting/test-data/newick	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863);
-
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/test-data/out_tree
--- a/Rooting/test-data/out_tree	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(ref:0.575788,(((((((((((((((((((((((PALAWAN:0.032789,KENDINGA5H:0.028863):0.031721,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.004581,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004869,DINORADO:0.065206):0.004898,((LUDAN:0.05423,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):8.8E-5):0.006838,CAAWA/FORT:0.05563):0.011439,CANELADEFE:0.050931):0.002897,PACHOLINHA:0.042509):0.002988,TRESMESES:0.028972):0.001209,((OS4:0.021016,OS6:0.01567):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.006303,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.004673,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.14437):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.04316,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.01418,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.05797):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.00344,(((((KUROKA:0.096901,IRAT144:0.032372):0.04063,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.03418):0.01106,CAIAPO:0.07222):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.001457,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.01125,(((IAC47:0.007321,(IAC165:5.0E-4,VARYLAVA90:0.00165):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.007912,IRAT234:0.037316):0.005647,MANDRIRAVI:0.049833):0.002593,RT1031-69:0.04352):0.005079,((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.00474):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):8.58E-4,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.02711,GRAZI:0.022678):7.63E-4):0.00987,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:0.0,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):9.71E-4):0.009442):0.002985):0.008281,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.02162,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.05943,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.001416,((GANIGI:0.040448,PULULAPA:0.03984):0.020258,GOGO:0.060904):0.005609):0.018877,CUIABANA:0.066182):0.020665,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.03265):0.012575,VIETNAM1:0.049323):0.00311,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.01445):0.01097):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.00624,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.043699,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.015245,(((JUMALI:0.07765,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607):0.14713500000000007);
diff -r 420b57c3c185 -r feb40a9a8eae Rooting/test-data/out_tree.log
diff -r 420b57c3c185 -r feb40a9a8eae SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl
--- a/SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-use Bio::SeqIO;
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -i, --input         <Hapmap input>
-    -o, --out           <output in tabular format>
-    -s, --step          <step (in bp)>
-~;
-$usage .= "\n";
-
-my ($input,$out,$step);
-
-GetOptions(
-	"input=s"    => \$input,
-	"out=s"      => \$out,
-	"step=s"     => \$step,
-);
-
-
-die $usage
-  if ( !$input || !$step || !$out );
-  
-my $max_chr_num = 100;
-
-my %counts;
-my %counts_by_ind;
-open(my $HAPMAP,$input);
-my $headers= <$HAPMAP>;
-$headers=~s/\n//g;
-$headers=~s/\r//g;
-my @ind_names = split(/\t/,$headers);
-my @individual_names;
-for (my $i = 12; $i <= $#ind_names; $i++)
-{
-	push(@individual_names,$ind_names[$i]);
-}
-my %maximums;
-while(<$HAPMAP>)
-{
-	my $line = $_;
-	$line=~s/\n//g;
-	$line=~s/\r//g;
-	my @infos = split(/\t/,$line);
-	my $chrom = $infos[2];
-	my $position = $infos[3];
-	if ($position > $maximums{$chrom}){$maximums{$chrom}=$position;}
-	my $classe_position = int($position/$step);
-	$counts{$chrom}{$classe_position}++;
-		
-	my $ref_allele = $infos[11];
-	for (my $i = 12; $i <= $#infos; $i++)
-	{
-		if (!$counts_by_ind{$chrom}{$classe_position}{$i}){$counts_by_ind{$chrom}{$classe_position}{$i} = 0;}
-		if ($infos[$i] ne $ref_allele)
-		{
-			$counts_by_ind{$chrom}{$classe_position}{$i}++;
-		}
-	}
-}
-close($HAPMAP);
-
-#######################################################
-# global
-#######################################################
-open(my $OUT,">$out");
-print $OUT "Chromosome	Position	SNPs\n";
-my $chr_num = 0;
-foreach my $chrom(sort keys(%counts))
-{
-	$chr_num++;
-	my $ref_counts = $counts{$chrom};
-	my %final_counts = %$ref_counts;
-	my $x = 0;
-	#foreach my $classe_position(sort {$a<=>$b} keys(%final_counts))
-	for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++)
-	{
-		my $nb = 0;
-		if ($counts{$chrom}{$classe_position})
-		{
-			$nb = $counts{$chrom}{$classe_position};
-		}
-		$x += $step;
-		print $OUT "$chrom	$x	$nb\n";
-	}
-	if ($chr_num >= $max_chr_num){last;}
-}
-close($OUT);
-
-#######################################################
-# For each individual
-#######################################################
-open(my $OUT2,">$out.by_sample");
-$chr_num = 0;
-print $OUT2 "Chromosome	".join("\t",@individual_names) . "\n";
-foreach my $chrom(sort keys(%counts_by_ind))
-{
-	$chr_num++;
-        my $ref_counts = $counts_by_ind{$chrom};
-        my %final_counts = %$ref_counts;
-	for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++)
-        {
-			print $OUT2 "$chrom";
-			my $num_ind = 12;
-			foreach my $indiv(@individual_names)
-			{
-				my $val = 0;
-				
-				if ($counts_by_ind{$chrom}{$classe_position}{$num_ind})
-				{
-					$val = $counts_by_ind{$chrom}{$classe_position}{$num_ind};
-				}
-				print $OUT2 "	$val";
-				$num_ind++;
-			}
-			print $OUT2 "\n";
-        }
-	if ($chr_num >= $max_chr_num){last;}
-}
-close($OUT2);
diff -r 420b57c3c185 -r feb40a9a8eae SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml
--- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,207 +0,0 @@
-<tool id="sniplay_density" name="SNP density" version="1.2.0">
-    
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
-    <description> Calculate SNP densities along chromosome from HapMap</description>
-    
-    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
-    <requirements>
-        <requirement type="binary">perl</requirement>
-    </requirements>
-    
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
-    
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="bash">
-	calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step
-    </command>
-   
-    <!-- [REQUIRED] Input files and tool parameters -->
-    <inputs>
-	<param name="filein" type="data" format="txt" optional="false" label="Hapmap input" />
-	<param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
-	<param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
-    </inputs>
-    
-    <!-- [REQUIRED] Output files -->
-    <outputs>
-	<data name="fileout" type="data" format="tabular" label="${fileout_label}" />
-	<data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
-    </outputs>
-    
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-<!--
-        <test>
-         <param name="input" value="input_test.txt" />
-         <output name="output" file="output_test.txt" />
-        </test>
--->
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-    
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
-
-.. class:: infomark
-
-**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform 
-
- | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
-
-.. class:: infomark
-
-**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
-
-.. class:: infomark
-
-**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
-
----------------------------------------------------
-
-
-
-=============
-SNP densities
-=============
-
------------
-Description
------------
-
-  Calculate SNP densities along chromosome from HapMap
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ====================== ===========
-Name            output file(s)         format 
-=============== ====================== ===========
-VCF to Hapmap   Hapmap file	       hapmap
-=============== ====================== ===========
-
-
-----------
-Input file
-----------	
-
-Hapmap file
-	File with SNPs
-
-
-----------
-Parameters
-----------
-
-Step
-        Step in bp for the window to calculate SNP density
-
-Output name
-        Output base name for the two ouput files
-
-
-------------
-Output files
-------------
-
-Output_name
-	Tabular file with SNP density in each postion 
-
-Output_name.by_sample
-	Tabular file with SNP density for each sample
-
-	
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-hapmap file
------------
-
-::
-
-	rs#       alleles chrom pos  strand          assembly# center                protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54
-	chr1:1774 [G/T]   chr1  1774 Cc01_g00010:47  exon      NON_SYNONYMOUS_CODING gCg/gAg  A/E       25.0%     4      GG  TT   TT   TT
-	chr1:1640 [G/A]   chr1  1640 Cc01_g00010:127 exon      NON_SYNONYMOUS_CODING Ccg/Tcg  P/S       37.5%     4      GG  GG   AA   GA
-	chr1:1629 [A/C]   chr1  1629 Cc01_g00010:138 exon      SYNONYMOUS_CODING     ctT/ctG  L/L       37.5%     4      AA  CC   CC   AC
-	chr1:1628 [C/G]   chr1  1628 Cc01_g00010:139 exon      NON_SYNONYMOUS_CODING Ggg/Cgg  G/R       12.5%     4      CC  CC   CC   CG
-	chr1:1619 [T/G]   chr1  1619 Cc01_g00010:148 exon      NON_SYNONYMOUS_CODING Aaa/Caa  K/Q       37.5%     4      TT  TT   GG   TG
-	chr1:1405 [C/T]   chr1  1405 Cc01_g00010:362 exon      NON_SYNONYMOUS_CODING cGg/cAg  R/Q       16.7%     3      CC  CC   NN   CT
-
-Parameters
-==========
-
-Step -> 200000
-
-Output name -> densities
-
-
-Output files
-============
-
-densities
----------
-
-::
-
-	Chromosome Position SNPs
-	chr1       200000   355
-	chr1       400000   228
-	chr1       600000   63
-	chr1       800000   191
-
-
-densities.by_sample
--------------------
-
-::
-
-	Chromosome BA58 BA59 BD54
-	chr1       220  197  225
-	chr1       130  119  133
-	chr1       43   43   40
-	chr1       139  167  141
-
-    </help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>    
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh
--- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-tool_path=$(dirname $0)
-hapmap=$1
-fileout=$2
-fileout_bysample=$3
-step=$4
-
-perl $tool_path/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl -i $hapmap -o $fileout -s $step
-
-cp  $fileout.by_sample $fileout_bysample
-rm $fileout.by_sample
-
diff -r 420b57c3c185 -r feb40a9a8eae SNP_density/test-data/hapmap
--- a/SNP_density/test-data/hapmap	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3584 +0,0 @@
-rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panelLSID	QCcode	ref	BA58	BA59	BD54
-chr1:1774	[G/T]	chr1	1774	Cc01_g00010:47	exon	NON_SYNONYMOUS_CODING	gCg/gAg	A/E	25.0%	4	GG	TT	TT	TT
-chr1:1640	[G/A]	chr1	1640	Cc01_g00010:127	exon	NON_SYNONYMOUS_CODING	Ccg/Tcg	P/S	37.5%	4	GG	GG	AA	GA
-chr1:1629	[A/C]	chr1	1629	Cc01_g00010:138	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	37.5%	4	AA	CC	CC	AC
-chr1:1628	[C/G]	chr1	1628	Cc01_g00010:139	exon	NON_SYNONYMOUS_CODING	Ggg/Cgg	G/R	12.5%	4	CC	CC	CC	CG
-chr1:1619	[T/G]	chr1	1619	Cc01_g00010:148	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	37.5%	4	TT	TT	GG	TG
-chr1:1405	[C/T]	chr1	1405	Cc01_g00010:362	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	16.7%	3	CC	CC	NN	CT
-chr1:1398	[T/G]	chr1	1398	Cc01_g00010:369	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	16.7%	3	TT	TT	NN	TG
-chr1:1394	[G/C]	chr1	1394	Cc01_g00010:373	exon	NON_SYNONYMOUS_CODING	Cgt/Ggt	R/G	16.7%	3	GG	GG	NN	GC
-chr1:1379	[A/T]	chr1	1379	Cc01_g00010:388	exon	NON_SYNONYMOUS_CODING	Tac/Aac	Y/N	16.7%	3	AA	AA	NN	AT
-chr1:1352	[T/C]	chr1	1352	Cc01_g00010:415	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	33.3%	3	TT	CC	NN	CC
-chr1:1252	[T/A]	chr1	1252	Cc01_g00010:515	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	12.5%	4	TT	TT	TT	TA
-chr1:17176	[T/G]	chr1	17176	Cc01_g00030:504	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	12.5%	4	TT	TT	TG	TT
-chr1:18041	[A/G]	chr1	18041	Cc01_g00030:661	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	37.5%	4	AA	AA	GG	AG
-chr1:18442	[C/A]	chr1	18442	Cc01_g00030:929	exon	NON_SYNONYMOUS_CODING	tCc/tAc	S/Y	25.0%	4	CC	CC	CA	CA
-chr1:18478	[T/C]	chr1	18478	Cc01_g00030:965	exon	NON_SYNONYMOUS_CODING	cTa/cCa	L/P	25.0%	4	TT	TT	TC	TC
-chr1:18554	[T/G]	chr1	18554	Cc01_g00030:1041	exon	SYNONYMOUS_CODING	tcT/tcG	S/S	25.0%	4	TT	TT	TG	TG
-chr1:19062	[T/A]	chr1	19062	Cc01_g00030:1151	exon	NON_SYNONYMOUS_CODING	tTc/tAc	F/Y	33.3%	3	TT	NN	TT	AA
-chr1:19078	[A/G]	chr1	19078	Cc01_g00030:1167	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	AA	AA	AG	AA
-chr1:19138	[T/C]	chr1	19138	Cc01_g00030:1227	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	25.0%	4	TT	TT	CT	TC
-chr1:22125	[C/T]	chr1	22125	Cc01_g00030:1773	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	25.0%	4	CC	CC	CT	CT
-chr1:22212	[T/C]	chr1	22212	Cc01_g00030:1860	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	TT	TT	TC	TT
-chr1:22342	[T/A]	chr1	22342	Cc01_g00030:1990	exon	NON_SYNONYMOUS_CODING	Tca/Aca	S/T	25.0%	4	TT	TT	TA	TA
-chr1:22404	[C/T]	chr1	22404	Cc01_g00030:2052	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	25.0%	4	CC	CC	CT	CT
-chr1:22478	[C/G]	chr1	22478	Cc01_g00030:2126	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	25.0%	4	CC	GG	CC	CC
-chr1:22613	[C/T]	chr1	22613	Cc01_g00030:2261	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	25.0%	4	CC	TT	CC	CC
-chr1:22657	[C/T]	chr1	22657	Cc01_g00030:2305	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	12.5%	4	CC	CC	CT	CC
-chr1:22758	[A/G]	chr1	22758	Cc01_g00030:2406	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	25.0%	4	AA	AA	AG	AG
-chr1:22903	[C/A]	chr1	22903	Cc01_g00030:2551	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	25.0%	4	CC	CC	CA	CA
-chr1:22965	[G/T]	chr1	22965	Cc01_g00030:2613	exon	NON_SYNONYMOUS_CODING	atG/atT	M/I	12.5%	4	GG	GG	TG	GG
-chr1:23037	[A/G]	chr1	23037	Cc01_g00030:2685	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	25.0%	4	AA	AA	AG	AG
-chr1:24151	[A/G]	chr1	24151	Cc01_g00030:3063	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	AA	AA	AG	AG
-chr1:24436	[T/C]	chr1	24436	Cc01_g00030:3240	exon	SYNONYMOUS_CODING	agT/agC	S/S	25.0%	4	TT	TT	TC	TC
-chr1:25763	[G/C]	chr1	25763	Cc01_g00030:3610	exon	NON_SYNONYMOUS_CODING	Gta/Cta	V/L	25.0%	4	GG	GG	GC	GC
-chr1:26910	[T/G]	chr1	26910	Cc01_g00030:3889	exon	NON_SYNONYMOUS_CODING	Tct/Gct	S/A	25.0%	4	TT	TT	TG	TG
-chr1:26996	[C/T]	chr1	26996	Cc01_g00030:3975	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	25.0%	4	CC	CC	CT	CT
-chr1:27095	[A/T]	chr1	27095	Cc01_g00030:4074	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	37.5%	4	AA	AA	TT	AT
-chr1:27755	[C/T]	chr1	27755	Cc01_g00030:4734	exon	SYNONYMOUS_CODING	agC/agT	S/S	25.0%	4	CC	CC	CT	CT
-chr1:30493	[C/T]	chr1	30493	Cc01_g00030:4992	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	CC	CC	CT	CC
-chr1:30505	[C/T]	chr1	30505	Cc01_g00030:5004	exon	SYNONYMOUS_CODING	acC/acT	T/T	37.5%	4	CC	CC	TT	CT
-chr1:30560	[A/G]	chr1	30560	Cc01_g00030:5059	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	12.5%	4	AA	AA	AG	AA
-chr1:30592	[T/C]	chr1	30592	Cc01_g00030:5091	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	TT	TT	TC	TT
-chr1:32950	[A/G]	chr1	32950	Cc01_g00030:5337	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	25.0%	4	AA	AA	AG	AG
-chr1:32968	[A/C]	chr1	32968	Cc01_g00030:5355	exon	SYNONYMOUS_CODING	acA/acC	T/T	25.0%	4	AA	CC	AA	AA
-chr1:33022	[A/T]	chr1	33022	Cc01_g00030:5409	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	AA	TT	AA	AA
-chr1:33025	[T/A]	chr1	33025	Cc01_g00030:5412	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	25.0%	4	TT	AA	TT	TT
-chr1:33167	[T/C]	chr1	33167	Cc01_g00030:5554	exon	NON_SYNONYMOUS_CODING	Tcg/Ccg	S/P	25.0%	4	TT	CC	TT	TT
-chr1:33196	[C/T]	chr1	33196	Cc01_g00030:5583	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	25.0%	4	CC	TT	CC	CC
-chr1:33467	[T/C]	chr1	33467	Cc01_g00030:5854	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	25.0%	4	TT	TT	TC	TC
-chr1:37303	[G/A]	chr1	37303	Cc01_g00040:129	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	50.0%	2	GG	NN	NN	AA
-chr1:37602	[C/G]	chr1	37602	Cc01_g00040:428	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	37.5%	4	CC	GG	GG	CG
-chr1:37607	[T/G]	chr1	37607	Cc01_g00040:433	exon	NON_SYNONYMOUS_CODING	Tta/Gta	L/V	50.0%	3	TT	GG	NN	TG
-chr1:38519	[A/C]	chr1	38519	Cc01_g00040:507	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	33.3%	3	AA	NN	CC	CC
-chr1:38606	[G/A]	chr1	38606	Cc01_g00040:594	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	50.0%	4	GG	AA	GA	GA
-chr1:38657	[C/T]	chr1	38657	Cc01_g00040:645	exon	SYNONYMOUS_CODING	caC/caT	H/H	37.5%	4	CC	TT	TT	CT
-chr1:38927	[G/A]	chr1	38927	Cc01_g00040:915	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	50.0%	2	GG	NN	NN	AA
-chr1:38942	[G/C]	chr1	38942	Cc01_g00040:930	exon	SYNONYMOUS_CODING	ggG/ggC	G/G	33.3%	3	GG	NN	CC	CC
-chr1:38952	[C/T]	chr1	38952	Cc01_g00040:940	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	50.0%	3	CC	NN	TT	CT
-chr1:38956	[T/C]	chr1	38956	Cc01_g00040:944	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	50.0%	3	TT	NN	CC	TC
-chr1:39103	[C/T]	chr1	39103	Cc01_g00040:1091	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	33.3%	3	CC	NN	TT	TT
-chr1:39113	[C/T]	chr1	39113	Cc01_g00040:1101	exon	SYNONYMOUS_CODING	acC/acT	T/T	37.5%	4	CC	TT	TT	CT
-chr1:39164	[T/G]	chr1	39164	Cc01_g00040:1152	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	12.5%	4	TT	TG	TT	TT
-chr1:39389	[T/C]	chr1	39389	Cc01_g00040:1377	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	2	TT	NN	NN	TC
-chr1:77092	[C/G]	chr1	77092	Cc01_g00050:8	exon	NON_SYNONYMOUS_CODING	gGg/gCg	G/A	25.0%	4	CC	GG	GG	GG
-chr1:77069	[C/A]	chr1	77069	Cc01_g00050:31	exon	NON_SYNONYMOUS_CODING	Gta/Tta	V/L	12.5%	4	CC	CA	CC	CC
-chr1:77040	[A/C]	chr1	77040	Cc01_g00050:60	exon	NON_SYNONYMOUS_CODING	atT/atG	I/M	25.0%	4	AA	CC	CC	CC
-chr1:77030	[T/C]	chr1	77030	Cc01_g00050:70	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	25.0%	4	TT	CC	CC	CC
-chr1:76998	[C/A]	chr1	76998	Cc01_g00050:102	exon	SYNONYMOUS_CODING	ccG/ccT	P/P	50.0%	4	CC	AA	CA	CA
-chr1:76995	[T/C]	chr1	76995	Cc01_g00050:105	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	TT	CC	CC	CC
-chr1:83837	[G/A]	chr1	83837	Cc01_g00060:12	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	25.0%	4	GG	AA	AA	AA
-chr1:84858	[A/C]	chr1	84858	Cc01_g00060:392	exon	NON_SYNONYMOUS_CODING	aAa/aCa	K/T	37.5%	4	AA	CC	AA	AC
-chr1:84868	[C/T]	chr1	84868	Cc01_g00060:402	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	50.0%	4	CC	TT	CC	TT
-chr1:84880	[G/A]	chr1	84880	Cc01_g00060:414	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	50.0%	4	GG	AA	GG	AA
-chr1:84991	[C/G]	chr1	84991	Cc01_g00060:525	exon	SYNONYMOUS_CODING	ctC/ctG	L/L	12.5%	4	CC	CC	CG	CC
-chr1:105491	[C/A]	chr1	105491	Cc01_g00070:36	exon	SYNONYMOUS_CODING	ctG/ctT	L/L	12.5%	4	CC	CC	CC	CA
-chr1:100754	[G/C]	chr1	100754	Cc01_g00070:660	exon	SYNONYMOUS_CODING	ccC/ccG	P/P	12.5%	4	GG	GC	GG	GG
-chr1:100458	[A/C]	chr1	100458	Cc01_g00070:720	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	37.5%	4	AA	CC	AA	AC
-chr1:100367	[C/A]	chr1	100367	Cc01_g00070:811	exon	STOP_GAINED	Gga/Tga	G/1	12.5%	4	CC	CC	CA	CC
-chr1:99870	[T/C]	chr1	99870	Cc01_g00070:1068	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	TT	TT	TT	TC
-chr1:99742	[C/G]	chr1	99742	Cc01_g00070:1196	exon	NON_SYNONYMOUS_CODING	gGt/gCt	G/A	12.5%	4	CC	CC	CC	CG
-chr1:99729	[G/A]	chr1	99729	Cc01_g00070:1209	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	GG	GG	GG	GA
-chr1:99727	[G/C]	chr1	99727	Cc01_g00070:1211	exon	NON_SYNONYMOUS_CODING	cCt/cGt	P/R	12.5%	4	GG	GG	GG	GC
-chr1:99642	[C/T]	chr1	99642	Cc01_g00070:1296	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	12.5%	4	CC	CC	CC	CT
-chr1:99567	[T/G]	chr1	99567	Cc01_g00070:1371	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	12.5%	4	TT	TT	TT	TG
-chr1:99549	[T/C]	chr1	99549	Cc01_g00070:1389	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	25.0%	4	TT	CC	TT	TT
-chr1:99448	[T/G]	chr1	99448	Cc01_g00070:1490	exon	NON_SYNONYMOUS_CODING	cAg/cCg	Q/P	12.5%	4	TT	TT	TT	TG
-chr1:99354	[T/C]	chr1	99354	Cc01_g00070:1584	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	12.5%	4	TT	TT	TT	TC
-chr1:99162	[T/C]	chr1	99162	Cc01_g00070:1776	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TT	TT	TC
-chr1:98368	[C/G]	chr1	98368	Cc01_g00070:2112	exon	NON_SYNONYMOUS_CODING	agG/agC	R/S	50.0%	2	CC	NN	NN	GG
-chr1:97071	[A/C]	chr1	97071	Cc01_g00070:2285	exon	NON_SYNONYMOUS_CODING	aTc/aGc	I/S	25.0%	4	AA	CC	CC	CC
-chr1:96611	[C/T]	chr1	96611	Cc01_g00070:2292	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	CC	CT	CC	CC
-chr1:95183	[T/C]	chr1	95183	Cc01_g00070:2748	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	TT	TT	TT	TC
-chr1:95134	[T/C]	chr1	95134	Cc01_g00070:2797	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	37.5%	4	TT	CC	TT	TC
-chr1:95116	[G/A]	chr1	95116	Cc01_g00070:2815	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	GG	GG	GG	GA
-chr1:94898	[G/A]	chr1	94898	Cc01_g00070:2895	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	12.5%	4	GG	GG	GG	GA
-chr1:94841	[A/T]	chr1	94841	Cc01_g00070:2952	exon	SYNONYMOUS_CODING	atT/atA	I/I	12.5%	4	AA	AA	AA	AT
-chr1:94700	[C/T]	chr1	94700	Cc01_g00070:2994	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	CC	CC	CC	CT
-chr1:94679	[A/G]	chr1	94679	Cc01_g00070:3015	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	AA	AA	AA	AG
-chr1:93879	[T/C]	chr1	93879	Cc01_g00070:3411	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	37.5%	4	TT	CC	TT	TC
-chr1:93873	[C/T]	chr1	93873	Cc01_g00070:3417	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	CC	CC	CC	CT
-chr1:92117	[A/T]	chr1	92117	Cc01_g00070:3663	exon	SYNONYMOUS_CODING	ctT/ctA	L/L	25.0%	4	AA	TT	AA	AA
-chr1:92011	[A/C]	chr1	92011	Cc01_g00070:3769	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	12.5%	4	AA	AA	AA	AC
-chr1:91347	[G/A]	chr1	91347	Cc01_g00070:4194	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	25.0%	4	GG	AA	GG	GG
-chr1:90731	[A/C]	chr1	90731	Cc01_g00070:4545	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	37.5%	4	AA	AC	AC	AC
-chr1:90332	[T/A]	chr1	90332	Cc01_g00070:4746	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	12.5%	4	TT	TT	TT	TA
-chr1:90303	[A/G]	chr1	90303	Cc01_g00070:4775	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	25.0%	4	AA	GG	AA	AA
-chr1:90289	[C/T]	chr1	90289	Cc01_g00070:4789	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	37.5%	4	CC	TT	CC	CT
-chr1:90161	[A/G]	chr1	90161	Cc01_g00070:4917	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AA	AG	AA
-chr1:90128	[G/A]	chr1	90128	Cc01_g00070:4950	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	GG	GG	GG	GA
-chr1:89792	[G/A]	chr1	89792	Cc01_g00070:5127	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	37.5%	4	GG	AA	GG	GA
-chr1:89745	[A/G]	chr1	89745	Cc01_g00070:5174	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	37.5%	4	AA	GG	AA	AG
-chr1:89720	[T/C]	chr1	89720	Cc01_g00070:5199	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	TT	CC	CC	CC
-chr1:89493	[A/G]	chr1	89493	Cc01_g00070:5304	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	37.5%	4	AA	AG	AG	AG
-chr1:89423	[A/C]	chr1	89423	Cc01_g00070:5374	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	12.5%	4	AA	AA	AA	AC
-chr1:89418	[A/T]	chr1	89418	Cc01_g00070:5379	exon	SYNONYMOUS_CODING	ggT/ggA	G/G	12.5%	4	AA	AA	AA	TA
-chr1:88516	[T/G]	chr1	88516	Cc01_g00070:5910	exon	SYNONYMOUS_CODING	atA/atC	I/I	12.5%	4	TT	TT	TT	TG
-chr1:87964	[T/C]	chr1	87964	Cc01_g00070:6237	exon	SYNONYMOUS_CODING	agA/agG	R/R	37.5%	4	TT	CC	TT	TC
-chr1:112990	[T/C]	chr1	112990	Cc01_g00080:4	exon	NON_SYNONYMOUS_CODING	Acg/Gcg	T/A	50.0%	4	TT	TT	CC	CC
-chr1:112983	[A/G]	chr1	112983	Cc01_g00080:11	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	50.0%	4	AA	AA	GG	GG
-chr1:112926	[A/T]	chr1	112926	Cc01_g00080:68	exon	NON_SYNONYMOUS_CODING	gTt/gAt	V/D	50.0%	4	AA	AA	TT	TT
-chr1:112910	[T/C]	chr1	112910	Cc01_g00080:84	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TT	TT	TC
-chr1:112909	[A/C]	chr1	112909	Cc01_g00080:85	exon	NON_SYNONYMOUS_CODING	Ttg/Gtg	L/V	25.0%	4	AA	CC	CC	CC
-chr1:112875	[C/A]	chr1	112875	Cc01_g00080:119	exon	NON_SYNONYMOUS_CODING	gGc/gTc	G/V	12.5%	4	CC	CC	CA	CC
-chr1:112874	[G/A]	chr1	112874	Cc01_g00080:120	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	25.0%	4	GG	GG	GA	GA
-chr1:112792	[A/G]	chr1	112792	Cc01_g00080:202	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	50.0%	4	AA	AA	GG	GG
-chr1:112070	[T/C]	chr1	112070	Cc01_g00080:274	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	37.5%	4	TT	TT	TC	CC
-chr1:111976	[T/C]	chr1	111976	Cc01_g00080:368	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	12.5%	4	TT	TT	TC	TT
-chr1:111966	[G/C]	chr1	111966	Cc01_g00080:378	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	12.5%	4	GG	GG	GC	GG
-chr1:111413	[T/C]	chr1	111413	Cc01_g00080:741	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	25.0%	4	TT	CC	TT	TT
-chr1:111011	[T/A]	chr1	111011	Cc01_g00080:879	exon	SYNONYMOUS_CODING	atA/atT	I/I	12.5%	4	TT	TT	TA	TT
-chr1:111002	[G/A]	chr1	111002	Cc01_g00080:888	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	25.0%	4	GG	AA	AA	AA
-chr1:110176	[A/G]	chr1	110176	Cc01_g00080:1233	exon	SYNONYMOUS_CODING	acT/acC	T/T	12.5%	4	AA	AA	AG	AA
-chr1:127984	[A/G]	chr1	127984	Cc01_g00090:15	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	AA	GG	GG	GG
-chr1:128022	[T/A]	chr1	128022	Cc01_g00090:53	exon	NON_SYNONYMOUS_CODING	cTg/cAg	L/Q	25.0%	4	TT	AA	AA	AA
-chr1:128047	[A/G]	chr1	128047	Cc01_g00090:78	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	AA	GG	GG	GG
-chr1:128072	[A/T]	chr1	128072	Cc01_g00090:103	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	25.0%	4	AA	TT	TT	TT
-chr1:128252	[T/C]	chr1	128252	Cc01_g00090:283	exon	NON_SYNONYMOUS_CODING	Tat/Cat	Y/H	25.0%	4	TT	CC	CC	CC
-chr1:133985	[C/T]	chr1	133985	Cc01_g00100:165	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	25.0%	4	CC	CC	TT	CC
-chr1:133990	[T/G]	chr1	133990	Cc01_g00100:170	exon	NON_SYNONYMOUS_CODING	aTt/aGt	I/S	12.5%	4	TT	TT	TT	TG
-chr1:134007	[G/T]	chr1	134007	Cc01_g00100:187	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	37.5%	4	GG	TT	TT	GT
-chr1:134174	[T/A]	chr1	134174	Cc01_g00100:354	exon	SYNONYMOUS_CODING	gtT/gtA	V/V	25.0%	4	TT	TT	TA	TA
-chr1:134262	[G/A]	chr1	134262	Cc01_g00100:442	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	25.0%	4	GG	GA	GA	GG
-chr1:134333	[T/C]	chr1	134333	Cc01_g00100:513	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	25.0%	4	TT	TT	TC	TC
-chr1:134393	[C/A]	chr1	134393	Cc01_g00100:573	exon	SYNONYMOUS_CODING	acC/acA	T/T	37.5%	4	CC	AA	CC	AC
-chr1:134403	[C/T]	chr1	134403	Cc01_g00100:583	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	12.5%	4	CC	CC	TC	CC
-chr1:134481	[C/A]	chr1	134481	Cc01_g00100:661	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	12.5%	4	CC	CC	CA	CC
-chr1:134514	[T/C]	chr1	134514	Cc01_g00100:694	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	37.5%	4	TT	TC	TC	TC
-chr1:134570	[T/C]	chr1	134570	Cc01_g00100:750	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	37.5%	4	TT	TT	CC	TC
-chr1:134580	[C/T]	chr1	134580	Cc01_g00100:760	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	25.0%	4	CC	TT	TT	TT
-chr1:134592	[C/G]	chr1	134592	Cc01_g00100:772	exon	NON_SYNONYMOUS_CODING	Ctt/Gtt	L/V	25.0%	4	CC	GG	CC	CC
-chr1:134603	[G/T]	chr1	134603	Cc01_g00100:783	exon	SYNONYMOUS_CODING	acG/acT	T/T	25.0%	4	GG	GG	TT	GG
-chr1:134957	[T/G]	chr1	134957	Cc01_g00100:1137	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	37.5%	4	TT	GG	TT	TG
-chr1:135249	[C/A]	chr1	135249	Cc01_g00100:1429	exon	NON_SYNONYMOUS_CODING	Cca/Aca	P/T	12.5%	4	CC	CC	CC	CA
-chr1:135260	[G/A]	chr1	135260	Cc01_g00100:1440	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	37.5%	4	GG	GG	AA	GA
-chr1:135922	[T/C]	chr1	135922	Cc01_g00110:53	exon	NON_SYNONYMOUS_CODING	aTc/aCc	I/T	37.5%	4	TT	CC	TT	TC
-chr1:135925	[A/G]	chr1	135925	Cc01_g00110:56	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	25.0%	4	AA	AG	AA	AG
-chr1:136539	[G/A]	chr1	136539	Cc01_g00120:13	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	25.0%	4	GG	GG	AA	GG
-chr1:136654	[A/T]	chr1	136654	Cc01_g00120:128	exon	NON_SYNONYMOUS_CODING	cAt/cTt	H/L	25.0%	4	AA	AA	TT	AA
-chr1:136658	[A/G]	chr1	136658	Cc01_g00120:132	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	25.0%	4	AA	GG	GG	GG
-chr1:136898	[A/G]	chr1	136898	Cc01_g00120:372	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	AA	AA	AA	AG
-chr1:136996	[A/G]	chr1	136996	Cc01_g00120:470	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	37.5%	4	AA	GG	GG	AG
-chr1:137035	[T/C]	chr1	137035	Cc01_g00120:509	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	TT	TT	TT	CT
-chr1:137064	[G/A]	chr1	137064	Cc01_g00120:538	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	37.5%	4	GG	AA	AA	GA
-chr1:137153	[A/G]	chr1	137153	Cc01_g00120:627	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	AA	AA	AG
-chr1:137300	[C/T]	chr1	137300	Cc01_g00120:774	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	25.0%	4	CC	CC	TT	CC
-chr1:137483	[G/A]	chr1	137483	Cc01_g00120:957	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	12.5%	4	GG	GG	GG	GA
-chr1:137525	[A/G]	chr1	137525	Cc01_g00120:999	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	AA	GG	AA
-chr1:137571	[A/G]	chr1	137571	Cc01_g00120:1045	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	37.5%	4	AA	GG	GG	AG
-chr1:137669	[C/T]	chr1	137669	Cc01_g00120:1143	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	CC	CC	CC	CT
-chr1:137725	[T/C]	chr1	137725	Cc01_g00120:1199	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	12.5%	4	TT	TT	TT	TC
-chr1:137873	[T/C]	chr1	137873	Cc01_g00120:1347	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	37.5%	4	TT	CC	CC	TC
-chr1:137891	[C/T]	chr1	137891	Cc01_g00120:1365	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CC	CC	TC
-chr1:138059	[T/C]	chr1	138059	Cc01_g00120:1533	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	25.0%	4	TT	CC	TT	TT
-chr1:138108	[C/T]	chr1	138108	Cc01_g00120:1582	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	CC	TT	CC	CT
-chr1:138227	[C/T]	chr1	138227	Cc01_g00120:1701	exon	SYNONYMOUS_CODING	agC/agT	S/S	25.0%	4	CC	CC	TT	CC
-chr1:138383	[C/T]	chr1	138383	Cc01_g00120:1857	exon	SYNONYMOUS_CODING	agC/agT	S/S	37.5%	4	CC	TT	TT	CT
-chr1:138386	[T/C]	chr1	138386	Cc01_g00120:1860	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	37.5%	4	TT	CC	CC	TC
-chr1:138497	[G/A]	chr1	138497	Cc01_g00120:1971	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	GG	GG	AA	GG
-chr1:144606	[G/C]	chr1	144606	Cc01_g00130:45	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	37.5%	4	GG	GG	CC	GC
-chr1:144576	[C/G]	chr1	144576	Cc01_g00130:75	exon	NON_SYNONYMOUS_CODING	ttG/ttC	L/F	25.0%	4	CC	GG	GG	GG
-chr1:144519	[A/G]	chr1	144519	Cc01_g00130:132	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	25.0%	4	AA	AA	GG	AA
-chr1:144434	[T/A]	chr1	144434	Cc01_g00130:217	exon	NON_SYNONYMOUS_CODING	Aat/Tat	N/Y	37.5%	4	TT	AA	TT	TA
-chr1:144286	[C/G]	chr1	144286	Cc01_g00130:365	exon	NON_SYNONYMOUS_CODING	gGt/gCt	G/A	50.0%	4	CC	GG	GG	CC
-chr1:147816	[C/T]	chr1	147816	Cc01_g00140:18	exon	SYNONYMOUS_CODING	agC/agT	S/S	50.0%	2	CC	TT	NN	NN
-chr1:147821	[G/T]	chr1	147821	Cc01_g00140:23	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	33.3%	3	GG	TT	NN	GG
-chr1:147823	[G/A]	chr1	147823	Cc01_g00140:25	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	33.3%	3	GG	AA	NN	GG
-chr1:147861	[G/A]	chr1	147861	Cc01_g00140:63	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	33.3%	3	GG	GG	NN	AA
-chr1:147863	[G/C]	chr1	147863	Cc01_g00140:65	exon	NON_SYNONYMOUS_CODING	aGc/aCc	S/T	33.3%	3	GG	GG	NN	CC
-chr1:147872	[C/T]	chr1	147872	Cc01_g00140:74	exon	NON_SYNONYMOUS_CODING	tCc/tTc	S/F	33.3%	3	CC	TT	NN	CC
-chr1:147974	[G/T]	chr1	147974	Cc01_g00140:176	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	25.0%	4	GG	TT	TT	TT
-chr1:148011	[T/G]	chr1	148011	Cc01_g00140:213	exon	SYNONYMOUS_CODING	tcT/tcG	S/S	25.0%	4	TT	GG	TT	TT
-chr1:148050	[T/C]	chr1	148050	Cc01_g00140:252	exon	SYNONYMOUS_CODING	atT/atC	I/I	25.0%	4	TT	TT	CC	TT
-chr1:148062	[G/A]	chr1	148062	Cc01_g00140:264	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	GG	AA	AA	AA
-chr1:148150	[A/G]	chr1	148150	Cc01_g00140:352	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	12.5%	4	AA	AG	AA	AA
-chr1:148165	[C/G]	chr1	148165	Cc01_g00140:367	exon	NON_SYNONYMOUS_CODING	Ccc/Gcc	P/A	25.0%	4	CC	CC	GG	CC
-chr1:148179	[C/G]	chr1	148179	Cc01_g00140:381	exon	NON_SYNONYMOUS_CODING	agC/agG	S/R	12.5%	4	CC	GC	CC	CC
-chr1:148184	[A/G]	chr1	148184	Cc01_g00140:386	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	25.0%	4	AA	GG	GG	GG
-chr1:148230	[C/T]	chr1	148230	Cc01_g00140:432	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	25.0%	4	CC	TT	CC	CC
-chr1:148933	[G/T]	chr1	148933	Cc01_g00140:447	exon	SYNONYMOUS_CODING	cgG/cgT	R/R	25.0%	4	GG	TT	TT	TT
-chr1:148935	[G/T]	chr1	148935	Cc01_g00140:449	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	25.0%	4	GG	TT	TT	TT
-chr1:148943	[G/A]	chr1	148943	Cc01_g00140:457	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	GG	AA	AA	AA
-chr1:148945	[A/G]	chr1	148945	Cc01_g00140:459	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	25.0%	4	AA	GG	GG	GG
-chr1:149174	[A/G]	chr1	149174	Cc01_g00140:492	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	50.0%	4	AA	AG	GG	AG
-chr1:149185	[A/G]	chr1	149185	Cc01_g00140:503	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	25.0%	4	AA	AA	GG	AA
-chr1:149253	[C/T]	chr1	149253	Cc01_g00140:571	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	25.0%	4	CC	TT	TT	TT
-chr1:149279	[G/A]	chr1	149279	Cc01_g00140:597	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	50.0%	4	GG	GA	AA	GA
-chr1:150025	[G/C]	chr1	150025	Cc01_g00140:698	exon	NON_SYNONYMOUS_CODING	aGa/aCa	R/T	12.5%	4	GG	GG	GG	GC
-chr1:150045	[G/A]	chr1	150045	Cc01_g00140:718	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	GG	GA	GG	GG
-chr1:150080	[A/T]	chr1	150080	Cc01_g00140:753	exon	SYNONYMOUS_CODING	atA/atT	I/I	12.5%	4	AA	AT	AA	AA
-chr1:150083	[G/A]	chr1	150083	Cc01_g00140:756	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	50.0%	4	GG	AG	AA	AG
-chr1:151272	[C/T]	chr1	151272	Cc01_g00140:847	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	CC	CC	CC	CT
-chr1:151277	[G/C]	chr1	151277	Cc01_g00140:852	exon	SYNONYMOUS_CODING	ccG/ccC	P/P	50.0%	4	GG	GC	CC	CG
-chr1:152592	[T/C]	chr1	152592	Cc01_g00140:903	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	TT	TT	TT	TC
-chr1:157051	[C/T]	chr1	157051	Cc01_g00140:960	exon	SYNONYMOUS_CODING	atC/atT	I/I	25.0%	4	CC	TT	TT	TT
-chr1:160171	[C/A]	chr1	160171	Cc01_g00140:1088	exon	NON_SYNONYMOUS_CODING	gCt/gAt	A/D	25.0%	4	CC	AA	AA	AA
-chr1:160217	[A/G]	chr1	160217	Cc01_g00140:1134	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	25.0%	4	AA	AG	AA	AG
-chr1:160786	[C/T]	chr1	160786	Cc01_g00140:1194	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	CC	CC	CC	TC
-chr1:161276	[A/G]	chr1	161276	Cc01_g00140:1312	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	12.5%	4	AA	AG	AA	AA
-chr1:161769	[A/T]	chr1	161769	Cc01_g00140:1461	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	50.0%	4	AA	AT	TT	AT
-chr1:161789	[A/C]	chr1	161789	Cc01_g00140:1481	exon	NON_SYNONYMOUS_CODING	gAt/gCt	D/A	12.5%	4	AA	CA	AA	AA
-chr1:161808	[A/T]	chr1	161808	Cc01_g00140:1500	exon	SYNONYMOUS_CODING	tcA/tcT	S/S	12.5%	4	AA	TA	AA	AA
-chr1:161819	[G/A]	chr1	161819	Cc01_g00140:1511	exon	NON_SYNONYMOUS_CODING	tGc/tAc	C/Y	12.5%	4	GG	GA	GG	GG
-chr1:161837	[T/C]	chr1	161837	Cc01_g00140:1529	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	TT	TT	TT	CT
-chr1:162050	[C/T]	chr1	162050	Cc01_g00140:1545	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	12.5%	4	CC	CC	CT	CC
-chr1:162069	[C/A]	chr1	162069	Cc01_g00140:1564	exon	NON_SYNONYMOUS_CODING	Cag/Aag	Q/K	12.5%	4	CC	CC	CC	AC
-chr1:162112	[A/T]	chr1	162112	Cc01_g00140:1607	exon	NON_SYNONYMOUS_CODING	aAa/aTa	K/I	12.5%	4	AA	AT	AA	AA
-chr1:162135	[A/C]	chr1	162135	Cc01_g00140:1630	exon	SYNONYMOUS_CODING	Aga/Cga	R/R	12.5%	4	AA	AA	AA	CA
-chr1:162634	[C/G]	chr1	162634	Cc01_g00140:1650	exon	SYNONYMOUS_CODING	acC/acG	T/T	12.5%	4	CC	CC	CC	GC
-chr1:163489	[A/T]	chr1	163489	Cc01_g00140:1854	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	12.5%	4	AA	AT	AA	AA
-chr1:168498	[C/T]	chr1	168498	Cc01_g00150:90	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	25.0%	4	CC	CC	TT	CC
-chr1:168595	[G/A]	chr1	168595	Cc01_g00150:187	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	12.5%	4	GG	GG	GG	GA
-chr1:168747	[A/T]	chr1	168747	Cc01_g00150:339	exon	SYNONYMOUS_CODING	ggA/ggT	G/G	25.0%	4	AA	AA	AA	TT
-chr1:174617	[C/G]	chr1	174617	Cc01_g00160:6	exon	SYNONYMOUS_CODING	gcG/gcC	A/A	25.0%	4	CC	CC	GG	CC
-chr1:174616	[C/T]	chr1	174616	Cc01_g00160:7	exon	NON_SYNONYMOUS_CODING	Gcg/Acg	A/T	25.0%	4	CC	CC	TT	CC
-chr1:174601	[G/C]	chr1	174601	Cc01_g00160:22	exon	NON_SYNONYMOUS_CODING	Ctg/Gtg	L/V	12.5%	4	GG	GC	GG	GG
-chr1:174600	[A/G]	chr1	174600	Cc01_g00160:23	exon	NON_SYNONYMOUS_CODING	cTg/cCg	L/P	12.5%	4	AA	AA	AG	AA
-chr1:174590	[C/A]	chr1	174590	Cc01_g00160:33	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	12.5%	4	CC	CC	CA	CC
-chr1:174580	[C/T]	chr1	174580	Cc01_g00160:43	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	37.5%	4	CC	TC	TC	CT
-chr1:174572	[C/T]	chr1	174572	Cc01_g00160:51	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	37.5%	4	CC	TC	TC	CT
-chr1:174565	[T/C]	chr1	174565	Cc01_g00160:58	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	37.5%	4	TT	CT	TC	TC
-chr1:174562	[A/G]	chr1	174562	Cc01_g00160:61	exon	NON_SYNONYMOUS_CODING	Tgt/Cgt	C/R	25.0%	4	AA	GA	AA	AG
-chr1:174533	[C/G]	chr1	174533	Cc01_g00160:90	exon	SYNONYMOUS_CODING	ctG/ctC	L/L	25.0%	4	CC	GG	GG	GG
-chr1:174501	[C/T]	chr1	174501	Cc01_g00160:122	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	37.5%	4	CC	TC	TT	CC
-chr1:174490	[C/T]	chr1	174490	Cc01_g00160:133	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	50.0%	4	CC	TC	TT	TC
-chr1:174472	[C/T]	chr1	174472	Cc01_g00160:151	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	12.5%	4	CC	TC	CC	CC
-chr1:174446	[T/C]	chr1	174446	Cc01_g00160:177	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	TT	TC	TT	TC
-chr1:174440	[G/A]	chr1	174440	Cc01_g00160:183	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	37.5%	4	GG	AG	AA	GG
-chr1:174419	[C/T]	chr1	174419	Cc01_g00160:204	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	CC	TC	CT	CC
-chr1:174413	[G/C]	chr1	174413	Cc01_g00160:210	exon	SYNONYMOUS_CODING	acC/acG	T/T	12.5%	4	GG	GC	GG	GG
-chr1:174411	[C/T]	chr1	174411	Cc01_g00160:212	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	25.0%	4	CC	TC	CT	CC
-chr1:174403	[T/C]	chr1	174403	Cc01_g00160:220	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	12.5%	4	TT	CT	TT	TT
-chr1:174401	[G/A]	chr1	174401	Cc01_g00160:222	exon	SYNONYMOUS_CODING	agC/agT	S/S	25.0%	4	GG	GA	AG	GG
-chr1:174374	[G/A]	chr1	174374	Cc01_g00160:249	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	25.0%	4	GG	GG	AA	GG
-chr1:174353	[G/A]	chr1	174353	Cc01_g00160:270	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	12.5%	4	GG	GG	GA	GG
-chr1:174324	[G/A]	chr1	174324	Cc01_g00160:299	exon	NON_SYNONYMOUS_CODING	cCc/cTc	P/L	37.5%	4	GG	GA	GA	GA
-chr1:174310	[C/T]	chr1	174310	Cc01_g00160:313	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	50.0%	4	CC	CT	TT	CT
-chr1:174297	[C/T]	chr1	174297	Cc01_g00160:326	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	25.0%	4	CC	CT	CC	CT
-chr1:174295	[G/A]	chr1	174295	Cc01_g00160:328	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	25.0%	4	GG	GA	GG	GA
-chr1:174280	[G/T]	chr1	174280	Cc01_g00160:343	exon	NON_SYNONYMOUS_CODING	Ctg/Atg	L/M	25.0%	4	GG	GT	GT	GG
-chr1:174257	[G/A]	chr1	174257	Cc01_g00160:366	exon	SYNONYMOUS_CODING	caC/caT	H/H	12.5%	4	GG	GG	GA	GG
-chr1:174251	[C/T]	chr1	174251	Cc01_g00160:372	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	12.5%	4	CC	CC	CT	CC
-chr1:174248	[G/A]	chr1	174248	Cc01_g00160:375	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	GG	GG	GA	GG
-chr1:174242	[A/T]	chr1	174242	Cc01_g00160:381	exon	SYNONYMOUS_CODING	atT/atA	I/I	12.5%	4	AA	AA	AA	AT
-chr1:174232	[C/T]	chr1	174232	Cc01_g00160:391	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	12.5%	4	CC	CC	CT	CC
-chr1:174225	[G/C]	chr1	174225	Cc01_g00160:398	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	12.5%	4	GG	GC	GG	GG
-chr1:174208	[C/G]	chr1	174208	Cc01_g00160:415	exon	NON_SYNONYMOUS_CODING	Gtt/Ctt	V/L	12.5%	4	CC	CG	CC	CC
-chr1:174205	[G/A]	chr1	174205	Cc01_g00160:418	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	25.0%	4	GG	GA	AG	GG
-chr1:174192	[G/A]	chr1	174192	Cc01_g00160:431	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	25.0%	4	GG	GA	GA	GG
-chr1:174190	[G/A]	chr1	174190	Cc01_g00160:433	exon	STOP_GAINED	Cag/Tag	Q/5	25.0%	4	GG	GA	AG	GG
-chr1:174185	[A/T]	chr1	174185	Cc01_g00160:438	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	4	AA	AT	TA	AA
-chr1:174174	[C/T]	chr1	174174	Cc01_g00160:449	exon	NON_SYNONYMOUS_CODING	gGc/gAc	G/D	25.0%	4	CC	CT	TC	CC
-chr1:174172	[T/C]	chr1	174172	Cc01_g00160:451	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	12.5%	4	TT	TT	TC	TT
-chr1:174068	[G/C]	chr1	174068	Cc01_g00160:555	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	16.7%	3	GG	GC	NN	GG
-chr1:174026	[G/T]	chr1	174026	Cc01_g00160:597	exon	NON_SYNONYMOUS_CODING	agC/agA	S/R	33.3%	3	GG	TT	NN	GG
-chr1:173945	[C/G]	chr1	173945	Cc01_g00160:678	exon	SYNONYMOUS_CODING	gcG/gcC	A/A	12.5%	4	CC	CG	CC	CC
-chr1:173942	[C/T]	chr1	173942	Cc01_g00160:681	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	37.5%	4	CC	TT	TT	CT
-chr1:173921	[G/A]	chr1	173921	Cc01_g00160:702	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	37.5%	4	GG	AA	AA	GA
-chr1:173846	[G/A]	chr1	173846	Cc01_g00160:777	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	50.0%	3	GG	AA	NN	GA
-chr1:173642	[A/T]	chr1	173642	Cc01_g00160:981	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	25.0%	4	AA	TT	AA	AA
-chr1:173627	[A/G]	chr1	173627	Cc01_g00160:996	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	25.0%	4	AA	GG	AA	AA
-chr1:173596	[C/A]	chr1	173596	Cc01_g00160:1027	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	CC	CA	CC	CC
-chr1:173585	[G/A]	chr1	173585	Cc01_g00160:1038	exon	SYNONYMOUS_CODING	atC/atT	I/I	37.5%	4	GG	AG	AA	AA
-chr1:173444	[G/T]	chr1	173444	Cc01_g00160:1179	exon	SYNONYMOUS_CODING	atC/atA	I/I	25.0%	2	GG	NN	NN	GT
-chr1:173410	[C/T]	chr1	173410	Cc01_g00160:1213	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	16.7%	3	CC	CC	NN	CT
-chr1:173230	[T/C]	chr1	173230	Cc01_g00160:1393	exon	NON_SYNONYMOUS_CODING	Acg/Gcg	T/A	16.7%	3	TT	TT	NN	TC
-chr1:173180	[C/T]	chr1	173180	Cc01_g00160:1443	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	33.3%	3	CC	TT	NN	CC
-chr1:173126	[A/G]	chr1	173126	Cc01_g00160:1497	exon	SYNONYMOUS_CODING	atT/atC	I/I	25.0%	4	AA	GG	AA	AA
-chr1:172613	[G/C]	chr1	172613	Cc01_g00160:2010	exon	SYNONYMOUS_CODING	ctC/ctG	L/L	50.0%	3	GG	CC	NN	GC
-chr1:172589	[G/T]	chr1	172589	Cc01_g00160:2034	exon	NON_SYNONYMOUS_CODING	ttC/ttA	F/L	16.7%	3	GG	GG	NN	TG
-chr1:172499	[A/G]	chr1	172499	Cc01_g00160:2124	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	50.0%	3	AA	NN	GG	AG
-chr1:172355	[T/C]	chr1	172355	Cc01_g00160:2268	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	16.7%	3	TT	TC	NN	TT
-chr1:172314	[T/C]	chr1	172314	Cc01_g00160:2309	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	16.7%	3	TT	TC	NN	TT
-chr1:172303	[G/A]	chr1	172303	Cc01_g00160:2320	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	33.3%	3	GG	AA	NN	GG
-chr1:172265	[T/C]	chr1	172265	Cc01_g00160:2358	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	16.7%	3	TT	TT	NN	TC
-chr1:172206	[G/A]	chr1	172206	Cc01_g00160:2417	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	16.7%	3	GG	GA	NN	GG
-chr1:172178	[T/C]	chr1	172178	Cc01_g00160:2445	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	2	TT	NN	NN	TC
-chr1:172150	[T/C]	chr1	172150	Cc01_g00160:2473	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	2	TT	NN	NN	TC
-chr1:181949	[A/C]	chr1	181949	Cc01_g00170:492	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	50.0%	2	AA	NN	NN	CC
-chr1:182195	[C/A]	chr1	182195	Cc01_g00170:738	exon	SYNONYMOUS_CODING	atC/atA	I/I	50.0%	2	CC	NN	NN	AA
-chr1:182231	[G/A]	chr1	182231	Cc01_g00170:774	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	33.3%	3	GG	NN	AA	AA
-chr1:182291	[A/G]	chr1	182291	Cc01_g00170:834	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	50.0%	3	AA	NN	AG	GG
-chr1:182424	[G/A]	chr1	182424	Cc01_g00170:861	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	33.3%	3	GG	NN	AA	AA
-chr1:182456	[A/G]	chr1	182456	Cc01_g00170:893	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	16.7%	3	AA	NN	AA	AG
-chr1:182483	[A/G]	chr1	182483	Cc01_g00170:920	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	12.5%	4	AA	AA	AA	AG
-chr1:182874	[A/G]	chr1	182874	Cc01_g00170:1113	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	33.3%	3	AA	NN	AA	GG
-chr1:183107	[T/C]	chr1	183107	Cc01_g00170:1346	exon	NON_SYNONYMOUS_CODING	aTc/aCc	I/T	33.3%	3	TT	NN	CC	TT
-chr1:188621	[G/A]	chr1	188621	Cc01_g00180:12	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	25.0%	4	GG	AA	AA	AA
-chr1:188690	[C/A]	chr1	188690	Cc01_g00180:81	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	12.5%	4	CC	CA	CC	CC
-chr1:189264	[A/G]	chr1	189264	Cc01_g00180:254	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	25.0%	4	AA	AA	AG	AG
-chr1:189346	[C/G]	chr1	189346	Cc01_g00180:336	exon	SYNONYMOUS_CODING	cgC/cgG	R/R	25.0%	4	CC	GG	GG	GG
-chr1:189357	[G/A]	chr1	189357	Cc01_g00180:347	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	25.0%	4	GG	AA	AA	AA
-chr1:189499	[G/C]	chr1	189499	Cc01_g00180:489	exon	SYNONYMOUS_CODING	ctG/ctC	L/L	50.0%	4	GG	CC	CC	GG
-chr1:189586	[C/T]	chr1	189586	Cc01_g00180:576	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	50.0%	4	CC	TT	TT	CC
-chr1:190066	[A/G]	chr1	190066	Cc01_g00180:780	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	AA	GG	AA	AA
-chr1:190127	[T/G]	chr1	190127	Cc01_g00180:841	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	25.0%	4	TT	GG	GG	GG
-chr1:190494	[C/T]	chr1	190494	Cc01_g00180:1023	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	25.0%	4	CC	TT	TT	TT
-chr1:190503	[A/G]	chr1	190503	Cc01_g00180:1032	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	AA	AA	AG
-chr1:190584	[T/C]	chr1	190584	Cc01_g00180:1113	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	25.0%	4	TT	TT	CC	TT
-chr1:190662	[A/G]	chr1	190662	Cc01_g00180:1191	exon	SYNONYMOUS_STOP	taA/taG	3/3	25.0%	4	AA	AA	GG	AA
-chr1:193899	[T/C]	chr1	193899	Cc01_g00190:67	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	25.0%	4	TT	CC	TT	TT
-chr1:193871	[T/C]	chr1	193871	Cc01_g00190:95	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	37.5%	4	TT	TT	CC	TC
-chr1:193809	[A/T]	chr1	193809	Cc01_g00190:157	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	12.5%	4	AA	AA	AA	TA
-chr1:193801	[G/C]	chr1	193801	Cc01_g00190:165	exon	NON_SYNONYMOUS_CODING	agC/agG	S/R	12.5%	4	GG	GG	GG	CG
-chr1:193793	[C/T]	chr1	193793	Cc01_g00190:173	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	25.0%	4	CC	CT	CC	TC
-chr1:193735	[C/T]	chr1	193735	Cc01_g00190:231	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	37.5%	4	CC	CT	CT	TC
-chr1:193681	[G/C]	chr1	193681	Cc01_g00190:240	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	25.0%	4	GG	GC	GG	GC
-chr1:193649	[T/G]	chr1	193649	Cc01_g00190:272	exon	NON_SYNONYMOUS_CODING	gAc/gCc	D/A	12.5%	4	TT	TT	TT	TG
-chr1:193584	[G/A]	chr1	193584	Cc01_g00190:337	exon	NON_SYNONYMOUS_CODING	Ccc/Tcc	P/S	25.0%	4	GG	GG	AA	GG
-chr1:193551	[T/A]	chr1	193551	Cc01_g00190:370	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	37.5%	4	TT	AA	TT	TA
-chr1:193129	[T/A]	chr1	193129	Cc01_g00190:445	exon	NON_SYNONYMOUS_CODING	Aca/Tca	T/S	25.0%	4	TT	TT	AA	TT
-chr1:192625	[A/G]	chr1	192625	Cc01_g00190:654	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	25.0%	4	AA	AA	GG	AA
-chr1:191959	[T/C]	chr1	191959	Cc01_g00190:689	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	25.0%	4	TT	TT	CC	TT
-chr1:191385	[T/A]	chr1	191385	Cc01_g00190:915	exon	SYNONYMOUS_CODING	tcA/tcT	S/S	25.0%	4	TT	AA	AA	AA
-chr1:191370	[A/G]	chr1	191370	Cc01_g00190:930	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	25.0%	4	AA	AA	GG	AA
-chr1:191325	[C/T]	chr1	191325	Cc01_g00190:975	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	CC	TT	TT	TT
-chr1:199253	[T/C]	chr1	199253	Cc01_g00200:6	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	TT	TT	CC	TT
-chr1:199193	[G/A]	chr1	199193	Cc01_g00200:66	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	GG	GG	GG	GA
-chr1:199148	[T/A]	chr1	199148	Cc01_g00200:111	exon	NON_SYNONYMOUS_CODING	ttA/ttT	L/F	12.5%	4	TT	TT	TT	AT
-chr1:199134	[G/A]	chr1	199134	Cc01_g00200:125	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	37.5%	4	GG	AA	GG	AG
-chr1:199093	[A/C]	chr1	199093	Cc01_g00200:166	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	37.5%	4	AA	CC	AA	CA
-chr1:199078	[T/C]	chr1	199078	Cc01_g00200:181	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	TT	CC	TT	TT
-chr1:198900	[A/T]	chr1	198900	Cc01_g00200:262	exon	NON_SYNONYMOUS_CODING	Tcg/Acg	S/T	12.5%	4	AA	AA	AA	AT
-chr1:198850	[G/A]	chr1	198850	Cc01_g00200:312	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	12.5%	4	GG	GG	GG	GA
-chr1:198811	[A/G]	chr1	198811	Cc01_g00200:351	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	25.0%	4	AA	GG	AA	AA
-chr1:198805	[A/G]	chr1	198805	Cc01_g00200:357	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	AA	AA	GG	AA
-chr1:198802	[C/G]	chr1	198802	Cc01_g00200:360	exon	SYNONYMOUS_CODING	gtG/gtC	V/V	25.0%	4	CC	CC	GG	CC
-chr1:197996	[A/G]	chr1	197996	Cc01_g00200:615	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	AA	AA	AA	AG
-chr1:197551	[A/G]	chr1	197551	Cc01_g00200:963	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	25.0%	4	AA	GG	AA	AA
-chr1:197200	[C/T]	chr1	197200	Cc01_g00200:1207	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	4	CC	TT	CT	CT
-chr1:197177	[C/T]	chr1	197177	Cc01_g00200:1230	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	25.0%	4	CC	TT	TT	TT
-chr1:196815	[C/T]	chr1	196815	Cc01_g00200:1344	exon	SYNONYMOUS_CODING	acG/acA	T/T	50.0%	4	CC	CT	TT	CT
-chr1:196570	[A/T]	chr1	196570	Cc01_g00200:1485	exon	SYNONYMOUS_CODING	acT/acA	T/T	12.5%	4	AA	AA	AA	AT
-chr1:196315	[G/A]	chr1	196315	Cc01_g00200:1584	exon	SYNONYMOUS_CODING	agC/agT	S/S	25.0%	4	GG	GG	AA	GG
-chr1:196047	[G/C]	chr1	196047	Cc01_g00200:1668	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	25.0%	4	GG	GG	CC	GG
-chr1:195875	[A/G]	chr1	195875	Cc01_g00200:1698	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	AA	GG	AA	AA
-chr1:195821	[A/G]	chr1	195821	Cc01_g00200:1752	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	AA	GG	AA	AA
-chr1:208818	[T/C]	chr1	208818	Cc01_g00220:430	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	TT	TC	TT	TC
-chr1:207744	[G/A]	chr1	207744	Cc01_g00220:618	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	25.0%	4	GG	GA	GG	GA
-chr1:207027	[T/C]	chr1	207027	Cc01_g00220:756	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	TT	TC	TT	TT
-chr1:206648	[A/G]	chr1	206648	Cc01_g00220:891	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AG	AA	AA
-chr1:206440	[T/C]	chr1	206440	Cc01_g00220:1099	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	12.5%	4	TT	TT	TT	TC
-chr1:206402	[A/G]	chr1	206402	Cc01_g00220:1137	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	50.0%	4	AA	AA	GG	GG
-chr1:216024	[C/T]	chr1	216024	Cc01_g00230:429	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	50.0%	2	CC	TT	NN	NN
-chr1:218860	[T/C]	chr1	218860	Cc01_g00230:1338	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	50.0%	4	TT	CC	TT	CC
-chr1:218862	[G/A]	chr1	218862	Cc01_g00230:1340	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	25.0%	4	GG	GG	AA	GG
-chr1:219273	[C/T]	chr1	219273	Cc01_g00230:1566	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	33.3%	3	CC	NN	TT	TT
-chr1:219413	[G/A]	chr1	219413	Cc01_g00230:1605	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	50.0%	3	GG	NN	GA	AA
-chr1:219545	[T/C]	chr1	219545	Cc01_g00230:1737	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	25.0%	4	TT	TT	TT	CC
-chr1:220134	[A/G]	chr1	220134	Cc01_g00230:2126	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	25.0%	4	AA	GG	GG	GG
-chr1:220340	[A/G]	chr1	220340	Cc01_g00230:2332	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	25.0%	4	AA	GG	GG	GG
-chr1:221669	[G/T]	chr1	221669	Cc01_g00240:79	exon	NON_SYNONYMOUS_CODING	Ggc/Tgc	G/C	50.0%	4	GG	TT	TT	GG
-chr1:221674	[T/C]	chr1	221674	Cc01_g00240:84	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	12.5%	4	TT	TT	TT	TC
-chr1:221714	[G/T]	chr1	221714	Cc01_g00240:124	exon	NON_SYNONYMOUS_CODING	Ggg/Tgg	G/W	25.0%	4	GG	TT	GG	GG
-chr1:221718	[G/A]	chr1	221718	Cc01_g00240:128	exon	NON_SYNONYMOUS_CODING	gGa/gAa	G/E	12.5%	4	GG	GG	GG	AG
-chr1:221746	[A/T]	chr1	221746	Cc01_g00240:156	exon	SYNONYMOUS_CODING	acA/acT	T/T	12.5%	4	AA	AT	AA	AA
-chr1:221763	[A/T]	chr1	221763	Cc01_g00240:173	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	12.5%	4	AA	AT	AA	AA
-chr1:221788	[C/T]	chr1	221788	Cc01_g00240:198	exon	SYNONYMOUS_CODING	agC/agT	S/S	12.5%	4	CC	CT	CC	CC
-chr1:221833	[T/C]	chr1	221833	Cc01_g00240:243	exon	SYNONYMOUS_CODING	acT/acC	T/T	12.5%	4	TT	CT	TT	TT
-chr1:221852	[C/T]	chr1	221852	Cc01_g00240:262	exon	NON_SYNONYMOUS_CODING	Cgc/Tgc	R/C	12.5%	4	CC	CC	CC	CT
-chr1:221853	[G/A]	chr1	221853	Cc01_g00240:263	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	25.0%	4	GG	GG	GG	AA
-chr1:221866	[A/T]	chr1	221866	Cc01_g00240:276	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	25.0%	4	AA	AA	AA	TT
-chr1:222383	[T/C]	chr1	222383	Cc01_g00240:354	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	TT	TC	TT	TT
-chr1:222633	[T/C]	chr1	222633	Cc01_g00240:417	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	CT	TT	TT
-chr1:222951	[T/C]	chr1	222951	Cc01_g00240:534	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	CT	TT	TT
-chr1:224386	[T/A]	chr1	224386	Cc01_g00240:726	exon	SYNONYMOUS_CODING	gtT/gtA	V/V	12.5%	4	TT	TA	TT	TT
-chr1:224660	[A/T]	chr1	224660	Cc01_g00240:825	exon	SYNONYMOUS_CODING	ggA/ggT	G/G	37.5%	4	AA	TT	AA	AT
-chr1:224706	[G/C]	chr1	224706	Cc01_g00240:871	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	12.5%	4	GG	GG	GC	GG
-chr1:225032	[G/A]	chr1	225032	Cc01_g00240:933	exon	SYNONYMOUS_CODING	acG/acA	T/T	12.5%	4	GG	GA	GG	GG
-chr1:225065	[C/T]	chr1	225065	Cc01_g00240:966	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	CC	TC	CC	CC
-chr1:225194	[C/T]	chr1	225194	Cc01_g00240:1008	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	CC	TT	CC	CT
-chr1:226501	[T/C]	chr1	226501	Cc01_g00240:1072	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	TT	TT	TC	CT
-chr1:226539	[C/A]	chr1	226539	Cc01_g00240:1110	exon	SYNONYMOUS_CODING	acC/acA	T/T	12.5%	4	CC	CC	CC	CA
-chr1:226575	[T/C]	chr1	226575	Cc01_g00240:1146	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	12.5%	4	TT	TC	TT	TT
-chr1:226694	[C/G]	chr1	226694	Cc01_g00240:1181	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	12.5%	4	CC	CC	CG	CC
-chr1:232340	[C/T]	chr1	232340	Cc01_g00250:33	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	25.0%	4	CC	CC	TT	CC
-chr1:232292	[G/A]	chr1	232292	Cc01_g00250:81	exon	SYNONYMOUS_CODING	acC/acT	T/T	25.0%	4	GG	AA	AA	AA
-chr1:229696	[A/G]	chr1	229696	Cc01_g00250:380	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	AA	AA	AA	AG
-chr1:228604	[A/G]	chr1	228604	Cc01_g00250:468	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	AA	AA	AG	AA
-chr1:250535	[A/C]	chr1	250535	Cc01_g00260:69	exon	NON_SYNONYMOUS_CODING	atT/atG	I/M	12.5%	4	AA	AA	AA	AC
-chr1:250487	[T/A]	chr1	250487	Cc01_g00260:117	exon	SYNONYMOUS_CODING	acA/acT	T/T	12.5%	4	TT	TA	TT	TT
-chr1:250388	[G/A]	chr1	250388	Cc01_g00260:216	exon	SYNONYMOUS_CODING	acC/acT	T/T	25.0%	4	GG	AA	GG	GG
-chr1:246857	[G/A]	chr1	246857	Cc01_g00260:529	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	12.5%	4	GG	GG	GA	GG
-chr1:246722	[T/C]	chr1	246722	Cc01_g00260:584	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	37.5%	4	TT	CC	TT	TC
-chr1:246700	[A/G]	chr1	246700	Cc01_g00260:606	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	AA	AA	AA	GA
-chr1:246674	[G/C]	chr1	246674	Cc01_g00260:632	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	12.5%	4	GG	GG	GG	GC
-chr1:244939	[T/C]	chr1	244939	Cc01_g00260:648	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	25.0%	4	TT	TC	TC	TT
-chr1:244750	[T/C]	chr1	244750	Cc01_g00260:726	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	12.5%	4	TT	TT	TT	TC
-chr1:254013	[C/T]	chr1	254013	Cc01_g00270:80	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	CC	CT	CC	CC
-chr1:254369	[A/G]	chr1	254369	Cc01_g00270:114	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	AA	AG	AA
-chr1:254414	[C/T]	chr1	254414	Cc01_g00270:159	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CT	CC	CC
-chr1:254486	[C/T]	chr1	254486	Cc01_g00270:231	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	CC	CT	CC	CC
-chr1:256173	[C/T]	chr1	256173	Cc01_g00270:426	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	50.0%	4	CC	CT	TT	CT
-chr1:256269	[T/A]	chr1	256269	Cc01_g00270:522	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	12.5%	4	TT	TT	TT	TA
-chr1:256296	[C/G]	chr1	256296	Cc01_g00270:549	exon	SYNONYMOUS_CODING	ggC/ggG	G/G	12.5%	4	CC	CC	CG	CC
-chr1:256351	[G/C]	chr1	256351	Cc01_g00270:604	exon	NON_SYNONYMOUS_CODING	Gca/Cca	A/P	12.5%	4	GG	GC	GG	GG
-chr1:269489	[G/A]	chr1	269489	Cc01_g00280:101	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	12.5%	4	GG	GG	GG	GA
-chr1:269514	[T/C]	chr1	269514	Cc01_g00280:126	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	TT	CC	CC	CC
-chr1:269516	[T/C]	chr1	269516	Cc01_g00280:128	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	TT	TT	TT	TC
-chr1:269724	[T/C]	chr1	269724	Cc01_g00280:336	exon	SYNONYMOUS_CODING	caT/caC	H/H	25.0%	4	TT	CC	CC	CC
-chr1:269781	[G/A]	chr1	269781	Cc01_g00280:393	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	12.5%	4	GG	GG	GG	GA
-chr1:269793	[T/C]	chr1	269793	Cc01_g00280:405	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	TT	TT	TT	TC
-chr1:269833	[G/T]	chr1	269833	Cc01_g00280:445	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	GG	GG	GG	GT
-chr1:269843	[T/C]	chr1	269843	Cc01_g00280:455	exon	NON_SYNONYMOUS_CODING	tTa/tCa	L/S	12.5%	4	TT	TT	TT	CT
-chr1:269847	[C/T]	chr1	269847	Cc01_g00280:459	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	CC	CC	CC	CT
-chr1:269904	[T/C]	chr1	269904	Cc01_g00280:516	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	TT	TT	TT	TC
-chr1:269928	[C/T]	chr1	269928	Cc01_g00280:540	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	CC	CC	CC	CT
-chr1:270027	[G/T]	chr1	270027	Cc01_g00280:639	exon	SYNONYMOUS_CODING	ggG/ggT	G/G	25.0%	4	GG	TT	TT	TT
-chr1:270312	[A/C]	chr1	270312	Cc01_g00280:924	exon	SYNONYMOUS_CODING	tcA/tcC	S/S	25.0%	4	AA	AA	CC	AA
-chr1:270383	[G/C]	chr1	270383	Cc01_g00280:995	exon	NON_SYNONYMOUS_CODING	gGt/gCt	G/A	12.5%	4	GG	GG	GG	GC
-chr1:270395	[G/T]	chr1	270395	Cc01_g00280:1007	exon	NON_SYNONYMOUS_CODING	gGt/gTt	G/V	12.5%	4	GG	GG	GT	GG
-chr1:270483	[T/C]	chr1	270483	Cc01_g00280:1095	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	TT	TT	TT	TC
-chr1:276780	[A/C]	chr1	276780	Cc01_g00290:10	exon	NON_SYNONYMOUS_CODING	Tcc/Gcc	S/A	25.0%	4	AA	CC	CC	CC
-chr1:274650	[T/G]	chr1	274650	Cc01_g00290:196	exon	NON_SYNONYMOUS_CODING	Att/Ctt	I/L	12.5%	4	TT	TT	TG	TT
-chr1:274413	[T/A]	chr1	274413	Cc01_g00290:433	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	12.5%	4	TT	TT	TA	TT
-chr1:274345	[A/G]	chr1	274345	Cc01_g00290:501	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	AA	AA	AG	AA
-chr1:273652	[G/A]	chr1	273652	Cc01_g00290:639	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	37.5%	4	GG	AA	GG	GA
-chr1:273576	[C/T]	chr1	273576	Cc01_g00290:715	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	25.0%	4	CC	CC	TT	CC
-chr1:273394	[C/T]	chr1	273394	Cc01_g00290:897	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	37.5%	4	CC	CC	TT	CT
-chr1:273220	[G/A]	chr1	273220	Cc01_g00290:1071	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	GG	GG	GA	GG
-chr1:273180	[C/G]	chr1	273180	Cc01_g00290:1111	exon	NON_SYNONYMOUS_CODING	Gcc/Ccc	A/P	37.5%	4	CC	CC	GG	CG
-chr1:273178	[G/A]	chr1	273178	Cc01_g00290:1113	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	GG	GG	AA	GA
-chr1:288461	[C/T]	chr1	288461	Cc01_g00300:50	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	CC	TT	CC	CC
-chr1:288120	[G/A]	chr1	288120	Cc01_g00300:228	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	12.5%	4	GG	GG	GA	GG
-chr1:287468	[G/A]	chr1	287468	Cc01_g00300:469	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	25.0%	4	GG	GG	AA	GG
-chr1:287403	[A/G]	chr1	287403	Cc01_g00300:534	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	25.0%	4	AA	GG	GG	GG
-chr1:287370	[C/T]	chr1	287370	Cc01_g00300:567	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	25.0%	4	CC	TT	TT	TT
-chr1:286545	[A/G]	chr1	286545	Cc01_g00300:774	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	AA	AA	GG	AA
-chr1:286507	[G/A]	chr1	286507	Cc01_g00300:812	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	37.5%	4	GG	AA	GG	GA
-chr1:286482	[G/C]	chr1	286482	Cc01_g00300:837	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	12.5%	4	GG	GG	GG	CG
-chr1:285910	[C/A]	chr1	285910	Cc01_g00300:942	exon	SYNONYMOUS_CODING	gtG/gtT	V/V	50.0%	4	CC	AA	CC	AA
-chr1:285897	[A/G]	chr1	285897	Cc01_g00300:955	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	25.0%	4	AA	GG	GG	GG
-chr1:285722	[T/G]	chr1	285722	Cc01_g00300:1031	exon	NON_SYNONYMOUS_CODING	gAt/gCt	D/A	25.0%	4	TT	TT	GG	TT
-chr1:283896	[T/C]	chr1	283896	Cc01_g00300:1335	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	TT	TT	TT	TC
-chr1:283878	[G/A]	chr1	283878	Cc01_g00300:1353	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	25.0%	4	GG	AA	AA	AA
-chr1:283455	[A/T]	chr1	283455	Cc01_g00300:1569	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	12.5%	4	AA	AT	AA	AA
-chr1:283107	[T/C]	chr1	283107	Cc01_g00300:1682	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	12.5%	4	TT	TC	TT	TT
-chr1:280180	[T/C]	chr1	280180	Cc01_g00300:1872	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	25.0%	4	TT	CC	CC	CC
-chr1:293608	[T/C]	chr1	293608	Cc01_g00310:9	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	TT	TC	TT	TC
-chr1:293593	[G/A]	chr1	293593	Cc01_g00310:24	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	GG	GA	GA	GA
-chr1:293581	[A/T]	chr1	293581	Cc01_g00310:36	exon	SYNONYMOUS_CODING	ctT/ctA	L/L	37.5%	4	AA	AT	AT	AT
-chr1:293556	[G/A]	chr1	293556	Cc01_g00310:61	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	37.5%	4	GG	GA	GA	GA
-chr1:293548	[G/A]	chr1	293548	Cc01_g00310:69	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	12.5%	4	GG	GG	GA	GG
-chr1:293524	[A/G]	chr1	293524	Cc01_g00310:93	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	37.5%	4	AA	GG	GG	AG
-chr1:290571	[T/C]	chr1	290571	Cc01_g00310:310	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	12.5%	4	TT	TT	TC	TT
-chr1:300689	[C/A]	chr1	300689	Cc01_g00320:60	exon	SYNONYMOUS_CODING	ctC/ctA	L/L	12.5%	4	CC	CC	CC	CA
-chr1:300911	[G/T]	chr1	300911	Cc01_g00320:111	exon	SYNONYMOUS_CODING	cgG/cgT	R/R	25.0%	4	GG	TT	TT	TT
-chr1:301164	[A/C]	chr1	301164	Cc01_g00320:219	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	12.5%	4	AA	AA	AC	AA
-chr1:301180	[G/T]	chr1	301180	Cc01_g00320:235	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	GG	GT	GG	GG
-chr1:304719	[T/A]	chr1	304719	Cc01_g00320:558	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	12.5%	4	TT	TT	TT	TA
-chr1:304779	[A/C]	chr1	304779	Cc01_g00320:618	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	12.5%	4	AA	AA	AC	AA
-chr1:329247	[C/A]	chr1	329247	Cc01_g00330:270	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	25.0%	4	CC	AA	CC	CC
-chr1:329217	[G/A]	chr1	329217	Cc01_g00330:300	exon	SYNONYMOUS_CODING	agC/agT	S/S	50.0%	4	GG	AA	GA	GA
-chr1:329108	[G/A]	chr1	329108	Cc01_g00330:409	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	GG	GA	GG	GG
-chr1:329088	[A/G]	chr1	329088	Cc01_g00330:429	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	AA	AA	AG	AA
-chr1:328149	[A/G]	chr1	328149	Cc01_g00330:456	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	AA	AA	GA	AA
-chr1:328065	[T/G]	chr1	328065	Cc01_g00330:540	exon	SYNONYMOUS_CODING	tcA/tcC	S/S	50.0%	4	TT	GG	TG	TG
-chr1:327708	[A/C]	chr1	327708	Cc01_g00330:644	exon	NON_SYNONYMOUS_CODING	gTg/gGg	V/G	12.5%	4	AA	AC	AA	AA
-chr1:327632	[C/T]	chr1	327632	Cc01_g00330:720	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	37.5%	4	CC	TT	CC	CT
-chr1:327519	[A/C]	chr1	327519	Cc01_g00330:760	exon	NON_SYNONYMOUS_CODING	Ttg/Gtg	L/V	25.0%	4	AA	CC	CC	CC
-chr1:327109	[T/C]	chr1	327109	Cc01_g00330:833	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	12.5%	4	TT	TT	TT	TC
-chr1:320096	[C/G]	chr1	320096	Cc01_g00330:1285	exon	NON_SYNONYMOUS_CODING	Gta/Cta	V/L	37.5%	4	CC	GG	GG	CG
-chr1:319913	[T/C]	chr1	319913	Cc01_g00330:1358	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	12.5%	4	TT	TT	TT	TC
-chr1:319903	[G/C]	chr1	319903	Cc01_g00330:1368	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	12.5%	4	GG	GG	GC	GG
-chr1:319887	[G/T]	chr1	319887	Cc01_g00330:1384	exon	NON_SYNONYMOUS_CODING	Cat/Aat	H/N	37.5%	4	GG	TT	GG	GT
-chr1:319879	[C/A]	chr1	319879	Cc01_g00330:1392	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	12.5%	4	CC	CC	CC	CA
-chr1:319682	[T/A]	chr1	319682	Cc01_g00330:1589	exon	NON_SYNONYMOUS_CODING	aAa/aTa	K/I	37.5%	4	TT	AA	AA	TA
-chr1:319581	[C/T]	chr1	319581	Cc01_g00330:1690	exon	NON_SYNONYMOUS_CODING	Ggt/Agt	G/S	12.5%	4	CC	CC	CT	CC
-chr1:319379	[A/G]	chr1	319379	Cc01_g00330:1892	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	12.5%	4	AA	AA	AA	AG
-chr1:319299	[A/C]	chr1	319299	Cc01_g00330:1972	exon	NON_SYNONYMOUS_CODING	Tta/Gta	L/V	12.5%	4	AA	AA	AC	AA
-chr1:319123	[G/A]	chr1	319123	Cc01_g00330:2148	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	GG	GG	GA	GG
-chr1:319112	[G/C]	chr1	319112	Cc01_g00330:2159	exon	NON_SYNONYMOUS_CODING	gCc/gGc	A/G	12.5%	4	GG	GG	GC	GG
-chr1:319087	[C/A]	chr1	319087	Cc01_g00330:2184	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	12.5%	4	CC	CC	CC	CA
-chr1:319073	[G/A]	chr1	319073	Cc01_g00330:2198	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	GG	GG	GG	GA
-chr1:319033	[A/G]	chr1	319033	Cc01_g00330:2238	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	AA	AA	AG	AA
-chr1:317552	[C/T]	chr1	317552	Cc01_g00330:2468	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	12.5%	4	CC	CC	CT	CC
-chr1:315675	[A/T]	chr1	315675	Cc01_g00330:2530	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	37.5%	4	AA	TT	TT	AT
-chr1:315443	[G/A]	chr1	315443	Cc01_g00330:2691	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	GG	GG	GA	GG
-chr1:315404	[C/T]	chr1	315404	Cc01_g00330:2730	exon	SYNONYMOUS_CODING	acG/acA	T/T	37.5%	4	CC	TT	TT	CT
-chr1:315126	[A/G]	chr1	315126	Cc01_g00330:2787	exon	SYNONYMOUS_CODING	agT/agC	S/S	25.0%	4	AA	GG	GG	GG
-chr1:315087	[C/G]	chr1	315087	Cc01_g00330:2826	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	12.5%	4	CC	CC	CC	CG
-chr1:312979	[T/C]	chr1	312979	Cc01_g00330:3198	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TT	TC	TT
-chr1:312964	[C/T]	chr1	312964	Cc01_g00330:3213	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	37.5%	4	CC	TT	TT	CT
-chr1:312879	[G/A]	chr1	312879	Cc01_g00330:3298	exon	NON_SYNONYMOUS_CODING	Ctc/Ttc	L/F	37.5%	4	GG	AA	AA	GA
-chr1:312680	[G/A]	chr1	312680	Cc01_g00330:3393	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	37.5%	4	GG	AA	AA	GA
-chr1:312672	[T/A]	chr1	312672	Cc01_g00330:3401	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	37.5%	4	TT	AA	AA	TA
-chr1:312546	[A/G]	chr1	312546	Cc01_g00330:3527	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	AA	AA	AG	AA
-chr1:312321	[G/C]	chr1	312321	Cc01_g00330:3752	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	12.5%	4	GG	GG	GG	GC
-chr1:312307	[C/G]	chr1	312307	Cc01_g00330:3766	exon	NON_SYNONYMOUS_CODING	Gca/Cca	A/P	50.0%	4	CC	GG	CG	GC
-chr1:312213	[G/A]	chr1	312213	Cc01_g00330:3860	exon	NON_SYNONYMOUS_CODING	cCt/cTt	P/L	12.5%	4	GG	GG	GG	GA
-chr1:312086	[T/C]	chr1	312086	Cc01_g00330:3987	exon	SYNONYMOUS_CODING	agA/agG	R/R	50.0%	4	TT	CC	TC	TC
-chr1:311898	[T/C]	chr1	311898	Cc01_g00330:4175	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	12.5%	4	TT	TT	TT	TC
-chr1:311859	[C/T]	chr1	311859	Cc01_g00330:4214	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	50.0%	4	CC	TT	CT	CT
-chr1:311729	[T/C]	chr1	311729	Cc01_g00330:4344	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	TT	TT	TC	TT
-chr1:311665	[C/T]	chr1	311665	Cc01_g00330:4408	exon	NON_SYNONYMOUS_CODING	Ggt/Agt	G/S	37.5%	4	CC	TT	CC	CT
-chr1:311522	[T/C]	chr1	311522	Cc01_g00330:4551	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TC	TT
-chr1:311476	[T/G]	chr1	311476	Cc01_g00330:4597	exon	NON_SYNONYMOUS_CODING	Act/Cct	T/P	12.5%	4	TT	TT	GT	TT
-chr1:311457	[C/A]	chr1	311457	Cc01_g00330:4616	exon	NON_SYNONYMOUS_CODING	gGg/gTg	G/V	37.5%	4	CC	AA	AA	CA
-chr1:311357	[G/C]	chr1	311357	Cc01_g00330:4716	exon	SYNONYMOUS_CODING	ccC/ccG	P/P	37.5%	4	GG	CC	GG	GC
-chr1:311161	[A/G]	chr1	311161	Cc01_g00330:4912	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	50.0%	4	AA	GG	AG	AG
-chr1:311057	[G/A]	chr1	311057	Cc01_g00330:5016	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	GG	GG	GA	GG
-chr1:311024	[T/C]	chr1	311024	Cc01_g00330:5049	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	12.5%	4	TT	TT	TC	TT
-chr1:310991	[A/G]	chr1	310991	Cc01_g00330:5082	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	37.5%	4	AA	GG	AA	AG
-chr1:310760	[T/C]	chr1	310760	Cc01_g00330:5229	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TT	TC	TT
-chr1:331033	[C/T]	chr1	331033	Cc01_g00340:332	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	33.3%	3	CC	TT	NN	TT
-chr1:339763	[C/T]	chr1	339763	Cc01_g00350:9	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	25.0%	4	CC	CC	CT	CT
-chr1:339901	[G/C]	chr1	339901	Cc01_g00350:147	exon	SYNONYMOUS_CODING	acG/acC	T/T	12.5%	4	GG	GG	GG	GC
-chr1:339988	[A/G]	chr1	339988	Cc01_g00350:234	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	AA	AA	AG	AA
-chr1:346095	[A/G]	chr1	346095	Cc01_g00350:384	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	AA	AA	AG
-chr1:346128	[C/G]	chr1	346128	Cc01_g00350:417	exon	NON_SYNONYMOUS_CODING	atC/atG	I/M	25.0%	4	CC	CC	GG	CC
-chr1:346300	[T/C]	chr1	346300	Cc01_g00350:489	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	25.0%	4	TT	CC	TT	TT
-chr1:346330	[A/G]	chr1	346330	Cc01_g00350:519	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	AA	GG	AA	AA
-chr1:346342	[T/C]	chr1	346342	Cc01_g00350:531	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	TT	CC	TT	TT
-chr1:349895	[T/C]	chr1	349895	Cc01_g00360:87	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	50.0%	2	TT	CC	NN	NN
-chr1:350036	[C/G]	chr1	350036	Cc01_g00360:228	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	25.0%	2	CC	CG	NN	NN
-chr1:350043	[T/C]	chr1	350043	Cc01_g00360:235	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	50.0%	2	TT	CC	NN	NN
-chr1:350373	[G/A]	chr1	350373	Cc01_g00360:565	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	16.7%	3	GG	GA	NN	GG
-chr1:350416	[A/G]	chr1	350416	Cc01_g00360:608	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	50.0%	2	AA	GG	NN	NN
-chr1:350429	[T/C]	chr1	350429	Cc01_g00360:621	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	33.3%	3	TT	TT	NN	CC
-chr1:350537	[A/T]	chr1	350537	Cc01_g00360:729	exon	SYNONYMOUS_CODING	atA/atT	I/I	25.0%	4	AA	AA	AA	TT
-chr1:350672	[G/A]	chr1	350672	Cc01_g00360:864	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	25.0%	2	GG	GA	NN	NN
-chr1:350729	[C/T]	chr1	350729	Cc01_g00360:921	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	25.0%	4	CC	CC	TT	CC
-chr1:350738	[A/C]	chr1	350738	Cc01_g00360:930	exon	SYNONYMOUS_CODING	ccA/ccC	P/P	25.0%	4	AA	AA	CC	AA
-chr1:351014	[T/C]	chr1	351014	Cc01_g00360:1206	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	50.0%	2	TT	CC	NN	NN
-chr1:351188	[G/C]	chr1	351188	Cc01_g00360:1380	exon	SYNONYMOUS_CODING	ccG/ccC	P/P	33.3%	3	GG	CC	NN	CC
-chr1:351329	[A/T]	chr1	351329	Cc01_g00360:1521	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	50.0%	3	AA	TT	NN	AT
-chr1:392985	[A/G]	chr1	392985	Cc01_g00370:84	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	AA	AA	AG	AA
-chr1:393004	[C/T]	chr1	393004	Cc01_g00370:103	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	CC	CC	CC	CT
-chr1:393006	[G/C]	chr1	393006	Cc01_g00370:105	exon	SYNONYMOUS_CODING	ctG/ctC	L/L	12.5%	4	GG	GG	CG	GG
-chr1:393015	[G/A]	chr1	393015	Cc01_g00370:114	exon	SYNONYMOUS_CODING	agG/agA	R/R	37.5%	4	GG	AA	AA	AG
-chr1:393081	[C/A]	chr1	393081	Cc01_g00370:180	exon	SYNONYMOUS_CODING	atC/atA	I/I	50.0%	3	CC	NN	AA	CA
-chr1:393089	[T/A]	chr1	393089	Cc01_g00370:188	exon	NON_SYNONYMOUS_CODING	cTg/cAg	L/Q	12.5%	4	TT	TT	TT	TA
-chr1:393111	[C/T]	chr1	393111	Cc01_g00370:210	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	37.5%	4	CC	TT	TT	CT
-chr1:393120	[C/T]	chr1	393120	Cc01_g00370:219	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	37.5%	4	CC	TT	TT	CT
-chr1:393139	[G/A]	chr1	393139	Cc01_g00370:238	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	50.0%	4	GG	AA	AA	GG
-chr1:393271	[G/A]	chr1	393271	Cc01_g00370:370	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	33.3%	3	GG	AA	NN	GG
-chr1:393315	[G/A]	chr1	393315	Cc01_g00370:414	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	16.7%	3	GG	GG	NN	GA
-chr1:393339	[G/T]	chr1	393339	Cc01_g00370:438	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	50.0%	3	GG	TT	NN	GT
-chr1:393342	[G/A]	chr1	393342	Cc01_g00370:441	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	2	GG	NN	NN	GA
-chr1:397208	[G/C]	chr1	397208	Cc01_g00380:63	exon	SYNONYMOUS_CODING	gcG/gcC	A/A	37.5%	4	GG	CC	CC	GC
-chr1:397217	[T/C]	chr1	397217	Cc01_g00380:72	exon	SYNONYMOUS_CODING	acT/acC	T/T	37.5%	4	TT	CC	CC	TC
-chr1:397228	[G/T]	chr1	397228	Cc01_g00380:83	exon	NON_SYNONYMOUS_CODING	tGc/tTc	C/F	25.0%	4	GG	TT	TT	TT
-chr1:397253	[T/C]	chr1	397253	Cc01_g00380:108	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	TT	CC	TT	TT
-chr1:397269	[T/A]	chr1	397269	Cc01_g00380:124	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	50.0%	4	TT	AA	AA	TT
-chr1:397270	[T/C]	chr1	397270	Cc01_g00380:125	exon	NON_SYNONYMOUS_CODING	tTt/tCt	F/S	50.0%	4	TT	CC	CC	TT
-chr1:397361	[G/T]	chr1	397361	Cc01_g00380:216	exon	SYNONYMOUS_CODING	gtG/gtT	V/V	50.0%	4	GG	GG	TT	TT
-chr1:397547	[C/A]	chr1	397547	Cc01_g00380:402	exon	SYNONYMOUS_CODING	gcC/gcA	A/A	25.0%	4	CC	AA	AA	AA
-chr1:397566	[T/G]	chr1	397566	Cc01_g00380:421	exon	NON_SYNONYMOUS_CODING	Tta/Gta	L/V	12.5%	4	TT	TT	TT	TG
-chr1:397576	[T/C]	chr1	397576	Cc01_g00380:431	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	12.5%	4	TT	TT	TC	TT
-chr1:398909	[G/C]	chr1	398909	Cc01_g00380:456	exon	SYNONYMOUS_CODING	ggG/ggC	G/G	12.5%	4	GG	GG	GC	GG
-chr1:398940	[A/G]	chr1	398940	Cc01_g00380:487	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	37.5%	4	AA	GG	GA	AA
-chr1:398942	[C/T]	chr1	398942	Cc01_g00380:489	exon	SYNONYMOUS_CODING	acC/acT	T/T	37.5%	4	CC	TT	TC	CC
-chr1:398951	[C/T]	chr1	398951	Cc01_g00380:498	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	37.5%	4	CC	TT	TC	CC
-chr1:399320	[T/C]	chr1	399320	Cc01_g00380:867	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	TT	TC	TT	TT
-chr1:399344	[C/T]	chr1	399344	Cc01_g00380:891	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	12.5%	4	CC	CC	CT	CC
-chr1:399368	[C/T]	chr1	399368	Cc01_g00380:915	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	25.0%	4	CC	TT	TT	TT
-chr1:399404	[A/T]	chr1	399404	Cc01_g00380:951	exon	SYNONYMOUS_CODING	ggA/ggT	G/G	12.5%	4	AA	AT	AA	AA
-chr1:399453	[T/G]	chr1	399453	Cc01_g00380:1000	exon	NON_SYNONYMOUS_CODING	Tcc/Gcc	S/A	25.0%	4	TT	GG	GG	GG
-chr1:399557	[C/T]	chr1	399557	Cc01_g00380:1104	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	CC	CC	CT	CC
-chr1:399739	[C/G]	chr1	399739	Cc01_g00380:1286	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	12.5%	4	CC	CC	CG	CC
-chr1:399765	[C/T]	chr1	399765	Cc01_g00380:1312	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	CC	CC	CC	CT
-chr1:399795	[C/A]	chr1	399795	Cc01_g00380:1342	exon	NON_SYNONYMOUS_CODING	Cac/Aac	H/N	12.5%	4	CC	CC	CC	AC
-chr1:399796	[A/G]	chr1	399796	Cc01_g00380:1343	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	25.0%	4	AA	AA	AA	GG
-chr1:399801	[A/G]	chr1	399801	Cc01_g00380:1348	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	50.0%	4	AA	GG	AA	GG
-chr1:399809	[C/G]	chr1	399809	Cc01_g00380:1356	exon	SYNONYMOUS_CODING	gtC/gtG	V/V	37.5%	4	CC	GG	CC	GC
-chr1:420355	[T/C]	chr1	420355	Cc01_g00390:538	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	50.0%	2	TT	NN	NN	CC
-chr1:421363	[C/T]	chr1	421363	Cc01_g00390:1546	exon	NON_SYNONYMOUS_CODING	Cgg/Tgg	R/W	50.0%	2	CC	NN	NN	TT
-chr1:421532	[A/C]	chr1	421532	Cc01_g00390:1715	exon	NON_SYNONYMOUS_CODING	aAt/aCt	N/T	37.5%	4	AA	CC	CC	AC
-chr1:421534	[A/G]	chr1	421534	Cc01_g00390:1717	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	25.0%	4	AA	AG	AG	AA
-chr1:421540	[G/A]	chr1	421540	Cc01_g00390:1723	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	37.5%	4	GG	AG	AG	GA
-chr1:421556	[T/A]	chr1	421556	Cc01_g00390:1739	exon	NON_SYNONYMOUS_CODING	aTt/aAt	I/N	12.5%	4	TT	TT	TA	TT
-chr1:421570	[T/C]	chr1	421570	Cc01_g00390:1753	exon	NON_SYNONYMOUS_CODING	Tac/Cac	Y/H	12.5%	4	TT	TC	TT	TT
-chr1:421572	[C/T]	chr1	421572	Cc01_g00390:1755	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	CC	CC	CC	CT
-chr1:421577	[C/T]	chr1	421577	Cc01_g00390:1760	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	12.5%	4	CC	CC	CC	CT
-chr1:421612	[A/G]	chr1	421612	Cc01_g00390:1795	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	12.5%	4	AA	AA	AG	AA
-chr1:422090	[G/C]	chr1	422090	Cc01_g00390:2123	exon	NON_SYNONYMOUS_CODING	aGt/aCt	S/T	33.3%	3	GG	NN	CC	GG
-chr1:422353	[G/A]	chr1	422353	Cc01_g00390:2386	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	2	GG	NN	NN	GA
-chr1:422467	[C/G]	chr1	422467	Cc01_g00390:2500	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	33.3%	3	CC	NN	CC	GG
-chr1:422483	[C/A]	chr1	422483	Cc01_g00390:2516	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	33.3%	3	CC	NN	AA	CC
-chr1:422740	[G/T]	chr1	422740	Cc01_g00390:2686	exon	NON_SYNONYMOUS_CODING	Ggt/Tgt	G/C	25.0%	2	GG	NN	NN	GT
-chr1:422742	[T/G]	chr1	422742	Cc01_g00390:2688	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	25.0%	2	TT	NN	NN	TG
-chr1:422746	[A/T]	chr1	422746	Cc01_g00390:2692	exon	STOP_GAINED	Aaa/Taa	K/8	25.0%	2	AA	NN	NN	AT
-chr1:422747	[A/C]	chr1	422747	Cc01_g00390:2693	exon	NON_SYNONYMOUS_CODING	aAa/aCa	K/T	25.0%	2	AA	NN	NN	AC
-chr1:422885	[A/C]	chr1	422885	Cc01_g00390:2831	exon	NON_SYNONYMOUS_CODING	cAa/cCa	Q/P	33.3%	3	AA	CC	NN	AA
-chr1:445244	[A/G]	chr1	445244	Cc01_g00410:59	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	12.5%	4	AA	AA	AA	AG
-chr1:445214	[A/T]	chr1	445214	Cc01_g00410:89	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	37.5%	4	AA	TT	AT	AA
-chr1:445148	[T/G]	chr1	445148	Cc01_g00410:155	exon	NON_SYNONYMOUS_CODING	aAg/aCg	K/T	16.7%	3	TT	TG	NN	TT
-chr1:445013	[T/C]	chr1	445013	Cc01_g00410:185	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	12.5%	4	TT	TC	TT	TT
-chr1:444990	[C/T]	chr1	444990	Cc01_g00410:208	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	CC	CC	CC	CT
-chr1:444968	[G/A]	chr1	444968	Cc01_g00410:230	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	12.5%	4	GG	GG	GA	GG
-chr1:444952	[A/G]	chr1	444952	Cc01_g00410:246	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AA	AA	AG
-chr1:444930	[G/A]	chr1	444930	Cc01_g00410:268	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	GG	GG	GG	GA
-chr1:444929	[T/C]	chr1	444929	Cc01_g00410:269	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	12.5%	4	TT	TT	TT	TC
-chr1:444921	[T/C]	chr1	444921	Cc01_g00410:277	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	25.0%	4	TT	TC	TT	CT
-chr1:444904	[G/A]	chr1	444904	Cc01_g00410:294	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	GG	GG	GG	GA
-chr1:444879	[G/A]	chr1	444879	Cc01_g00410:319	exon	STOP_GAINED	Cag/Tag	Q/7	12.5%	4	GG	GG	GG	GA
-chr1:561287	[C/G]	chr1	561287	Cc01_g00420:1568	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	50.0%	2	CC	NN	NN	GG
-chr1:562257	[A/G]	chr1	562257	Cc01_g00420:2449	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	33.3%	3	AA	GG	NN	AA
-chr1:562260	[A/G]	chr1	562260	Cc01_g00420:2452	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	33.3%	3	AA	GG	NN	AA
-chr1:562358	[T/C]	chr1	562358	Cc01_g00420:2550	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	25.0%	2	TT	NN	NN	TC
-chr1:563082	[G/C]	chr1	563082	Cc01_g00420:3274	exon	NON_SYNONYMOUS_CODING	Gtg/Ctg	V/L	33.3%	3	GG	CC	NN	GG
-chr1:563087	[A/G]	chr1	563087	Cc01_g00420:3279	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	33.3%	3	AA	GG	NN	AA
-chr1:563172	[C/T]	chr1	563172	Cc01_g00420:3364	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	16.7%	3	CC	CC	NN	CT
-chr1:563178	[G/A]	chr1	563178	Cc01_g00420:3370	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	16.7%	3	GG	GG	NN	GA
-chr1:563217	[A/G]	chr1	563217	Cc01_g00420:3409	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	33.3%	3	AA	NN	GG	AA
-chr1:563316	[A/G]	chr1	563316	Cc01_g00420:3439	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	33.3%	3	AA	NN	AA	GG
-chr1:563359	[C/A]	chr1	563359	Cc01_g00420:3482	exon	NON_SYNONYMOUS_CODING	aCc/aAc	T/N	50.0%	2	CC	NN	AA	NN
-chr1:563503	[T/C]	chr1	563503	Cc01_g00420:3626	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	25.0%	4	TT	TT	TC	TC
-chr1:563700	[T/A]	chr1	563700	Cc01_g00420:3784	exon	NON_SYNONYMOUS_CODING	Tgg/Agg	W/R	50.0%	2	TT	NN	NN	AA
-chr1:563763	[G/A]	chr1	563763	Cc01_g00420:3847	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	GG	AA	GG	GG
-chr1:563764	[A/T]	chr1	563764	Cc01_g00420:3848	exon	NON_SYNONYMOUS_CODING	gAa/gTa	E/V	25.0%	4	AA	TT	AA	AA
-chr1:563780	[G/C]	chr1	563780	Cc01_g00420:3864	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	25.0%	4	GG	GG	GG	CC
-chr1:563788	[G/A]	chr1	563788	Cc01_g00420:3872	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	25.0%	4	GG	AA	GG	GG
-chr1:563836	[T/C]	chr1	563836	Cc01_g00420:3920	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	50.0%	2	TT	NN	CC	NN
-chr1:564119	[C/T]	chr1	564119	Cc01_g00420:4122	exon	SYNONYMOUS_CODING	agC/agT	S/S	50.0%	2	CC	NN	TT	NN
-chr1:564245	[G/A]	chr1	564245	Cc01_g00420:4248	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	50.0%	2	GG	NN	AA	NN
-chr1:564250	[A/C]	chr1	564250	Cc01_g00420:4253	exon	NON_SYNONYMOUS_CODING	cAt/cCt	H/P	50.0%	2	AA	NN	CC	NN
-chr1:564302	[A/G]	chr1	564302	Cc01_g00420:4305	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	50.0%	4	AA	GG	GG	AA
-chr1:564307	[C/T]	chr1	564307	Cc01_g00420:4310	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	33.3%	3	CC	NN	TT	CC
-chr1:564313	[T/A]	chr1	564313	Cc01_g00420:4316	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	25.0%	4	TT	TT	TT	AA
-chr1:564315	[G/T]	chr1	564315	Cc01_g00420:4318	exon	NON_SYNONYMOUS_CODING	Gac/Tac	D/Y	12.5%	4	GG	GG	GG	GT
-chr1:564335	[C/G]	chr1	564335	Cc01_g00420:4338	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	25.0%	4	CC	CC	GG	CC
-chr1:564360	[T/G]	chr1	564360	Cc01_g00420:4363	exon	NON_SYNONYMOUS_CODING	Tcg/Gcg	S/A	33.3%	3	TT	GG	NN	GG
-chr1:564391	[G/T]	chr1	564391	Cc01_g00420:4394	exon	NON_SYNONYMOUS_CODING	tGc/tTc	C/F	33.3%	3	GG	GG	NN	TT
-chr1:564393	[C/G]	chr1	564393	Cc01_g00420:4396	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	16.7%	3	CC	CG	NN	CC
-chr1:564416	[T/C]	chr1	564416	Cc01_g00420:4419	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	33.3%	3	TT	CC	NN	CC
-chr1:564424	[C/A]	chr1	564424	Cc01_g00420:4427	exon	NON_SYNONYMOUS_CODING	gCc/gAc	A/D	25.0%	2	CC	CA	NN	NN
-chr1:564550	[T/A]	chr1	564550	Cc01_g00420:4553	exon	NON_SYNONYMOUS_CODING	gTt/gAt	V/D	33.3%	3	TT	AA	AA	NN
-chr1:624837	[T/G]	chr1	624837	Cc01_g00430:60	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	50.0%	2	TT	NN	NN	GG
-chr1:624841	[C/G]	chr1	624841	Cc01_g00430:64	exon	NON_SYNONYMOUS_CODING	Cat/Gat	H/D	50.0%	2	CC	NN	NN	GG
-chr1:625917	[T/G]	chr1	625917	Cc01_g00430:987	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	50.0%	2	TT	NN	NN	GG
-chr1:625940	[G/C]	chr1	625940	Cc01_g00430:1010	exon	NON_SYNONYMOUS_CODING	aGa/aCa	R/T	50.0%	2	GG	NN	NN	CC
-chr1:626077	[A/C]	chr1	626077	Cc01_g00430:1147	exon	NON_SYNONYMOUS_CODING	Aca/Cca	T/P	50.0%	2	AA	CC	NN	NN
-chr1:626259	[G/A]	chr1	626259	Cc01_g00430:1329	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	25.0%	2	GG	NN	NN	GA
-chr1:626317	[G/C]	chr1	626317	Cc01_g00430:1387	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	25.0%	2	GG	NN	NN	GC
-chr1:626491	[A/G]	chr1	626491	Cc01_g00430:1561	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	50.0%	2	AA	NN	NN	GG
-chr1:626499	[A/T]	chr1	626499	Cc01_g00430:1569	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	50.0%	2	AA	NN	NN	TT
-chr1:626536	[C/T]	chr1	626536	Cc01_g00430:1606	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	50.0%	2	CC	NN	TT	NN
-chr1:626555	[C/G]	chr1	626555	Cc01_g00430:1625	exon	NON_SYNONYMOUS_CODING	aCa/aGa	T/R	50.0%	2	CC	NN	GG	NN
-chr1:626820	[T/C]	chr1	626820	Cc01_g00430:1857	exon	SYNONYMOUS_CODING	cgT/cgC	R/R	16.7%	3	TT	NN	TT	TC
-chr1:626826	[A/T]	chr1	626826	Cc01_g00430:1863	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	16.7%	3	AA	NN	AA	AT
-chr1:626895	[G/A]	chr1	626895	Cc01_g00430:1932	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	50.0%	2	GG	NN	AA	NN
-chr1:626907	[G/A]	chr1	626907	Cc01_g00430:1944	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	GG	GG	GA	GG
-chr1:626917	[T/C]	chr1	626917	Cc01_g00430:1954	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	12.5%	4	TT	TT	TC	TT
-chr1:626930	[G/C]	chr1	626930	Cc01_g00430:1967	exon	NON_SYNONYMOUS_CODING	aGt/aCt	S/T	12.5%	4	GG	GG	GG	GC
-chr1:626944	[G/A]	chr1	626944	Cc01_g00430:1981	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	4	GG	GA	AG	GG
-chr1:626953	[G/A]	chr1	626953	Cc01_g00430:1990	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	4	GG	GA	AA	AG
-chr1:626958	[A/C]	chr1	626958	Cc01_g00430:1995	exon	NON_SYNONYMOUS_CODING	ttA/ttC	L/F	12.5%	4	AA	AA	AC	AA
-chr1:626960	[T/G]	chr1	626960	Cc01_g00430:1997	exon	NON_SYNONYMOUS_CODING	gTg/gGg	V/G	25.0%	4	TT	TG	GT	TT
-chr1:626962	[A/G]	chr1	626962	Cc01_g00430:1999	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	25.0%	4	AA	GA	AA	AG
-chr1:626990	[T/A]	chr1	626990	Cc01_g00430:2027	exon	NON_SYNONYMOUS_CODING	gTt/gAt	V/D	12.5%	4	TT	TT	TT	TA
-chr1:626992	[G/A]	chr1	626992	Cc01_g00430:2029	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	25.0%	4	GG	GA	GG	AG
-chr1:627002	[G/A]	chr1	627002	Cc01_g00430:2039	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	GG	GG	AA	GG
-chr1:627009	[C/T]	chr1	627009	Cc01_g00430:2046	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	25.0%	4	CC	CC	TT	CC
-chr1:627032	[G/T]	chr1	627032	Cc01_g00430:2069	exon	NON_SYNONYMOUS_CODING	tGt/tTt	C/F	25.0%	4	GG	GT	GG	GT
-chr1:627051	[A/G]	chr1	627051	Cc01_g00430:2088	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	AA	GG	GG	GG
-chr1:627058	[G/C]	chr1	627058	Cc01_g00430:2095	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	37.5%	4	GG	CC	CC	GC
-chr1:627068	[C/T]	chr1	627068	Cc01_g00430:2105	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	37.5%	4	CC	TT	TT	CT
-chr1:627110	[C/T]	chr1	627110	Cc01_g00430:2147	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	CC	CC	CC	CT
-chr1:627131	[C/T]	chr1	627131	Cc01_g00430:2168	exon	NON_SYNONYMOUS_CODING	gCc/gTc	A/V	50.0%	2	CC	NN	NN	TT
-chr1:627366	[G/T]	chr1	627366	Cc01_g00430:2307	exon	NON_SYNONYMOUS_CODING	aaG/aaT	K/N	50.0%	2	GG	TT	NN	NN
-chr1:627379	[T/G]	chr1	627379	Cc01_g00430:2320	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	50.0%	2	TT	GG	NN	NN
-chr1:627697	[G/A]	chr1	627697	Cc01_g00430:2548	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	50.0%	2	GG	NN	AA	NN
-chr1:627713	[A/T]	chr1	627713	Cc01_g00430:2564	exon	NON_SYNONYMOUS_CODING	cAt/cTt	H/L	50.0%	2	AA	NN	TT	NN
-chr1:627715	[G/C]	chr1	627715	Cc01_g00430:2566	exon	NON_SYNONYMOUS_CODING	Ggg/Cgg	G/R	50.0%	2	GG	NN	CC	NN
-chr1:627727	[T/C]	chr1	627727	Cc01_g00430:2578	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	50.0%	2	TT	NN	CC	NN
-chr1:627753	[T/G]	chr1	627753	Cc01_g00430:2604	exon	NON_SYNONYMOUS_CODING	tgT/tgG	C/W	50.0%	2	TT	NN	GG	NN
-chr1:627759	[C/A]	chr1	627759	Cc01_g00430:2610	exon	NON_SYNONYMOUS_CODING	caC/caA	H/Q	50.0%	2	CC	NN	AA	NN
-chr1:627760	[G/A]	chr1	627760	Cc01_g00430:2611	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	2	GG	NN	GA	NN
-chr1:627858	[C/T]	chr1	627858	Cc01_g00430:2709	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	50.0%	2	CC	NN	NN	TT
-chr1:694337	[T/C]	chr1	694337	Cc01_g00440:1131	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	50.0%	2	TT	CC	NN	NN
-chr1:694724	[A/C]	chr1	694724	Cc01_g00440:1518	exon	SYNONYMOUS_CODING	gtA/gtC	V/V	50.0%	2	AA	NN	NN	CC
-chr1:694734	[G/A]	chr1	694734	Cc01_g00440:1528	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	2	GG	NN	NN	GA
-chr1:695273	[C/G]	chr1	695273	Cc01_g00440:2067	exon	NON_SYNONYMOUS_CODING	aaC/aaG	N/K	25.0%	2	CC	NN	NN	CG
-chr1:695280	[A/G]	chr1	695280	Cc01_g00440:2074	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	50.0%	2	AA	NN	NN	GG
-chr1:695301	[T/A]	chr1	695301	Cc01_g00440:2095	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	25.0%	2	TT	NN	NN	TA
-chr1:695306	[A/G]	chr1	695306	Cc01_g00440:2100	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	25.0%	2	AA	NN	NN	AG
-chr1:695389	[A/C]	chr1	695389	Cc01_g00440:2183	exon	NON_SYNONYMOUS_CODING	aAa/aCa	K/T	33.3%	3	AA	NN	AC	AC
-chr1:695751	[A/G]	chr1	695751	Cc01_g00440:2506	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	50.0%	4	AA	GG	AA	GG
-chr1:696170	[A/G]	chr1	696170	Cc01_g00440:2790	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	50.0%	2	AA	NN	NN	GG
-chr1:696187	[A/T]	chr1	696187	Cc01_g00440:2807	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	50.0%	2	AA	NN	NN	TT
-chr1:696190	[T/C]	chr1	696190	Cc01_g00440:2810	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	50.0%	2	TT	NN	NN	CC
-chr1:696193	[C/A]	chr1	696193	Cc01_g00440:2813	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	50.0%	2	CC	NN	NN	AA
-chr1:696194	[A/G]	chr1	696194	Cc01_g00440:2814	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	50.0%	2	AA	NN	NN	GG
-chr1:696282	[A/T]	chr1	696282	Cc01_g00440:2902	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	50.0%	2	AA	NN	NN	TT
-chr1:696283	[C/T]	chr1	696283	Cc01_g00440:2903	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	50.0%	2	CC	NN	NN	TT
-chr1:696299	[T/A]	chr1	696299	Cc01_g00440:2919	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	2	TT	NN	NN	TA
-chr1:696368	[T/G]	chr1	696368	Cc01_g00440:2988	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	50.0%	2	TT	NN	NN	GG
-chr1:696565	[A/G]	chr1	696565	Cc01_g00440:3131	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	33.3%	3	AA	NN	GG	AA
-chr1:696569	[C/T]	chr1	696569	Cc01_g00440:3135	exon	SYNONYMOUS_CODING	caC/caT	H/H	33.3%	3	CC	NN	TT	CC
-chr1:696578	[G/A]	chr1	696578	Cc01_g00440:3144	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	33.3%	3	GG	NN	AA	GG
-chr1:696580	[A/G]	chr1	696580	Cc01_g00440:3146	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	33.3%	3	AA	NN	GG	AA
-chr1:696589	[A/T]	chr1	696589	Cc01_g00440:3155	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	33.3%	3	AA	NN	TT	AA
-chr1:696664	[C/A]	chr1	696664	Cc01_g00440:3230	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	33.3%	3	CC	AA	CC	NN
-chr1:698121	[T/A]	chr1	698121	Cc01_g00450:9	exon	STOP_GAINED	taT/taA	Y3*	25.0%	4	TT	TA	TT	TA
-chr1:698290	[C/A]	chr1	698290	Cc01_g00450:59	exon	NON_SYNONYMOUS_CODING	gCc/gAc	A/D	12.5%	4	CC	CC	CC	CA
-chr1:698302	[A/G]	chr1	698302	Cc01_g00450:71	exon	NON_SYNONYMOUS_CODING	gAa/gGa	E/G	25.0%	4	AA	AG	AG	AA
-chr1:698316	[G/T]	chr1	698316	Cc01_g00450:85	exon	STOP_GAINED	Gga/Tga	G/9	37.5%	4	GG	TG	TG	TG
-chr1:698328	[G/A]	chr1	698328	Cc01_g00450:97	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	37.5%	4	GG	AG	GA	GA
-chr1:698331	[A/G]	chr1	698331	Cc01_g00450:100	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	37.5%	4	AA	GA	AG	AG
-chr1:698332	[G/A]	chr1	698332	Cc01_g00450:101	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	37.5%	4	GG	GA	AG	AG
-chr1:698333	[A/G]	chr1	698333	Cc01_g00450:102	exon	SYNONYMOUS_CODING	agA/agG	R/R	25.0%	4	AA	GG	GG	GG
-chr1:698339	[A/G]	chr1	698339	Cc01_g00450:108	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	37.5%	4	AA	AG	GG	GG
-chr1:698350	[C/T]	chr1	698350	Cc01_g00450:119	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	37.5%	4	CC	TC	CT	CT
-chr1:698355	[A/G]	chr1	698355	Cc01_g00450:124	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	25.0%	4	AA	GG	GG	GG
-chr1:698372	[C/G]	chr1	698372	Cc01_g00450:141	exon	NON_SYNONYMOUS_CODING	aaC/aaG	N/K	25.0%	4	CC	GG	GG	GG
-chr1:698398	[T/G]	chr1	698398	Cc01_g00450:167	exon	STOP_GAINED	tTa/tGa	L/6	33.3%	3	TT	TT	NN	GG
-chr1:698411	[T/C]	chr1	698411	Cc01_g00450:180	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	TT	CC	TT	TT
-chr1:698426	[G/A]	chr1	698426	Cc01_g00450:195	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	25.0%	4	GG	GA	GG	GA
-chr1:698432	[G/A]	chr1	698432	Cc01_g00450:201	exon	STOP_GAINED	tgG/tgA	W/7	50.0%	4	GG	AA	GA	GA
-chr1:698434	[A/G]	chr1	698434	Cc01_g00450:203	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	37.5%	4	AA	GG	GG	AG
-chr1:714525	[A/G]	chr1	714525	Cc01_g00470:91	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	50.0%	2	AA	NN	GG	NN
-chr1:714606	[C/A]	chr1	714606	Cc01_g00470:172	exon	NON_SYNONYMOUS_CODING	Cgt/Agt	R/S	50.0%	4	CC	AA	CC	AA
-chr1:714611	[G/A]	chr1	714611	Cc01_g00470:177	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	GG	GG	AA	GG
-chr1:714616	[T/A]	chr1	714616	Cc01_g00470:182	exon	NON_SYNONYMOUS_CODING	gTa/gAa	V/E	33.3%	3	TT	NN	TT	AA
-chr1:714635	[G/A]	chr1	714635	Cc01_g00470:201	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	33.3%	3	GG	NN	AA	AA
-chr1:714636	[C/G]	chr1	714636	Cc01_g00470:202	exon	NON_SYNONYMOUS_CODING	Cat/Gat	H/D	33.3%	3	CC	NN	GG	GG
-chr1:715733	[C/G]	chr1	715733	Cc01_g00470:1198	exon	NON_SYNONYMOUS_CODING	Cat/Gat	H/D	50.0%	4	CC	GG	GG	CC
-chr1:715736	[T/G]	chr1	715736	Cc01_g00470:1201	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	12.5%	4	TT	TT	TT	TG
-chr1:715743	[C/A]	chr1	715743	Cc01_g00470:1208	exon	NON_SYNONYMOUS_CODING	aCa/aAa	T/K	50.0%	4	CC	AA	AA	CC
-chr1:715749	[G/T]	chr1	715749	Cc01_g00470:1214	exon	NON_SYNONYMOUS_CODING	cGc/cTc	R/L	50.0%	4	GG	TT	TT	GG
-chr1:715750	[C/T]	chr1	715750	Cc01_g00470:1215	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	12.5%	4	CC	CC	CC	TC
-chr1:715751	[G/A]	chr1	715751	Cc01_g00470:1216	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	GG	GG	GG	GA
-chr1:715769	[G/A]	chr1	715769	Cc01_g00470:1234	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	25.0%	2	GG	NN	NN	GA
-chr1:715779	[A/G]	chr1	715779	Cc01_g00470:1244	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	50.0%	2	AA	NN	NN	GG
-chr1:715853	[G/C]	chr1	715853	Cc01_g00470:1318	exon	NON_SYNONYMOUS_CODING	Ggg/Cgg	G/R	50.0%	2	GG	NN	NN	CC
-chr1:716060	[A/C]	chr1	716060	Cc01_g00470:1525	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	50.0%	2	AA	NN	CC	NN
-chr1:716123	[G/A]	chr1	716123	Cc01_g00470:1588	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	2	GG	NN	AA	NN
-chr1:716482	[G/A]	chr1	716482	Cc01_g00470:1836	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	33.3%	3	GG	NN	AA	GG
-chr1:716498	[G/C]	chr1	716498	Cc01_g00470:1852	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	16.7%	3	GG	NN	GG	GC
-chr1:716510	[G/A]	chr1	716510	Cc01_g00470:1864	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	25.0%	4	GG	GG	GA	GA
-chr1:716535	[A/G]	chr1	716535	Cc01_g00470:1889	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	25.0%	4	AA	GG	AA	AA
-chr1:716594	[T/C]	chr1	716594	Cc01_g00470:1948	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	37.5%	4	TT	CC	TC	CC
-chr1:716622	[A/G]	chr1	716622	Cc01_g00470:1976	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	12.5%	4	AA	AA	AA	AG
-chr1:716696	[C/T]	chr1	716696	Cc01_g00470:2050	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	33.3%	3	CC	NN	TT	CC
-chr1:716714	[G/C]	chr1	716714	Cc01_g00470:2068	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	16.7%	3	GG	NN	GG	GC
-chr1:716724	[A/G]	chr1	716724	Cc01_g00470:2078	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	50.0%	3	AA	NN	GG	AG
-chr1:716729	[G/C]	chr1	716729	Cc01_g00470:2083	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	33.3%	3	GG	NN	CC	GG
-chr1:716741	[G/A]	chr1	716741	Cc01_g00470:2095	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	50.0%	2	GG	NN	NN	AA
-chr1:716770	[C/T]	chr1	716770	Cc01_g00470:2124	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	50.0%	2	CC	NN	NN	TT
-chr1:716789	[C/A]	chr1	716789	Cc01_g00470:2143	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	50.0%	2	CC	NN	NN	AA
-chr1:716793	[C/A]	chr1	716793	Cc01_g00470:2147	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	25.0%	2	CC	NN	NN	CA
-chr1:716863	[T/C]	chr1	716863	Cc01_g00470:2217	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	33.3%	3	TT	NN	CC	TT
-chr1:716867	[G/C]	chr1	716867	Cc01_g00470:2221	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	33.3%	3	GG	NN	CC	GG
-chr1:716879	[A/T]	chr1	716879	Cc01_g00470:2233	exon	NON_SYNONYMOUS_CODING	Aat/Tat	N/Y	16.7%	3	AA	NN	AA	AT
-chr1:716880	[A/T]	chr1	716880	Cc01_g00470:2234	exon	NON_SYNONYMOUS_CODING	aAt/aTt	N/I	33.3%	3	AA	NN	TT	AA
-chr1:717010	[T/C]	chr1	717010	Cc01_g00470:2364	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	50.0%	2	TT	NN	NN	CC
-chr1:717382	[A/G]	chr1	717382	Cc01_g00470:2502	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	16.7%	3	AA	NN	AA	AG
-chr1:717405	[A/G]	chr1	717405	Cc01_g00470:2525	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	12.5%	4	AA	AA	AA	AG
-chr1:718555	[G/T]	chr1	718555	Cc01_g00480:7	exon	STOP_GAINED	Gga/Tga	G3*	50.0%	4	GG	TT	GT	GT
-chr1:718570	[A/G]	chr1	718570	Cc01_g00480:22	exon	NON_SYNONYMOUS_CODING	Agg/Ggg	R/G	25.0%	4	AA	GG	GG	GG
-chr1:718578	[A/G]	chr1	718578	Cc01_g00480:30	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	25.0%	4	AA	GG	GG	GG
-chr1:718579	[A/G]	chr1	718579	Cc01_g00480:31	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	25.0%	4	AA	GG	GG	GG
-chr1:718589	[T/C]	chr1	718589	Cc01_g00480:41	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	37.5%	4	TT	TC	CT	CT
-chr1:718602	[A/G]	chr1	718602	Cc01_g00480:54	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	GA	AA	AA
-chr1:718616	[A/G]	chr1	718616	Cc01_g00480:68	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	37.5%	4	AA	GA	AG	AG
-chr1:718623	[A/G]	chr1	718623	Cc01_g00480:75	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	AA	GA	AG	AG
-chr1:718626	[A/C]	chr1	718626	Cc01_g00480:78	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	37.5%	4	AA	AC	CA	CA
-chr1:718632	[A/G]	chr1	718632	Cc01_g00480:84	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	37.5%	4	AA	GG	GG	GA
-chr1:718633	[C/T]	chr1	718633	Cc01_g00480:85	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	12.5%	4	CC	CC	CC	CT
-chr1:718636	[G/A]	chr1	718636	Cc01_g00480:88	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	37.5%	4	GG	AG	GA	GA
-chr1:718676	[A/G]	chr1	718676	Cc01_g00480:128	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	12.5%	4	AA	GA	AA	AA
-chr1:719091	[T/A]	chr1	719091	Cc01_g00480:135	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	25.0%	4	TT	TA	AT	TT
-chr1:720709	[G/A]	chr1	720709	Cc01_g00490:200	exon	NON_SYNONYMOUS_CODING	aCc/aTc	T/I	33.3%	3	GG	NN	AA	AA
-chr1:757845	[A/T]	chr1	757845	Cc01_g00500:54	exon	SYNONYMOUS_CODING	acT/acA	T/T	50.0%	3	AA	TT	AT	NN
-chr1:757827	[A/T]	chr1	757827	Cc01_g00500:72	exon	SYNONYMOUS_CODING	acT/acA	T/T	37.5%	4	AA	TT	AT	TT
-chr1:757176	[T/A]	chr1	757176	Cc01_g00500:160	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	12.5%	4	TT	TT	TT	TA
-chr1:757171	[A/C]	chr1	757171	Cc01_g00500:165	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	37.5%	4	AA	AC	AC	CA
-chr1:757169	[C/G]	chr1	757169	Cc01_g00500:167	exon	NON_SYNONYMOUS_CODING	aGt/aCt	S/T	12.5%	4	CC	CC	GC	CC
-chr1:757141	[T/C]	chr1	757141	Cc01_g00500:195	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TT	TT	TC
-chr1:756891	[T/C]	chr1	756891	Cc01_g00500:213	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	CT	TT	TT
-chr1:756475	[G/A]	chr1	756475	Cc01_g00500:399	exon	SYNONYMOUS_CODING	atC/atT	I/I	33.3%	3	GG	NN	GG	AA
-chr1:756448	[T/C]	chr1	756448	Cc01_g00500:426	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	33.3%	3	TT	NN	TT	CC
-chr1:763230	[A/C]	chr1	763230	Cc01_g00510:245	exon	NON_SYNONYMOUS_CODING	cTa/cGa	L/R	50.0%	2	AA	NN	NN	CC
-chr1:765710	[A/G]	chr1	765710	Cc01_g00520:150	exon	SYNONYMOUS_CODING	acA/acG	T/T	50.0%	3	AA	NN	AG	GG
-chr1:765774	[C/G]	chr1	765774	Cc01_g00520:214	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	50.0%	2	CC	NN	NN	GG
-chr1:767708	[C/T]	chr1	767708	Cc01_g00520:2019	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	50.0%	3	CC	TT	NN	CT
-chr1:767754	[T/C]	chr1	767754	Cc01_g00520:2065	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	TT	TC	TT	TT
-chr1:767773	[T/C]	chr1	767773	Cc01_g00520:2084	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	12.5%	4	TT	TC	TT	TT
-chr1:767784	[A/G]	chr1	767784	Cc01_g00520:2095	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	37.5%	4	AA	GG	AA	AG
-chr1:768089	[T/G]	chr1	768089	Cc01_g00520:2142	exon	NON_SYNONYMOUS_CODING	agT/agG	S/R	16.7%	3	TT	NN	TG	TT
-chr1:768095	[G/T]	chr1	768095	Cc01_g00520:2148	exon	NON_SYNONYMOUS_CODING	gaG/gaT	E/D	16.7%	3	GG	NN	GT	GG
-chr1:768097	[G/T]	chr1	768097	Cc01_g00520:2150	exon	NON_SYNONYMOUS_CODING	gGc/gTc	G/V	16.7%	3	GG	NN	GT	GG
-chr1:768140	[A/T]	chr1	768140	Cc01_g00520:2193	exon	SYNONYMOUS_CODING	ctA/ctT	L/L	50.0%	3	AA	NN	AT	TT
-chr1:768149	[G/T]	chr1	768149	Cc01_g00520:2202	exon	SYNONYMOUS_CODING	gcG/gcT	A/A	50.0%	3	GG	NN	GT	TT
-chr1:768210	[A/G]	chr1	768210	Cc01_g00520:2263	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	50.0%	3	AA	NN	AG	GG
-chr1:768322	[G/A]	chr1	768322	Cc01_g00520:2375	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	16.7%	3	GG	NN	GA	GG
-chr1:768476	[T/G]	chr1	768476	Cc01_g00520:2529	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	25.0%	4	TT	GG	TT	TT
-chr1:768570	[G/A]	chr1	768570	Cc01_g00520:2623	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	50.0%	3	GG	NN	GA	AA
-chr1:768621	[A/C]	chr1	768621	Cc01_g00520:2674	exon	NON_SYNONYMOUS_CODING	Aag/Cag	K/Q	33.3%	3	AA	NN	CC	AA
-chr1:768623	[G/C]	chr1	768623	Cc01_g00520:2676	exon	NON_SYNONYMOUS_CODING	aaG/aaC	K/N	50.0%	3	GG	NN	GC	CC
-chr1:768653	[C/T]	chr1	768653	Cc01_g00520:2706	exon	SYNONYMOUS_CODING	atC/atT	I/I	33.3%	3	CC	NN	TT	CC
-chr1:768703	[C/T]	chr1	768703	Cc01_g00520:2756	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	16.7%	3	CC	NN	CC	CT
-chr1:768709	[T/G]	chr1	768709	Cc01_g00520:2762	exon	NON_SYNONYMOUS_CODING	tTt/tGt	F/C	16.7%	3	TT	NN	TT	TG
-chr1:768710	[T/G]	chr1	768710	Cc01_g00520:2763	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	16.7%	3	TT	NN	TT	TG
-chr1:768718	[G/C]	chr1	768718	Cc01_g00520:2771	exon	NON_SYNONYMOUS_CODING	cGt/cCt	R/P	33.3%	3	GG	NN	CC	CC
-chr1:768724	[C/T]	chr1	768724	Cc01_g00520:2777	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	16.7%	3	CC	NN	CC	CT
-chr1:768748	[A/G]	chr1	768748	Cc01_g00520:2801	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	33.3%	3	AA	NN	AA	GG
-chr1:768806	[A/G]	chr1	768806	Cc01_g00520:2859	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	50.0%	3	AA	NN	AG	GG
-chr1:768948	[G/A]	chr1	768948	Cc01_g00520:2917	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	4	GG	AA	AA	GG
-chr1:768971	[T/C]	chr1	768971	Cc01_g00520:2940	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	33.3%	3	TT	CC	NN	TT
-chr1:772576	[A/T]	chr1	772576	Cc01_g00530:220	exon	STOP_GAINED	Aaa/Taa	K/4	37.5%	4	AA	TT	TT	AT
-chr1:772604	[A/G]	chr1	772604	Cc01_g00530:248	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	50.0%	3	AA	NN	GG	AG
-chr1:787097	[G/A]	chr1	787097	Cc01_g00550:1089	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	50.0%	3	GG	NN	AA	GA
-chr1:787673	[T/G]	chr1	787673	Cc01_g00550:1596	exon	NON_SYNONYMOUS_CODING	caT/caG	H/Q	33.3%	3	TT	GG	NN	GG
-chr1:788087	[C/T]	chr1	788087	Cc01_g00550:1680	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	16.7%	3	CC	NN	CC	CT
-chr1:788159	[G/A]	chr1	788159	Cc01_g00550:1752	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	GG	GA	GG	GG
-chr1:788273	[C/A]	chr1	788273	Cc01_g00550:1866	exon	NON_SYNONYMOUS_CODING	aaC/aaA	N/K	25.0%	4	CC	AA	CC	CC
-chr1:788275	[C/T]	chr1	788275	Cc01_g00550:1868	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	50.0%	4	CC	TT	CT	CT
-chr1:788383	[C/G]	chr1	788383	Cc01_g00550:1886	exon	NON_SYNONYMOUS_CODING	aCa/aGa	T/R	50.0%	2	CC	NN	GG	NN
-chr1:788482	[C/T]	chr1	788482	Cc01_g00550:1985	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	12.5%	4	CC	CC	CT	CC
-chr1:788491	[G/A]	chr1	788491	Cc01_g00550:1994	exon	NON_SYNONYMOUS_CODING	gGc/gAc	G/D	12.5%	4	GG	GG	GA	GG
-chr1:788516	[A/G]	chr1	788516	Cc01_g00550:2019	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	AA	AG	AG
-chr1:788558	[A/G]	chr1	788558	Cc01_g00550:2061	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	25.0%	4	AA	GG	AA	AA
-chr1:788560	[T/C]	chr1	788560	Cc01_g00550:2063	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	25.0%	4	TT	CC	TT	TT
-chr1:788561	[C/G]	chr1	788561	Cc01_g00550:2064	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	25.0%	4	CC	GG	CC	CC
-chr1:788694	[G/A]	chr1	788694	Cc01_g00550:2197	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	37.5%	4	GG	AA	GG	GA
-chr1:788708	[G/A]	chr1	788708	Cc01_g00550:2211	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	GG	GA	GG	GG
-chr1:788716	[A/C]	chr1	788716	Cc01_g00550:2219	exon	NON_SYNONYMOUS_CODING	aAa/aCa	K/T	12.5%	4	AA	AC	AA	AA
-chr1:836275	[A/G]	chr1	836275	Cc01_g00570:39	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	2	AA	NN	NN	AG
-chr1:836319	[C/T]	chr1	836319	Cc01_g00570:83	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	CC	CT	CC	CC
-chr1:836362	[T/A]	chr1	836362	Cc01_g00570:126	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	12.5%	4	TT	TA	TT	TT
-chr1:837674	[G/C]	chr1	837674	Cc01_g00570:1378	exon	NON_SYNONYMOUS_CODING	Gtg/Ctg	V/L	50.0%	2	GG	NN	NN	CC
-chr1:837956	[A/G]	chr1	837956	Cc01_g00570:1660	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	33.3%	3	AA	GG	NN	AA
-chr1:837958	[T/A]	chr1	837958	Cc01_g00570:1662	exon	SYNONYMOUS_CODING	atT/atA	I/I	33.3%	3	TT	AA	NN	TT
-chr1:837989	[A/G]	chr1	837989	Cc01_g00570:1693	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	50.0%	2	AA	GG	NN	NN
-chr1:838599	[A/T]	chr1	838599	Cc01_g00570:2303	exon	NON_SYNONYMOUS_CODING	gAa/gTa	E/V	16.7%	3	AA	AA	NN	AT
-chr1:838628	[T/C]	chr1	838628	Cc01_g00570:2332	exon	NON_SYNONYMOUS_CODING	Tac/Cac	Y/H	33.3%	3	TT	CC	NN	CC
-chr1:838667	[T/A]	chr1	838667	Cc01_g00570:2338	exon	NON_SYNONYMOUS_CODING	Tca/Aca	S/T	25.0%	2	TT	TA	NN	NN
-chr1:838670	[A/G]	chr1	838670	Cc01_g00570:2341	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	25.0%	2	AA	GA	NN	NN
-chr1:838676	[A/G]	chr1	838676	Cc01_g00570:2347	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	50.0%	2	AA	GG	NN	NN
-chr1:838683	[C/G]	chr1	838683	Cc01_g00570:2354	exon	NON_SYNONYMOUS_CODING	aCa/aGa	T/R	50.0%	2	CC	GG	NN	NN
-chr1:838689	[C/T]	chr1	838689	Cc01_g00570:2360	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	33.3%	3	CC	TT	CC	NN
-chr1:838705	[C/T]	chr1	838705	Cc01_g00570:2376	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	33.3%	3	CC	CC	TT	NN
-chr1:838717	[T/A]	chr1	838717	Cc01_g00570:2388	exon	SYNONYMOUS_CODING	tcT/tcA	S/S	50.0%	2	TT	AA	NN	NN
-chr1:839122	[G/A]	chr1	839122	Cc01_g00570:2689	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	50.0%	2	GG	AA	NN	NN
-chr1:839352	[G/A]	chr1	839352	Cc01_g00570:2919	exon	SYNONYMOUS_CODING	agG/agA	R/R	50.0%	2	GG	NN	NN	AA
-chr1:839601	[A/T]	chr1	839601	Cc01_g00570:3168	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	50.0%	2	AA	NN	NN	TT
-chr1:839786	[G/A]	chr1	839786	Cc01_g00570:3353	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	50.0%	2	GG	NN	NN	AA
-chr1:839932	[G/A]	chr1	839932	Cc01_g00570:3499	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	2	GG	NN	NN	GA
-chr1:928733	[T/C]	chr1	928733	Cc01_g00580:26	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	16.7%	3	TT	NN	TT	TC
-chr1:928809	[A/G]	chr1	928809	Cc01_g00580:102	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	50.0%	2	AA	NN	NN	GG
-chr1:928827	[A/G]	chr1	928827	Cc01_g00580:120	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	25.0%	2	AA	NN	NN	AG
-chr1:928836	[A/G]	chr1	928836	Cc01_g00580:129	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	25.0%	2	AA	NN	NN	GA
-chr1:928904	[A/G]	chr1	928904	Cc01_g00580:197	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	25.0%	2	AA	NN	NN	GA
-chr1:966451	[A/G]	chr1	966451	Cc01_g00590:185	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	50.0%	2	AA	NN	NN	GG
-chr1:966652	[A/G]	chr1	966652	Cc01_g00590:386	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	50.0%	2	AA	NN	NN	GG
-chr1:966654	[A/G]	chr1	966654	Cc01_g00590:388	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	50.0%	2	AA	NN	NN	GG
-chr1:966661	[A/C]	chr1	966661	Cc01_g00590:395	exon	NON_SYNONYMOUS_CODING	aAg/aCg	K/T	50.0%	2	AA	NN	NN	CC
-chr1:966719	[A/G]	chr1	966719	Cc01_g00590:453	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	50.0%	2	AA	NN	NN	GG
-chr1:966803	[T/C]	chr1	966803	Cc01_g00590:486	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	50.0%	2	TT	NN	NN	CC
-chr1:966831	[G/C]	chr1	966831	Cc01_g00590:514	exon	NON_SYNONYMOUS_CODING	Gtt/Ctt	V/L	12.5%	4	GG	GG	GG	GC
-chr1:966834	[A/G]	chr1	966834	Cc01_g00590:517	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	25.0%	4	AA	GG	GG	GG
-chr1:966846	[G/A]	chr1	966846	Cc01_g00590:529	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	37.5%	4	GG	AA	AA	AG
-chr1:966866	[C/T]	chr1	966866	Cc01_g00590:549	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	50.0%	2	CC	NN	NN	TT
-chr1:967049	[G/T]	chr1	967049	Cc01_g00590:732	exon	NON_SYNONYMOUS_CODING	aaG/aaT	K/N	50.0%	2	GG	NN	NN	TT
-chr1:967059	[G/A]	chr1	967059	Cc01_g00590:742	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	50.0%	2	GG	NN	NN	AA
-chr1:967062	[A/G]	chr1	967062	Cc01_g00590:745	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	50.0%	2	AA	NN	NN	GG
-chr1:967063	[A/T]	chr1	967063	Cc01_g00590:746	exon	NON_SYNONYMOUS_CODING	aAt/aTt	N/I	50.0%	2	AA	NN	NN	TT
-chr1:967183	[C/G]	chr1	967183	Cc01_g00590:866	exon	NON_SYNONYMOUS_CODING	gCg/gGg	A/G	33.3%	3	CC	CC	NN	GG
-chr1:967752	[G/T]	chr1	967752	Cc01_g00590:1435	exon	NON_SYNONYMOUS_CODING	Gat/Tat	D/Y	50.0%	3	GG	TT	NN	GT
-chr1:967768	[C/G]	chr1	967768	Cc01_g00590:1451	exon	NON_SYNONYMOUS_CODING	tCg/tGg	S/W	33.3%	3	CC	GG	NN	GG
-chr1:967992	[G/A]	chr1	967992	Cc01_g00590:1675	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	33.3%	3	GG	NN	AA	AA
-chr1:986447	[C/A]	chr1	986447	Cc01_g00610:57	exon	SYNONYMOUS_CODING	cgC/cgA	R/R	12.5%	4	CC	CC	CC	CA
-chr1:986448	[G/A]	chr1	986448	Cc01_g00610:58	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	GG	GA	GG	AG
-chr1:986456	[A/G]	chr1	986456	Cc01_g00610:66	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	AA	GG	AG	GG
-chr1:986518	[T/G]	chr1	986518	Cc01_g00610:128	exon	NON_SYNONYMOUS_CODING	cTt/cGt	L/R	25.0%	4	TT	TG	TG	TT
-chr1:986525	[G/T]	chr1	986525	Cc01_g00610:135	exon	NON_SYNONYMOUS_CODING	gaG/gaT	E/D	12.5%	4	GG	GG	GG	TG
-chr1:986546	[G/A]	chr1	986546	Cc01_g00610:156	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	2	GG	NN	NN	GA
-chr1:986690	[G/A]	chr1	986690	Cc01_g00610:300	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	12.5%	4	GG	GG	GG	GA
-chr1:986709	[G/A]	chr1	986709	Cc01_g00610:319	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	GG	GG	GG	GA
-chr1:986710	[A/T]	chr1	986710	Cc01_g00610:320	exon	NON_SYNONYMOUS_CODING	gAa/gTa	E/V	12.5%	4	AA	AA	AA	AT
-chr1:986736	[C/G]	chr1	986736	Cc01_g00610:346	exon	NON_SYNONYMOUS_CODING	Cac/Gac	H/D	37.5%	4	CC	CG	CC	GG
-chr1:987100	[C/T]	chr1	987100	Cc01_g00610:546	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	16.7%	3	CC	NN	CC	CT
-chr1:987154	[T/A]	chr1	987154	Cc01_g00610:600	exon	NON_SYNONYMOUS_CODING	agT/agA	S/R	50.0%	4	TT	AA	TA	TA
-chr1:987159	[A/T]	chr1	987159	Cc01_g00610:605	exon	NON_SYNONYMOUS_CODING	gAt/gTt	D/V	12.5%	4	AA	AA	AA	TA
-chr1:987178	[A/G]	chr1	987178	Cc01_g00610:624	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	50.0%	4	AA	GG	AG	AG
-chr1:987200	[G/A]	chr1	987200	Cc01_g00610:646	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	GG	GA	GG	GG
-chr1:987232	[T/G]	chr1	987232	Cc01_g00610:678	exon	SYNONYMOUS_CODING	tcT/tcG	S/S	50.0%	4	TT	GG	TG	TG
-chr1:987567	[A/T]	chr1	987567	Cc01_g00610:1013	exon	NON_SYNONYMOUS_CODING	aAt/aTt	N/I	25.0%	4	AA	AA	AA	TT
-chr1:987582	[A/C]	chr1	987582	Cc01_g00610:1028	exon	NON_SYNONYMOUS_CODING	aAa/aCa	K/T	33.3%	3	AA	NN	AA	CC
-chr1:987606	[G/A]	chr1	987606	Cc01_g00610:1052	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	33.3%	3	GG	NN	GG	AA
-chr1:987613	[T/C]	chr1	987613	Cc01_g00610:1059	exon	SYNONYMOUS_CODING	acT/acC	T/T	33.3%	3	TT	NN	TT	CC
-chr1:987648	[T/C]	chr1	987648	Cc01_g00610:1094	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	16.7%	3	TT	NN	TT	TC
-chr1:987704	[A/C]	chr1	987704	Cc01_g00610:1150	exon	NON_SYNONYMOUS_CODING	Agt/Cgt	S/R	16.7%	3	AA	NN	AA	AC
-chr1:987875	[C/G]	chr1	987875	Cc01_g00610:1286	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	33.3%	3	CC	NN	GG	GG
-chr1:988107	[A/G]	chr1	988107	Cc01_g00610:1518	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	AA	AG	AG	AG
-chr1:988121	[A/G]	chr1	988121	Cc01_g00610:1532	exon	NON_SYNONYMOUS_CODING	gAa/gGa	E/G	12.5%	4	AA	AA	AA	AG
-chr1:988128	[T/A]	chr1	988128	Cc01_g00610:1539	exon	NON_SYNONYMOUS_CODING	agT/agA	S/R	12.5%	4	TT	TT	TA	TT
-chr1:988129	[C/T]	chr1	988129	Cc01_g00610:1540	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	25.0%	4	CC	TC	CC	TC
-chr1:988136	[C/G]	chr1	988136	Cc01_g00610:1547	exon	NON_SYNONYMOUS_CODING	cCt/cGt	P/R	12.5%	4	CC	CC	CC	GC
-chr1:988162	[G/C]	chr1	988162	Cc01_g00610:1573	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	25.0%	4	GG	GG	GC	GC
-chr1:997411	[A/G]	chr1	997411	Cc01_g00620:25	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	33.3%	3	AA	NN	AG	AG
-chr1:997409	[G/A]	chr1	997409	Cc01_g00620:27	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	33.3%	3	GG	NN	AA	AA
-chr1:997392	[T/C]	chr1	997392	Cc01_g00620:44	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	16.7%	3	TT	NN	TT	CT
-chr1:997300	[C/G]	chr1	997300	Cc01_g00620:60	exon	SYNONYMOUS_CODING	ctG/ctC	L/L	12.5%	4	CC	CC	CG	CC
-chr1:997296	[G/A]	chr1	997296	Cc01_g00620:64	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	12.5%	4	GG	GA	GG	GG
-chr1:997213	[G/A]	chr1	997213	Cc01_g00620:147	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	25.0%	4	GG	AA	AA	AA
-chr1:997200	[C/A]	chr1	997200	Cc01_g00620:160	exon	NON_SYNONYMOUS_CODING	Gcg/Tcg	A/S	50.0%	3	CC	AA	NN	CA
-chr1:997185	[T/G]	chr1	997185	Cc01_g00620:175	exon	NON_SYNONYMOUS_CODING	Aac/Cac	N/H	50.0%	2	TT	NN	NN	GG
-chr1:997169	[A/G]	chr1	997169	Cc01_g00620:191	exon	NON_SYNONYMOUS_CODING	gTc/gCc	V/A	25.0%	2	AA	NN	NN	AG
-chr1:997094	[A/G]	chr1	997094	Cc01_g00620:266	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	25.0%	2	AA	NN	NN	AG
-chr1:997051	[G/C]	chr1	997051	Cc01_g00620:309	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	50.0%	2	GG	NN	NN	CC
-chr1:995391	[A/G]	chr1	995391	Cc01_g00620:348	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	16.7%	3	AA	AG	NN	AA
-chr1:995363	[T/C]	chr1	995363	Cc01_g00620:376	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	25.0%	2	TT	TC	NN	NN
-chr1:994056	[G/T]	chr1	994056	Cc01_g00620:1180	exon	SYNONYMOUS_CODING	Cgg/Agg	R/R	50.0%	2	GG	NN	NN	TT
-chr1:994012	[A/C]	chr1	994012	Cc01_g00620:1224	exon	SYNONYMOUS_CODING	cgT/cgG	R/R	50.0%	2	AA	NN	NN	CC
-chr1:1105670	[T/C]	chr1	1105670	Cc01_g00630:393	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TT	TC	TT
-chr1:1105722	[A/G]	chr1	1105722	Cc01_g00630:445	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	25.0%	4	AA	GG	GG	GG
-chr1:1124006	[T/C]	chr1	1124006	Cc01_g00640:198	exon	SYNONYMOUS_CODING	atT/atC	I/I	33.3%	3	TT	CC	NN	TT
-chr1:1124349	[T/C]	chr1	1124349	Cc01_g00640:426	exon	SYNONYMOUS_CODING	agT/agC	S/S	25.0%	4	TT	TT	CC	TT
-chr1:1125855	[G/A]	chr1	1125855	Cc01_g00640:1414	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	16.7%	3	GG	GA	NN	GG
-chr1:1125920	[T/A]	chr1	1125920	Cc01_g00640:1479	exon	SYNONYMOUS_CODING	acT/acA	T/T	33.3%	3	TT	AA	NN	TT
-chr1:1125966	[A/T]	chr1	1125966	Cc01_g00640:1525	exon	NON_SYNONYMOUS_CODING	Att/Ttt	I/F	33.3%	3	AA	TT	NN	AA
-chr1:1126013	[A/G]	chr1	1126013	Cc01_g00640:1572	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	50.0%	2	AA	GG	NN	NN
-chr1:1151834	[G/C]	chr1	1151834	Cc01_g00670:239	exon	NON_SYNONYMOUS_CODING	cGa/cCa	R/P	12.5%	4	GG	GC	GG	GG
-chr1:1153859	[G/A]	chr1	1153859	Cc01_g00670:410	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	GG	GG	GG	GA
-chr1:1153862	[A/G]	chr1	1153862	Cc01_g00670:413	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	37.5%	4	AA	GG	AG	GG
-chr1:1153873	[A/C]	chr1	1153873	Cc01_g00670:424	exon	SYNONYMOUS_CODING	Aga/Cga	R/R	12.5%	4	AA	AA	AA	AC
-chr1:1154467	[T/G]	chr1	1154467	Cc01_g00670:486	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	25.0%	4	TT	TT	TG	TG
-chr1:1154473	[T/C]	chr1	1154473	Cc01_g00670:492	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	12.5%	4	TT	TT	TT	TC
-chr1:1154482	[T/G]	chr1	1154482	Cc01_g00670:501	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	25.0%	4	TT	TT	TG	TG
-chr1:1154490	[C/G]	chr1	1154490	Cc01_g00670:509	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	25.0%	4	CC	CC	CG	CG
-chr1:1154495	[A/G]	chr1	1154495	Cc01_g00670:514	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	12.5%	4	AA	AG	AA	AA
-chr1:1154499	[T/C]	chr1	1154499	Cc01_g00670:518	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	TT	TC	TT	TT
-chr1:1154515	[C/G]	chr1	1154515	Cc01_g00670:534	exon	SYNONYMOUS_CODING	ggC/ggG	G/G	12.5%	4	CC	CG	CC	CC
-chr1:1154527	[G/T]	chr1	1154527	Cc01_g00670:546	exon	NON_SYNONYMOUS_CODING	gaG/gaT	E/D	12.5%	4	GG	GT	GG	GG
-chr1:1154549	[A/G]	chr1	1154549	Cc01_g00670:568	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	12.5%	4	AA	AA	GA	AA
-chr1:1154550	[A/T]	chr1	1154550	Cc01_g00670:569	exon	NON_SYNONYMOUS_CODING	aAa/aTa	K/I	37.5%	4	AA	AT	TA	AT
-chr1:1154579	[A/G]	chr1	1154579	Cc01_g00670:598	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	12.5%	4	AA	AG	AA	AA
-chr1:1154582	[T/G]	chr1	1154582	Cc01_g00670:601	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	12.5%	4	TT	TG	TT	TT
-chr1:1154588	[A/C]	chr1	1154588	Cc01_g00670:607	exon	NON_SYNONYMOUS_CODING	Aac/Cac	N/H	12.5%	4	AA	AC	AA	AA
-chr1:1154849	[G/A]	chr1	1154849	Cc01_g00670:711	exon	SYNONYMOUS_CODING	acG/acA	T/T	37.5%	4	GG	AA	GA	AA
-chr1:1154858	[G/A]	chr1	1154858	Cc01_g00670:720	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	GG	GA	GG	GG
-chr1:1154868	[A/G]	chr1	1154868	Cc01_g00670:730	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	12.5%	4	AA	GA	AA	AA
-chr1:1154885	[G/A]	chr1	1154885	Cc01_g00670:747	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	12.5%	4	GG	AG	GG	GG
-chr1:1154894	[A/G]	chr1	1154894	Cc01_g00670:756	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	AA	GA	AA	AA
-chr1:1154916	[T/A]	chr1	1154916	Cc01_g00670:778	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	12.5%	4	TT	AT	TT	TT
-chr1:1154924	[T/C]	chr1	1154924	Cc01_g00670:786	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	12.5%	4	TT	CT	TT	TT
-chr1:1154929	[C/G]	chr1	1154929	Cc01_g00670:791	exon	STOP_GAINED	tCa/tGa	S/4	12.5%	4	CC	GC	CC	CC
-chr1:1154930	[A/G]	chr1	1154930	Cc01_g00670:792	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	GA	AA	AA
-chr1:1154936	[G/C]	chr1	1154936	Cc01_g00670:798	exon	NON_SYNONYMOUS_CODING	agG/agC	R/S	12.5%	4	GG	CG	GG	GG
-chr1:1154941	[T/C]	chr1	1154941	Cc01_g00670:803	exon	NON_SYNONYMOUS_CODING	tTt/tCt	F/S	12.5%	4	TT	CT	TT	TT
-chr1:1154946	[G/A]	chr1	1154946	Cc01_g00670:808	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	12.5%	4	GG	GA	GG	GG
-chr1:1154952	[A/T]	chr1	1154952	Cc01_g00670:814	exon	NON_SYNONYMOUS_CODING	Ata/Tta	I/L	25.0%	4	AA	TT	AA	AA
-chr1:1154976	[A/G]	chr1	1154976	Cc01_g00670:838	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	12.5%	4	AA	GA	AA	AA
-chr1:1154985	[C/G]	chr1	1154985	Cc01_g00670:847	exon	NON_SYNONYMOUS_CODING	Ctg/Gtg	L/V	12.5%	4	CC	GC	CC	CC
-chr1:1155000	[G/A]	chr1	1155000	Cc01_g00670:862	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	AG	GG	GG
-chr1:1155003	[C/A]	chr1	1155003	Cc01_g00670:865	exon	NON_SYNONYMOUS_CODING	Cta/Ata	L/I	12.5%	4	CC	AC	CC	CC
-chr1:1155015	[T/A]	chr1	1155015	Cc01_g00670:877	exon	NON_SYNONYMOUS_CODING	Tta/Ata	L/I	12.5%	4	TT	AT	TT	TT
-chr1:1155017	[A/G]	chr1	1155017	Cc01_g00670:879	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	GA	AA	AA
-chr1:1155021	[C/T]	chr1	1155021	Cc01_g00670:883	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	12.5%	4	CC	TC	CC	CC
-chr1:1155927	[G/A]	chr1	1155927	Cc01_g00670:906	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	AG	GG	GG
-chr1:1155945	[C/G]	chr1	1155945	Cc01_g00670:924	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	12.5%	4	CC	CC	CC	CG
-chr1:1155970	[G/A]	chr1	1155970	Cc01_g00670:949	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	AG	GG	GG
-chr1:1155978	[G/A]	chr1	1155978	Cc01_g00670:957	exon	SYNONYMOUS_CODING	acG/acA	T/T	12.5%	4	GG	AG	GG	GG
-chr1:1156036	[C/G]	chr1	1156036	Cc01_g00670:1015	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	12.5%	4	CC	GC	CC	CC
-chr1:1156056	[G/T]	chr1	1156056	Cc01_g00670:1035	exon	NON_SYNONYMOUS_CODING	aaG/aaT	K/N	12.5%	4	GG	GG	GG	GT
-chr1:1156075	[C/T]	chr1	1156075	Cc01_g00670:1054	exon	NON_SYNONYMOUS_CODING	Ccc/Tcc	P/S	12.5%	4	CC	CT	CC	CC
-chr1:1156086	[A/T]	chr1	1156086	Cc01_g00670:1065	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	12.5%	4	AA	TA	AA	AA
-chr1:1156095	[A/G]	chr1	1156095	Cc01_g00670:1074	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	AA	GG	AG	GG
-chr1:1156099	[A/C]	chr1	1156099	Cc01_g00670:1078	exon	NON_SYNONYMOUS_CODING	Atg/Ctg	M/L	12.5%	4	AA	CA	AA	AA
-chr1:1156677	[C/T]	chr1	1156677	Cc01_g00670:1089	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	CC	CT	CC	CC
-chr1:1156701	[T/G]	chr1	1156701	Cc01_g00670:1113	exon	NON_SYNONYMOUS_CODING	agT/agG	S/R	12.5%	4	TT	GT	TT	TT
-chr1:1156712	[T/A]	chr1	1156712	Cc01_g00670:1124	exon	NON_SYNONYMOUS_CODING	cTa/cAa	L/Q	12.5%	4	TT	AT	TT	TT
-chr1:1156733	[T/C]	chr1	1156733	Cc01_g00670:1145	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	37.5%	4	TT	CC	TC	CC
-chr1:1156813	[G/A]	chr1	1156813	Cc01_g00670:1225	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	12.5%	4	GG	GA	GG	GG
-chr1:1156819	[A/G]	chr1	1156819	Cc01_g00670:1231	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	12.5%	4	AA	AG	AA	AA
-chr1:1156820	[G/A]	chr1	1156820	Cc01_g00670:1232	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	GG	GA	GG	GG
-chr1:1156883	[T/C]	chr1	1156883	Cc01_g00670:1295	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	TT	TC	TT	TT
-chr1:1156892	[A/G]	chr1	1156892	Cc01_g00670:1304	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	12.5%	4	AA	AG	AA	AA
-chr1:1156901	[T/A]	chr1	1156901	Cc01_g00670:1313	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	12.5%	4	TT	TA	TT	TT
-chr1:1156908	[C/T]	chr1	1156908	Cc01_g00670:1320	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	37.5%	4	CC	CT	CT	CT
-chr1:1165679	[A/T]	chr1	1165679	Cc01_g00680:45	exon	STOP_GAINED	tgT/tgA	C/5	37.5%	4	AA	TT	AT	TT
-chr1:1165649	[C/T]	chr1	1165649	Cc01_g00680:75	exon	SYNONYMOUS_CODING	acG/acA	T/T	37.5%	4	CC	TT	CT	TT
-chr1:1165641	[A/G]	chr1	1165641	Cc01_g00680:83	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	12.5%	4	AA	AA	AG	AA
-chr1:1165640	[G/A]	chr1	1165640	Cc01_g00680:84	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	25.0%	4	GG	AA	AA	AA
-chr1:1165637	[A/G]	chr1	1165637	Cc01_g00680:87	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	25.0%	4	AA	GG	GG	GG
-chr1:1165630	[G/T]	chr1	1165630	Cc01_g00680:94	exon	NON_SYNONYMOUS_CODING	Ccc/Acc	P/T	25.0%	4	GG	TT	TT	TT
-chr1:1166386	[C/A]	chr1	1166386	Cc01_g00690:200	exon	NON_SYNONYMOUS_CODING	aCt/aAt	T/N	33.3%	3	CC	NN	CC	AA
-chr1:1166466	[A/C]	chr1	1166466	Cc01_g00690:280	exon	NON_SYNONYMOUS_CODING	Act/Cct	T/P	16.7%	3	AA	NN	AA	AC
-chr1:1166542	[T/G]	chr1	1166542	Cc01_g00690:356	exon	NON_SYNONYMOUS_CODING	gTc/gGc	V/G	33.3%	3	TT	NN	TT	GG
-chr1:1166804	[C/A]	chr1	1166804	Cc01_g00690:618	exon	SYNONYMOUS_CODING	gcC/gcA	A/A	25.0%	4	CC	CC	CC	AA
-chr1:1167034	[G/C]	chr1	1167034	Cc01_g00700:60	exon	NON_SYNONYMOUS_CODING	agG/agC	R/S	33.3%	3	GG	NN	GG	CC
-chr1:1167354	[A/G]	chr1	1167354	Cc01_g00700:380	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	33.3%	3	AA	NN	AA	GG
-chr1:1167571	[G/T]	chr1	1167571	Cc01_g00700:597	exon	NON_SYNONYMOUS_CODING	agG/agT	R/S	33.3%	3	GG	NN	GG	TT
-chr1:1179790	[G/A]	chr1	1179790	Cc01_g00710:105	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	GG	GG	AA	GG
-chr1:1179828	[C/G]	chr1	1179828	Cc01_g00710:143	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	25.0%	4	CC	GG	GG	GG
-chr1:1179917	[A/T]	chr1	1179917	Cc01_g00710:232	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	25.0%	4	AA	TT	TT	TT
-chr1:1179943	[C/T]	chr1	1179943	Cc01_g00710:258	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	25.0%	4	CC	TT	TT	TT
-chr1:1179952	[T/C]	chr1	1179952	Cc01_g00710:267	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	TT	CC	CC	CC
-chr1:1179953	[G/A]	chr1	1179953	Cc01_g00710:268	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	25.0%	4	GG	AA	AA	AA
-chr1:1179985	[C/T]	chr1	1179985	Cc01_g00710:300	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	25.0%	4	CC	TT	TT	TT
-chr1:1180012	[A/G]	chr1	1180012	Cc01_g00710:327	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	25.0%	4	AA	GG	GG	GG
-chr1:1180056	[T/C]	chr1	1180056	Cc01_g00710:371	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	25.0%	4	TT	CC	CC	CC
-chr1:1180061	[T/C]	chr1	1180061	Cc01_g00710:376	exon	STOP_LOST	Tag/Cag	1/Q	25.0%	4	TT	CC	CC	CC
-chr1:1180063	[G/C]	chr1	1180063	Cc01_g00710:378	exon	STOP_LOST	taG/taC	1/Y	33.3%	3	GG	NN	CC	CC
-chr1:1212493	[G/C]	chr1	1212493	Cc01_g00720:7	exon	NON_SYNONYMOUS_CODING	Ctc/Gtc	L/V	33.3%	3	GG	CC	NN	GG
-chr1:1212477	[T/C]	chr1	1212477	Cc01_g00720:23	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	25.0%	4	TT	CC	TT	TT
-chr1:1212194	[A/T]	chr1	1212194	Cc01_g00720:160	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	25.0%	4	AA	TT	AA	AA
-chr1:1212184	[C/G]	chr1	1212184	Cc01_g00720:170	exon	NON_SYNONYMOUS_CODING	gGg/gCg	G/A	12.5%	4	CC	CG	CC	CC
-chr1:1212161	[G/A]	chr1	1212161	Cc01_g00720:193	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	25.0%	4	GG	AA	GG	GG
-chr1:1212152	[A/G]	chr1	1212152	Cc01_g00720:202	exon	NON_SYNONYMOUS_CODING	Ttt/Ctt	F/L	25.0%	4	AA	GG	AA	AA
-chr1:1212124	[C/A]	chr1	1212124	Cc01_g00720:230	exon	NON_SYNONYMOUS_CODING	aGt/aTt	S/I	25.0%	4	CC	AA	CC	CC
-chr1:1211997	[A/T]	chr1	1211997	Cc01_g00720:357	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	4	AA	TT	AA	AA
-chr1:1211930	[T/C]	chr1	1211930	Cc01_g00720:424	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	25.0%	4	TT	CC	TT	TT
-chr1:1211567	[A/G]	chr1	1211567	Cc01_g00720:530	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	25.0%	4	AA	GG	AA	AA
-chr1:1211520	[G/T]	chr1	1211520	Cc01_g00720:577	exon	NON_SYNONYMOUS_CODING	Cag/Aag	Q/K	25.0%	4	GG	TT	GG	GG
-chr1:1211473	[C/A]	chr1	1211473	Cc01_g00720:624	exon	SYNONYMOUS_CODING	ctG/ctT	L/L	25.0%	4	CC	AA	CC	CC
-chr1:1211425	[A/G]	chr1	1211425	Cc01_g00720:672	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	AA	GG	AA	AA
-chr1:1211423	[A/C]	chr1	1211423	Cc01_g00720:674	exon	NON_SYNONYMOUS_CODING	tTc/tGc	F/C	25.0%	4	AA	CC	AA	AA
-chr1:1211422	[G/C]	chr1	1211422	Cc01_g00720:675	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	25.0%	4	GG	CC	GG	GG
-chr1:1211398	[G/C]	chr1	1211398	Cc01_g00720:699	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	25.0%	4	GG	CC	GG	GG
-chr1:1211397	[G/T]	chr1	1211397	Cc01_g00720:700	exon	NON_SYNONYMOUS_CODING	Cac/Aac	H/N	25.0%	4	GG	TT	GG	GG
-chr1:1211383	[C/T]	chr1	1211383	Cc01_g00720:714	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	25.0%	4	CC	TT	CC	CC
-chr1:1211377	[C/T]	chr1	1211377	Cc01_g00720:720	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	37.5%	4	CC	TT	CT	CC
-chr1:1211364	[T/G]	chr1	1211364	Cc01_g00720:733	exon	NON_SYNONYMOUS_CODING	Ata/Cta	I/L	25.0%	4	TT	GG	TT	TT
-chr1:1211349	[C/T]	chr1	1211349	Cc01_g00720:748	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	37.5%	4	CC	TT	CT	CC
-chr1:1210891	[T/A]	chr1	1210891	Cc01_g00720:758	exon	NON_SYNONYMOUS_CODING	cAt/cTt	H/L	25.0%	4	TT	AA	TT	TT
-chr1:1210874	[A/G]	chr1	1210874	Cc01_g00720:775	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	AA	GG	AA	AA
-chr1:1210869	[A/G]	chr1	1210869	Cc01_g00720:780	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	AA	GG	AA	AA
-chr1:1210831	[T/A]	chr1	1210831	Cc01_g00720:818	exon	NON_SYNONYMOUS_CODING	gAa/gTa	E/V	12.5%	4	TT	TA	TT	TT
-chr1:1210823	[G/A]	chr1	1210823	Cc01_g00720:826	exon	NON_SYNONYMOUS_CODING	Cgc/Tgc	R/C	25.0%	4	GG	AA	GG	GG
-chr1:1210781	[C/T]	chr1	1210781	Cc01_g00720:868	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	4	CC	TT	CC	CC
-chr1:1210772	[A/T]	chr1	1210772	Cc01_g00720:877	exon	NON_SYNONYMOUS_CODING	Tat/Aat	Y/N	25.0%	4	AA	TT	TT	TT
-chr1:1210770	[A/C]	chr1	1210770	Cc01_g00720:879	exon	STOP_GAINED	taT/taG	Y/3	25.0%	4	AA	CC	AA	AA
-chr1:1210745	[T/C]	chr1	1210745	Cc01_g00720:904	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	TT	TT	TT	CC
-chr1:1210744	[A/G]	chr1	1210744	Cc01_g00720:905	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	25.0%	4	AA	GG	AA	AA
-chr1:1210728	[T/C]	chr1	1210728	Cc01_g00720:921	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	TT	CC	TT	TT
-chr1:1210710	[A/T]	chr1	1210710	Cc01_g00720:939	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	25.0%	4	AA	TT	AA	AA
-chr1:1210708	[A/G]	chr1	1210708	Cc01_g00720:941	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	25.0%	4	AA	GG	AA	AA
-chr1:1210663	[A/G]	chr1	1210663	Cc01_g00720:986	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	25.0%	4	AA	GG	AA	AA
-chr1:1210651	[T/A]	chr1	1210651	Cc01_g00720:998	exon	NON_SYNONYMOUS_CODING	tAc/tTc	Y/F	25.0%	4	TT	AA	TT	TT
-chr1:1210640	[G/C]	chr1	1210640	Cc01_g00720:1009	exon	NON_SYNONYMOUS_CODING	Ctc/Gtc	L/V	25.0%	4	GG	CC	GG	GG
-chr1:1210632	[A/G]	chr1	1210632	Cc01_g00720:1017	exon	SYNONYMOUS_CODING	agT/agC	S/S	37.5%	4	AA	AA	AG	GG
-chr1:1210613	[A/T]	chr1	1210613	Cc01_g00720:1036	exon	NON_SYNONYMOUS_CODING	Tta/Ata	L/I	25.0%	4	AA	TT	AA	AA
-chr1:1210611	[T/C]	chr1	1210611	Cc01_g00720:1038	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	25.0%	4	TT	CC	TT	TT
-chr1:1210566	[G/A]	chr1	1210566	Cc01_g00720:1083	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	25.0%	4	GG	AA	GG	GG
-chr1:1210546	[T/A]	chr1	1210546	Cc01_g00720:1103	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	25.0%	4	TT	AA	TT	TT
-chr1:1210538	[C/T]	chr1	1210538	Cc01_g00720:1111	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	25.0%	4	CC	TT	CC	CC
-chr1:1210516	[T/A]	chr1	1210516	Cc01_g00720:1133	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	25.0%	4	TT	TT	TT	AA
-chr1:1210512	[C/T]	chr1	1210512	Cc01_g00720:1137	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	4	CC	TT	CC	CC
-chr1:1210505	[C/A]	chr1	1210505	Cc01_g00720:1144	exon	NON_SYNONYMOUS_CODING	Gca/Tca	A/S	25.0%	4	CC	AA	CC	CC
-chr1:1242676	[A/G]	chr1	1242676	Cc01_g00730:1	exon	START_LOST	Atg/Gtg	M/V	25.0%	4	AA	GG	AA	AA
-chr1:1242683	[C/T]	chr1	1242683	Cc01_g00730:8	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	12.5%	4	CC	CT	CC	CC
-chr1:1242684	[A/G]	chr1	1242684	Cc01_g00730:9	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	37.5%	4	AA	GG	AG	AA
-chr1:1242698	[C/T]	chr1	1242698	Cc01_g00730:23	exon	NON_SYNONYMOUS_CODING	tCc/tTc	S/F	12.5%	4	CC	CC	CT	CC
-chr1:1242721	[C/G]	chr1	1242721	Cc01_g00730:46	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	37.5%	4	CC	GG	CC	CG
-chr1:1242729	[T/G]	chr1	1242729	Cc01_g00730:54	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	37.5%	4	TT	GG	TT	TG
-chr1:1242731	[C/A]	chr1	1242731	Cc01_g00730:56	exon	NON_SYNONYMOUS_CODING	aCt/aAt	T/N	12.5%	4	CC	CA	CC	CC
-chr1:1242744	[A/T]	chr1	1242744	Cc01_g00730:69	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	50.0%	4	AA	TT	AT	AT
-chr1:1242762	[T/C]	chr1	1242762	Cc01_g00730:87	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	50.0%	4	TT	CC	TC	TC
-chr1:1242783	[A/G]	chr1	1242783	Cc01_g00730:108	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	50.0%	4	AA	GG	AG	AG
-chr1:1242791	[G/C]	chr1	1242791	Cc01_g00730:116	exon	NON_SYNONYMOUS_CODING	tGt/tCt	C/S	12.5%	4	GG	GC	GG	GG
-chr1:1242950	[G/T]	chr1	1242950	Cc01_g00730:275	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	25.0%	4	GG	TT	GG	GG
-chr1:1243019	[G/C]	chr1	1243019	Cc01_g00730:344	exon	NON_SYNONYMOUS_CODING	cGt/cCt	R/P	25.0%	4	GG	CC	GG	GG
-chr1:1243020	[T/A]	chr1	1243020	Cc01_g00730:345	exon	SYNONYMOUS_CODING	cgT/cgA	R/R	25.0%	4	TT	AA	TT	TT
-chr1:1244895	[G/T]	chr1	1244895	Cc01_g00730:369	exon	SYNONYMOUS_CODING	tcG/tcT	S/S	25.0%	4	GG	TT	GG	GG
-chr1:1244933	[T/A]	chr1	1244933	Cc01_g00730:407	exon	NON_SYNONYMOUS_CODING	cTa/cAa	L/Q	25.0%	4	TT	AA	TT	TT
-chr1:1245002	[C/A]	chr1	1245002	Cc01_g00730:476	exon	NON_SYNONYMOUS_CODING	cCt/cAt	P/H	25.0%	4	CC	CC	CC	AA
-chr1:1245030	[G/A]	chr1	1245030	Cc01_g00730:504	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	4	GG	AA	GG	GG
-chr1:1245060	[T/A]	chr1	1245060	Cc01_g00730:534	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	12.5%	4	TT	TA	TT	TT
-chr1:1245492	[A/G]	chr1	1245492	Cc01_g00730:553	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	AA	AA	AG	AG
-chr1:1245530	[A/G]	chr1	1245530	Cc01_g00730:591	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	AA	AG	AG
-chr1:1245533	[T/C]	chr1	1245533	Cc01_g00730:594	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	TT	TT	TC	TT
-chr1:1245549	[C/A]	chr1	1245549	Cc01_g00730:610	exon	NON_SYNONYMOUS_CODING	Ctg/Atg	L/M	25.0%	4	CC	CC	CA	CA
-chr1:1245553	[A/G]	chr1	1245553	Cc01_g00730:614	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	12.5%	4	AA	AA	AA	AG
-chr1:1245566	[G/C]	chr1	1245566	Cc01_g00730:627	exon	SYNONYMOUS_CODING	tcG/tcC	S/S	25.0%	4	GG	CC	GG	GG
-chr1:1253676	[T/C]	chr1	1253676	Cc01_g00740:865	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	TT	TT	TC	TC
-chr1:1256457	[G/T]	chr1	1256457	Cc01_g00750:100	exon	NON_SYNONYMOUS_CODING	Cac/Aac	H/N	25.0%	2	GG	NN	NN	GT
-chr1:1262785	[G/T]	chr1	1262785	Cc01_g00760:45	exon	SYNONYMOUS_CODING	tcC/tcA	S/S	50.0%	2	GG	NN	NN	TT
-chr1:1269842	[C/T]	chr1	1269842	Cc01_g00770:45	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	16.7%	3	CC	CC	NN	CT
-chr1:1269935	[C/G]	chr1	1269935	Cc01_g00770:138	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	37.5%	4	CC	GG	GG	CG
-chr1:1269943	[G/A]	chr1	1269943	Cc01_g00770:146	exon	STOP_GAINED	tGg/tAg	W/9	37.5%	4	GG	AA	AA	GA
-chr1:1269976	[T/C]	chr1	1269976	Cc01_g00770:179	exon	NON_SYNONYMOUS_CODING	cTa/cCa	L/P	12.5%	4	TT	TT	TC	TT
-chr1:1270017	[T/C]	chr1	1270017	Cc01_g00770:220	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	TT	TT	TC	TT
-chr1:1270071	[A/C]	chr1	1270071	Cc01_g00770:274	exon	NON_SYNONYMOUS_CODING	Agt/Cgt	S/R	12.5%	4	AA	AA	AA	AC
-chr1:1270072	[G/A]	chr1	1270072	Cc01_g00770:275	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	GG	GG	GA	GG
-chr1:1270081	[T/C]	chr1	1270081	Cc01_g00770:284	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	12.5%	4	TT	TT	TT	CT
-chr1:1270085	[T/C]	chr1	1270085	Cc01_g00770:288	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	12.5%	4	TT	TT	TT	CT
-chr1:1270104	[A/T]	chr1	1270104	Cc01_g00770:307	exon	NON_SYNONYMOUS_CODING	Agg/Tgg	R/W	12.5%	4	AA	AA	AT	AA
-chr1:1276100	[G/T]	chr1	1276100	Cc01_g00770:317	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	25.0%	4	GG	TT	TT	TT
-chr1:1278052	[G/A]	chr1	1278052	Cc01_g00780:52	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	37.5%	4	GG	AA	AA	GA
-chr1:1278096	[A/T]	chr1	1278096	Cc01_g00780:96	exon	NON_SYNONYMOUS_CODING	agA/agT	R/S	50.0%	4	AA	TT	AT	AT
-chr1:1278097	[A/G]	chr1	1278097	Cc01_g00780:97	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	50.0%	4	AA	GG	AG	AG
-chr1:1278180	[T/C]	chr1	1278180	Cc01_g00780:180	exon	SYNONYMOUS_CODING	agT/agC	S/S	25.0%	4	TT	CC	CC	CC
-chr1:1278211	[T/C]	chr1	1278211	Cc01_g00780:211	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	37.5%	4	TT	CC	TC	TT
-chr1:1279216	[A/G]	chr1	1279216	Cc01_g00780:409	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	25.0%	4	AA	AA	AG	AG
-chr1:1287721	[T/C]	chr1	1287721	Cc01_g00790:16	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	50.0%	3	TT	TC	NN	CC
-chr1:1287672	[C/T]	chr1	1287672	Cc01_g00790:31	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	25.0%	4	CC	CC	TT	CC
-chr1:1287643	[T/C]	chr1	1287643	Cc01_g00790:60	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TC	TT
-chr1:1287637	[C/T]	chr1	1287637	Cc01_g00790:66	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	12.5%	4	CC	CC	CC	CT
-chr1:1286824	[G/A]	chr1	1286824	Cc01_g00790:136	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	25.0%	4	GG	AA	AA	AA
-chr1:1286808	[T/C]	chr1	1286808	Cc01_g00790:152	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	12.5%	4	TT	TC	TT	TT
-chr1:1285473	[T/C]	chr1	1285473	Cc01_g00790:246	exon	SYNONYMOUS_CODING	acA/acG	T/T	37.5%	4	TT	CC	TC	CC
-chr1:1285472	[G/A]	chr1	1285472	Cc01_g00790:247	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	GG	GA	GG	GG
-chr1:1284801	[T/C]	chr1	1284801	Cc01_g00790:399	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	TT	TT	TC	TT
-chr1:1287857	[C/A]	chr1	1287857	Cc01_g00800:142	exon	NON_SYNONYMOUS_CODING	Gca/Tca	A/S	50.0%	2	CC	NN	NN	AA
-chr1:1287818	[C/G]	chr1	1287818	Cc01_g00800:181	exon	NON_SYNONYMOUS_CODING	Gta/Cta	V/L	50.0%	2	CC	GG	NN	NN
-chr1:1291612	[T/C]	chr1	1291612	Cc01_g00810:61	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	12.5%	4	TT	TT	TC	TT
-chr1:1291633	[A/T]	chr1	1291633	Cc01_g00810:82	exon	NON_SYNONYMOUS_CODING	Aat/Tat	N/Y	25.0%	4	AA	AA	AA	TT
-chr1:1291665	[T/C]	chr1	1291665	Cc01_g00810:114	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	TT	TT	TT	CC
-chr1:1291715	[A/G]	chr1	1291715	Cc01_g00810:164	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	37.5%	4	AA	GG	AG	AA
-chr1:1291716	[C/T]	chr1	1291716	Cc01_g00810:165	exon	SYNONYMOUS_CODING	caC/caT	H/H	25.0%	4	CC	CC	CC	TT
-chr1:1291740	[G/T]	chr1	1291740	Cc01_g00810:189	exon	SYNONYMOUS_CODING	ccG/ccT	P/P	25.0%	4	GG	GG	GG	TT
-chr1:1292034	[T/A]	chr1	1292034	Cc01_g00810:396	exon	SYNONYMOUS_CODING	ggT/ggA	G/G	25.0%	4	TT	AA	AA	AA
-chr1:1292248	[A/G]	chr1	1292248	Cc01_g00810:510	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	AA	AA	AG
-chr1:1293103	[C/T]	chr1	1293103	Cc01_g00810:767	exon	NON_SYNONYMOUS_CODING	gCc/gTc	A/V	12.5%	4	CC	CT	CC	CC
-chr1:1293122	[C/G]	chr1	1293122	Cc01_g00810:786	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	25.0%	4	CC	CC	CC	GG
-chr1:1293811	[T/C]	chr1	1293811	Cc01_g00810:813	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	25.0%	4	TT	TT	TT	CC
-chr1:1293815	[C/A]	chr1	1293815	Cc01_g00810:817	exon	NON_SYNONYMOUS_CODING	Cat/Aat	H/N	50.0%	4	CC	AA	AA	CC
-chr1:1293824	[C/T]	chr1	1293824	Cc01_g00810:826	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	50.0%	4	CC	TT	TT	CC
-chr1:1293825	[A/G]	chr1	1293825	Cc01_g00810:827	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	50.0%	4	AA	GG	GG	AA
-chr1:1293978	[A/T]	chr1	1293978	Cc01_g00810:882	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	25.0%	4	AA	AA	AA	TT
-chr1:1294013	[G/A]	chr1	1294013	Cc01_g00810:917	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	12.5%	4	GG	GG	GG	GA
-chr1:1294044	[A/T]	chr1	1294044	Cc01_g00810:948	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	AA	AA	AA	TT
-chr1:1294134	[C/T]	chr1	1294134	Cc01_g00810:1038	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	25.0%	4	CC	CC	CC	TT
-chr1:1294702	[C/T]	chr1	1294702	Cc01_g00810:1221	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	CC	CC	CT	CC
-chr1:1294781	[G/C]	chr1	1294781	Cc01_g00810:1300	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	12.5%	4	GG	GG	GC	GG
-chr1:1294832	[A/T]	chr1	1294832	Cc01_g00810:1351	exon	NON_SYNONYMOUS_CODING	Att/Ttt	I/F	50.0%	4	AA	TT	TT	AA
-chr1:1294843	[G/T]	chr1	1294843	Cc01_g00810:1362	exon	SYNONYMOUS_CODING	ggG/ggT	G/G	25.0%	4	GG	TT	TT	TT
-chr1:1294891	[T/G]	chr1	1294891	Cc01_g00810:1410	exon	NON_SYNONYMOUS_CODING	atT/atG	I/M	37.5%	4	TT	GG	TG	GG
-chr1:1294916	[G/T]	chr1	1294916	Cc01_g00810:1435	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	25.0%	4	GG	GT	GT	GG
-chr1:1299931	[A/C]	chr1	1299931	Cc01_g00820:42	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	25.0%	4	AA	AC	AA	AC
-chr1:1299953	[G/A]	chr1	1299953	Cc01_g00820:64	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	12.5%	4	GG	GG	GG	GA
-chr1:1300252	[C/T]	chr1	1300252	Cc01_g00820:219	exon	SYNONYMOUS_CODING	atC/atT	I/I	25.0%	4	CC	CC	TT	CC
-chr1:1300382	[C/T]	chr1	1300382	Cc01_g00820:349	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	25.0%	4	CC	CC	TT	CC
-chr1:1300390	[T/C]	chr1	1300390	Cc01_g00820:357	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	25.0%	4	TT	TT	CC	TT
-chr1:1300457	[T/C]	chr1	1300457	Cc01_g00820:424	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	TT	TT	CC	TT
-chr1:1300540	[T/C]	chr1	1300540	Cc01_g00820:507	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	TT	TT	CC	TT
-chr1:1300948	[C/T]	chr1	1300948	Cc01_g00820:915	exon	SYNONYMOUS_CODING	agC/agT	S/S	37.5%	4	CC	TT	TT	CT
-chr1:1301593	[T/C]	chr1	1301593	Cc01_g00820:1152	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	25.0%	4	TT	TT	CC	TT
-chr1:1302393	[T/C]	chr1	1302393	Cc01_g00820:1332	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	25.0%	4	TT	TT	CC	TT
-chr1:1304941	[C/T]	chr1	1304941	Cc01_g00820:2055	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	CC	CT	TT	CC
-chr1:1306040	[A/T]	chr1	1306040	Cc01_g00820:2256	exon	SYNONYMOUS_CODING	ggA/ggT	G/G	25.0%	4	AA	AA	TT	AA
-chr1:1306100	[A/G]	chr1	1306100	Cc01_g00820:2316	exon	SYNONYMOUS_CODING	acA/acG	T/T	25.0%	4	AA	AA	GG	AA
-chr1:1306364	[T/C]	chr1	1306364	Cc01_g00820:2482	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	TT	TT	CC	TT
-chr1:1306387	[A/G]	chr1	1306387	Cc01_g00820:2505	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	AG	AA	AA
-chr1:1307153	[T/C]	chr1	1307153	Cc01_g00820:2580	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	TT	TC	TT	TT
-chr1:1307312	[T/C]	chr1	1307312	Cc01_g00820:2652	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	25.0%	4	TT	TT	CC	TT
-chr1:1307738	[A/T]	chr1	1307738	Cc01_g00820:2802	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	25.0%	4	AA	AA	TT	AA
-chr1:1308482	[A/T]	chr1	1308482	Cc01_g00820:2964	exon	SYNONYMOUS_CODING	tcA/tcT	S/S	12.5%	4	AA	AT	AA	AA
-chr1:1308494	[G/A]	chr1	1308494	Cc01_g00820:2976	exon	SYNONYMOUS_CODING	agG/agA	R/R	16.7%	3	GG	GA	NN	GG
-chr1:1308608	[C/A]	chr1	1308608	Cc01_g00830:24	exon	STOP_GAINED	tgC/tgA	C8*	16.7%	3	CC	CA	NN	CC
-chr1:1309677	[C/G]	chr1	1309677	Cc01_g00830:163	exon	NON_SYNONYMOUS_CODING	Ctt/Gtt	L/V	25.0%	4	CC	CG	CG	CC
-chr1:1314539	[G/A]	chr1	1314539	Cc01_g00840:25	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	50.0%	3	GG	AA	NN	GA
-chr1:1314673	[G/A]	chr1	1314673	Cc01_g00840:159	exon	SYNONYMOUS_CODING	acG/acA	T/T	37.5%	4	GG	AA	GG	GA
-chr1:1314823	[C/G]	chr1	1314823	Cc01_g00840:309	exon	SYNONYMOUS_CODING	ggC/ggG	G/G	25.0%	4	CC	GG	GG	GG
-chr1:1314984	[G/A]	chr1	1314984	Cc01_g00840:470	exon	NON_SYNONYMOUS_CODING	aGc/aAc	S/N	37.5%	4	GG	GG	AA	GA
-chr1:1315015	[G/C]	chr1	1315015	Cc01_g00840:501	exon	SYNONYMOUS_CODING	gcG/gcC	A/A	37.5%	4	GG	GG	CC	GC
-chr1:1315050	[A/G]	chr1	1315050	Cc01_g00840:536	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	16.7%	3	AA	AG	NN	AA
-chr1:1315120	[C/A]	chr1	1315120	Cc01_g00840:606	exon	SYNONYMOUS_CODING	acC/acA	T/T	12.5%	4	CC	CC	CC	CA
-chr1:1315139	[T/A]	chr1	1315139	Cc01_g00840:625	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	16.7%	3	TT	TT	NN	TA
-chr1:1315156	[T/G]	chr1	1315156	Cc01_g00840:642	exon	SYNONYMOUS_CODING	tcT/tcG	S/S	16.7%	3	TT	TT	NN	TG
-chr1:1315218	[T/C]	chr1	1315218	Cc01_g00840:704	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	50.0%	3	TT	NN	CC	TC
-chr1:1315234	[C/T]	chr1	1315234	Cc01_g00840:720	exon	SYNONYMOUS_CODING	agC/agT	S/S	33.3%	3	CC	CC	NN	TT
-chr1:1315240	[C/T]	chr1	1315240	Cc01_g00840:726	exon	SYNONYMOUS_CODING	caC/caT	H/H	33.3%	3	CC	CC	NN	TT
-chr1:1315338	[A/T]	chr1	1315338	Cc01_g00840:824	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	33.3%	3	AA	TT	NN	AA
-chr1:1324380	[G/A]	chr1	1324380	Cc01_g00850:82	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	25.0%	4	GG	AA	AA	AA
-chr1:1324392	[A/G]	chr1	1324392	Cc01_g00850:94	exon	NON_SYNONYMOUS_CODING	Aac/Gac	N/D	37.5%	4	AA	GG	GG	AG
-chr1:1324409	[G/C]	chr1	1324409	Cc01_g00850:111	exon	NON_SYNONYMOUS_CODING	caG/caC	Q/H	12.5%	4	GG	GG	GG	CG
-chr1:1326674	[T/C]	chr1	1326674	Cc01_g00850:270	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	37.5%	4	TT	CC	CC	TC
-chr1:1326698	[A/G]	chr1	1326698	Cc01_g00850:294	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	25.0%	4	AA	GG	AA	AA
-chr1:1327530	[G/C]	chr1	1327530	Cc01_g00850:418	exon	NON_SYNONYMOUS_CODING	Gac/Cac	D/H	25.0%	4	GG	CC	CC	CC
-chr1:1327531	[A/G]	chr1	1327531	Cc01_g00850:419	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	37.5%	4	AA	GG	GG	AG
-chr1:1327575	[C/G]	chr1	1327575	Cc01_g00850:463	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	12.5%	4	CC	CC	CC	GC
-chr1:1327581	[G/A]	chr1	1327581	Cc01_g00850:469	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	12.5%	4	GG	GG	GA	GG
-chr1:1327613	[C/T]	chr1	1327613	Cc01_g00850:501	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	25.0%	4	CC	TT	TT	TT
-chr1:1327618	[C/T]	chr1	1327618	Cc01_g00850:506	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	25.0%	4	CC	TT	TT	TT
-chr1:1327624	[C/A]	chr1	1327624	Cc01_g00850:512	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	37.5%	4	CC	AA	AA	CA
-chr1:1327630	[G/T]	chr1	1327630	Cc01_g00850:518	exon	NON_SYNONYMOUS_CODING	aGg/aTg	R/M	25.0%	4	GG	TT	TT	TT
-chr1:1327639	[T/G]	chr1	1327639	Cc01_g00850:527	exon	NON_SYNONYMOUS_CODING	gTt/gGt	V/G	25.0%	4	TT	GG	GG	GG
-chr1:1327826	[T/C]	chr1	1327826	Cc01_g00850:714	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	TT	CC	CC	CC
-chr1:1327904	[C/T]	chr1	1327904	Cc01_g00850:792	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	37.5%	4	CC	TT	CT	CC
-chr1:1328126	[A/G]	chr1	1328126	Cc01_g00850:859	exon	NON_SYNONYMOUS_CODING	Aac/Gac	N/D	12.5%	4	AA	AA	AA	AG
-chr1:1328127	[A/T]	chr1	1328127	Cc01_g00850:860	exon	NON_SYNONYMOUS_CODING	aAc/aTc	N/I	12.5%	4	AA	AA	AA	AT
-chr1:1332539	[C/A]	chr1	1332539	Cc01_g00860:529	exon	NON_SYNONYMOUS_CODING	Gta/Tta	V/L	37.5%	4	CC	CA	CA	CA
-chr1:1332405	[T/C]	chr1	1332405	Cc01_g00860:663	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TC	TT	TT
-chr1:1332138	[T/C]	chr1	1332138	Cc01_g00860:930	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	50.0%	4	TT	TC	TC	CC
-chr1:1331004	[A/G]	chr1	1331004	Cc01_g00860:1047	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	AA	GG	AA	AA
-chr1:1330827	[G/A]	chr1	1330827	Cc01_g00860:1224	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	GG	GA	GG	GG
-chr1:1330803	[T/A]	chr1	1330803	Cc01_g00860:1248	exon	SYNONYMOUS_CODING	ggA/ggT	G/G	12.5%	4	TT	TA	TT	TT
-chr1:1330755	[A/G]	chr1	1330755	Cc01_g00860:1296	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	AA	AG	AA	AA
-chr1:1349945	[T/C]	chr1	1349945	Cc01_g00870:84	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	TT	TC	TT
-chr1:1349954	[T/C]	chr1	1349954	Cc01_g00870:93	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TT	TC	TT
-chr1:1350532	[C/T]	chr1	1350532	Cc01_g00870:144	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	37.5%	4	CC	CC	TC	TT
-chr1:1350732	[C/T]	chr1	1350732	Cc01_g00870:344	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	37.5%	4	CC	CC	CT	TT
-chr1:1400299	[A/G]	chr1	1400299	Cc01_g00880:23	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	25.0%	4	AA	GG	GG	GG
-chr1:1400306	[C/T]	chr1	1400306	Cc01_g00880:30	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	25.0%	4	CC	CC	CC	TT
-chr1:1400308	[A/G]	chr1	1400308	Cc01_g00880:32	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	25.0%	4	AA	GG	GG	GG
-chr1:1400337	[T/G]	chr1	1400337	Cc01_g00880:61	exon	NON_SYNONYMOUS_CODING	Tgg/Ggg	W/G	25.0%	4	TT	GG	GG	GG
-chr1:1400339	[G/A]	chr1	1400339	Cc01_g00880:63	exon	STOP_GAINED	tgG/tgA	W/1	25.0%	4	GG	AA	AA	AA
-chr1:1400381	[A/C]	chr1	1400381	Cc01_g00880:105	exon	SYNONYMOUS_CODING	ccA/ccC	P/P	33.3%	3	AA	CC	NN	CC
-chr1:1410529	[A/G]	chr1	1410529	Cc01_g00890:10	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	50.0%	2	AA	NN	NN	GG
-chr1:1410533	[C/T]	chr1	1410533	Cc01_g00890:14	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	33.3%	3	CC	CC	NN	TT
-chr1:1410555	[T/C]	chr1	1410555	Cc01_g00890:36	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	25.0%	4	TT	CC	TT	TT
-chr1:1410556	[T/C]	chr1	1410556	Cc01_g00890:37	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	50.0%	4	TT	TT	CC	CC
-chr1:1410561	[C/T]	chr1	1410561	Cc01_g00890:42	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	50.0%	4	CC	CC	TT	TT
-chr1:1410563	[A/G]	chr1	1410563	Cc01_g00890:44	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	25.0%	4	AA	GG	GG	GG
-chr1:1410566	[C/T]	chr1	1410566	Cc01_g00890:47	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	50.0%	4	CC	CC	TT	TT
-chr1:1410569	[A/C]	chr1	1410569	Cc01_g00890:50	exon	NON_SYNONYMOUS_CODING	aAg/aCg	K/T	25.0%	4	AA	CC	CC	CC
-chr1:1410570	[G/A]	chr1	1410570	Cc01_g00890:51	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	50.0%	4	GG	GG	AA	AA
-chr1:1410580	[A/C]	chr1	1410580	Cc01_g00890:61	exon	SYNONYMOUS_CODING	Agg/Cgg	R/R	12.5%	4	AA	AC	AA	AA
-chr1:1410597	[C/G]	chr1	1410597	Cc01_g00890:78	exon	NON_SYNONYMOUS_CODING	caC/caG	H/Q	25.0%	4	CC	GG	GG	GG
-chr1:1427295	[C/G]	chr1	1427295	Cc01_g00900:7	exon	NON_SYNONYMOUS_CODING	Gct/Cct	A/P	25.0%	4	CC	CG	CC	CG
-chr1:1427282	[G/A]	chr1	1427282	Cc01_g00900:20	exon	NON_SYNONYMOUS_CODING	aCc/aTc	T/I	37.5%	4	GG	AA	AA	GA
-chr1:1427281	[G/A]	chr1	1427281	Cc01_g00900:21	exon	SYNONYMOUS_CODING	acC/acT	T/T	25.0%	4	GG	GG	GA	AG
-chr1:1427279	[G/A]	chr1	1427279	Cc01_g00900:23	exon	NON_SYNONYMOUS_CODING	cCg/cTg	P/L	25.0%	4	GG	GG	GA	AG
-chr1:1427275	[A/T]	chr1	1427275	Cc01_g00900:27	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	12.5%	4	AA	AA	AA	TA
-chr1:1427274	[A/G]	chr1	1427274	Cc01_g00900:28	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	12.5%	4	AA	AA	AA	GA
-chr1:1427261	[C/A]	chr1	1427261	Cc01_g00900:41	exon	NON_SYNONYMOUS_CODING	gGt/gTt	G/V	12.5%	4	CC	CC	CC	AC
-chr1:1427118	[T/C]	chr1	1427118	Cc01_g00900:66	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	16.7%	3	TT	NN	TT	CT
-chr1:1427056	[T/C]	chr1	1427056	Cc01_g00900:128	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	25.0%	4	TT	TC	TC	TT
-chr1:1427054	[C/T]	chr1	1427054	Cc01_g00900:130	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	CC	CC	CT	CC
-chr1:1427045	[G/A]	chr1	1427045	Cc01_g00900:139	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	GG	GA	GA	AG
-chr1:1427039	[G/T]	chr1	1427039	Cc01_g00900:145	exon	NON_SYNONYMOUS_CODING	Cag/Aag	Q/K	37.5%	4	GG	TG	TG	GT
-chr1:1427035	[G/A]	chr1	1427035	Cc01_g00900:149	exon	NON_SYNONYMOUS_CODING	aCc/aTc	T/I	37.5%	4	GG	GA	AG	AG
-chr1:1427030	[A/T]	chr1	1427030	Cc01_g00900:154	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	37.5%	4	AA	AT	AT	TA
-chr1:1427016	[T/C]	chr1	1427016	Cc01_g00900:168	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	TT	TC	CT	TC
-chr1:1427004	[G/A]	chr1	1427004	Cc01_g00900:180	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	GG	GG	GG	GA
-chr1:1427003	[C/T]	chr1	1427003	Cc01_g00900:181	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	25.0%	4	CC	CC	CT	CT
-chr1:1426994	[A/T]	chr1	1426994	Cc01_g00900:190	exon	NON_SYNONYMOUS_CODING	Ttc/Atc	F/I	25.0%	4	AA	TA	AA	AT
-chr1:1426981	[A/G]	chr1	1426981	Cc01_g00900:203	exon	NON_SYNONYMOUS_CODING	cTc/cCc	L/P	12.5%	4	AA	AA	AA	AG
-chr1:1426962	[T/C]	chr1	1426962	Cc01_g00900:222	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	TT	CT	CT	TC
-chr1:1426958	[C/T]	chr1	1426958	Cc01_g00900:226	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	4	CC	TC	CC	CT
-chr1:1426939	[A/T]	chr1	1426939	Cc01_g00900:245	exon	NON_SYNONYMOUS_CODING	cTg/cAg	L/Q	12.5%	4	AA	AA	TA	AA
-chr1:1426936	[A/G]	chr1	1426936	Cc01_g00900:248	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	25.0%	4	AA	AG	AA	GA
-chr1:1426925	[A/G]	chr1	1426925	Cc01_g00900:259	exon	NON_SYNONYMOUS_CODING	Tgt/Cgt	C/R	25.0%	4	AA	AA	AG	GA
-chr1:1426907	[T/A]	chr1	1426907	Cc01_g00900:277	exon	NON_SYNONYMOUS_CODING	Atc/Ttc	I/F	25.0%	4	TT	TA	AT	TT
-chr1:1426905	[G/A]	chr1	1426905	Cc01_g00900:279	exon	SYNONYMOUS_CODING	atC/atT	I/I	25.0%	4	GG	AA	AA	AA
-chr1:1433418	[A/G]	chr1	1433418	Cc01_g00910:102	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AA	AG	AA
-chr1:1433394	[G/A]	chr1	1433394	Cc01_g00910:126	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	50.0%	4	GG	GA	AA	GA
-chr1:1433392	[C/T]	chr1	1433392	Cc01_g00910:128	exon	NON_SYNONYMOUS_CODING	gGc/gAc	G/D	25.0%	4	CC	CT	CC	CT
-chr1:1433373	[C/G]	chr1	1433373	Cc01_g00910:147	exon	SYNONYMOUS_CODING	ctG/ctC	L/L	12.5%	4	CC	CC	CG	CC
-chr1:1432755	[C/T]	chr1	1432755	Cc01_g00910:549	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	12.5%	4	CC	CC	CT	CC
-chr1:1432742	[C/T]	chr1	1432742	Cc01_g00910:562	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	12.5%	4	CC	CT	CC	CC
-chr1:1432732	[C/T]	chr1	1432732	Cc01_g00910:572	exon	NON_SYNONYMOUS_CODING	gGa/gAa	G/E	25.0%	4	CC	TC	CT	CC
-chr1:1432730	[T/C]	chr1	1432730	Cc01_g00910:574	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	25.0%	4	TT	CT	TC	TT
-chr1:1432728	[T/G]	chr1	1432728	Cc01_g00910:576	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	25.0%	4	TT	GT	TG	TT
-chr1:1432698	[A/G]	chr1	1432698	Cc01_g00910:606	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	AA	GA	AA	AA
-chr1:1432697	[A/G]	chr1	1432697	Cc01_g00910:607	exon	NON_SYNONYMOUS_CODING	Ttc/Ctc	F/L	12.5%	4	AA	GA	AA	AA
-chr1:1432689	[G/C]	chr1	1432689	Cc01_g00910:615	exon	SYNONYMOUS_CODING	gtC/gtG	V/V	12.5%	4	GG	GC	GG	GG
-chr1:1432664	[C/A]	chr1	1432664	Cc01_g00910:640	exon	STOP_GAINED	Gag/Tag	E/4	12.5%	4	CC	CA	CC	CC
-chr1:1432663	[T/A]	chr1	1432663	Cc01_g00910:641	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	12.5%	4	TT	TA	TT	TT
-chr1:1432611	[A/G]	chr1	1432611	Cc01_g00910:693	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	AA	AG	AA	AA
-chr1:1432605	[G/A]	chr1	1432605	Cc01_g00910:699	exon	SYNONYMOUS_CODING	agC/agT	S/S	37.5%	4	GG	GA	AA	GG
-chr1:1432569	[C/T]	chr1	1432569	Cc01_g00910:735	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	16.7%	3	CC	CC	NN	CT
-chr1:1500031	[G/T]	chr1	1500031	Cc01_g00920:49	exon	NON_SYNONYMOUS_CODING	Cca/Aca	P/T	37.5%	4	GG	GT	GG	TT
-chr1:1500013	[A/T]	chr1	1500013	Cc01_g00920:67	exon	NON_SYNONYMOUS_CODING	Tgt/Agt	C/S	25.0%	4	AA	TA	AT	AA
-chr1:1499982	[C/T]	chr1	1499982	Cc01_g00920:98	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	50.0%	2	CC	NN	TT	NN
-chr1:1499966	[C/T]	chr1	1499966	Cc01_g00920:114	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	50.0%	2	CC	NN	TT	NN
-chr1:1499954	[T/C]	chr1	1499954	Cc01_g00920:126	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	33.3%	3	TT	CC	CC	NN
-chr1:1499939	[C/T]	chr1	1499939	Cc01_g00920:141	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	33.3%	3	CC	TT	TT	NN
-chr1:1499937	[T/A]	chr1	1499937	Cc01_g00920:143	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	33.3%	3	TT	AA	AA	NN
-chr1:1499906	[T/C]	chr1	1499906	Cc01_g00920:174	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	50.0%	4	TT	CC	CC	TT
-chr1:1499782	[C/G]	chr1	1499782	Cc01_g00920:298	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	25.0%	2	CC	NN	CG	NN
-chr1:1499780	[C/G]	chr1	1499780	Cc01_g00920:300	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	25.0%	2	CC	NN	CG	NN
-chr1:1499449	[G/A]	chr1	1499449	Cc01_g00920:631	exon	NON_SYNONYMOUS_CODING	Cgg/Tgg	R/W	50.0%	2	GG	NN	AA	NN
-chr1:1500757	[A/G]	chr1	1500757	Cc01_g00930:205	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	16.7%	3	AA	NN	AA	AG
-chr1:1500735	[C/G]	chr1	1500735	Cc01_g00930:227	exon	NON_SYNONYMOUS_CODING	aGa/aCa	R/T	16.7%	3	CC	NN	CC	CG
-chr1:1500625	[A/G]	chr1	1500625	Cc01_g00930:337	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	25.0%	2	AA	NN	NN	AG
-chr1:1500270	[T/C]	chr1	1500270	Cc01_g00930:605	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	12.5%	4	TT	TT	TC	TT
-chr1:1500265	[G/T]	chr1	1500265	Cc01_g00930:610	exon	NON_SYNONYMOUS_CODING	Cgc/Agc	R/S	12.5%	4	GG	GG	GT	GG
-chr1:1500257	[C/A]	chr1	1500257	Cc01_g00930:618	exon	SYNONYMOUS_CODING	ctG/ctT	L/L	12.5%	4	CC	CC	CC	CA
-chr1:1527537	[A/C]	chr1	1527537	Cc01_g00940:47	exon	NON_SYNONYMOUS_CODING	gTa/gGa	V/G	12.5%	4	AA	AC	AA	AA
-chr1:1527535	[G/C]	chr1	1527535	Cc01_g00940:49	exon	NON_SYNONYMOUS_CODING	Cga/Gga	R/G	37.5%	4	GG	CG	GC	GC
-chr1:1527534	[C/A]	chr1	1527534	Cc01_g00940:50	exon	NON_SYNONYMOUS_CODING	cGa/cTa	R/L	12.5%	4	CC	CC	CA	CC
-chr1:1527525	[G/C]	chr1	1527525	Cc01_g00940:59	exon	STOP_GAINED	tCa/tGa	S/0	37.5%	4	GG	CG	GC	GC
-chr1:1527523	[C/T]	chr1	1527523	Cc01_g00940:61	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	25.0%	4	CC	CT	CC	CT
-chr1:1527516	[A/G]	chr1	1527516	Cc01_g00940:68	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	25.0%	4	AA	AG	GA	AA
-chr1:1527513	[T/C]	chr1	1527513	Cc01_g00940:71	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	25.0%	4	TT	CC	CC	CC
-chr1:1527501	[T/C]	chr1	1527501	Cc01_g00940:83	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	25.0%	4	TT	TT	CT	TC
-chr1:1527490	[C/A]	chr1	1527490	Cc01_g00940:94	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	12.5%	4	CC	CC	AC	CC
-chr1:1527489	[A/G]	chr1	1527489	Cc01_g00940:95	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	AA	AA	AG	AA
-chr1:1527479	[A/T]	chr1	1527479	Cc01_g00940:105	exon	NON_SYNONYMOUS_CODING	agT/agA	S/R	37.5%	4	AA	AT	TT	TT
-chr1:1527475	[A/G]	chr1	1527475	Cc01_g00940:109	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	25.0%	4	AA	AG	GA	AA
-chr1:1527337	[T/C]	chr1	1527337	Cc01_g00940:124	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	37.5%	4	TT	TC	CT	TC
-chr1:1527336	[G/A]	chr1	1527336	Cc01_g00940:125	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	12.5%	4	GG	GA	GG	GG
-chr1:1527333	[G/A]	chr1	1527333	Cc01_g00940:128	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	37.5%	4	GG	AG	GA	AG
-chr1:1527325	[C/T]	chr1	1527325	Cc01_g00940:136	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	12.5%	4	CC	CT	CC	CC
-chr1:1527324	[A/G]	chr1	1527324	Cc01_g00940:137	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	AA	AA	AG	AA
-chr1:1527323	[C/T]	chr1	1527323	Cc01_g00940:138	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	12.5%	4	CC	CC	CC	TC
-chr1:1527310	[G/T]	chr1	1527310	Cc01_g00940:151	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	12.5%	4	GG	GG	GG	TG
-chr1:1527283	[G/A]	chr1	1527283	Cc01_g00940:178	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	37.5%	4	GG	GA	GA	GA
-chr1:1527277	[T/C]	chr1	1527277	Cc01_g00940:184	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	12.5%	4	TT	TT	TC	TT
-chr1:1527264	[C/A]	chr1	1527264	Cc01_g00940:197	exon	NON_SYNONYMOUS_CODING	tGc/tTc	C/F	12.5%	4	CC	CA	CC	CC
-chr1:1527261	[T/C]	chr1	1527261	Cc01_g00940:200	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	25.0%	4	TT	CC	CC	CC
-chr1:1527259	[G/A]	chr1	1527259	Cc01_g00940:202	exon	NON_SYNONYMOUS_CODING	Cac/Tac	H/Y	25.0%	4	GG	AA	AA	AA
-chr1:1527237	[G/A]	chr1	1527237	Cc01_g00940:224	exon	NON_SYNONYMOUS_CODING	cCg/cTg	P/L	25.0%	4	GG	GG	GA	AG
-chr1:1527236	[C/T]	chr1	1527236	Cc01_g00940:225	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	CC	CT	CC	CC
-chr1:1531686	[A/G]	chr1	1531686	Cc01_g00950:645	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	33.3%	3	AA	GG	NN	GG
-chr1:1531682	[A/G]	chr1	1531682	Cc01_g00950:649	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	33.3%	3	AA	GG	NN	GG
-chr1:1531673	[C/T]	chr1	1531673	Cc01_g00950:658	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	37.5%	4	CC	TT	CC	CT
-chr1:1531659	[A/G]	chr1	1531659	Cc01_g00950:672	exon	SYNONYMOUS_CODING	atT/atC	I/I	12.5%	4	AA	AA	AA	AG
-chr1:1531644	[A/T]	chr1	1531644	Cc01_g00950:687	exon	SYNONYMOUS_CODING	cgT/cgA	R/R	50.0%	4	AA	TT	TT	AA
-chr1:1531643	[A/T]	chr1	1531643	Cc01_g00950:688	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	37.5%	4	AA	TT	TT	TA
-chr1:1531641	[C/T]	chr1	1531641	Cc01_g00950:690	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	50.0%	4	CC	TT	TT	CC
-chr1:1531626	[C/G]	chr1	1531626	Cc01_g00950:705	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	50.0%	4	CC	GG	GG	CC
-chr1:1531625	[A/G]	chr1	1531625	Cc01_g00950:706	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	25.0%	4	AA	AA	GG	AA
-chr1:1531616	[T/C]	chr1	1531616	Cc01_g00950:715	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	TT	TT	CC	TT
-chr1:1531606	[T/C]	chr1	1531606	Cc01_g00950:725	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	33.3%	3	TT	NN	CC	TT
-chr1:1531575	[A/G]	chr1	1531575	Cc01_g00950:756	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	33.3%	3	AA	NN	AG	AG
-chr1:1531524	[G/A]	chr1	1531524	Cc01_g00950:807	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	GG	GG	GA	GG
-chr1:1531385	[A/C]	chr1	1531385	Cc01_g00950:946	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	12.5%	4	AA	AA	AA	AC
-chr1:1531373	[T/G]	chr1	1531373	Cc01_g00950:958	exon	NON_SYNONYMOUS_CODING	Att/Ctt	I/L	12.5%	4	TT	TT	TG	TT
-chr1:1531330	[C/T]	chr1	1531330	Cc01_g00950:1001	exon	NON_SYNONYMOUS_CODING	gGg/gAg	G/E	12.5%	4	CC	CC	CC	CT
-chr1:1531324	[C/G]	chr1	1531324	Cc01_g00950:1007	exon	NON_SYNONYMOUS_CODING	aGa/aCa	R/T	37.5%	4	CC	GG	GG	GC
-chr1:1530921	[T/A]	chr1	1530921	Cc01_g00950:1410	exon	NON_SYNONYMOUS_CODING	agA/agT	R/S	33.3%	3	TT	AA	NN	AA
-chr1:1530898	[T/A]	chr1	1530898	Cc01_g00950:1433	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	50.0%	3	TT	AA	NN	TA
-chr1:1530757	[C/T]	chr1	1530757	Cc01_g00950:1574	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	50.0%	2	CC	TT	NN	NN
-chr1:1530731	[T/G]	chr1	1530731	Cc01_g00950:1600	exon	NON_SYNONYMOUS_CODING	Aac/Cac	N/H	50.0%	2	TT	GG	NN	NN
-chr1:1530707	[G/A]	chr1	1530707	Cc01_g00950:1624	exon	NON_SYNONYMOUS_CODING	Cgc/Tgc	R/C	50.0%	2	GG	AA	NN	NN
-chr1:1530676	[G/C]	chr1	1530676	Cc01_g00950:1655	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	50.0%	3	GG	GC	NN	CC
-chr1:1530668	[T/C]	chr1	1530668	Cc01_g00950:1663	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	25.0%	4	TT	CC	TT	TT
-chr1:1530661	[T/G]	chr1	1530661	Cc01_g00950:1670	exon	NON_SYNONYMOUS_CODING	aAa/aCa	K/T	12.5%	4	TT	TG	TT	TT
-chr1:1530629	[T/G]	chr1	1530629	Cc01_g00950:1702	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	25.0%	4	TT	TT	TT	GG
-chr1:1530627	[T/C]	chr1	1530627	Cc01_g00950:1704	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	TT	CT	TT	TT
-chr1:1530607	[C/T]	chr1	1530607	Cc01_g00950:1724	exon	STOP_GAINED	tGg/tAg	W/5	16.7%	3	CC	TC	CC	NN
-chr1:1530606	[C/A]	chr1	1530606	Cc01_g00950:1725	exon	NON_SYNONYMOUS_CODING	tgG/tgT	W/C	16.7%	3	CC	AC	CC	NN
-chr1:1530597	[T/G]	chr1	1530597	Cc01_g00950:1734	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	16.7%	3	TT	GT	TT	NN
-chr1:1530532	[T/C]	chr1	1530532	Cc01_g00950:1799	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	33.3%	3	TT	CC	TT	NN
-chr1:1530520	[T/G]	chr1	1530520	Cc01_g00950:1811	exon	NON_SYNONYMOUS_CODING	gAg/gCg	E/A	16.7%	3	TT	TG	TT	NN
-chr1:1530290	[T/C]	chr1	1530290	Cc01_g00950:2041	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	33.3%	3	TT	TT	NN	CC
-chr1:1530289	[A/G]	chr1	1530289	Cc01_g00950:2042	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	33.3%	3	AA	AA	NN	GG
-chr1:1530287	[C/A]	chr1	1530287	Cc01_g00950:2044	exon	NON_SYNONYMOUS_CODING	Ggt/Tgt	G/C	33.3%	3	CC	CC	NN	AA
-chr1:1530286	[C/T]	chr1	1530286	Cc01_g00950:2045	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	25.0%	4	CC	CC	CC	TT
-chr1:1538660	[T/G]	chr1	1538660	Cc01_g00960:57	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	12.5%	4	TT	TG	TT	TT
-chr1:1538676	[T/C]	chr1	1538676	Cc01_g00960:73	exon	NON_SYNONYMOUS_CODING	Tat/Cat	Y/H	12.5%	4	TT	TC	TT	TT
-chr1:1538690	[A/G]	chr1	1538690	Cc01_g00960:87	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	AA	AG	AA	AA
-chr1:1538747	[G/A]	chr1	1538747	Cc01_g00960:144	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	12.5%	4	GG	GA	GG	GG
-chr1:1538777	[T/C]	chr1	1538777	Cc01_g00960:174	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	TT	TC	TT	TT
-chr1:1538784	[G/T]	chr1	1538784	Cc01_g00960:181	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	GG	GT	GG	GG
-chr1:1538792	[T/G]	chr1	1538792	Cc01_g00960:189	exon	NON_SYNONYMOUS_CODING	aaT/aaG	N/K	12.5%	4	TT	TG	TT	TT
-chr1:1538814	[G/C]	chr1	1538814	Cc01_g00960:211	exon	NON_SYNONYMOUS_CODING	Gcc/Ccc	A/P	12.5%	4	GG	GC	GG	GG
-chr1:1538834	[T/C]	chr1	1538834	Cc01_g00960:231	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	TT	TC	TT	TT
-chr1:1538885	[C/T]	chr1	1538885	Cc01_g00960:282	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CT	CC	CC
-chr1:1539091	[G/A]	chr1	1539091	Cc01_g00960:488	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	25.0%	4	GG	AA	GG	GG
-chr1:1539183	[A/G]	chr1	1539183	Cc01_g00960:580	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	12.5%	4	AA	AG	AA	AA
-chr1:1539211	[C/G]	chr1	1539211	Cc01_g00960:608	exon	NON_SYNONYMOUS_CODING	tCc/tGc	S/C	12.5%	4	CC	CC	CC	CG
-chr1:1539272	[G/T]	chr1	1539272	Cc01_g00960:669	exon	SYNONYMOUS_CODING	tcG/tcT	S/S	12.5%	4	GG	GT	GG	GG
-chr1:1539343	[G/A]	chr1	1539343	Cc01_g00960:740	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	GG	GA	GG	GG
-chr1:1539365	[A/G]	chr1	1539365	Cc01_g00960:762	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	12.5%	4	AA	AG	AA	AA
-chr1:1539374	[T/G]	chr1	1539374	Cc01_g00960:771	exon	SYNONYMOUS_CODING	gtT/gtG	V/V	12.5%	4	TT	GT	TT	TT
-chr1:1539408	[T/C]	chr1	1539408	Cc01_g00960:805	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	12.5%	4	TT	CT	TT	TT
-chr1:1539428	[C/T]	chr1	1539428	Cc01_g00960:825	exon	SYNONYMOUS_CODING	caC/caT	H/H	12.5%	4	CC	CT	CC	CC
-chr1:1539430	[G/T]	chr1	1539430	Cc01_g00960:827	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	12.5%	4	GG	GT	GG	GG
-chr1:1539431	[G/T]	chr1	1539431	Cc01_g00960:828	exon	NON_SYNONYMOUS_CODING	tgG/tgT	W/C	12.5%	4	GG	GT	GG	GG
-chr1:1539509	[A/T]	chr1	1539509	Cc01_g00960:906	exon	SYNONYMOUS_CODING	ggA/ggT	G/G	12.5%	4	AA	AT	AA	AA
-chr1:1539636	[T/G]	chr1	1539636	Cc01_g00960:1033	exon	NON_SYNONYMOUS_CODING	Ttg/Gtg	L/V	12.5%	4	TT	TG	TT	TT
-chr1:1539709	[C/G]	chr1	1539709	Cc01_g00960:1106	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	12.5%	4	CC	CG	CC	CC
-chr1:1539758	[C/T]	chr1	1539758	Cc01_g00960:1155	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CT	CC	CC
-chr1:1539788	[A/G]	chr1	1539788	Cc01_g00960:1185	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	AA	GA	AA	AA
-chr1:1539824	[A/G]	chr1	1539824	Cc01_g00960:1221	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AG	AA	AA
-chr1:1540980	[G/A]	chr1	1540980	Cc01_g00960:1273	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	GG	AG	GG	GG
-chr1:1540985	[T/A]	chr1	1540985	Cc01_g00960:1278	exon	SYNONYMOUS_CODING	atT/atA	I/I	12.5%	4	TT	TA	TT	TT
-chr1:1541027	[G/A]	chr1	1541027	Cc01_g00960:1320	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	25.0%	4	GG	AA	GG	GG
-chr1:1541065	[A/G]	chr1	1541065	Cc01_g00960:1358	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	12.5%	4	AA	AG	AA	AA
-chr1:1542189	[G/A]	chr1	1542189	Cc01_g00960:1460	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	12.5%	4	GG	GA	GG	GG
-chr1:1542199	[C/A]	chr1	1542199	Cc01_g00960:1470	exon	SYNONYMOUS_CODING	ggC/ggA	G/G	37.5%	4	CC	AA	CA	AA
-chr1:1542239	[G/A]	chr1	1542239	Cc01_g00960:1510	exon	NON_SYNONYMOUS_CODING	Ggt/Agt	G/S	12.5%	4	GG	GA	GG	GG
-chr1:1542286	[T/C]	chr1	1542286	Cc01_g00960:1557	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	TC	TT	TT
-chr1:1542364	[A/G]	chr1	1542364	Cc01_g00960:1635	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	37.5%	4	AA	GG	AG	GG
-chr1:1542404	[T/G]	chr1	1542404	Cc01_g00960:1675	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	12.5%	4	TT	TG	TT	TT
-chr1:1542434	[A/C]	chr1	1542434	Cc01_g00960:1705	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	12.5%	4	AA	CA	AA	AA
-chr1:1546352	[C/G]	chr1	1546352	Cc01_g00970:32	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	50.0%	4	CC	GG	CG	CG
-chr1:1546365	[A/G]	chr1	1546365	Cc01_g00970:45	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	37.5%	4	AA	GG	AG	GG
-chr1:1546409	[G/T]	chr1	1546409	Cc01_g00970:89	exon	NON_SYNONYMOUS_CODING	aGc/aTc	S/I	50.0%	4	GG	TT	GT	GT
-chr1:1546414	[A/C]	chr1	1546414	Cc01_g00970:94	exon	SYNONYMOUS_CODING	Agg/Cgg	R/R	50.0%	4	AA	CC	AC	AC
-chr1:1546454	[G/C]	chr1	1546454	Cc01_g00970:134	exon	NON_SYNONYMOUS_CODING	cGc/cCc	R/P	50.0%	4	GG	CC	GC	GC
-chr1:1546477	[C/G]	chr1	1546477	Cc01_g00970:157	exon	NON_SYNONYMOUS_CODING	Ctt/Gtt	L/V	37.5%	4	CC	GG	CG	GG
-chr1:1546480	[A/G]	chr1	1546480	Cc01_g00970:160	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	37.5%	4	AA	GG	AG	GG
-chr1:1546484	[T/G]	chr1	1546484	Cc01_g00970:164	exon	NON_SYNONYMOUS_CODING	cTt/cGt	L/R	50.0%	4	TT	GG	TG	TG
-chr1:1546521	[C/G]	chr1	1546521	Cc01_g00970:201	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	37.5%	4	CC	GG	CG	GG
-chr1:1546531	[A/T]	chr1	1546531	Cc01_g00970:211	exon	NON_SYNONYMOUS_CODING	Acg/Tcg	T/S	25.0%	4	AA	TT	AA	AA
-chr1:1546532	[C/G]	chr1	1546532	Cc01_g00970:212	exon	NON_SYNONYMOUS_CODING	aCg/aGg	T/R	12.5%	4	CC	CG	CC	CC
-chr1:1546549	[C/G]	chr1	1546549	Cc01_g00970:229	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	25.0%	4	CC	GG	CC	CC
-chr1:1546652	[C/A]	chr1	1546652	Cc01_g00970:257	exon	NON_SYNONYMOUS_CODING	aCt/aAt	T/N	37.5%	4	CC	AA	CA	CC
-chr1:1546674	[G/A]	chr1	1546674	Cc01_g00970:279	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	GG	GG	GG	GA
-chr1:1546728	[A/G]	chr1	1546728	Cc01_g00970:333	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	AA	GG	AG	GG
-chr1:1547036	[C/T]	chr1	1547036	Cc01_g00970:641	exon	NON_SYNONYMOUS_CODING	gCc/gTc	A/V	25.0%	4	CC	CT	CT	CC
-chr1:1547145	[G/A]	chr1	1547145	Cc01_g00970:750	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	37.5%	4	GG	AA	GA	AA
-chr1:1547237	[A/G]	chr1	1547237	Cc01_g00970:842	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	37.5%	4	AA	GG	AG	GG
-chr1:1547280	[A/G]	chr1	1547280	Cc01_g00970:885	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	37.5%	4	AA	GG	AG	GG
-chr1:1547353	[T/A]	chr1	1547353	Cc01_g00970:958	exon	NON_SYNONYMOUS_CODING	Tgt/Agt	C/S	37.5%	4	TT	AA	TA	TT
-chr1:1547421	[G/A]	chr1	1547421	Cc01_g00970:1026	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	12.5%	4	GG	GA	GG	GG
-chr1:1547527	[G/A]	chr1	1547527	Cc01_g00970:1132	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	12.5%	4	GG	GA	GG	GG
-chr1:1547536	[T/A]	chr1	1547536	Cc01_g00970:1141	exon	NON_SYNONYMOUS_CODING	Tta/Ata	L/I	25.0%	4	TT	TT	TT	AA
-chr1:1547613	[T/C]	chr1	1547613	Cc01_g00970:1218	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TC	TT	TT
-chr1:1547682	[G/A]	chr1	1547682	Cc01_g00970:1287	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	12.5%	4	GG	GA	GG	GG
-chr1:1547853	[C/G]	chr1	1547853	Cc01_g00970:1458	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	12.5%	4	CC	CG	CC	CC
-chr1:1547901	[A/G]	chr1	1547901	Cc01_g00970:1506	exon	SYNONYMOUS_CODING	acA/acG	T/T	37.5%	4	AA	GG	AG	GG
-chr1:1547985	[C/T]	chr1	1547985	Cc01_g00970:1590	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	CC	CT	CC	CC
-chr1:1548006	[G/A]	chr1	1548006	Cc01_g00970:1611	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	4	GG	GG	GG	AA
-chr1:1548171	[A/C]	chr1	1548171	Cc01_g00970:1776	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	25.0%	4	AA	AA	AA	CC
-chr1:1548194	[C/A]	chr1	1548194	Cc01_g00970:1799	exon	NON_SYNONYMOUS_CODING	aCg/aAg	T/K	37.5%	4	CC	AA	CA	AA
-chr1:1548347	[G/A]	chr1	1548347	Cc01_g00970:1952	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	GG	GA	GG	GG
-chr1:1548414	[G/A]	chr1	1548414	Cc01_g00970:2019	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	GA	GG	GG
-chr1:1548432	[T/C]	chr1	1548432	Cc01_g00970:2037	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	CT	TT	TT
-chr1:1548609	[A/G]	chr1	1548609	Cc01_g00970:2214	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	12.5%	4	AA	AA	AA	AG
-chr1:1548632	[C/T]	chr1	1548632	Cc01_g00970:2237	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	37.5%	4	CC	TT	CT	TT
-chr1:1548721	[A/C]	chr1	1548721	Cc01_g00970:2326	exon	NON_SYNONYMOUS_CODING	Aag/Cag	K/Q	25.0%	4	AA	AC	AA	AC
-chr1:1565335	[T/C]	chr1	1565335	Cc01_g00980:2	exon	START_LOST	aTg/aCg	M/T	12.5%	4	TT	TC	TT	TT
-chr1:1565363	[T/A]	chr1	1565363	Cc01_g00980:30	exon	SYNONYMOUS_CODING	ggT/ggA	G/G	12.5%	4	TT	TA	TT	TT
-chr1:1566976	[A/G]	chr1	1566976	Cc01_g00980:324	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	AA	AG	AA	AA
-chr1:1567002	[G/A]	chr1	1567002	Cc01_g00980:350	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	GG	GA	GG	GG
-chr1:1567012	[C/T]	chr1	1567012	Cc01_g00980:360	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	CC	CT	CC	CC
-chr1:1568715	[T/C]	chr1	1568715	Cc01_g00980:465	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TT	TT	TC
-chr1:1568812	[A/G]	chr1	1568812	Cc01_g00980:562	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	12.5%	4	AA	AG	AA	AA
-chr1:1568822	[T/C]	chr1	1568822	Cc01_g00980:572	exon	NON_SYNONYMOUS_CODING	gTc/gCc	V/A	12.5%	4	TT	TC	TT	TT
-chr1:1569214	[G/A]	chr1	1569214	Cc01_g00980:702	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	12.5%	4	GG	GA	GG	GG
-chr1:1570049	[T/G]	chr1	1570049	Cc01_g00980:976	exon	NON_SYNONYMOUS_CODING	Tcc/Gcc	S/A	12.5%	4	TT	TG	TT	TT
-chr1:1570069	[G/C]	chr1	1570069	Cc01_g00980:996	exon	SYNONYMOUS_CODING	gtG/gtC	V/V	12.5%	4	GG	GC	GG	GG
-chr1:1570255	[A/G]	chr1	1570255	Cc01_g00980:1068	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	AA	AG	AA	AA
-chr1:1570279	[A/T]	chr1	1570279	Cc01_g00980:1092	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	AA	TA	AA	AT
-chr1:1570408	[C/T]	chr1	1570408	Cc01_g00980:1221	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	CC	CC	CC	CT
-chr1:1578648	[G/A]	chr1	1578648	Cc01_g00990:84	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	25.0%	4	GG	GG	GG	AA
-chr1:1577422	[G/C]	chr1	1577422	Cc01_g00990:216	exon	SYNONYMOUS_CODING	cgC/cgG	R/R	12.5%	4	GG	GC	GG	GG
-chr1:1574681	[T/G]	chr1	1574681	Cc01_g00990:474	exon	SYNONYMOUS_CODING	gtA/gtC	V/V	12.5%	4	TT	TT	TG	TT
-chr1:1589010	[G/A]	chr1	1589010	Cc01_g01000:168	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	GG	GG	GA	GG
-chr1:1588986	[T/A]	chr1	1588986	Cc01_g01000:192	exon	SYNONYMOUS_CODING	atA/atT	I/I	12.5%	4	TT	TA	TT	TT
-chr1:1588914	[T/G]	chr1	1588914	Cc01_g01000:264	exon	SYNONYMOUS_CODING	ctA/ctC	L/L	25.0%	4	TT	GG	TT	TT
-chr1:1588838	[G/A]	chr1	1588838	Cc01_g01000:340	exon	STOP_GAINED	Cga/Tga	R/4	25.0%	4	GG	AA	GG	GG
-chr1:1588837	[C/A]	chr1	1588837	Cc01_g01000:341	exon	NON_SYNONYMOUS_CODING	cGa/cTa	R/L	25.0%	4	CC	AA	CC	CC
-chr1:1588277	[T/C]	chr1	1588277	Cc01_g01000:901	exon	NON_SYNONYMOUS_CODING	Aac/Gac	N/D	25.0%	4	TT	CC	TT	TT
-chr1:1588220	[G/A]	chr1	1588220	Cc01_g01000:958	exon	NON_SYNONYMOUS_CODING	Cct/Tct	P/S	12.5%	4	GG	GG	GA	GG
-chr1:1588137	[G/A]	chr1	1588137	Cc01_g01000:1041	exon	SYNONYMOUS_CODING	caC/caT	H/H	25.0%	4	GG	AA	GG	GG
-chr1:1588135	[A/G]	chr1	1588135	Cc01_g01000:1043	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	12.5%	4	AA	AA	AA	AG
-chr1:1587967	[G/A]	chr1	1587967	Cc01_g01000:1211	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	25.0%	4	GG	GG	GA	GA
-chr1:1587921	[A/G]	chr1	1587921	Cc01_g01000:1257	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	50.0%	4	AA	GG	AG	AG
-chr1:1587798	[C/T]	chr1	1587798	Cc01_g01000:1380	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	25.0%	4	CC	TT	CC	CC
-chr1:1587708	[C/T]	chr1	1587708	Cc01_g01000:1470	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	4	CC	TT	CC	CC
-chr1:1587646	[G/C]	chr1	1587646	Cc01_g01000:1532	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	25.0%	4	GG	GC	GC	GG
-chr1:1587588	[T/A]	chr1	1587588	Cc01_g01000:1590	exon	SYNONYMOUS_CODING	atA/atT	I/I	25.0%	4	TT	AA	TT	TT
-chr1:1587577	[C/T]	chr1	1587577	Cc01_g01000:1601	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	CC	TT	CC	CC
-chr1:1587576	[A/T]	chr1	1587576	Cc01_g01000:1602	exon	NON_SYNONYMOUS_CODING	agT/agA	S/R	25.0%	4	AA	TT	AA	AA
-chr1:1587527	[G/T]	chr1	1587527	Cc01_g01000:1651	exon	NON_SYNONYMOUS_CODING	Cta/Ata	L/I	25.0%	4	GG	TT	GG	GG
-chr1:1587435	[G/T]	chr1	1587435	Cc01_g01000:1743	exon	SYNONYMOUS_CODING	gtC/gtA	V/V	25.0%	4	GG	TT	GG	GG
-chr1:1595916	[A/T]	chr1	1595916	Cc01_g01010:153	exon	SYNONYMOUS_CODING	gtT/gtA	V/V	37.5%	4	AA	AT	AT	AT
-chr1:1595665	[A/C]	chr1	1595665	Cc01_g01010:278	exon	NON_SYNONYMOUS_CODING	gTt/gGt	V/G	25.0%	4	AA	AC	AC	AA
-chr1:1594252	[G/A]	chr1	1594252	Cc01_g01010:651	exon	SYNONYMOUS_CODING	acC/acT	T/T	37.5%	4	GG	GA	GA	GA
-chr1:1594186	[T/C]	chr1	1594186	Cc01_g01010:717	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	37.5%	4	TT	CC	TC	CC
-chr1:1593925	[G/A]	chr1	1593925	Cc01_g01010:858	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	37.5%	4	GG	GA	GA	GA
-chr1:1593817	[T/G]	chr1	1593817	Cc01_g01010:966	exon	SYNONYMOUS_CODING	cgA/cgC	R/R	37.5%	4	TT	TG	TG	TG
-chr1:1593814	[T/C]	chr1	1593814	Cc01_g01010:969	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	TT	TT	TC	TT
-chr1:1593634	[C/T]	chr1	1593634	Cc01_g01010:1056	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	CC	CT	CC	CC
-chr1:1593035	[T/A]	chr1	1593035	Cc01_g01010:1221	exon	SYNONYMOUS_CODING	tcA/tcT	S/S	12.5%	4	TT	TA	TT	TT
-chr1:1593017	[G/A]	chr1	1593017	Cc01_g01010:1239	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	GG	AA	GA	AA
-chr1:1592810	[A/G]	chr1	1592810	Cc01_g01010:1341	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	37.5%	4	AA	AG	AG	AG
-chr1:1591963	[T/C]	chr1	1591963	Cc01_g01010:1515	exon	SYNONYMOUS_CODING	cgA/cgG	R/R	37.5%	4	TT	TC	TC	TC
-chr1:1591951	[A/G]	chr1	1591951	Cc01_g01010:1527	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	37.5%	4	AA	AG	AG	AG
-chr1:1591930	[G/A]	chr1	1591930	Cc01_g01010:1548	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	25.0%	4	GG	GG	GA	GA
-chr1:1591377	[A/G]	chr1	1591377	Cc01_g01010:1560	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	12.5%	4	AA	AA	AG	AA
-chr1:1590960	[G/A]	chr1	1590960	Cc01_g01010:1788	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	37.5%	4	GG	GA	GA	GA
-chr1:1590951	[A/G]	chr1	1590951	Cc01_g01010:1797	exon	SYNONYMOUS_CODING	acT/acC	T/T	12.5%	4	AA	AG	AA	AA
-chr1:1605944	[G/T]	chr1	1605944	Cc01_g01020:27	exon	SYNONYMOUS_CODING	acG/acT	T/T	12.5%	4	GG	GT	GG	GG
-chr1:1605987	[T/G]	chr1	1605987	Cc01_g01020:70	exon	NON_SYNONYMOUS_CODING	Tcg/Gcg	S/A	12.5%	4	TT	TT	TG	TT
-chr1:1606067	[C/G]	chr1	1606067	Cc01_g01020:150	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	37.5%	4	CC	GG	CG	GG
-chr1:1606163	[A/C]	chr1	1606163	Cc01_g01020:246	exon	SYNONYMOUS_CODING	acA/acC	T/T	12.5%	4	AA	AA	AA	AC
-chr1:1609099	[T/C]	chr1	1609099	Cc01_g01020:536	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	TT	TC	TT	TT
-chr1:1609547	[G/C]	chr1	1609547	Cc01_g01020:822	exon	SYNONYMOUS_CODING	ccG/ccC	P/P	12.5%	4	GG	GC	GG	GG
-chr1:1609736	[C/A]	chr1	1609736	Cc01_g01020:912	exon	SYNONYMOUS_CODING	gtC/gtA	V/V	25.0%	4	CC	CA	CC	CA
-chr1:1609752	[G/C]	chr1	1609752	Cc01_g01020:928	exon	NON_SYNONYMOUS_CODING	Gac/Cac	D/H	37.5%	4	GG	CC	GC	CC
-chr1:1609769	[A/C]	chr1	1609769	Cc01_g01020:945	exon	SYNONYMOUS_CODING	ctA/ctC	L/L	12.5%	4	AA	AA	AC	AA
-chr1:1610622	[A/G]	chr1	1610622	Cc01_g01020:1431	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	12.5%	4	AA	AG	AA	AA
-chr1:1610842	[A/G]	chr1	1610842	Cc01_g01020:1560	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AG	AA	AA
-chr1:1612395	[C/A]	chr1	1612395	Cc01_g01020:2229	exon	NON_SYNONYMOUS_CODING	aaC/aaA	N/K	12.5%	4	CC	CA	CC	CC
-chr1:1613838	[C/T]	chr1	1613838	Cc01_g01020:2532	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	50.0%	4	CC	TT	CC	TT
-chr1:1613901	[C/T]	chr1	1613901	Cc01_g01020:2595	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	CC	CC	CC	CT
-chr1:1615545	[T/G]	chr1	1615545	Cc01_g01030:18	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	12.5%	4	TT	TG	TT	TT
-chr1:1615529	[T/C]	chr1	1615529	Cc01_g01030:34	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	12.5%	4	TT	TC	TT	TT
-chr1:1615508	[C/T]	chr1	1615508	Cc01_g01030:55	exon	NON_SYNONYMOUS_CODING	Gcg/Acg	A/T	37.5%	4	CC	TT	CT	TT
-chr1:1615506	[C/T]	chr1	1615506	Cc01_g01030:57	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	CC	CC	CC	CT
-chr1:1615500	[T/G]	chr1	1615500	Cc01_g01030:63	exon	SYNONYMOUS_CODING	ggA/ggC	G/G	12.5%	4	TT	TT	TT	GT
-chr1:1615496	[T/C]	chr1	1615496	Cc01_g01030:67	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	12.5%	4	TT	TT	TT	CT
-chr1:1615491	[C/T]	chr1	1615491	Cc01_g01030:72	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	37.5%	4	CC	TT	CT	TT
-chr1:1615477	[G/A]	chr1	1615477	Cc01_g01030:86	exon	NON_SYNONYMOUS_CODING	cCt/cTt	P/L	12.5%	4	GG	GG	GG	AG
-chr1:1615472	[T/G]	chr1	1615472	Cc01_g01030:91	exon	NON_SYNONYMOUS_CODING	Atc/Ctc	I/L	37.5%	4	TT	GG	TG	GG
-chr1:1615458	[C/T]	chr1	1615458	Cc01_g01030:105	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	CC	TC	CC	CC
-chr1:1615440	[T/C]	chr1	1615440	Cc01_g01030:123	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	TT	TT	TT	CT
-chr1:1615335	[C/T]	chr1	1615335	Cc01_g01030:132	exon	SYNONYMOUS_CODING	agG/agA	R/R	37.5%	4	CC	TT	CT	TT
-chr1:1615256	[A/T]	chr1	1615256	Cc01_g01030:211	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	12.5%	4	AA	AA	AA	AT
-chr1:1620903	[A/T]	chr1	1620903	Cc01_g01040:366	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	12.5%	4	AA	AT	AA	AA
-chr1:1619369	[G/A]	chr1	1619369	Cc01_g01040:648	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	37.5%	4	GG	GA	GA	GA
-chr1:1619341	[G/C]	chr1	1619341	Cc01_g01040:676	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	37.5%	4	GG	CC	GC	CC
-chr1:1619334	[C/T]	chr1	1619334	Cc01_g01040:683	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	37.5%	4	CC	TT	CT	TT
-chr1:1619270	[C/G]	chr1	1619270	Cc01_g01040:747	exon	SYNONYMOUS_CODING	tcG/tcC	S/S	37.5%	4	CC	GG	CG	GG
-chr1:1619124	[A/G]	chr1	1619124	Cc01_g01040:893	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	AA	AA	AG	AA
-chr1:1618988	[A/G]	chr1	1618988	Cc01_g01040:1029	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	AA	AA	AA	AG
-chr1:1618984	[C/G]	chr1	1618984	Cc01_g01040:1033	exon	NON_SYNONYMOUS_CODING	Gta/Cta	V/L	12.5%	4	CC	CC	CC	CG
-chr1:1618978	[C/G]	chr1	1618978	Cc01_g01040:1039	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	37.5%	4	CC	CG	CG	CG
-chr1:1618886	[A/G]	chr1	1618886	Cc01_g01040:1131	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	AA	AA	AA	AG
-chr1:1618879	[T/A]	chr1	1618879	Cc01_g01040:1138	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	12.5%	4	TT	TT	TT	TA
-chr1:1618858	[T/G]	chr1	1618858	Cc01_g01040:1159	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	37.5%	4	TT	GG	TG	GG
-chr1:1618504	[G/A]	chr1	1618504	Cc01_g01040:1396	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	12.5%	4	GG	GG	GG	GA
-chr1:1618376	[T/G]	chr1	1618376	Cc01_g01040:1524	exon	SYNONYMOUS_CODING	ccA/ccC	P/P	12.5%	4	TT	TG	TT	TT
-chr1:1618358	[G/C]	chr1	1618358	Cc01_g01040:1542	exon	SYNONYMOUS_CODING	ggC/ggG	G/G	25.0%	4	GG	GG	GC	GC
-chr1:1618326	[C/T]	chr1	1618326	Cc01_g01040:1574	exon	NON_SYNONYMOUS_CODING	gGc/gAc	G/D	12.5%	4	CC	CC	CT	CC
-chr1:1618307	[G/C]	chr1	1618307	Cc01_g01040:1593	exon	SYNONYMOUS_CODING	ctC/ctG	L/L	12.5%	4	GG	GG	GG	CG
-chr1:1618184	[A/G]	chr1	1618184	Cc01_g01040:1716	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AG	AA	AA
-chr1:1618117	[G/C]	chr1	1618117	Cc01_g01040:1783	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	37.5%	4	GG	CG	GG	CC
-chr1:1618040	[C/G]	chr1	1618040	Cc01_g01040:1860	exon	NON_SYNONYMOUS_CODING	caG/caC	Q/H	12.5%	4	CC	CC	CG	CC
-chr1:1618037	[G/A]	chr1	1618037	Cc01_g01040:1863	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	37.5%	4	GG	GA	GA	GA
-chr1:1618016	[T/C]	chr1	1618016	Cc01_g01040:1884	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	TT	TT	TC	TT
-chr1:1617998	[G/C]	chr1	1617998	Cc01_g01040:1902	exon	SYNONYMOUS_CODING	ggC/ggG	G/G	25.0%	4	GG	GG	GC	CG
-chr1:1617793	[C/T]	chr1	1617793	Cc01_g01040:2107	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	37.5%	4	CC	CT	CT	CT
-chr1:1617773	[T/C]	chr1	1617773	Cc01_g01040:2127	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TT	TC
-chr1:1617769	[T/C]	chr1	1617769	Cc01_g01040:2131	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	12.5%	4	TT	TT	TT	TC
-chr1:1617757	[C/T]	chr1	1617757	Cc01_g01040:2143	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	CC	CC	CC	CT
-chr1:1617670	[C/T]	chr1	1617670	Cc01_g01040:2230	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	37.5%	4	CC	CT	CC	TT
-chr1:1617634	[C/T]	chr1	1617634	Cc01_g01040:2266	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	CC	CC	CC	CT
-chr1:1617479	[A/G]	chr1	1617479	Cc01_g01040:2421	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	25.0%	4	AA	GG	AA	AA
-chr1:1617238	[G/A]	chr1	1617238	Cc01_g01040:2662	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	GG	GA	GG	GG
-chr1:1617119	[A/T]	chr1	1617119	Cc01_g01040:2725	exon	NON_SYNONYMOUS_CODING	Tgt/Agt	C/S	25.0%	4	AA	AT	AT	AA
-chr1:1626903	[A/C]	chr1	1626903	Cc01_g01050:132	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	37.5%	4	AA	CC	AC	CC
-chr1:1626922	[C/G]	chr1	1626922	Cc01_g01050:151	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	25.0%	4	CC	CG	CG	CC
-chr1:1626973	[G/T]	chr1	1626973	Cc01_g01050:202	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	37.5%	4	GG	GT	GG	TT
-chr1:1627071	[T/C]	chr1	1627071	Cc01_g01050:300	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	37.5%	4	TT	TC	TT	CC
-chr1:1627227	[T/C]	chr1	1627227	Cc01_g01050:456	exon	SYNONYMOUS_CODING	atT/atC	I/I	25.0%	4	TT	TC	TC	TT
-chr1:1628554	[A/G]	chr1	1628554	Cc01_g01050:650	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	25.0%	4	AA	AG	AG	AA
-chr1:1628584	[A/G]	chr1	1628584	Cc01_g01050:680	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	37.5%	4	AA	GA	AA	GG
-chr1:1628763	[G/A]	chr1	1628763	Cc01_g01050:859	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	12.5%	4	GG	GG	GG	GA
-chr1:1628787	[G/C]	chr1	1628787	Cc01_g01050:883	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	37.5%	4	GG	GC	GG	CC
-chr1:1628828	[A/G]	chr1	1628828	Cc01_g01050:924	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	37.5%	4	AA	AG	AA	GG
-chr1:1628942	[A/G]	chr1	1628942	Cc01_g01050:1038	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	37.5%	4	AA	GG	AG	GG
-chr1:1630053	[T/C]	chr1	1630053	Cc01_g01050:1464	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	TT	TC	TC	TT
-chr1:1633739	[A/G]	chr1	1633739	Cc01_g01060:12	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	37.5%	4	AA	AG	AG	AG
-chr1:1633649	[T/C]	chr1	1633649	Cc01_g01060:102	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	37.5%	4	TT	TC	TC	TC
-chr1:1633602	[T/C]	chr1	1633602	Cc01_g01060:149	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	12.5%	4	TT	CT	TT	TT
-chr1:1633503	[G/A]	chr1	1633503	Cc01_g01060:248	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	12.5%	4	GG	GA	GG	GG
-chr1:1633430	[A/T]	chr1	1633430	Cc01_g01060:321	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	12.5%	4	AA	AT	AA	AA
-chr1:1633429	[G/T]	chr1	1633429	Cc01_g01060:322	exon	NON_SYNONYMOUS_CODING	Ctc/Atc	L/I	12.5%	4	GG	GT	GG	GG
-chr1:1633388	[A/T]	chr1	1633388	Cc01_g01060:363	exon	SYNONYMOUS_CODING	cgT/cgA	R/R	12.5%	4	AA	AA	AT	AA
-chr1:1752682	[C/T]	chr1	1752682	Cc01_g01120:21	exon	SYNONYMOUS_CODING	acG/acA	T/T	33.3%	3	CC	TT	NN	TT
-chr1:1752654	[A/T]	chr1	1752654	Cc01_g01120:49	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	37.5%	4	AA	AT	TT	AA
-chr1:1752632	[G/T]	chr1	1752632	Cc01_g01120:71	exon	NON_SYNONYMOUS_CODING	aCc/aAc	T/N	37.5%	4	GG	GT	TT	GG
-chr1:1752577	[C/A]	chr1	1752577	Cc01_g01120:126	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	25.0%	4	CC	CA	CA	CC
-chr1:1752535	[T/C]	chr1	1752535	Cc01_g01120:168	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	25.0%	4	TT	TT	CC	TT
-chr1:1752526	[C/T]	chr1	1752526	Cc01_g01120:177	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	4	CC	CC	TT	CC
-chr1:1750532	[T/G]	chr1	1750532	Cc01_g01120:970	exon	NON_SYNONYMOUS_CODING	Atg/Ctg	M/L	50.0%	2	TT	NN	NN	GG
-chr1:1750461	[C/T]	chr1	1750461	Cc01_g01120:1041	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	37.5%	4	CC	TT	CT	TT
-chr1:1750442	[C/T]	chr1	1750442	Cc01_g01120:1060	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	37.5%	4	CC	TT	CT	TT
-chr1:1760523	[C/A]	chr1	1760523	Cc01_g01130:135	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	12.5%	4	CC	CC	CA	CC
-chr1:1760522	[G/C]	chr1	1760522	Cc01_g01130:136	exon	NON_SYNONYMOUS_CODING	Ctc/Gtc	L/V	12.5%	4	GG	GG	GC	GG
-chr1:1760486	[A/C]	chr1	1760486	Cc01_g01130:172	exon	NON_SYNONYMOUS_CODING	Tcg/Gcg	S/A	12.5%	4	AA	AA	AA	AC
-chr1:1760383	[C/T]	chr1	1760383	Cc01_g01130:275	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	12.5%	4	CC	CT	CC	CC
-chr1:1760328	[T/A]	chr1	1760328	Cc01_g01130:330	exon	SYNONYMOUS_CODING	atA/atT	I/I	50.0%	4	TT	AA	TT	AA
-chr1:1760185	[T/A]	chr1	1760185	Cc01_g01130:473	exon	NON_SYNONYMOUS_CODING	tAc/tTc	Y/F	25.0%	4	TT	TA	TA	TT
-chr1:1760173	[C/A]	chr1	1760173	Cc01_g01130:485	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	12.5%	4	CC	CC	CC	CA
-chr1:1760172	[T/G]	chr1	1760172	Cc01_g01130:486	exon	NON_SYNONYMOUS_CODING	agA/agC	R/S	12.5%	4	TT	TT	TT	TG
-chr1:1759408	[A/G]	chr1	1759408	Cc01_g01130:603	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	25.0%	4	AA	AG	AG	AA
-chr1:1759378	[G/A]	chr1	1759378	Cc01_g01130:633	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	25.0%	4	GG	GA	GA	GG
-chr1:1759372	[A/G]	chr1	1759372	Cc01_g01130:639	exon	SYNONYMOUS_CODING	atT/atC	I/I	25.0%	4	AA	AG	AG	AA
-chr1:1759371	[T/A]	chr1	1759371	Cc01_g01130:640	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	25.0%	4	TT	TA	TA	TT
-chr1:1759364	[T/G]	chr1	1759364	Cc01_g01130:647	exon	NON_SYNONYMOUS_CODING	gAt/gCt	D/A	12.5%	4	TT	TG	TT	TT
-chr1:1759335	[G/A]	chr1	1759335	Cc01_g01130:676	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	25.0%	4	GG	GA	GA	GG
-chr1:1758971	[A/G]	chr1	1758971	Cc01_g01130:1040	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	50.0%	3	AA	GG	AG	NN
-chr1:1758937	[G/A]	chr1	1758937	Cc01_g01130:1074	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	50.0%	3	GG	AA	GA	NN
-chr1:1758885	[C/G]	chr1	1758885	Cc01_g01130:1126	exon	NON_SYNONYMOUS_CODING	Gct/Cct	A/P	33.3%	3	CC	GG	CC	NN
-chr1:1758882	[C/T]	chr1	1758882	Cc01_g01130:1129	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	50.0%	3	CC	TT	CT	NN
-chr1:1758778	[G/A]	chr1	1758778	Cc01_g01130:1233	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	GG	GA	GG	GG
-chr1:1758772	[A/G]	chr1	1758772	Cc01_g01130:1239	exon	SYNONYMOUS_CODING	caT/caC	H/H	12.5%	4	AA	AG	AA	AA
-chr1:1758762	[T/C]	chr1	1758762	Cc01_g01130:1249	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	12.5%	4	TT	TC	TT	TT
-chr1:1768762	[G/C]	chr1	1768762	Cc01_g01140:100	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	25.0%	4	GG	GC	GG	GC
-chr1:1768873	[T/C]	chr1	1768873	Cc01_g01140:211	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	12.5%	4	TT	TT	TT	TC
-chr1:1768956	[T/A]	chr1	1768956	Cc01_g01140:294	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	12.5%	4	TT	TT	TT	TA
-chr1:1768961	[C/A]	chr1	1768961	Cc01_g01140:299	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	12.5%	4	CC	CC	CC	CA
-chr1:1768967	[C/G]	chr1	1768967	Cc01_g01140:305	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	50.0%	4	CC	CG	CG	GG
-chr1:1769000	[A/G]	chr1	1769000	Cc01_g01140:338	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	12.5%	4	AA	AA	AA	AG
-chr1:1769038	[T/C]	chr1	1769038	Cc01_g01140:376	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	12.5%	4	TT	TC	TT	TT
-chr1:1769040	[T/G]	chr1	1769040	Cc01_g01140:378	exon	SYNONYMOUS_CODING	tcT/tcG	S/S	12.5%	4	TT	TT	TT	TG
-chr1:1769074	[T/C]	chr1	1769074	Cc01_g01140:412	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	TT	TT	TT	TC
-chr1:1769115	[T/C]	chr1	1769115	Cc01_g01140:453	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	TT	TT	TT	TC
-chr1:1769145	[C/T]	chr1	1769145	Cc01_g01140:483	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	50.0%	4	CC	CT	CT	TT
-chr1:1769183	[C/T]	chr1	1769183	Cc01_g01140:521	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	25.0%	4	CC	CT	CC	CT
-chr1:1769193	[A/T]	chr1	1769193	Cc01_g01140:531	exon	SYNONYMOUS_CODING	atA/atT	I/I	12.5%	4	AA	AT	AA	AA
-chr1:1769201	[C/T]	chr1	1769201	Cc01_g01140:539	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	25.0%	4	CC	CT	CC	CT
-chr1:1769253	[A/C]	chr1	1769253	Cc01_g01140:591	exon	SYNONYMOUS_CODING	tcA/tcC	S/S	12.5%	4	AA	AA	AA	AC
-chr1:1769277	[T/A]	chr1	1769277	Cc01_g01140:615	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	25.0%	4	TT	TA	TT	TA
-chr1:1769279	[G/A]	chr1	1769279	Cc01_g01140:617	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	25.0%	4	GG	GA	GG	GA
-chr1:1769288	[A/C]	chr1	1769288	Cc01_g01140:626	exon	NON_SYNONYMOUS_CODING	gAa/gCa	E/A	12.5%	4	AA	AA	AA	CA
-chr1:1769296	[A/G]	chr1	1769296	Cc01_g01140:634	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	25.0%	4	AA	AG	AA	AG
-chr1:1769367	[T/C]	chr1	1769367	Cc01_g01140:705	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	TT	TT	TC	TC
-chr1:1769374	[G/A]	chr1	1769374	Cc01_g01140:712	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	GG	GG	GA
-chr1:1769389	[C/T]	chr1	1769389	Cc01_g01140:727	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	CC	CT	CT	CT
-chr1:1769398	[T/C]	chr1	1769398	Cc01_g01140:736	exon	NON_SYNONYMOUS_CODING	Ttt/Ctt	F/L	25.0%	4	TT	TC	TT	TC
-chr1:1769433	[T/G]	chr1	1769433	Cc01_g01140:771	exon	NON_SYNONYMOUS_CODING	aaT/aaG	N/K	12.5%	4	TT	TG	TT	TT
-chr1:1769441	[C/T]	chr1	1769441	Cc01_g01140:779	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	37.5%	4	CC	CT	CT	CT
-chr1:1769448	[A/T]	chr1	1769448	Cc01_g01140:786	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	37.5%	4	AA	AT	AT	AT
-chr1:1769482	[A/T]	chr1	1769482	Cc01_g01140:820	exon	STOP_GAINED	Aga/Tga	R/4	12.5%	4	AA	AA	AA	TA
-chr1:1769483	[G/T]	chr1	1769483	Cc01_g01140:821	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	12.5%	4	GG	GG	GG	TG
-chr1:1769501	[C/G]	chr1	1769501	Cc01_g01140:839	exon	NON_SYNONYMOUS_CODING	tCc/tGc	S/C	12.5%	4	CC	CG	CC	CC
-chr1:1769639	[A/G]	chr1	1769639	Cc01_g01140:977	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	12.5%	4	AA	AA	AA	AG
-chr1:1769671	[C/A]	chr1	1769671	Cc01_g01140:1009	exon	NON_SYNONYMOUS_CODING	Cat/Aat	H/N	12.5%	4	CC	CA	CC	CC
-chr1:1769978	[A/G]	chr1	1769978	Cc01_g01140:1256	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	25.0%	4	AA	AG	AA	AG
-chr1:1769992	[A/G]	chr1	1769992	Cc01_g01140:1270	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	37.5%	4	AA	AG	AG	AG
-chr1:1770017	[G/T]	chr1	1770017	Cc01_g01140:1295	exon	NON_SYNONYMOUS_CODING	aGt/aTt	S/I	37.5%	4	GG	GT	GT	GT
-chr1:1770029	[C/T]	chr1	1770029	Cc01_g01140:1307	exon	NON_SYNONYMOUS_CODING	aCc/aTc	T/I	37.5%	4	CC	CT	CT	CT
-chr1:1770045	[C/T]	chr1	1770045	Cc01_g01140:1323	exon	SYNONYMOUS_CODING	atC/atT	I/I	37.5%	4	CC	CT	CT	CT
-chr1:1770067	[C/T]	chr1	1770067	Cc01_g01140:1345	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	25.0%	4	CC	CC	CT	CT
-chr1:1770389	[C/G]	chr1	1770389	Cc01_g01140:1667	exon	STOP_GAINED	tCa/tGa	S/6	12.5%	4	CC	CG	CC	CC
-chr1:1770417	[A/C]	chr1	1770417	Cc01_g01140:1695	exon	SYNONYMOUS_CODING	atA/atC	I/I	12.5%	4	AA	AC	AA	AA
-chr1:1770420	[C/A]	chr1	1770420	Cc01_g01140:1698	exon	SYNONYMOUS_CODING	tcC/tcA	S/S	12.5%	4	CC	CA	CC	CC
-chr1:1770531	[A/G]	chr1	1770531	Cc01_g01140:1809	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	AG	AA	AA
-chr1:1770535	[A/G]	chr1	1770535	Cc01_g01140:1813	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	12.5%	4	AA	AG	AA	AA
-chr1:1770536	[G/A]	chr1	1770536	Cc01_g01140:1814	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	GG	GA	GG	GA
-chr1:1770538	[C/T]	chr1	1770538	Cc01_g01140:1816	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	CC	CC	CC	CT
-chr1:1770756	[G/A]	chr1	1770756	Cc01_g01140:1972	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	4	GG	GA	GA	AA
-chr1:1770764	[A/G]	chr1	1770764	Cc01_g01140:1980	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	37.5%	4	AA	AG	AG	AG
-chr1:1770768	[A/T]	chr1	1770768	Cc01_g01140:1984	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	12.5%	4	AA	AA	AA	AT
-chr1:1770781	[G/T]	chr1	1770781	Cc01_g01140:1997	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	12.5%	4	GG	GG	GG	GT
-chr1:1770792	[C/G]	chr1	1770792	Cc01_g01140:2008	exon	NON_SYNONYMOUS_CODING	Ctt/Gtt	L/V	25.0%	4	CC	CC	GC	GC
-chr1:1770794	[T/C]	chr1	1770794	Cc01_g01140:2010	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	TT	TT	TT	TC
-chr1:1770795	[G/A]	chr1	1770795	Cc01_g01140:2011	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	GG	GA	GG	GG
-chr1:1770797	[A/T]	chr1	1770797	Cc01_g01140:2013	exon	SYNONYMOUS_CODING	gtA/gtT	V/V	12.5%	4	AA	AT	AA	AA
-chr1:1770804	[G/C]	chr1	1770804	Cc01_g01140:2020	exon	NON_SYNONYMOUS_CODING	Gca/Cca	A/P	12.5%	4	GG	GC	GG	GG
-chr1:1770806	[A/G]	chr1	1770806	Cc01_g01140:2022	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	AA	AG	AA	AA
-chr1:1770807	[A/T]	chr1	1770807	Cc01_g01140:2023	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	12.5%	4	AA	AT	AA	AA
-chr1:1771162	[C/T]	chr1	1771162	Cc01_g01140:2032	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	CC	TT	TC	TT
-chr1:1771185	[T/A]	chr1	1771185	Cc01_g01140:2055	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	37.5%	4	TT	AA	AT	AA
-chr1:1771201	[C/A]	chr1	1771201	Cc01_g01140:2071	exon	NON_SYNONYMOUS_CODING	Cta/Ata	L/I	37.5%	4	CC	AA	AC	AA
-chr1:1775047	[T/C]	chr1	1775047	Cc01_g01150:43	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	25.0%	2	TT	TC	NN	NN
-chr1:1774997	[A/G]	chr1	1774997	Cc01_g01150:93	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	33.3%	3	AA	AG	NN	AG
-chr1:1774994	[A/G]	chr1	1774994	Cc01_g01150:96	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	50.0%	4	AA	AG	GG	GA
-chr1:1774991	[C/T]	chr1	1774991	Cc01_g01150:99	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	25.0%	4	CC	TT	TT	TT
-chr1:1774981	[A/G]	chr1	1774981	Cc01_g01150:109	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	37.5%	4	AA	AG	AG	AG
-chr1:1774977	[C/T]	chr1	1774977	Cc01_g01150:113	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	25.0%	4	CC	TT	TT	TT
-chr1:1774975	[C/T]	chr1	1774975	Cc01_g01150:115	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	37.5%	4	CC	TC	TC	TC
-chr1:1774972	[T/G]	chr1	1774972	Cc01_g01150:118	exon	NON_SYNONYMOUS_CODING	Act/Cct	T/P	37.5%	4	TT	TG	TG	TG
-chr1:1774959	[A/G]	chr1	1774959	Cc01_g01150:131	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	37.5%	4	AA	GA	GA	GA
-chr1:1774957	[A/C]	chr1	1774957	Cc01_g01150:133	exon	NON_SYNONYMOUS_CODING	Ttg/Gtg	L/V	37.5%	4	AA	CC	CC	AC
-chr1:1774955	[C/A]	chr1	1774955	Cc01_g01150:135	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	37.5%	4	CC	AA	AA	CA
-chr1:1774925	[A/C]	chr1	1774925	Cc01_g01150:165	exon	NON_SYNONYMOUS_CODING	tgT/tgG	C/W	37.5%	4	AA	AC	AC	AC
-chr1:1774919	[A/G]	chr1	1774919	Cc01_g01150:171	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	37.5%	4	AA	AG	AG	AG
-chr1:1774915	[C/G]	chr1	1774915	Cc01_g01150:175	exon	NON_SYNONYMOUS_CODING	Gta/Cta	V/L	12.5%	4	CC	CG	CC	CC
-chr1:1774911	[C/T]	chr1	1774911	Cc01_g01150:179	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	37.5%	4	CC	TT	TT	CT
-chr1:1774901	[C/A]	chr1	1774901	Cc01_g01150:189	exon	NON_SYNONYMOUS_CODING	agG/agT	R/S	25.0%	4	CC	AA	AA	AA
-chr1:1774894	[G/A]	chr1	1774894	Cc01_g01150:196	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	37.5%	4	GG	GA	GA	GA
-chr1:1800628	[A/T]	chr1	1800628	Cc01_g01180:18	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	37.5%	4	AA	AT	AA	TT
-chr1:1800604	[A/G]	chr1	1800604	Cc01_g01180:42	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	50.0%	4	AA	GG	AA	GG
-chr1:1800591	[A/C]	chr1	1800591	Cc01_g01180:55	exon	NON_SYNONYMOUS_CODING	Ttg/Gtg	L/V	12.5%	4	AA	CA	AA	AA
-chr1:1800153	[G/A]	chr1	1800153	Cc01_g01180:237	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	12.5%	4	GG	GG	GA	GG
-chr1:1800141	[C/A]	chr1	1800141	Cc01_g01180:249	exon	SYNONYMOUS_CODING	tcG/tcT	S/S	12.5%	4	CC	CA	CC	CC
-chr1:1800037	[A/T]	chr1	1800037	Cc01_g01180:353	exon	NON_SYNONYMOUS_CODING	cTa/cAa	L/Q	37.5%	4	AA	TT	AT	TT
-chr1:1799883	[A/G]	chr1	1799883	Cc01_g01180:507	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	12.5%	4	AA	AG	AA	AA
-chr1:1799858	[C/A]	chr1	1799858	Cc01_g01180:532	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	25.0%	4	CC	AC	CC	CA
-chr1:1799772	[C/T]	chr1	1799772	Cc01_g01180:618	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	CC	CC	CC	CT
-chr1:1799746	[C/A]	chr1	1799746	Cc01_g01180:644	exon	NON_SYNONYMOUS_CODING	gGt/gTt	G/V	25.0%	4	CC	CA	CC	AC
-chr1:1799703	[T/A]	chr1	1799703	Cc01_g01180:687	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	37.5%	4	TT	AT	TA	TA
-chr1:1799683	[C/T]	chr1	1799683	Cc01_g01180:707	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	CC	CC	CT	CC
-chr1:1799560	[G/A]	chr1	1799560	Cc01_g01180:830	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	12.5%	4	GG	GG	GG	GA
-chr1:1799253	[G/A]	chr1	1799253	Cc01_g01180:1137	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	GG	GG	GG	GA
-chr1:1799138	[C/G]	chr1	1799138	Cc01_g01180:1252	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	12.5%	4	CC	CC	CC	CG
-chr1:1799114	[C/T]	chr1	1799114	Cc01_g01180:1276	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	12.5%	4	CC	CC	CC	CT
-chr1:1799096	[T/C]	chr1	1799096	Cc01_g01180:1294	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	25.0%	4	TT	TC	TC	TT
-chr1:1798930	[C/T]	chr1	1798930	Cc01_g01180:1460	exon	NON_SYNONYMOUS_CODING	gGa/gAa	G/E	37.5%	4	CC	CT	CT	CT
-chr1:1798825	[T/C]	chr1	1798825	Cc01_g01180:1565	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	12.5%	4	TT	TT	TT	TC
-chr1:1798812	[A/C]	chr1	1798812	Cc01_g01180:1578	exon	NON_SYNONYMOUS_CODING	aaT/aaG	N/K	12.5%	4	AA	AA	AA	AC
-chr1:1798782	[T/C]	chr1	1798782	Cc01_g01180:1608	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	12.5%	4	TT	TT	TT	TC
-chr1:1798753	[T/A]	chr1	1798753	Cc01_g01180:1637	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	12.5%	4	TT	TT	TT	TA
-chr1:1798733	[T/C]	chr1	1798733	Cc01_g01180:1657	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	37.5%	4	TT	TC	TC	TC
-chr1:1798724	[G/A]	chr1	1798724	Cc01_g01180:1666	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	GG	GG	GG	GA
-chr1:1798690	[C/A]	chr1	1798690	Cc01_g01180:1700	exon	NON_SYNONYMOUS_CODING	gGg/gTg	G/V	12.5%	4	CC	CC	CC	CA
-chr1:1798665	[T/C]	chr1	1798665	Cc01_g01180:1725	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	12.5%	4	TT	TT	TC	TT
-chr1:1798471	[T/A]	chr1	1798471	Cc01_g01180:1919	exon	NON_SYNONYMOUS_CODING	aAt/aTt	N/I	12.5%	4	TT	TT	TT	TA
-chr1:1798453	[A/G]	chr1	1798453	Cc01_g01180:1937	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	12.5%	4	AA	AA	AA	AG
-chr1:1798341	[G/A]	chr1	1798341	Cc01_g01180:2049	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	37.5%	4	GG	AA	GA	AA
-chr1:1798269	[T/C]	chr1	1798269	Cc01_g01180:2121	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	TT	TT	TT	TC
-chr1:1798206	[A/G]	chr1	1798206	Cc01_g01180:2184	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AA	AA	AG
-chr1:1798185	[A/T]	chr1	1798185	Cc01_g01180:2205	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	12.5%	4	AA	AA	AA	AT
-chr1:1798172	[G/A]	chr1	1798172	Cc01_g01180:2218	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	GG	GG	GG	GA
-chr1:1798019	[A/G]	chr1	1798019	Cc01_g01180:2277	exon	SYNONYMOUS_CODING	caT/caC	H/H	12.5%	4	AA	AA	AA	AG
-chr1:1797997	[A/C]	chr1	1797997	Cc01_g01180:2299	exon	NON_SYNONYMOUS_CODING	Tgc/Ggc	C/G	12.5%	4	AA	AA	AC	AA
-chr1:1796639	[G/T]	chr1	1796639	Cc01_g01180:2517	exon	SYNONYMOUS_CODING	ctC/ctA	L/L	12.5%	4	GG	GG	GG	GT
-chr1:1796548	[C/T]	chr1	1796548	Cc01_g01180:2608	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	CC	CC	CC	CT
-chr1:1796523	[G/C]	chr1	1796523	Cc01_g01180:2633	exon	NON_SYNONYMOUS_CODING	tCc/tGc	S/C	12.5%	4	GG	GG	GG	GC
-chr1:1796504	[G/A]	chr1	1796504	Cc01_g01180:2652	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	GG	GG	GA	GG
-chr1:1796501	[C/T]	chr1	1796501	Cc01_g01180:2655	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	CC	CC	CC	CT
-chr1:1796477	[A/G]	chr1	1796477	Cc01_g01180:2679	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	12.5%	4	AA	AA	AA	AG
-chr1:1794530	[C/A]	chr1	1794530	Cc01_g01180:2830	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	12.5%	4	CC	CC	CC	CA
-chr1:1793183	[A/G]	chr1	1793183	Cc01_g01180:2975	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	AA	AA	AA	AG
-chr1:1793145	[G/T]	chr1	1793145	Cc01_g01180:3013	exon	NON_SYNONYMOUS_CODING	Ctc/Atc	L/I	12.5%	4	GG	GG	GG	GT
-chr1:1793065	[C/T]	chr1	1793065	Cc01_g01180:3093	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	CC	CT	CC	CC
-chr1:1793054	[A/G]	chr1	1793054	Cc01_g01180:3104	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	12.5%	4	AA	AG	AA	AA
-chr1:1793045	[G/T]	chr1	1793045	Cc01_g01180:3113	exon	NON_SYNONYMOUS_CODING	aCa/aAa	T/K	12.5%	4	GG	GT	GG	GG
-chr1:1792939	[G/T]	chr1	1792939	Cc01_g01180:3147	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	12.5%	4	GG	GT	GG	GG
-chr1:1792909	[A/T]	chr1	1792909	Cc01_g01180:3177	exon	SYNONYMOUS_CODING	acT/acA	T/T	12.5%	4	AA	TA	AA	AA
-chr1:1813729	[G/T]	chr1	1813729	Cc01_g01190:306	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	16.7%	3	GG	GT	NN	GG
-chr1:1813726	[A/T]	chr1	1813726	Cc01_g01190:309	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	16.7%	3	AA	AT	NN	AA
-chr1:1813696	[T/G]	chr1	1813696	Cc01_g01190:339	exon	SYNONYMOUS_CODING	atA/atC	I/I	16.7%	3	TT	TG	NN	TT
-chr1:1818371	[T/C]	chr1	1818371	Cc01_g01200:87	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	50.0%	4	TT	TC	CC	TC
-chr1:1818296	[A/T]	chr1	1818296	Cc01_g01200:162	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	4	AA	AA	TT	AA
-chr1:1818188	[A/G]	chr1	1818188	Cc01_g01200:270	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	AA	AA	AG	AA
-chr1:1818116	[A/C]	chr1	1818116	Cc01_g01200:342	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	12.5%	4	AA	AC	AA	AA
-chr1:1818035	[A/G]	chr1	1818035	Cc01_g01200:423	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	50.0%	4	AA	AG	AG	GG
-chr1:1818018	[T/A]	chr1	1818018	Cc01_g01200:440	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	50.0%	4	TT	TA	TA	AA
-chr1:1818013	[T/G]	chr1	1818013	Cc01_g01200:445	exon	NON_SYNONYMOUS_CODING	Atg/Ctg	M/L	25.0%	4	TT	TT	TG	TG
-chr1:1822497	[A/G]	chr1	1822497	Cc01_g01210:153	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	AA	AG	AA	AG
-chr1:1822491	[C/G]	chr1	1822491	Cc01_g01210:159	exon	SYNONYMOUS_CODING	ccG/ccC	P/P	12.5%	4	CC	CC	CC	CG
-chr1:1822434	[C/T]	chr1	1822434	Cc01_g01210:216	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	12.5%	4	CC	CT	CC	CC
-chr1:1822365	[A/G]	chr1	1822365	Cc01_g01210:285	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	37.5%	4	AA	GG	AA	AG
-chr1:1822344	[G/C]	chr1	1822344	Cc01_g01210:306	exon	SYNONYMOUS_CODING	ccC/ccG	P/P	37.5%	4	GG	CC	GG	GC
-chr1:1822311	[G/C]	chr1	1822311	Cc01_g01210:339	exon	SYNONYMOUS_CODING	gtC/gtG	V/V	12.5%	4	GG	GG	GC	GG
-chr1:1822251	[G/A]	chr1	1822251	Cc01_g01210:399	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	37.5%	4	GG	GA	AG	GA
-chr1:1822215	[G/T]	chr1	1822215	Cc01_g01210:435	exon	NON_SYNONYMOUS_CODING	aaC/aaA	N/K	12.5%	4	GG	GG	TG	GG
-chr1:1822206	[G/A]	chr1	1822206	Cc01_g01210:444	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	37.5%	4	GG	AA	AG	AA
-chr1:1871413	[G/T]	chr1	1871413	Cc01_g01220:7	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	37.5%	4	GG	TT	GT	TT
-chr1:1871774	[T/C]	chr1	1871774	Cc01_g01220:65	exon	NON_SYNONYMOUS_CODING	tTt/tCt	F/S	12.5%	4	TT	TT	TT	TC
-chr1:1871782	[G/C]	chr1	1871782	Cc01_g01220:73	exon	NON_SYNONYMOUS_CODING	Gtg/Ctg	V/L	12.5%	4	GG	GG	GG	GC
-chr1:1871785	[G/T]	chr1	1871785	Cc01_g01220:76	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	25.0%	4	GG	GT	GG	GT
-chr1:1871959	[C/T]	chr1	1871959	Cc01_g01220:118	exon	NON_SYNONYMOUS_CODING	Ctc/Ttc	L/F	12.5%	4	CC	CT	CC	CC
-chr1:1871977	[G/C]	chr1	1871977	Cc01_g01220:136	exon	NON_SYNONYMOUS_CODING	Gtt/Ctt	V/L	25.0%	4	GG	GC	GC	GG
-chr1:1871980	[T/G]	chr1	1871980	Cc01_g01220:139	exon	NON_SYNONYMOUS_CODING	Ttt/Gtt	F/V	12.5%	4	TT	TG	TT	TT
-chr1:1871994	[C/A]	chr1	1871994	Cc01_g01220:153	exon	NON_SYNONYMOUS_CODING	ttC/ttA	F/L	12.5%	4	CC	AC	CC	CC
-chr1:1872001	[T/C]	chr1	1872001	Cc01_g01220:160	exon	NON_SYNONYMOUS_CODING	Tcc/Ccc	S/P	12.5%	4	TT	CT	TT	TT
-chr1:1872003	[C/T]	chr1	1872003	Cc01_g01220:162	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	37.5%	4	CC	CT	CT	CT
-chr1:1872004	[A/G]	chr1	1872004	Cc01_g01220:163	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	37.5%	4	AA	AG	AG	AG
-chr1:1872020	[G/A]	chr1	1872020	Cc01_g01220:179	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	12.5%	4	GG	GG	GA	GG
-chr1:1872035	[G/A]	chr1	1872035	Cc01_g01220:194	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	25.0%	4	GG	GA	GG	GA
-chr1:1872037	[A/G]	chr1	1872037	Cc01_g01220:196	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	12.5%	4	AA	AA	AA	AG
-chr1:1872051	[A/G]	chr1	1872051	Cc01_g01220:210	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	AA	GG	GA	GG
-chr1:1873065	[C/T]	chr1	1873065	Cc01_g01220:247	exon	NON_SYNONYMOUS_CODING	Cct/Tct	P/S	12.5%	4	CC	CC	CC	CT
-chr1:1873088	[T/C]	chr1	1873088	Cc01_g01220:270	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	TT	TT	TC
-chr1:1874574	[C/T]	chr1	1874574	Cc01_g01230:34	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	12.5%	4	CC	CC	CC	CT
-chr1:1874587	[T/G]	chr1	1874587	Cc01_g01230:47	exon	NON_SYNONYMOUS_CODING	tTc/tGc	F/C	12.5%	4	TT	TT	TG	TT
-chr1:1874774	[C/G]	chr1	1874774	Cc01_g01230:135	exon	STOP_GAINED	taC/taG	Y/5	12.5%	4	CC	CC	CG	CC
-chr1:1874797	[T/A]	chr1	1874797	Cc01_g01230:158	exon	NON_SYNONYMOUS_CODING	aTt/aAt	I/N	25.0%	4	TT	TT	TA	TA
-chr1:1874808	[G/T]	chr1	1874808	Cc01_g01230:169	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	GG	GG	GG	GT
-chr1:1874816	[G/T]	chr1	1874816	Cc01_g01230:177	exon	NON_SYNONYMOUS_CODING	agG/agT	R/S	12.5%	4	GG	GT	GG	GG
-chr1:1874818	[G/T]	chr1	1874818	Cc01_g01230:179	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	25.0%	4	GG	GG	GT	GT
-chr1:1879776	[A/C]	chr1	1879776	Cc01_g01240:27	exon	NON_SYNONYMOUS_CODING	tgT/tgG	C/W	50.0%	4	AA	AC	AC	CC
-chr1:1879628	[G/C]	chr1	1879628	Cc01_g01240:175	exon	NON_SYNONYMOUS_CODING	Ctc/Gtc	L/V	25.0%	4	GG	GC	GG	GC
-chr1:1879623	[T/C]	chr1	1879623	Cc01_g01240:180	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TC	TT
-chr1:1907384	[G/A]	chr1	1907384	Cc01_g01250:29	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	GG	GA	GG	GA
-chr1:1907400	[C/G]	chr1	1907400	Cc01_g01250:45	exon	SYNONYMOUS_CODING	ctC/ctG	L/L	25.0%	4	CC	GG	GG	GG
-chr1:1907401	[A/G]	chr1	1907401	Cc01_g01250:46	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	37.5%	4	AA	AG	AG	GA
-chr1:1907418	[G/A]	chr1	1907418	Cc01_g01250:63	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	37.5%	4	GG	GA	GA	AG
-chr1:1907454	[A/C]	chr1	1907454	Cc01_g01250:99	exon	NON_SYNONYMOUS_CODING	caA/caC	Q/H	37.5%	4	AA	AC	AC	CA
-chr1:1907455	[A/G]	chr1	1907455	Cc01_g01250:100	exon	NON_SYNONYMOUS_CODING	Aac/Gac	N/D	12.5%	4	AA	AA	AG	AA
-chr1:1907457	[C/G]	chr1	1907457	Cc01_g01250:102	exon	NON_SYNONYMOUS_CODING	aaC/aaG	N/K	25.0%	4	CC	GG	GG	GG
-chr1:1907460	[T/A]	chr1	1907460	Cc01_g01250:105	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	25.0%	4	TT	TT	AT	TA
-chr1:1907483	[A/C]	chr1	1907483	Cc01_g01250:128	exon	NON_SYNONYMOUS_CODING	aAt/aCt	N/T	12.5%	4	AA	AA	AA	CA
-chr1:1907485	[G/A]	chr1	1907485	Cc01_g01250:130	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	12.5%	4	GG	GG	GG	GA
-chr1:1907487	[C/T]	chr1	1907487	Cc01_g01250:132	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	37.5%	4	CC	CT	CT	TC
-chr1:1907489	[T/G]	chr1	1907489	Cc01_g01250:134	exon	NON_SYNONYMOUS_CODING	aTc/aGc	I/S	12.5%	4	TT	TT	TT	GT
-chr1:1907499	[G/A]	chr1	1907499	Cc01_g01250:144	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	25.0%	4	GG	GG	AG	GA
-chr1:1907514	[T/C]	chr1	1907514	Cc01_g01250:159	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	37.5%	4	TT	TC	TC	CT
-chr1:1907532	[G/C]	chr1	1907532	Cc01_g01250:177	exon	SYNONYMOUS_CODING	ggG/ggC	G/G	25.0%	4	GG	CC	CC	CC
-chr1:1907552	[A/G]	chr1	1907552	Cc01_g01250:197	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	37.5%	4	AA	AG	AG	GA
-chr1:1907554	[G/A]	chr1	1907554	Cc01_g01250:199	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	25.0%	4	GG	GG	AG	GA
-chr1:1907571	[A/G]	chr1	1907571	Cc01_g01250:216	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	37.5%	4	AA	AG	AG	GA
-chr1:1907577	[G/A]	chr1	1907577	Cc01_g01250:222	exon	SYNONYMOUS_CODING	agG/agA	R/R	12.5%	4	GG	GG	GA	GG
-chr1:1907584	[A/G]	chr1	1907584	Cc01_g01250:229	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	37.5%	4	AA	AG	AG	GA
-chr1:1907613	[C/T]	chr1	1907613	Cc01_g01250:258	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	37.5%	4	CC	CT	CT	TC
-chr1:1907628	[G/A]	chr1	1907628	Cc01_g01250:273	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	37.5%	4	GG	GA	GA	AG
-chr1:1907636	[C/G]	chr1	1907636	Cc01_g01250:281	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	37.5%	4	CC	CG	CG	GC
-chr1:1907643	[A/G]	chr1	1907643	Cc01_g01250:288	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	37.5%	4	AA	AG	AG	GA
-chr1:1907649	[G/T]	chr1	1907649	Cc01_g01250:294	exon	SYNONYMOUS_CODING	ctG/ctT	L/L	37.5%	4	GG	GT	GT	TG
-chr1:1907663	[A/T]	chr1	1907663	Cc01_g01250:308	exon	NON_SYNONYMOUS_CODING	cAa/cTa	Q/L	12.5%	4	AA	AA	TA	AA
-chr1:1907745	[T/G]	chr1	1907745	Cc01_g01250:390	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	25.0%	4	TT	GG	GG	GG
-chr1:1907751	[G/A]	chr1	1907751	Cc01_g01250:396	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	37.5%	4	GG	GA	GA	GA
-chr1:1907865	[G/A]	chr1	1907865	Cc01_g01250:438	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	GG	AA	AA	AA
-chr1:1907867	[C/T]	chr1	1907867	Cc01_g01250:440	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	50.0%	4	CC	CT	TT	CT
-chr1:1907913	[G/A]	chr1	1907913	Cc01_g01250:486	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	12.5%	4	GG	AG	GG	GG
-chr1:1907925	[C/T]	chr1	1907925	Cc01_g01250:498	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	CC	CT	CT	CT
-chr1:1907951	[T/A]	chr1	1907951	Cc01_g01250:524	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	37.5%	4	TT	TA	TA	TA
-chr1:1907955	[C/T]	chr1	1907955	Cc01_g01250:528	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	37.5%	4	CC	CT	CT	CT
-chr1:1907970	[G/A]	chr1	1907970	Cc01_g01250:543	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	GG	AG	GG
-chr1:1907971	[G/C]	chr1	1907971	Cc01_g01250:544	exon	NON_SYNONYMOUS_CODING	Ggg/Cgg	G/R	12.5%	4	GG	GG	CG	GG
-chr1:1907976	[A/G]	chr1	1907976	Cc01_g01250:549	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	25.0%	4	AA	GA	AA	GA
-chr1:1907998	[G/A]	chr1	1907998	Cc01_g01250:571	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	GG	AG	GG
-chr1:1908013	[C/G]	chr1	1908013	Cc01_g01250:586	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	12.5%	4	CC	CC	CC	GC
-chr1:1908043	[T/C]	chr1	1908043	Cc01_g01250:616	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	37.5%	4	TT	TC	TC	TC
-chr1:1908051	[G/C]	chr1	1908051	Cc01_g01250:624	exon	NON_SYNONYMOUS_CODING	atG/atC	M/I	25.0%	4	GG	CG	GG	CG
-chr1:1908071	[A/T]	chr1	1908071	Cc01_g01250:644	exon	NON_SYNONYMOUS_CODING	aAa/aTa	K/I	25.0%	4	AA	TT	TT	TT
-chr1:1908072	[A/T]	chr1	1908072	Cc01_g01250:645	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	37.5%	4	AA	AT	AT	AT
-chr1:1908080	[G/C]	chr1	1908080	Cc01_g01250:653	exon	NON_SYNONYMOUS_CODING	gGc/gCc	G/A	37.5%	4	GG	GC	GC	GC
-chr1:1908088	[A/G]	chr1	1908088	Cc01_g01250:661	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	37.5%	4	AA	AG	AG	AG
-chr1:1908103	[C/T]	chr1	1908103	Cc01_g01250:676	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	37.5%	4	CC	CT	CT	CT
-chr1:1908119	[G/A]	chr1	1908119	Cc01_g01250:692	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	25.0%	4	GG	GG	GA	GA
-chr1:1908120	[G/T]	chr1	1908120	Cc01_g01250:693	exon	NON_SYNONYMOUS_CODING	agG/agT	R/S	25.0%	4	GG	GG	GT	GT
-chr1:1908140	[A/G]	chr1	1908140	Cc01_g01250:713	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	12.5%	4	AA	AA	AA	GA
-chr1:1908345	[G/C]	chr1	1908345	Cc01_g01250:738	exon	NON_SYNONYMOUS_CODING	ttG/ttC	L/F	25.0%	4	GG	GC	GG	GC
-chr1:1908360	[C/G]	chr1	1908360	Cc01_g01250:753	exon	NON_SYNONYMOUS_CODING	agC/agG	S/R	37.5%	4	CC	GC	CG	GC
-chr1:1908383	[A/T]	chr1	1908383	Cc01_g01250:776	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	37.5%	4	AA	TA	AT	TA
-chr1:1908403	[C/G]	chr1	1908403	Cc01_g01250:796	exon	NON_SYNONYMOUS_CODING	Ctc/Gtc	L/V	12.5%	4	CC	CC	GC	CC
-chr1:1908407	[G/A]	chr1	1908407	Cc01_g01250:800	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	12.5%	4	GG	GA	GG	GG
-chr1:1908410	[G/A]	chr1	1908410	Cc01_g01250:803	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	37.5%	4	GG	AG	GA	AG
-chr1:1908447	[T/C]	chr1	1908447	Cc01_g01250:840	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	37.5%	4	TT	CT	TC	CT
-chr1:1908449	[T/C]	chr1	1908449	Cc01_g01250:842	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	TT	TC	TT	TT
-chr1:1908471	[C/G]	chr1	1908471	Cc01_g01250:864	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	37.5%	4	CC	GC	CG	GC
-chr1:1908474	[C/T]	chr1	1908474	Cc01_g01250:867	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	37.5%	4	CC	TC	CT	TC
-chr1:1908527	[T/C]	chr1	1908527	Cc01_g01250:920	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	25.0%	4	TT	CC	CC	CC
-chr1:1908549	[A/G]	chr1	1908549	Cc01_g01250:942	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	AA	AG	AG	AA
-chr1:1908765	[G/A]	chr1	1908765	Cc01_g01250:954	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	AG	GG	GG
-chr1:1908789	[C/A]	chr1	1908789	Cc01_g01250:978	exon	NON_SYNONYMOUS_CODING	aaC/aaA	N/K	37.5%	4	CC	CA	CA	CA
-chr1:1908791	[A/C]	chr1	1908791	Cc01_g01250:980	exon	NON_SYNONYMOUS_CODING	aAg/aCg	K/T	12.5%	4	AA	CA	AA	AA
-chr1:1908792	[G/A]	chr1	1908792	Cc01_g01250:981	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	25.0%	4	GG	AA	AA	AA
-chr1:1908828	[C/T]	chr1	1908828	Cc01_g01250:1017	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	37.5%	4	CC	CT	CT	CT
-chr1:1908831	[G/A]	chr1	1908831	Cc01_g01250:1020	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	37.5%	4	GG	GA	GA	GA
-chr1:1908907	[A/G]	chr1	1908907	Cc01_g01250:1096	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	25.0%	4	AA	GG	GG	GG
-chr1:1908909	[A/G]	chr1	1908909	Cc01_g01250:1098	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	37.5%	4	AA	AG	AG	AG
-chr1:1908915	[T/C]	chr1	1908915	Cc01_g01250:1104	exon	SYNONYMOUS_CODING	agT/agC	S/S	37.5%	4	TT	TC	TC	TC
-chr1:1908942	[G/A]	chr1	1908942	Cc01_g01250:1131	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	25.0%	4	GG	AA	AA	AA
-chr1:1908962	[G/A]	chr1	1908962	Cc01_g01250:1151	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	12.5%	4	GG	GG	GG	AG
-chr1:1908976	[A/G]	chr1	1908976	Cc01_g01250:1165	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	12.5%	4	AA	AA	GA	AA
-chr1:1909020	[A/G]	chr1	1909020	Cc01_g01250:1209	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	AA	AA	AG	AA
-chr1:1909071	[A/C]	chr1	1909071	Cc01_g01250:1260	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	33.3%	3	AA	AC	NN	AC
-chr1:1909091	[G/A]	chr1	1909091	Cc01_g01250:1280	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	37.5%	4	GG	AG	GA	AG
-chr1:1909122	[G/A]	chr1	1909122	Cc01_g01250:1311	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	25.0%	4	GG	AA	AA	AA
-chr1:1909165	[C/A]	chr1	1909165	Cc01_g01250:1354	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	12.5%	4	CC	CC	CA	CC
-chr1:1909186	[G/A]	chr1	1909186	Cc01_g01250:1375	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	GG	GG	GA	GG
-chr1:1909203	[C/T]	chr1	1909203	Cc01_g01250:1392	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	12.5%	4	CC	CC	TC	CC
-chr1:1909210	[G/T]	chr1	1909210	Cc01_g01250:1399	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	12.5%	4	GG	GT	GG	GG
-chr1:1909247	[G/C]	chr1	1909247	Cc01_g01250:1436	exon	NON_SYNONYMOUS_CODING	tGt/tCt	C/S	25.0%	4	GG	CC	CC	CC
-chr1:1909284	[G/A]	chr1	1909284	Cc01_g01250:1473	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	37.5%	4	GG	GA	GA	GA
-chr1:1909294	[C/G]	chr1	1909294	Cc01_g01250:1483	exon	NON_SYNONYMOUS_CODING	Cac/Gac	H/D	25.0%	4	CC	GG	GG	GG
-chr1:1909302	[T/C]	chr1	1909302	Cc01_g01250:1491	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	25.0%	4	TT	CC	CC	CC
-chr1:1909308	[C/T]	chr1	1909308	Cc01_g01250:1497	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	CC	CC	CC	CT
-chr1:1909332	[C/T]	chr1	1909332	Cc01_g01250:1521	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	37.5%	4	CC	TC	TC	TC
-chr1:1909361	[G/A]	chr1	1909361	Cc01_g01250:1550	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	37.5%	4	GG	GA	GA	GA
-chr1:1909447	[G/A]	chr1	1909447	Cc01_g01250:1636	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	37.5%	4	GG	GA	GA	GA
-chr1:1909475	[C/T]	chr1	1909475	Cc01_g01250:1664	exon	NON_SYNONYMOUS_CODING	aCc/aTc	T/I	25.0%	4	CC	TT	TT	TT
-chr1:1909487	[A/G]	chr1	1909487	Cc01_g01250:1676	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	25.0%	4	AA	GA	AA	GA
-chr1:1909530	[A/G]	chr1	1909530	Cc01_g01250:1719	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	37.5%	4	AA	AG	AG	AG
-chr1:1909566	[A/G]	chr1	1909566	Cc01_g01250:1755	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	GA	AA	AA
-chr1:1909582	[C/T]	chr1	1909582	Cc01_g01250:1771	exon	STOP_GAINED	Cga/Tga	R/1	12.5%	4	CC	CC	CC	CT
-chr1:1909609	[G/A]	chr1	1909609	Cc01_g01250:1798	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	GG	GG	GG	AG
-chr1:1909635	[C/T]	chr1	1909635	Cc01_g01250:1824	exon	SYNONYMOUS_CODING	atC/atT	I/I	37.5%	4	CC	CT	CT	CT
-chr1:1909662	[C/T]	chr1	1909662	Cc01_g01250:1851	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	50.0%	4	CC	CT	TT	CT
-chr1:1909686	[C/T]	chr1	1909686	Cc01_g01250:1875	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	37.5%	4	CC	CT	CT	CT
-chr1:1909689	[A/T]	chr1	1909689	Cc01_g01250:1878	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	12.5%	4	AA	AA	TA	AA
-chr1:1909703	[A/G]	chr1	1909703	Cc01_g01250:1892	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	12.5%	4	AA	AG	AA	AA
-chr1:1909742	[G/T]	chr1	1909742	Cc01_g01250:1931	exon	NON_SYNONYMOUS_CODING	aGg/aTg	R/M	37.5%	4	GG	GT	GT	TG
-chr1:1909746	[T/G]	chr1	1909746	Cc01_g01250:1935	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	37.5%	4	TT	TG	TG	GT
-chr1:1909748	[G/A]	chr1	1909748	Cc01_g01250:1937	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	25.0%	4	GG	AA	AA	AA
-chr1:1909805	[G/A]	chr1	1909805	Cc01_g01250:1994	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	37.5%	4	GG	GA	GA	AG
-chr1:1909856	[C/T]	chr1	1909856	Cc01_g01250:2045	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	25.0%	4	CC	TC	CC	CT
-chr1:1909857	[A/T]	chr1	1909857	Cc01_g01250:2046	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	AA	TA	AA	AT
-chr1:1909887	[G/A]	chr1	1909887	Cc01_g01250:2076	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	AG	GG	GG
-chr1:1909896	[A/G]	chr1	1909896	Cc01_g01250:2085	exon	SYNONYMOUS_CODING	agA/agG	R/R	25.0%	4	AA	GG	GG	GG
-chr1:1909917	[A/G]	chr1	1909917	Cc01_g01250:2106	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	37.5%	4	AA	AG	AG	AG
-chr1:1909941	[G/A]	chr1	1909941	Cc01_g01250:2130	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	37.5%	4	GG	GA	GA	GA
-chr1:1909992	[C/G]	chr1	1909992	Cc01_g01250:2181	exon	NON_SYNONYMOUS_CODING	agC/agG	S/R	12.5%	4	CC	GC	CC	CC
-chr1:2012155	[G/A]	chr1	2012155	Cc01_g01280:207	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	16.7%	3	GG	GA	NN	GG
-chr1:2012138	[G/A]	chr1	2012138	Cc01_g01280:224	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	25.0%	4	GG	AA	AA	AA
-chr1:2012066	[A/G]	chr1	2012066	Cc01_g01280:296	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	33.3%	3	AA	GG	GG	NN
-chr1:2011950	[C/G]	chr1	2011950	Cc01_g01280:412	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	25.0%	4	CC	GG	CC	CC
-chr1:2011879	[G/A]	chr1	2011879	Cc01_g01280:483	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	16.7%	3	GG	GA	NN	GG
-chr1:2029017	[G/C]	chr1	2029017	Cc01_g01300:239	exon	NON_SYNONYMOUS_CODING	gCg/gGg	A/G	37.5%	4	GG	CC	CC	GC
-chr1:2028341	[A/G]	chr1	2028341	Cc01_g01300:366	exon	SYNONYMOUS_CODING	atT/atC	I/I	50.0%	4	AA	AG	GG	AG
-chr1:2028339	[G/A]	chr1	2028339	Cc01_g01300:368	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	12.5%	4	GG	AG	GG	GG
-chr1:2028335	[A/C]	chr1	2028335	Cc01_g01300:372	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	25.0%	4	AA	CC	CC	CC
-chr1:2028322	[C/T]	chr1	2028322	Cc01_g01300:385	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	12.5%	4	CC	TC	CC	CC
-chr1:2028306	[C/G]	chr1	2028306	Cc01_g01300:401	exon	NON_SYNONYMOUS_CODING	gGt/gCt	G/A	12.5%	4	CC	CC	CG	CC
-chr1:2028289	[T/C]	chr1	2028289	Cc01_g01300:418	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	33.3%	3	TT	CC	NN	CC
-chr1:2084455	[A/G]	chr1	2084455	Cc01_g01330:36	exon	SYNONYMOUS_CODING	agA/agG	R/R	50.0%	4	AA	AG	AG	GG
-chr1:2084476	[G/C]	chr1	2084476	Cc01_g01330:57	exon	NON_SYNONYMOUS_CODING	atG/atC	M/I	37.5%	4	GG	CG	CC	CC
-chr1:2084479	[C/T]	chr1	2084479	Cc01_g01330:60	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	CC	TC	CC	CC
-chr1:2084490	[C/A]	chr1	2084490	Cc01_g01330:71	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	12.5%	4	CC	AC	CC	CC
-chr1:2084532	[A/G]	chr1	2084532	Cc01_g01330:113	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	50.0%	4	AA	AG	AG	GG
-chr1:2084551	[A/G]	chr1	2084551	Cc01_g01330:132	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	AA	GA	AA	AA
-chr1:2084565	[C/G]	chr1	2084565	Cc01_g01330:146	exon	NON_SYNONYMOUS_CODING	tCc/tGc	S/C	50.0%	4	CC	CG	CG	GG
-chr1:2084606	[G/T]	chr1	2084606	Cc01_g01330:187	exon	NON_SYNONYMOUS_CODING	Gat/Tat	D/Y	50.0%	4	GG	GT	GT	TT
-chr1:2084666	[A/G]	chr1	2084666	Cc01_g01330:247	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	50.0%	4	AA	AG	AG	GG
-chr1:2084667	[C/T]	chr1	2084667	Cc01_g01330:248	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	25.0%	4	CC	TT	TT	TT
-chr1:2084687	[G/A]	chr1	2084687	Cc01_g01330:268	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	50.0%	4	GG	GA	GA	AA
-chr1:2084690	[C/G]	chr1	2084690	Cc01_g01330:271	exon	NON_SYNONYMOUS_CODING	Cga/Gga	R/G	12.5%	4	CC	GC	CC	CC
-chr1:2084692	[A/G]	chr1	2084692	Cc01_g01330:273	exon	SYNONYMOUS_CODING	cgA/cgG	R/R	12.5%	4	AA	AG	AA	AA
-chr1:2084718	[C/T]	chr1	2084718	Cc01_g01330:299	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	33.3%	3	CC	TT	TT	NN
-chr1:2084791	[T/A]	chr1	2084791	Cc01_g01330:372	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	12.5%	4	TT	TT	TA	TT
-chr1:2084820	[A/G]	chr1	2084820	Cc01_g01330:401	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	25.0%	4	AA	AA	GA	AG
-chr1:2084834	[G/A]	chr1	2084834	Cc01_g01330:415	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	GG	GG	AG
-chr1:2084842	[G/C]	chr1	2084842	Cc01_g01330:423	exon	NON_SYNONYMOUS_CODING	atG/atC	M/I	25.0%	4	GG	GG	GC	CG
-chr1:2084851	[A/G]	chr1	2084851	Cc01_g01330:432	exon	SYNONYMOUS_CODING	acA/acG	T/T	25.0%	4	AA	AA	GA	AG
-chr1:2084863	[C/T]	chr1	2084863	Cc01_g01330:444	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	12.5%	4	CC	CC	TC	CC
-chr1:2084924	[A/T]	chr1	2084924	Cc01_g01330:505	exon	NON_SYNONYMOUS_CODING	Att/Ttt	I/F	33.3%	3	AA	AT	AT	NN
-chr1:2085060	[T/C]	chr1	2085060	Cc01_g01330:641	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	50.0%	2	TT	NN	CC	NN
-chr1:2085102	[A/C]	chr1	2085102	Cc01_g01330:683	exon	NON_SYNONYMOUS_CODING	gAa/gCa	E/A	25.0%	4	AA	AA	CC	AA
-chr1:2085109	[T/G]	chr1	2085109	Cc01_g01330:690	exon	NON_SYNONYMOUS_CODING	atT/atG	I/M	25.0%	4	TT	TT	GG	TT
-chr1:2085145	[G/A]	chr1	2085145	Cc01_g01330:726	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	25.0%	4	GG	GG	AA	GG
-chr1:2085162	[C/G]	chr1	2085162	Cc01_g01330:743	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	37.5%	4	CC	CG	GG	CC
-chr1:2085194	[G/A]	chr1	2085194	Cc01_g01330:775	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	25.0%	4	GG	GA	GG	GA
-chr1:2085203	[C/A]	chr1	2085203	Cc01_g01330:784	exon	NON_SYNONYMOUS_CODING	Cag/Aag	Q/K	37.5%	4	CC	CA	CA	CA
-chr1:2085208	[A/G]	chr1	2085208	Cc01_g01330:789	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	37.5%	4	AA	AG	AA	GG
-chr1:2085218	[G/C]	chr1	2085218	Cc01_g01330:799	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	37.5%	4	GG	GC	GG	CC
-chr1:2085227	[T/G]	chr1	2085227	Cc01_g01330:808	exon	NON_SYNONYMOUS_CODING	Tta/Gta	L/V	37.5%	4	TT	TG	TT	GG
-chr1:2085271	[A/G]	chr1	2085271	Cc01_g01330:852	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	16.7%	3	AA	AG	AA	NN
-chr1:2085356	[C/G]	chr1	2085356	Cc01_g01330:937	exon	NON_SYNONYMOUS_CODING	Cat/Gat	H/D	16.7%	3	CC	CC	CG	NN
-chr1:2085358	[T/A]	chr1	2085358	Cc01_g01330:939	exon	NON_SYNONYMOUS_CODING	caT/caA	H/Q	16.7%	3	TT	TT	TA	NN
-chr1:2086315	[G/T]	chr1	2086315	Cc01_g01330:1073	exon	NON_SYNONYMOUS_CODING	tGt/tTt	C/F	25.0%	4	GG	GG	GT	GT
-chr1:2086354	[A/G]	chr1	2086354	Cc01_g01330:1112	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	37.5%	4	AA	GG	GA	AA
-chr1:2086380	[C/A]	chr1	2086380	Cc01_g01330:1138	exon	NON_SYNONYMOUS_CODING	Cat/Aat	H/N	37.5%	4	CC	CC	CA	AA
-chr1:2086424	[A/G]	chr1	2086424	Cc01_g01330:1182	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	37.5%	4	AA	AA	AG	GG
-chr1:2086438	[C/T]	chr1	2086438	Cc01_g01330:1196	exon	NON_SYNONYMOUS_CODING	cCc/cTc	P/L	25.0%	4	CC	TT	TT	TT
-chr1:2086581	[G/T]	chr1	2086581	Cc01_g01330:1261	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	12.5%	4	GG	GG	GT	GG
-chr1:2086594	[T/C]	chr1	2086594	Cc01_g01330:1274	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	25.0%	4	TT	TT	TC	TC
-chr1:2086608	[T/C]	chr1	2086608	Cc01_g01330:1288	exon	NON_SYNONYMOUS_CODING	Ttt/Ctt	F/L	37.5%	4	TT	TC	TC	TC
-chr1:2086613	[T/C]	chr1	2086613	Cc01_g01330:1293	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	37.5%	4	TT	TC	TC	TC
-chr1:2086637	[C/A]	chr1	2086637	Cc01_g01330:1317	exon	SYNONYMOUS_CODING	atC/atA	I/I	37.5%	4	CC	CA	CC	AA
-chr1:2086679	[G/A]	chr1	2086679	Cc01_g01330:1359	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	12.5%	4	GG	GG	GG	GA
-chr1:2086682	[C/T]	chr1	2086682	Cc01_g01330:1362	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	25.0%	4	CC	CC	CT	CT
-chr1:2086716	[G/A]	chr1	2086716	Cc01_g01330:1396	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	25.0%	4	GG	GG	GG	AA
-chr1:2086756	[G/A]	chr1	2086756	Cc01_g01330:1436	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	12.5%	4	GG	GG	GG	GA
-chr1:2086758	[C/G]	chr1	2086758	Cc01_g01330:1438	exon	NON_SYNONYMOUS_CODING	Cac/Gac	H/D	25.0%	4	CC	CC	CG	GC
-chr1:2086789	[T/A]	chr1	2086789	Cc01_g01330:1469	exon	NON_SYNONYMOUS_CODING	gTg/gAg	V/E	25.0%	4	TT	AA	AA	AA
-chr1:2086811	[A/G]	chr1	2086811	Cc01_g01330:1491	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	25.0%	4	AA	GG	AA	AA
-chr1:2086840	[T/A]	chr1	2086840	Cc01_g01330:1520	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	25.0%	4	TT	AA	TT	TT
-chr1:2093852	[C/T]	chr1	2093852	Cc01_g01340:4	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	16.7%	3	CC	CT	NN	CC
-chr1:2093847	[C/A]	chr1	2093847	Cc01_g01340:9	exon	SYNONYMOUS_CODING	ggG/ggT	G/G	50.0%	4	CC	AC	AA	CA
-chr1:2093810	[G/A]	chr1	2093810	Cc01_g01340:46	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	GG	AG	GG	GG
-chr1:2093799	[A/G]	chr1	2093799	Cc01_g01340:57	exon	SYNONYMOUS_CODING	caT/caC	H/H	37.5%	4	AA	GA	GG	AA
-chr1:2093778	[A/G]	chr1	2093778	Cc01_g01340:78	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	16.7%	3	AA	AA	NN	GA
-chr1:2093758	[G/A]	chr1	2093758	Cc01_g01340:98	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	33.3%	3	GG	GA	NN	GA
-chr1:2093731	[C/A]	chr1	2093731	Cc01_g01340:125	exon	NON_SYNONYMOUS_CODING	tGc/tTc	C/F	16.7%	3	CC	CC	NN	CA
-chr1:2093721	[C/G]	chr1	2093721	Cc01_g01340:135	exon	SYNONYMOUS_CODING	tcG/tcC	S/S	50.0%	4	CC	CG	GG	CG
-chr1:2093714	[A/C]	chr1	2093714	Cc01_g01340:142	exon	NON_SYNONYMOUS_CODING	Ttc/Gtc	F/V	50.0%	4	AA	AC	CC	AC
-chr1:2093686	[A/G]	chr1	2093686	Cc01_g01340:170	exon	NON_SYNONYMOUS_CODING	tTt/tCt	F/S	50.0%	4	AA	AG	GG	AG
-chr1:2093684	[T/C]	chr1	2093684	Cc01_g01340:172	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	50.0%	4	TT	TC	CC	TC
-chr1:2093683	[G/C]	chr1	2093683	Cc01_g01340:173	exon	NON_SYNONYMOUS_CODING	aCc/aGc	T/S	12.5%	4	GG	GC	GG	GG
-chr1:2093672	[C/A]	chr1	2093672	Cc01_g01340:184	exon	STOP_GAINED	Gag/Tag	E/2	37.5%	4	CC	CA	CA	CA
-chr1:2093663	[G/A]	chr1	2093663	Cc01_g01340:193	exon	NON_SYNONYMOUS_CODING	Cgc/Tgc	R/C	12.5%	4	GG	GG	GG	AG
-chr1:2093646	[A/G]	chr1	2093646	Cc01_g01340:210	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	25.0%	4	AA	AG	AG	AA
-chr1:2093644	[T/C]	chr1	2093644	Cc01_g01340:212	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	37.5%	4	TT	TC	TC	TC
-chr1:2093642	[C/T]	chr1	2093642	Cc01_g01340:214	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	37.5%	4	CC	TC	TC	TC
-chr1:2093636	[T/G]	chr1	2093636	Cc01_g01340:220	exon	NON_SYNONYMOUS_CODING	Acc/Ccc	T/P	25.0%	4	TT	TG	TG	TT
-chr1:2093635	[G/T]	chr1	2093635	Cc01_g01340:221	exon	NON_SYNONYMOUS_CODING	aCc/aAc	T/N	25.0%	4	GG	GT	GG	GT
-chr1:2093634	[G/A]	chr1	2093634	Cc01_g01340:222	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	GG	GA	GG	GG
-chr1:2093633	[C/T]	chr1	2093633	Cc01_g01340:223	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	12.5%	4	CC	CC	CC	CT
-chr1:2093602	[A/T]	chr1	2093602	Cc01_g01340:254	exon	NON_SYNONYMOUS_CODING	gTc/gAc	V/D	33.3%	3	AA	AT	NN	AT
-chr1:2093600	[C/G]	chr1	2093600	Cc01_g01340:256	exon	NON_SYNONYMOUS_CODING	Gga/Cga	G/R	16.7%	3	CC	CG	NN	CC
-chr1:2093588	[T/G]	chr1	2093588	Cc01_g01340:268	exon	NON_SYNONYMOUS_CODING	Aag/Cag	K/Q	16.7%	3	TT	TG	NN	TT
-chr1:2093575	[A/G]	chr1	2093575	Cc01_g01340:281	exon	NON_SYNONYMOUS_CODING	tTa/tCa	L/S	50.0%	3	AA	GG	NN	AG
-chr1:2093569	[G/A]	chr1	2093569	Cc01_g01340:287	exon	NON_SYNONYMOUS_CODING	gCc/gTc	A/V	16.7%	3	GG	GG	NN	GA
-chr1:2093565	[G/A]	chr1	2093565	Cc01_g01340:291	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	16.7%	3	GG	GG	NN	GA
-chr1:2093525	[C/G]	chr1	2093525	Cc01_g01340:331	exon	NON_SYNONYMOUS_CODING	Gac/Cac	D/H	50.0%	3	CC	GG	NN	CG
-chr1:2093515	[T/C]	chr1	2093515	Cc01_g01340:341	exon	SYNONYMOUS_STOP	tAa/tGa	1/1	33.3%	3	TT	CC	NN	TT
-chr1:2095269	[G/A]	chr1	2095269	Cc01_g01350:16	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	GG	GA	GG	GG
-chr1:2095295	[A/G]	chr1	2095295	Cc01_g01350:42	exon	SYNONYMOUS_CODING	cgA/cgG	R/R	12.5%	4	AA	AG	AA	AA
-chr1:2095321	[A/T]	chr1	2095321	Cc01_g01350:68	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	12.5%	4	AA	AT	AA	AA
-chr1:2095431	[C/A]	chr1	2095431	Cc01_g01350:178	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	12.5%	4	CC	CA	CC	CC
-chr1:2095629	[C/T]	chr1	2095629	Cc01_g01350:376	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	25.0%	4	CC	CC	CT	CT
-chr1:2095745	[G/A]	chr1	2095745	Cc01_g01350:492	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	37.5%	4	GG	GA	AA	GG
-chr1:2095959	[C/G]	chr1	2095959	Cc01_g01350:706	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	12.5%	4	CC	CC	CG	CC
-chr1:2095960	[A/G]	chr1	2095960	Cc01_g01350:707	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	25.0%	4	AA	AG	GA	AA
-chr1:2095964	[C/T]	chr1	2095964	Cc01_g01350:711	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	CC	CC	TC	CC
-chr1:2095974	[C/T]	chr1	2095974	Cc01_g01350:721	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	CC	CC	TC	CC
-chr1:2095975	[A/C]	chr1	2095975	Cc01_g01350:722	exon	NON_SYNONYMOUS_CODING	cAt/cCt	H/P	12.5%	4	AA	AA	CA	AA
-chr1:2095983	[A/C]	chr1	2095983	Cc01_g01350:730	exon	NON_SYNONYMOUS_CODING	Aca/Cca	T/P	12.5%	4	AA	AC	AA	AA
-chr1:2096351	[T/A]	chr1	2096351	Cc01_g01350:980	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	12.5%	4	TT	TA	TT	TT
-chr1:2096710	[C/G]	chr1	2096710	Cc01_g01350:1261	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	12.5%	4	CC	CC	CG	CC
-chr1:2100328	[A/C]	chr1	2100328	Cc01_g01360:24	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	50.0%	3	AA	NN	AC	CC
-chr1:2100313	[T/A]	chr1	2100313	Cc01_g01360:39	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	TT	AA	AA	AA
-chr1:2100304	[T/C]	chr1	2100304	Cc01_g01360:48	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	37.5%	4	TT	CC	CC	TC
-chr1:2100300	[C/T]	chr1	2100300	Cc01_g01360:52	exon	NON_SYNONYMOUS_CODING	Gcg/Acg	A/T	25.0%	4	CC	TT	TT	TT
-chr1:2100299	[G/A]	chr1	2100299	Cc01_g01360:53	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	37.5%	4	GG	AA	AA	GA
-chr1:2100295	[A/G]	chr1	2100295	Cc01_g01360:57	exon	SYNONYMOUS_CODING	agT/agC	S/S	37.5%	4	AA	GG	GG	AG
-chr1:2100286	[A/G]	chr1	2100286	Cc01_g01360:66	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	50.0%	4	AA	GG	GG	AA
-chr1:2100277	[C/T]	chr1	2100277	Cc01_g01360:75	exon	SYNONYMOUS_CODING	acG/acA	T/T	25.0%	4	CC	TT	TT	TT
-chr1:2100255	[C/T]	chr1	2100255	Cc01_g01360:97	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	37.5%	4	CC	TT	CT	TT
-chr1:2100252	[A/T]	chr1	2100252	Cc01_g01360:100	exon	NON_SYNONYMOUS_CODING	Ttc/Atc	F/I	37.5%	4	AA	TT	AT	TT
-chr1:2100249	[C/T]	chr1	2100249	Cc01_g01360:103	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	37.5%	4	CC	TT	CT	TT
-chr1:2100244	[A/T]	chr1	2100244	Cc01_g01360:108	exon	SYNONYMOUS_CODING	ctT/ctA	L/L	37.5%	4	AA	TT	AT	TT
-chr1:2100237	[T/C]	chr1	2100237	Cc01_g01360:115	exon	NON_SYNONYMOUS_CODING	Acg/Gcg	T/A	37.5%	4	TT	CC	TC	CC
-chr1:2100226	[G/A]	chr1	2100226	Cc01_g01360:126	exon	SYNONYMOUS_CODING	atC/atT	I/I	33.3%	3	GG	NN	GG	AA
-chr1:2100223	[A/C]	chr1	2100223	Cc01_g01360:129	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	50.0%	3	AA	NN	AC	CC
-chr1:2100218	[C/T]	chr1	2100218	Cc01_g01360:134	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	2	CC	NN	CT	NN
-chr1:2100189	[T/C]	chr1	2100189	Cc01_g01360:163	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	37.5%	4	TT	CC	TT	TC
-chr1:2100184	[G/A]	chr1	2100184	Cc01_g01360:168	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	25.0%	4	GG	GA	GG	GA
-chr1:2100164	[A/G]	chr1	2100164	Cc01_g01360:188	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	50.0%	3	AA	GG	NN	AG
-chr1:2100139	[A/G]	chr1	2100139	Cc01_g01360:213	exon	SYNONYMOUS_CODING	agT/agC	S/S	25.0%	2	AA	NN	NN	AG
-chr1:2105898	[A/G]	chr1	2105898	Cc01_g01370:23	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	25.0%	4	AA	AG	AA	AG
-chr1:2105943	[C/G]	chr1	2105943	Cc01_g01370:68	exon	NON_SYNONYMOUS_CODING	gCa/gGa	A/G	12.5%	4	CC	CC	CG	CC
-chr1:2105974	[T/G]	chr1	2105974	Cc01_g01370:99	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	25.0%	4	TT	TG	TT	TG
-chr1:2105998	[T/C]	chr1	2105998	Cc01_g01370:123	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TT	CT	TT
-chr1:2106006	[G/C]	chr1	2106006	Cc01_g01370:131	exon	NON_SYNONYMOUS_CODING	aGc/aCc	S/T	50.0%	4	GG	CC	GC	GC
-chr1:2106086	[G/A]	chr1	2106086	Cc01_g01370:211	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	12.5%	4	GG	GG	GA	GG
-chr1:2106188	[G/C]	chr1	2106188	Cc01_g01370:313	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	25.0%	4	GG	GC	GG	GC
-chr1:2106190	[G/A]	chr1	2106190	Cc01_g01370:315	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	4	GG	GA	GG	GA
-chr1:2106216	[C/G]	chr1	2106216	Cc01_g01370:341	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	25.0%	4	CC	CG	CC	CG
-chr1:2106220	[T/C]	chr1	2106220	Cc01_g01370:345	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	25.0%	4	TT	TC	TT	TC
-chr1:2106236	[T/C]	chr1	2106236	Cc01_g01370:361	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	25.0%	4	TT	TC	TT	TC
-chr1:2106264	[G/A]	chr1	2106264	Cc01_g01370:389	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	GG	GG	GA	GG
-chr1:2106271	[C/A]	chr1	2106271	Cc01_g01370:396	exon	NON_SYNONYMOUS_CODING	gaC/gaA	D/E	25.0%	4	CC	CC	CA	CA
-chr1:2106279	[G/A]	chr1	2106279	Cc01_g01370:404	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	25.0%	4	GG	GG	GA	GA
-chr1:2106291	[A/C]	chr1	2106291	Cc01_g01370:416	exon	NON_SYNONYMOUS_CODING	gAa/gCa	E/A	37.5%	4	AA	AC	AC	AC
-chr1:2106302	[A/G]	chr1	2106302	Cc01_g01370:427	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	50.0%	4	AA	AG	GG	AG
-chr1:2106324	[T/G]	chr1	2106324	Cc01_g01370:449	exon	NON_SYNONYMOUS_CODING	cTt/cGt	L/R	37.5%	4	TT	TG	TG	TG
-chr1:2106332	[C/G]	chr1	2106332	Cc01_g01370:457	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	12.5%	4	CC	CC	CG	CC
-chr1:2106375	[A/G]	chr1	2106375	Cc01_g01370:500	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	37.5%	4	AA	AG	AG	AG
-chr1:2106435	[A/T]	chr1	2106435	Cc01_g01370:560	exon	NON_SYNONYMOUS_CODING	tAc/tTc	Y/F	25.0%	4	AA	AT	AA	AT
-chr1:2106441	[T/G]	chr1	2106441	Cc01_g01370:566	exon	NON_SYNONYMOUS_CODING	aTg/aGg	M/R	25.0%	4	TT	TG	TT	TG
-chr1:2106443	[C/G]	chr1	2106443	Cc01_g01370:568	exon	NON_SYNONYMOUS_CODING	Cga/Gga	R/G	12.5%	4	CC	GC	CC	CC
-chr1:2106602	[A/G]	chr1	2106602	Cc01_g01370:633	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	AA	AG	AG	AG
-chr1:2106604	[T/G]	chr1	2106604	Cc01_g01370:635	exon	NON_SYNONYMOUS_CODING	gTc/gGc	V/G	37.5%	4	TT	TG	TG	TG
-chr1:2106695	[G/C]	chr1	2106695	Cc01_g01370:726	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	25.0%	4	GG	CC	GG	GG
-chr1:2106696	[A/G]	chr1	2106696	Cc01_g01370:727	exon	NON_SYNONYMOUS_CODING	Agg/Ggg	R/G	50.0%	4	AA	GG	GG	AA
-chr1:2106708	[G/A]	chr1	2106708	Cc01_g01370:739	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	GA	GG	GG
-chr1:2106774	[A/G]	chr1	2106774	Cc01_g01370:805	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	AA	AG	AA	AG
-chr1:2106839	[T/C]	chr1	2106839	Cc01_g01370:870	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	TT	TC	TT	TC
-chr1:2106857	[T/A]	chr1	2106857	Cc01_g01370:888	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	50.0%	4	TT	AA	TA	TA
-chr1:2106878	[G/A]	chr1	2106878	Cc01_g01370:909	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	37.5%	4	GG	GA	GA	GA
-chr1:2106908	[A/G]	chr1	2106908	Cc01_g01370:939	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	AA	GG	AA	AA
-chr1:2107068	[C/A]	chr1	2107068	Cc01_g01370:980	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	12.5%	4	CC	CA	CC	CC
-chr1:2107109	[G/C]	chr1	2107109	Cc01_g01370:1021	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	12.5%	4	GG	GG	GC	GG
-chr1:2107131	[A/C]	chr1	2107131	Cc01_g01370:1043	exon	NON_SYNONYMOUS_CODING	cAt/cCt	H/P	25.0%	4	AA	CA	AA	AC
-chr1:2107150	[G/A]	chr1	2107150	Cc01_g01370:1062	exon	STOP_GAINED	tgG/tgA	W/4	12.5%	4	GG	GA	GG	GG
-chr1:2107161	[T/C]	chr1	2107161	Cc01_g01370:1073	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	TT	TT	CT	TT
-chr1:2107171	[C/G]	chr1	2107171	Cc01_g01370:1083	exon	NON_SYNONYMOUS_CODING	aaC/aaG	N/K	12.5%	4	CC	CC	GC	CC
-chr1:2107215	[G/A]	chr1	2107215	Cc01_g01370:1127	exon	NON_SYNONYMOUS_CODING	gGg/gAg	G/E	50.0%	4	GG	AA	GA	GA
-chr1:2107325	[A/C]	chr1	2107325	Cc01_g01370:1159	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	37.5%	4	AA	AC	AC	AC
-chr1:2107345	[A/G]	chr1	2107345	Cc01_g01370:1179	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	37.5%	4	AA	AG	AG	AG
-chr1:2107361	[T/A]	chr1	2107361	Cc01_g01370:1195	exon	NON_SYNONYMOUS_CODING	Tct/Act	S/T	37.5%	4	TT	TA	TA	TA
-chr1:2107390	[A/C]	chr1	2107390	Cc01_g01370:1224	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	25.0%	4	AA	AC	AA	AC
-chr1:2107405	[T/A]	chr1	2107405	Cc01_g01370:1239	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	4	TT	AA	AA	AA
-chr1:2107431	[C/T]	chr1	2107431	Cc01_g01370:1265	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	37.5%	4	CC	CT	CT	CT
-chr1:2107467	[A/T]	chr1	2107467	Cc01_g01370:1301	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	12.5%	4	AA	TA	AA	AA
-chr1:2107472	[G/A]	chr1	2107472	Cc01_g01370:1306	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	12.5%	4	GG	GG	AG	GG
-chr1:2107516	[T/C]	chr1	2107516	Cc01_g01370:1350	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	50.0%	4	TT	CC	TC	TC
-chr1:2107607	[C/T]	chr1	2107607	Cc01_g01370:1441	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	CC	CT	CT	CT
-chr1:2117223	[A/G]	chr1	2117223	Cc01_g01380:117	exon	SYNONYMOUS_CODING	cgT/cgC	R/R	33.3%	3	AA	GG	NN	GG
-chr1:2117210	[T/G]	chr1	2117210	Cc01_g01380:130	exon	NON_SYNONYMOUS_CODING	Att/Ctt	I/L	33.3%	3	TT	GG	NN	GG
-chr1:2117175	[C/G]	chr1	2117175	Cc01_g01380:165	exon	SYNONYMOUS_CODING	ctG/ctC	L/L	50.0%	2	CC	GG	NN	NN
-chr1:2117171	[C/T]	chr1	2117171	Cc01_g01380:169	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	50.0%	2	CC	TT	NN	NN
-chr1:2116944	[A/G]	chr1	2116944	Cc01_g01380:240	exon	SYNONYMOUS_CODING	caT/caC	H/H	50.0%	2	AA	NN	NN	GG
-chr1:2116934	[T/A]	chr1	2116934	Cc01_g01380:250	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	50.0%	2	TT	NN	NN	AA
-chr1:2116932	[C/G]	chr1	2116932	Cc01_g01380:252	exon	NON_SYNONYMOUS_CODING	atG/atC	M/I	50.0%	2	CC	NN	NN	GG
-chr1:2116917	[C/A]	chr1	2116917	Cc01_g01380:267	exon	SYNONYMOUS_CODING	ggG/ggT	G/G	50.0%	2	CC	NN	NN	AA
-chr1:2116877	[T/A]	chr1	2116877	Cc01_g01380:307	exon	NON_SYNONYMOUS_CODING	Ata/Tta	I/L	50.0%	2	TT	NN	NN	AA
-chr1:2116873	[T/C]	chr1	2116873	Cc01_g01380:311	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	50.0%	2	TT	NN	NN	CC
-chr1:2116861	[A/G]	chr1	2116861	Cc01_g01380:323	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	50.0%	2	AA	NN	NN	GG
-chr1:2169162	[C/G]	chr1	2169162	Cc01_g01390:5	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	12.5%	4	CC	CG	CC	CC
-chr1:2169167	[C/G]	chr1	2169167	Cc01_g01390:10	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	37.5%	4	CC	CG	CG	CG
-chr1:2169279	[A/G]	chr1	2169279	Cc01_g01390:122	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	25.0%	4	AA	GG	GG	GG
-chr1:2169286	[A/T]	chr1	2169286	Cc01_g01390:129	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	12.5%	4	AA	AA	AT	AA
-chr1:2169346	[T/C]	chr1	2169346	Cc01_g01390:189	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	25.0%	4	TT	TC	TC	TT
-chr1:2169353	[G/A]	chr1	2169353	Cc01_g01390:196	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	25.0%	4	GG	GA	GA	GG
-chr1:2169630	[T/A]	chr1	2169630	Cc01_g01390:473	exon	NON_SYNONYMOUS_CODING	gTa/gAa	V/E	37.5%	4	TT	AA	TA	AA
-chr1:2169828	[C/A]	chr1	2169828	Cc01_g01390:671	exon	NON_SYNONYMOUS_CODING	aCg/aAg	T/K	25.0%	4	CC	CA	CA	CC
-chr1:2169829	[G/C]	chr1	2169829	Cc01_g01390:672	exon	SYNONYMOUS_CODING	acG/acC	T/T	25.0%	4	GG	GC	GC	GG
-chr1:2169862	[C/T]	chr1	2169862	Cc01_g01390:705	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CT	CC	CC
-chr1:2169958	[T/C]	chr1	2169958	Cc01_g01390:801	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	TT	TT	TC	TT
-chr1:2169967	[C/T]	chr1	2169967	Cc01_g01390:810	exon	SYNONYMOUS_CODING	caC/caT	H/H	12.5%	4	CC	CC	CT	CC
-chr1:2170037	[G/C]	chr1	2170037	Cc01_g01390:880	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	12.5%	4	GG	GG	GC	GG
-chr1:2170043	[G/A]	chr1	2170043	Cc01_g01390:886	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	25.0%	4	GG	GA	GA	GG
-chr1:2170057	[C/T]	chr1	2170057	Cc01_g01390:900	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CC	TC	CC
-chr1:2170129	[T/C]	chr1	2170129	Cc01_g01390:972	exon	SYNONYMOUS_CODING	acT/acC	T/T	12.5%	4	TT	TT	TC	TT
-chr1:2170192	[G/T]	chr1	2170192	Cc01_g01390:1035	exon	SYNONYMOUS_CODING	gtG/gtT	V/V	12.5%	4	GG	GT	GG	GG
-chr1:2170204	[T/C]	chr1	2170204	Cc01_g01390:1047	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	TT	TC	TT	TT
-chr1:2170362	[A/T]	chr1	2170362	Cc01_g01390:1080	exon	NON_SYNONYMOUS_CODING	ttA/ttT	L/F	25.0%	4	AA	AT	AT	AA
-chr1:2170446	[T/C]	chr1	2170446	Cc01_g01390:1164	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	37.5%	4	TT	CC	TC	CC
-chr1:2170635	[T/C]	chr1	2170635	Cc01_g01390:1275	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	50.0%	4	TT	CC	TT	CC
-chr1:2170650	[T/C]	chr1	2170650	Cc01_g01390:1290	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	TT	TT	TC	TT
-chr1:2170761	[T/G]	chr1	2170761	Cc01_g01390:1401	exon	NON_SYNONYMOUS_CODING	aaT/aaG	N/K	37.5%	4	TT	GG	TG	GG
-chr1:2170780	[C/T]	chr1	2170780	Cc01_g01390:1420	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	CC	CC	CT	CC
-chr1:2170800	[G/A]	chr1	2170800	Cc01_g01390:1440	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	50.0%	4	GG	AA	GG	AA
-chr1:2170865	[C/A]	chr1	2170865	Cc01_g01390:1505	exon	NON_SYNONYMOUS_CODING	gCg/gAg	A/E	12.5%	4	CC	CC	CA	CC
-chr1:2170868	[A/C]	chr1	2170868	Cc01_g01390:1508	exon	NON_SYNONYMOUS_CODING	cAa/cCa	Q/P	50.0%	4	AA	CC	AA	CC
-chr1:2170873	[A/G]	chr1	2170873	Cc01_g01390:1513	exon	NON_SYNONYMOUS_CODING	Aac/Gac	N/D	12.5%	4	AA	AG	AA	AA
-chr1:2170884	[C/T]	chr1	2170884	Cc01_g01390:1524	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	50.0%	4	CC	TT	CC	TT
-chr1:2174798	[C/T]	chr1	2174798	Cc01_g01400:21	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	50.0%	4	CC	CT	CT	TT
-chr1:2174809	[A/G]	chr1	2174809	Cc01_g01400:32	exon	NON_SYNONYMOUS_CODING	gAa/gGa	E/G	25.0%	4	AA	AA	AG	AG
-chr1:2174843	[G/A]	chr1	2174843	Cc01_g01400:66	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	4	GG	GG	GA	GA
-chr1:2174851	[G/A]	chr1	2174851	Cc01_g01400:74	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	GG	GG	AG	GG
-chr1:2174873	[C/A]	chr1	2174873	Cc01_g01400:96	exon	NON_SYNONYMOUS_CODING	gaC/gaA	D/E	25.0%	4	CC	CC	CA	CA
-chr1:2174883	[T/C]	chr1	2174883	Cc01_g01400:106	exon	NON_SYNONYMOUS_CODING	Tat/Cat	Y/H	25.0%	4	TT	TT	TC	TC
-chr1:2174888	[T/C]	chr1	2174888	Cc01_g01400:111	exon	SYNONYMOUS_CODING	atT/atC	I/I	25.0%	4	TT	TT	TC	TC
-chr1:2174899	[T/C]	chr1	2174899	Cc01_g01400:122	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	12.5%	4	TT	TT	TT	CT
-chr1:2174901	[C/T]	chr1	2174901	Cc01_g01400:124	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	25.0%	4	CC	CC	CT	CT
-chr1:2174903	[T/C]	chr1	2174903	Cc01_g01400:126	exon	SYNONYMOUS_CODING	cgT/cgC	R/R	25.0%	4	TT	TT	TC	TC
-chr1:2174906	[T/G]	chr1	2174906	Cc01_g01400:129	exon	SYNONYMOUS_CODING	acT/acG	T/T	25.0%	4	TT	TT	TG	TG
-chr1:2174908	[C/A]	chr1	2174908	Cc01_g01400:131	exon	NON_SYNONYMOUS_CODING	aCa/aAa	T/K	25.0%	4	CC	CC	CA	CA
-chr1:2174912	[T/G]	chr1	2174912	Cc01_g01400:135	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	12.5%	4	TT	TG	TT	TT
-chr1:2174940	[C/A]	chr1	2174940	Cc01_g01400:163	exon	SYNONYMOUS_CODING	Cgg/Agg	R/R	25.0%	4	CC	CC	CA	CA
-chr1:2174949	[T/G]	chr1	2174949	Cc01_g01400:172	exon	NON_SYNONYMOUS_CODING	Tac/Gac	Y/D	25.0%	4	TT	TT	TG	TG
-chr1:2174958	[G/A]	chr1	2174958	Cc01_g01400:181	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	25.0%	4	GG	GG	GA	GA
-chr1:2174961	[C/T]	chr1	2174961	Cc01_g01400:184	exon	NON_SYNONYMOUS_CODING	Cgg/Tgg	R/W	37.5%	4	CC	CC	TT	CT
-chr1:2174991	[G/A]	chr1	2174991	Cc01_g01400:214	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	GG	GA	GG	GG
-chr1:2174992	[A/G]	chr1	2174992	Cc01_g01400:215	exon	NON_SYNONYMOUS_CODING	gAa/gGa	E/G	25.0%	4	AA	GA	AA	GA
-chr1:2174997	[C/T]	chr1	2174997	Cc01_g01400:220	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	50.0%	4	CC	CT	CT	TT
-chr1:2174999	[T/C]	chr1	2174999	Cc01_g01400:222	exon	SYNONYMOUS_CODING	caT/caC	H/H	25.0%	4	TT	TT	TC	TC
-chr1:2175021	[G/C]	chr1	2175021	Cc01_g01400:244	exon	NON_SYNONYMOUS_CODING	Ggt/Cgt	G/R	25.0%	4	GG	GG	GC	GC
-chr1:2175025	[C/G]	chr1	2175025	Cc01_g01400:248	exon	NON_SYNONYMOUS_CODING	cCt/cGt	P/R	25.0%	4	CC	CC	CG	CG
-chr1:2175026	[T/C]	chr1	2175026	Cc01_g01400:249	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	25.0%	4	TT	TT	TC	TC
-chr1:2175072	[A/C]	chr1	2175072	Cc01_g01400:295	exon	NON_SYNONYMOUS_CODING	Aag/Cag	K/Q	12.5%	4	AA	AC	AA	AA
-chr1:2175151	[T/G]	chr1	2175151	Cc01_g01400:374	exon	NON_SYNONYMOUS_CODING	cTt/cGt	L/R	12.5%	4	TT	TT	TT	TG
-chr1:2175157	[C/A]	chr1	2175157	Cc01_g01400:380	exon	NON_SYNONYMOUS_CODING	gCg/gAg	A/E	12.5%	4	CC	CC	CC	AC
-chr1:2175167	[C/T]	chr1	2175167	Cc01_g01400:390	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CC	CC	TC
-chr1:2175183	[A/G]	chr1	2175183	Cc01_g01400:406	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	12.5%	4	AA	AG	AA	AA
-chr1:2175248	[C/T]	chr1	2175248	Cc01_g01400:471	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	33.3%	3	CC	TT	NN	TT
-chr1:2175317	[A/C]	chr1	2175317	Cc01_g01400:540	exon	SYNONYMOUS_CODING	gtA/gtC	V/V	12.5%	4	AA	AA	AA	AC
-chr1:2175371	[T/C]	chr1	2175371	Cc01_g01400:594	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	TT	TT	TT	TC
-chr1:2175512	[C/T]	chr1	2175512	Cc01_g01400:735	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CC	CC	CT
-chr1:2175561	[G/T]	chr1	2175561	Cc01_g01400:784	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	25.0%	4	GG	TT	GG	GG
-chr1:2175562	[C/G]	chr1	2175562	Cc01_g01400:785	exon	NON_SYNONYMOUS_CODING	gCt/gGt	A/G	25.0%	4	CC	GG	CC	CC
-chr1:2175613	[G/T]	chr1	2175613	Cc01_g01400:836	exon	NON_SYNONYMOUS_CODING	cGt/cTt	R/L	25.0%	4	GG	GG	GG	TT
-chr1:2175705	[T/A]	chr1	2175705	Cc01_g01400:928	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	12.5%	4	TT	TT	TA	TT
-chr1:2175977	[G/A]	chr1	2175977	Cc01_g01400:1088	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	12.5%	4	GG	GG	GG	GA
-chr1:2176009	[G/A]	chr1	2176009	Cc01_g01400:1120	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	GG	GA	GG	GG
-chr1:2176010	[A/C]	chr1	2176010	Cc01_g01400:1121	exon	NON_SYNONYMOUS_CODING	gAt/gCt	D/A	12.5%	4	AA	AC	AA	AA
-chr1:2176046	[C/A]	chr1	2176046	Cc01_g01400:1157	exon	NON_SYNONYMOUS_CODING	aCg/aAg	T/K	12.5%	4	CC	CA	CC	CC
-chr1:2176075	[G/C]	chr1	2176075	Cc01_g01400:1186	exon	NON_SYNONYMOUS_CODING	Gtg/Ctg	V/L	12.5%	4	GG	GG	GC	GG
-chr1:2176085	[G/A]	chr1	2176085	Cc01_g01400:1196	exon	NON_SYNONYMOUS_CODING	aGc/aAc	S/N	12.5%	4	GG	GG	GA	GG
-chr1:2176089	[A/G]	chr1	2176089	Cc01_g01400:1200	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	AA	AG	AA
-chr1:2176098	[C/T]	chr1	2176098	Cc01_g01400:1209	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	CC	CT	CC	CC
-chr1:2176099	[G/A]	chr1	2176099	Cc01_g01400:1210	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	12.5%	4	GG	AG	GG	GG
-chr1:2176255	[G/A]	chr1	2176255	Cc01_g01400:1285	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	GA	GG	GG
-chr1:2176279	[T/A]	chr1	2176279	Cc01_g01400:1309	exon	NON_SYNONYMOUS_CODING	Tgc/Agc	C/S	12.5%	4	TT	TT	TT	TA
-chr1:2176311	[C/A]	chr1	2176311	Cc01_g01400:1341	exon	SYNONYMOUS_CODING	atC/atA	I/I	12.5%	4	CC	CA	CC	CC
-chr1:2176321	[G/A]	chr1	2176321	Cc01_g01400:1351	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	37.5%	4	GG	AA	AA	GA
-chr1:2176345	[C/G]	chr1	2176345	Cc01_g01400:1375	exon	NON_SYNONYMOUS_CODING	Cta/Gta	L/V	12.5%	4	CC	CG	CC	CC
-chr1:2176383	[A/G]	chr1	2176383	Cc01_g01400:1413	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AG	AA	AA
-chr1:2176387	[A/T]	chr1	2176387	Cc01_g01400:1417	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	12.5%	4	AA	AT	AA	AA
-chr1:2177071	[T/G]	chr1	2177071	Cc01_g01410:37	exon	NON_SYNONYMOUS_CODING	Tgt/Ggt	C/G	33.3%	3	TT	GG	NN	TT
-chr1:2177072	[G/T]	chr1	2177072	Cc01_g01410:38	exon	NON_SYNONYMOUS_CODING	tGt/tTt	C/F	33.3%	3	GG	GG	NN	TT
-chr1:2177953	[T/C]	chr1	2177953	Cc01_g01410:198	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	50.0%	2	TT	NN	NN	CC
-chr1:2185597	[C/A]	chr1	2185597	Cc01_g01420:45	exon	SYNONYMOUS_CODING	tcG/tcT	S/S	25.0%	4	CC	CA	CC	CA
-chr1:2185587	[T/C]	chr1	2185587	Cc01_g01420:55	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	12.5%	4	TT	TC	TT	TT
-chr1:2185534	[T/C]	chr1	2185534	Cc01_g01420:108	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	TT	TT	TC	TT
-chr1:2185452	[G/C]	chr1	2185452	Cc01_g01420:190	exon	NON_SYNONYMOUS_CODING	Cat/Gat	H/D	12.5%	4	GG	GG	GC	GG
-chr1:2185431	[T/C]	chr1	2185431	Cc01_g01420:211	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	12.5%	4	TT	TT	TT	TC
-chr1:2185418	[T/C]	chr1	2185418	Cc01_g01420:224	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	12.5%	4	TT	TT	CT	TT
-chr1:2185408	[C/T]	chr1	2185408	Cc01_g01420:234	exon	SYNONYMOUS_CODING	agG/agA	R/R	37.5%	4	CC	TT	TT	CT
-chr1:2185315	[A/C]	chr1	2185315	Cc01_g01420:327	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	12.5%	4	AA	AA	AA	AC
-chr1:2185281	[A/G]	chr1	2185281	Cc01_g01420:361	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	AA	AG	AA	AA
-chr1:2185274	[G/T]	chr1	2185274	Cc01_g01420:368	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	25.0%	4	GG	GG	TT	GG
-chr1:2185232	[C/T]	chr1	2185232	Cc01_g01420:410	exon	NON_SYNONYMOUS_CODING	gGg/gAg	G/E	12.5%	4	CC	CC	CT	CC
-chr1:2185228	[A/T]	chr1	2185228	Cc01_g01420:414	exon	SYNONYMOUS_CODING	atT/atA	I/I	12.5%	4	AA	AA	TA	AA
-chr1:2185186	[A/G]	chr1	2185186	Cc01_g01420:456	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	AA	AG	AA	AA
-chr1:2185185	[T/A]	chr1	2185185	Cc01_g01420:457	exon	NON_SYNONYMOUS_CODING	Att/Ttt	I/F	25.0%	4	TT	AT	TT	TA
-chr1:2185150	[A/G]	chr1	2185150	Cc01_g01420:492	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	AA	GA	AA	AG
-chr1:2185136	[T/G]	chr1	2185136	Cc01_g01420:506	exon	NON_SYNONYMOUS_CODING	aAc/aCc	N/T	12.5%	4	TT	TG	TT	TT
-chr1:2185131	[A/T]	chr1	2185131	Cc01_g01420:511	exon	NON_SYNONYMOUS_CODING	Tgg/Agg	W/R	50.0%	4	AA	TT	AT	AT
-chr1:2185130	[C/G]	chr1	2185130	Cc01_g01420:512	exon	NON_SYNONYMOUS_CODING	tGg/tCg	W/S	50.0%	4	CC	GG	CG	CG
-chr1:2185056	[C/T]	chr1	2185056	Cc01_g01420:586	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	CC	CT	CC	CC
-chr1:2185024	[C/G]	chr1	2185024	Cc01_g01420:618	exon	SYNONYMOUS_CODING	cgG/cgC	R/R	12.5%	4	CC	CC	CG	CC
-chr1:2184985	[C/T]	chr1	2184985	Cc01_g01420:657	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	12.5%	4	CC	CC	CT	CC
-chr1:2184978	[A/G]	chr1	2184978	Cc01_g01420:664	exon	NON_SYNONYMOUS_CODING	Tat/Cat	Y/H	12.5%	4	AA	AA	AG	AA
-chr1:2184967	[C/T]	chr1	2184967	Cc01_g01420:675	exon	SYNONYMOUS_CODING	agG/agA	R/R	12.5%	4	CC	CC	CT	CC
-chr1:2184923	[T/C]	chr1	2184923	Cc01_g01420:719	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	12.5%	4	TT	TT	TC	TT
-chr1:2184900	[G/A]	chr1	2184900	Cc01_g01420:742	exon	NON_SYNONYMOUS_CODING	Ctc/Ttc	L/F	12.5%	4	GG	GG	GA	GG
-chr1:2184858	[C/T]	chr1	2184858	Cc01_g01420:784	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	CC	CC	CT	CC
-chr1:2184847	[T/G]	chr1	2184847	Cc01_g01420:795	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	12.5%	4	TT	TT	TG	TT
-chr1:2184843	[A/G]	chr1	2184843	Cc01_g01420:799	exon	NON_SYNONYMOUS_CODING	Ttt/Ctt	F/L	25.0%	4	AA	GG	GG	GG
-chr1:2184715	[A/G]	chr1	2184715	Cc01_g01420:927	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AG	AA	AA
-chr1:2184631	[A/G]	chr1	2184631	Cc01_g01420:1011	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	12.5%	4	AA	AG	AA	AA
-chr1:2184436	[C/T]	chr1	2184436	Cc01_g01420:1087	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	37.5%	4	CC	TT	CT	TT
-chr1:2184420	[C/T]	chr1	2184420	Cc01_g01420:1103	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	CC	CC	TC	CC
-chr1:2184375	[A/C]	chr1	2184375	Cc01_g01420:1148	exon	NON_SYNONYMOUS_CODING	tTt/tGt	F/C	25.0%	4	AA	CC	CC	CC
-chr1:2184365	[C/T]	chr1	2184365	Cc01_g01420:1158	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	12.5%	4	CC	CC	CC	CT
-chr1:2184361	[T/C]	chr1	2184361	Cc01_g01420:1162	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	50.0%	4	TT	CC	CC	TT
-chr1:2184164	[T/A]	chr1	2184164	Cc01_g01420:1280	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	37.5%	4	TT	AA	AA	AT
-chr1:2184085	[C/T]	chr1	2184085	Cc01_g01420:1359	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	25.0%	4	CC	CC	TT	CC
-chr1:2184069	[A/G]	chr1	2184069	Cc01_g01420:1375	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	AA	GG	GG	GG
-chr1:2184058	[T/A]	chr1	2184058	Cc01_g01420:1386	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	TT	AA	AA	AA
-chr1:2184010	[T/C]	chr1	2184010	Cc01_g01420:1434	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	12.5%	4	TT	TT	TT	TC
-chr1:2183902	[T/C]	chr1	2183902	Cc01_g01420:1542	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	TT	CC	CC	CC
-chr1:2191614	[T/C]	chr1	2191614	Cc01_g01430:14	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	37.5%	4	TT	TC	TC	TC
-chr1:2190583	[G/T]	chr1	2190583	Cc01_g01430:511	exon	NON_SYNONYMOUS_CODING	Ctc/Atc	L/I	25.0%	4	GG	GT	GG	GT
-chr1:2190560	[C/G]	chr1	2190560	Cc01_g01430:534	exon	SYNONYMOUS_CODING	gtG/gtC	V/V	12.5%	4	CC	CC	CC	GC
-chr1:2190508	[A/G]	chr1	2190508	Cc01_g01430:586	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	AA	AG	AA	AA
-chr1:2190494	[A/G]	chr1	2190494	Cc01_g01430:600	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	25.0%	4	AA	AG	AG	AA
-chr1:2189807	[A/T]	chr1	2189807	Cc01_g01430:897	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	25.0%	4	AA	AT	AT	AA
-chr1:2189651	[T/C]	chr1	2189651	Cc01_g01430:1053	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	37.5%	4	TT	CC	TC	CC
-chr1:2189636	[A/G]	chr1	2189636	Cc01_g01430:1068	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	AA	GG	GG	GG
-chr1:2189634	[A/T]	chr1	2189634	Cc01_g01430:1070	exon	NON_SYNONYMOUS_CODING	aTt/aAt	I/N	12.5%	4	AA	AA	TA	AA
-chr1:2188570	[T/C]	chr1	2188570	Cc01_g01430:1166	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	12.5%	4	TT	TT	TC	TT
-chr1:2188551	[A/G]	chr1	2188551	Cc01_g01430:1185	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AA	AG	AA
-chr1:2196422	[A/G]	chr1	2196422	Cc01_g01440:36	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	25.0%	4	AA	AG	AA	AG
-chr1:2196341	[T/C]	chr1	2196341	Cc01_g01440:117	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	TT	TC	TC	TC
-chr1:2196333	[G/C]	chr1	2196333	Cc01_g01440:125	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	12.5%	4	GG	CG	GG	GG
-chr1:2196286	[C/A]	chr1	2196286	Cc01_g01440:172	exon	NON_SYNONYMOUS_CODING	Gca/Tca	A/S	37.5%	4	CC	AA	CC	CA
-chr1:2196284	[T/G]	chr1	2196284	Cc01_g01440:174	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	12.5%	4	TT	GT	TT	TT
-chr1:2196257	[A/G]	chr1	2196257	Cc01_g01440:201	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	AA	GG	AA	AA
-chr1:2196212	[A/G]	chr1	2196212	Cc01_g01440:246	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	AA	AA	AG	AA
-chr1:2196172	[A/G]	chr1	2196172	Cc01_g01440:286	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	25.0%	4	AA	AA	GG	AA
-chr1:2196160	[A/G]	chr1	2196160	Cc01_g01440:298	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	37.5%	4	AA	GG	AA	AG
-chr1:2196140	[A/G]	chr1	2196140	Cc01_g01440:318	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	25.0%	4	AA	AA	GG	AA
-chr1:2196134	[G/C]	chr1	2196134	Cc01_g01440:324	exon	NON_SYNONYMOUS_CODING	caC/caG	H/Q	12.5%	4	GG	GC	GG	GG
-chr1:2196132	[C/T]	chr1	2196132	Cc01_g01440:326	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	12.5%	4	CC	CT	CC	CC
-chr1:2196068	[T/A]	chr1	2196068	Cc01_g01440:390	exon	NON_SYNONYMOUS_CODING	ttA/ttT	L/F	37.5%	4	TT	TA	TA	TA
-chr1:2196065	[T/C]	chr1	2196065	Cc01_g01440:393	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	37.5%	4	TT	TC	TC	TC
-chr1:2195449	[A/G]	chr1	2195449	Cc01_g01440:536	exon	NON_SYNONYMOUS_CODING	tTa/tCa	L/S	12.5%	4	AA	AA	AA	AG
-chr1:2195438	[T/A]	chr1	2195438	Cc01_g01440:547	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	37.5%	4	TT	TA	TA	TA
-chr1:2195424	[C/A]	chr1	2195424	Cc01_g01440:561	exon	SYNONYMOUS_CODING	ctG/ctT	L/L	25.0%	4	CC	CA	CA	CC
-chr1:2195362	[G/A]	chr1	2195362	Cc01_g01440:623	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	25.0%	4	GG	AG	GG	GA
-chr1:2195350	[A/G]	chr1	2195350	Cc01_g01440:635	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	12.5%	4	AA	AA	AA	AG
-chr1:2195327	[T/C]	chr1	2195327	Cc01_g01440:658	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	TT	CT	TT	TC
-chr1:2195242	[C/G]	chr1	2195242	Cc01_g01440:743	exon	NON_SYNONYMOUS_CODING	gGa/gCa	G/A	12.5%	4	CC	CG	CC	CC
-chr1:2195189	[A/G]	chr1	2195189	Cc01_g01440:796	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	12.5%	4	AA	GA	AA	AA
-chr1:2195153	[T/C]	chr1	2195153	Cc01_g01440:832	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	37.5%	4	TT	TT	TC	CC
-chr1:2195139	[A/G]	chr1	2195139	Cc01_g01440:846	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	AA	AG	AA	AA
-chr1:2194136	[C/T]	chr1	2194136	Cc01_g01440:878	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	CC	TC	CC	CC
-chr1:2194114	[G/A]	chr1	2194114	Cc01_g01440:900	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	25.0%	4	GG	AA	AA	AA
-chr1:2194101	[G/T]	chr1	2194101	Cc01_g01440:913	exon	NON_SYNONYMOUS_CODING	Caa/Aaa	Q/K	12.5%	4	GG	TG	GG	GG
-chr1:2194096	[T/G]	chr1	2194096	Cc01_g01440:918	exon	SYNONYMOUS_CODING	tcA/tcC	S/S	12.5%	4	TT	TG	TT	TT
-chr1:2194092	[C/T]	chr1	2194092	Cc01_g01440:922	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	CC	TC	CC	CC
-chr1:2194052	[T/A]	chr1	2194052	Cc01_g01440:962	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	12.5%	4	TT	TT	TA	TT
-chr1:2193981	[A/G]	chr1	2193981	Cc01_g01440:1033	exon	NON_SYNONYMOUS_CODING	Tac/Cac	Y/H	12.5%	4	AA	AG	AA	AA
-chr1:2193975	[T/C]	chr1	2193975	Cc01_g01440:1039	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	12.5%	4	TT	TT	TC	TT
-chr1:2193955	[C/A]	chr1	2193955	Cc01_g01440:1059	exon	SYNONYMOUS_CODING	gcG/gcT	A/A	37.5%	4	CC	AA	CC	CA
-chr1:2209238	[C/T]	chr1	2209238	Cc01_g01450:478	exon	NON_SYNONYMOUS_CODING	Ggt/Agt	G/S	25.0%	4	CC	CC	CC	TT
-chr1:2209206	[G/T]	chr1	2209206	Cc01_g01450:510	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	33.3%	3	GG	GG	TT	NN
-chr1:2208545	[T/C]	chr1	2208545	Cc01_g01450:868	exon	NON_SYNONYMOUS_CODING	Agc/Ggc	S/G	12.5%	4	TT	TC	TT	TT
-chr1:2208543	[G/T]	chr1	2208543	Cc01_g01450:870	exon	NON_SYNONYMOUS_CODING	agC/agA	S/R	12.5%	4	GG	GT	GG	GG
-chr1:2208524	[T/A]	chr1	2208524	Cc01_g01450:889	exon	NON_SYNONYMOUS_CODING	Aat/Tat	N/Y	12.5%	4	TT	TA	TT	TT
-chr1:2208480	[C/T]	chr1	2208480	Cc01_g01450:933	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	CC	CT	CC	CC
-chr1:2208471	[A/G]	chr1	2208471	Cc01_g01450:942	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	12.5%	4	AA	GA	AA	AA
-chr1:2208398	[C/T]	chr1	2208398	Cc01_g01450:1015	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	33.3%	3	CC	TT	NN	TT
-chr1:2208295	[T/G]	chr1	2208295	Cc01_g01450:1118	exon	NON_SYNONYMOUS_CODING	aAt/aCt	N/T	12.5%	4	TT	TG	TT	TT
-chr1:2208265	[G/A]	chr1	2208265	Cc01_g01450:1148	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	12.5%	4	GG	GA	GG	GG
-chr1:2208247	[G/T]	chr1	2208247	Cc01_g01450:1166	exon	NON_SYNONYMOUS_CODING	cCa/cAa	P/Q	25.0%	4	GG	GT	GG	GT
-chr1:2208199	[T/A]	chr1	2208199	Cc01_g01450:1214	exon	NON_SYNONYMOUS_CODING	aAc/aTc	N/I	12.5%	4	TT	TT	TA	TT
-chr1:2208185	[C/T]	chr1	2208185	Cc01_g01450:1228	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	12.5%	4	CC	CC	TC	CC
-chr1:2208178	[T/C]	chr1	2208178	Cc01_g01450:1235	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	12.5%	4	TT	TT	TC	TT
-chr1:2208133	[G/A]	chr1	2208133	Cc01_g01450:1280	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	12.5%	4	GG	GA	GG	GG
-chr1:2274354	[C/T]	chr1	2274354	Cc01_g01460:831	exon	SYNONYMOUS_CODING	atC/atT	I/I	33.3%	3	CC	TT	NN	TT
-chr1:2274363	[T/C]	chr1	2274363	Cc01_g01460:840	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	33.3%	3	TT	CC	NN	CC
-chr1:2274385	[G/C]	chr1	2274385	Cc01_g01460:862	exon	NON_SYNONYMOUS_CODING	Gac/Cac	D/H	33.3%	3	GG	CC	NN	CC
-chr1:2274390	[A/T]	chr1	2274390	Cc01_g01460:867	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	33.3%	3	AA	AA	NN	TT
-chr1:2274408	[A/C]	chr1	2274408	Cc01_g01460:885	exon	SYNONYMOUS_CODING	atA/atC	I/I	50.0%	2	AA	NN	NN	CC
-chr1:2274417	[C/T]	chr1	2274417	Cc01_g01460:894	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	33.3%	3	CC	TT	NN	TT
-chr1:2300221	[C/T]	chr1	2300221	Cc01_g01470:1228	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	2	CC	NN	NN	TT
-chr1:2300215	[T/C]	chr1	2300215	Cc01_g01470:1234	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	50.0%	2	TT	NN	NN	CC
-chr1:2300214	[G/A]	chr1	2300214	Cc01_g01470:1235	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	50.0%	2	GG	NN	NN	AA
-chr1:2343380	[T/C]	chr1	2343380	Cc01_g01490:11	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	12.5%	4	TT	TT	TT	TC
-chr1:2343353	[T/C]	chr1	2343353	Cc01_g01490:38	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	25.0%	4	TT	CC	CC	CC
-chr1:2343351	[G/C]	chr1	2343351	Cc01_g01490:40	exon	NON_SYNONYMOUS_CODING	Ccc/Gcc	P/A	25.0%	4	GG	CC	CC	CC
-chr1:2343348	[T/C]	chr1	2343348	Cc01_g01490:43	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	25.0%	4	TT	CC	CC	CC
-chr1:2343347	[A/G]	chr1	2343347	Cc01_g01490:44	exon	NON_SYNONYMOUS_CODING	aTg/aCg	M/T	25.0%	4	AA	GG	GG	GG
-chr1:2343346	[C/T]	chr1	2343346	Cc01_g01490:45	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	37.5%	4	CC	CC	TT	TC
-chr1:2343313	[A/G]	chr1	2343313	Cc01_g01490:78	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	37.5%	4	AA	AA	GG	GA
-chr1:2343300	[G/A]	chr1	2343300	Cc01_g01490:91	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	GG	GG	GG	AG
-chr1:2343296	[C/T]	chr1	2343296	Cc01_g01490:95	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	25.0%	4	CC	TT	TT	TT
-chr1:2343283	[A/G]	chr1	2343283	Cc01_g01490:108	exon	SYNONYMOUS_CODING	atT/atC	I/I	50.0%	4	AA	AG	AG	GG
-chr1:2343280	[T/G]	chr1	2343280	Cc01_g01490:111	exon	SYNONYMOUS_CODING	acA/acC	T/T	50.0%	4	TT	TG	TG	GG
-chr1:2343274	[A/C]	chr1	2343274	Cc01_g01490:117	exon	SYNONYMOUS_CODING	gcT/gcG	A/A	25.0%	4	AA	AA	AC	CA
-chr1:2343261	[C/A]	chr1	2343261	Cc01_g01490:130	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	37.5%	4	CC	CA	CC	AA
-chr1:2343259	[C/G]	chr1	2343259	Cc01_g01490:132	exon	SYNONYMOUS_CODING	gtG/gtC	V/V	37.5%	4	CC	CG	CC	GG
-chr1:2343244	[G/T]	chr1	2343244	Cc01_g01490:147	exon	NON_SYNONYMOUS_CODING	caC/caA	H/Q	25.0%	4	GG	GG	GG	TT
-chr1:2343241	[T/G]	chr1	2343241	Cc01_g01490:150	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	37.5%	4	TT	TT	TG	GG
-chr1:2343235	[G/C]	chr1	2343235	Cc01_g01490:156	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	37.5%	4	GG	GG	GC	CC
-chr1:2343232	[A/C]	chr1	2343232	Cc01_g01490:159	exon	SYNONYMOUS_CODING	ggT/ggG	G/G	37.5%	4	AA	AA	AC	CC
-chr1:2343229	[A/T]	chr1	2343229	Cc01_g01490:162	exon	SYNONYMOUS_CODING	tcT/tcA	S/S	37.5%	4	AA	AA	AT	TT
-chr1:2343225	[T/C]	chr1	2343225	Cc01_g01490:166	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	37.5%	4	TT	TT	TC	CC
-chr1:2343092	[T/C]	chr1	2343092	Cc01_g01490:299	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	25.0%	4	TT	TT	TT	CC
-chr1:2342875	[G/A]	chr1	2342875	Cc01_g01490:516	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	33.3%	3	GG	AA	NN	AA
-chr1:2342772	[C/T]	chr1	2342772	Cc01_g01490:619	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	4	CC	TT	CC	CC
-chr1:2342382	[C/T]	chr1	2342382	Cc01_g01490:636	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	33.3%	3	CC	TT	NN	CC
-chr1:2342352	[A/T]	chr1	2342352	Cc01_g01490:666	exon	SYNONYMOUS_CODING	atT/atA	I/I	37.5%	4	AA	TT	TT	AT
-chr1:2342154	[T/G]	chr1	2342154	Cc01_g01490:774	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	37.5%	4	TT	TT	TG	GG
-chr1:2342153	[A/G]	chr1	2342153	Cc01_g01490:775	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	37.5%	4	AA	AA	AG	GG
-chr1:2342152	[C/T]	chr1	2342152	Cc01_g01490:776	exon	STOP_GAINED	tGg/tAg	W/9	37.5%	4	CC	CC	CT	TT
-chr1:2342133	[G/A]	chr1	2342133	Cc01_g01490:795	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	50.0%	4	GG	GA	GA	AA
-chr1:2342078	[G/A]	chr1	2342078	Cc01_g01490:850	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	25.0%	4	GG	AA	AA	AA
-chr1:2342048	[C/A]	chr1	2342048	Cc01_g01490:880	exon	NON_SYNONYMOUS_CODING	Gtc/Ttc	V/F	25.0%	4	CC	AA	AA	AA
-chr1:2342034	[A/G]	chr1	2342034	Cc01_g01490:894	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	25.0%	4	AA	GG	GG	GG
-chr1:2342013	[T/G]	chr1	2342013	Cc01_g01490:915	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	25.0%	4	TT	GG	GG	GG
-chr1:2342007	[T/A]	chr1	2342007	Cc01_g01490:921	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	12.5%	4	TT	TT	TT	TA
-chr1:2342001	[G/T]	chr1	2342001	Cc01_g01490:927	exon	SYNONYMOUS_CODING	atC/atA	I/I	37.5%	4	GG	TT	GT	TT
-chr1:2341971	[A/G]	chr1	2341971	Cc01_g01490:957	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	AA	AA	AG	AA
-chr1:2341944	[T/C]	chr1	2341944	Cc01_g01490:984	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	50.0%	4	TT	TC	TC	CC
-chr1:2341934	[C/T]	chr1	2341934	Cc01_g01490:994	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	50.0%	4	CC	CT	CT	TT
-chr1:2341930	[A/C]	chr1	2341930	Cc01_g01490:998	exon	NON_SYNONYMOUS_CODING	gTc/gGc	V/G	37.5%	4	AA	AC	AA	CC
-chr1:2341921	[C/T]	chr1	2341921	Cc01_g01490:1007	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	37.5%	4	CC	CT	CC	TT
-chr1:2341915	[G/A]	chr1	2341915	Cc01_g01490:1013	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	37.5%	4	GG	GA	GG	AA
-chr1:2341914	[T/G]	chr1	2341914	Cc01_g01490:1014	exon	SYNONYMOUS_CODING	acA/acC	T/T	37.5%	4	TT	TG	TT	GG
-chr1:2341905	[G/A]	chr1	2341905	Cc01_g01490:1023	exon	SYNONYMOUS_CODING	agC/agT	S/S	50.0%	4	GG	GA	GA	AA
-chr1:2341899	[A/G]	chr1	2341899	Cc01_g01490:1029	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	50.0%	4	AA	AG	AG	GG
-chr1:2341885	[G/A]	chr1	2341885	Cc01_g01490:1043	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	25.0%	4	GG	AA	AA	AA
-chr1:2341855	[C/T]	chr1	2341855	Cc01_g01490:1073	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	25.0%	4	CC	TT	TT	TT
-chr1:2341853	[A/G]	chr1	2341853	Cc01_g01490:1075	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	25.0%	4	AA	GG	GG	GG
-chr1:2341843	[T/G]	chr1	2341843	Cc01_g01490:1085	exon	NON_SYNONYMOUS_CODING	aAt/aCt	N/T	25.0%	4	TT	GG	GG	GG
-chr1:2341816	[C/T]	chr1	2341816	Cc01_g01490:1112	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	25.0%	4	CC	TT	TT	TT
-chr1:2341814	[G/C]	chr1	2341814	Cc01_g01490:1114	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	25.0%	4	GG	CC	CC	CC
-chr1:2341761	[A/G]	chr1	2341761	Cc01_g01490:1167	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	25.0%	4	AA	GG	GG	GG
-chr1:2341752	[T/G]	chr1	2341752	Cc01_g01490:1176	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	25.0%	4	TT	GG	GG	GG
-chr1:2341742	[G/A]	chr1	2341742	Cc01_g01490:1186	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	25.0%	4	GG	AA	AA	AA
-chr1:2341734	[T/C]	chr1	2341734	Cc01_g01490:1194	exon	SYNONYMOUS_CODING	agA/agG	R/R	50.0%	4	TT	TC	TC	CC
-chr1:2341733	[G/T]	chr1	2341733	Cc01_g01490:1195	exon	NON_SYNONYMOUS_CODING	Cat/Aat	H/N	50.0%	4	GG	GT	GT	TT
-chr1:2341731	[A/C]	chr1	2341731	Cc01_g01490:1197	exon	NON_SYNONYMOUS_CODING	caT/caG	H/Q	50.0%	4	AA	AC	AC	CC
-chr1:2341728	[G/A]	chr1	2341728	Cc01_g01490:1200	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	50.0%	4	GG	GA	GA	AA
-chr1:2341719	[C/G]	chr1	2341719	Cc01_g01490:1209	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	25.0%	4	CC	GG	GG	GG
-chr1:2341697	[T/C]	chr1	2341697	Cc01_g01490:1231	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	12.5%	4	TT	TT	TT	TC
-chr1:2341685	[C/G]	chr1	2341685	Cc01_g01490:1243	exon	NON_SYNONYMOUS_CODING	Gta/Cta	V/L	12.5%	4	CC	CG	CC	CC
-chr1:2340685	[G/A]	chr1	2340685	Cc01_g01490:1261	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	25.0%	4	GG	AA	AA	AA
-chr1:2340667	[T/C]	chr1	2340667	Cc01_g01490:1279	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	25.0%	4	TT	CC	CC	CC
-chr1:2334881	[A/G]	chr1	2334881	Cc01_g01490:1362	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	AA	AA	AG	AA
-chr1:2334835	[T/C]	chr1	2334835	Cc01_g01490:1408	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	37.5%	4	TT	CC	CT	CC
-chr1:2334831	[G/T]	chr1	2334831	Cc01_g01490:1412	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	50.0%	4	GG	GT	TG	TT
-chr1:2334799	[A/C]	chr1	2334799	Cc01_g01490:1444	exon	NON_SYNONYMOUS_CODING	Tta/Gta	L/V	25.0%	4	AA	AC	AA	AC
-chr1:2334780	[A/T]	chr1	2334780	Cc01_g01490:1463	exon	NON_SYNONYMOUS_CODING	tTc/tAc	F/Y	12.5%	4	AA	TA	AA	AA
-chr1:2334662	[A/T]	chr1	2334662	Cc01_g01490:1581	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	12.5%	4	AA	AA	AT	AA
-chr1:2334642	[G/T]	chr1	2334642	Cc01_g01490:1601	exon	NON_SYNONYMOUS_CODING	aCt/aAt	T/N	37.5%	4	GG	TT	GT	TT
-chr1:2334620	[A/C]	chr1	2334620	Cc01_g01490:1623	exon	NON_SYNONYMOUS_CODING	atT/atG	I/M	12.5%	4	AA	AA	AA	AC
-chr1:2334584	[G/A]	chr1	2334584	Cc01_g01490:1659	exon	SYNONYMOUS_CODING	atC/atT	I/I	37.5%	4	GG	AA	GA	AA
-chr1:2334185	[G/A]	chr1	2334185	Cc01_g01490:1719	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	GG	GG	GG	GA
-chr1:2334144	[C/G]	chr1	2334144	Cc01_g01490:1760	exon	NON_SYNONYMOUS_CODING	aGt/aCt	S/T	50.0%	4	CC	GG	CC	GG
-chr1:2334140	[A/C]	chr1	2334140	Cc01_g01490:1764	exon	NON_SYNONYMOUS_CODING	atT/atG	I/M	12.5%	4	AA	AC	AA	AA
-chr1:2334026	[T/C]	chr1	2334026	Cc01_g01490:1878	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	TT	TC	TT	TC
-chr1:2333864	[T/C]	chr1	2333864	Cc01_g01490:1978	exon	NON_SYNONYMOUS_CODING	Agg/Ggg	R/G	50.0%	4	TT	CC	TC	TC
-chr1:2360212	[G/A]	chr1	2360212	Cc01_g01510:67	exon	NON_SYNONYMOUS_CODING	Gcg/Acg	A/T	33.3%	3	GG	AA	NN	GG
-chr1:2360304	[G/T]	chr1	2360304	Cc01_g01510:159	exon	SYNONYMOUS_CODING	ggG/ggT	G/G	33.3%	3	GG	TT	NN	GG
-chr1:2360308	[C/T]	chr1	2360308	Cc01_g01510:163	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	33.3%	3	CC	TT	NN	CC
-chr1:2360310	[A/G]	chr1	2360310	Cc01_g01510:165	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	33.3%	3	AA	GG	NN	AA
-chr1:2360316	[A/G]	chr1	2360316	Cc01_g01510:171	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	33.3%	3	AA	AA	NN	GG
-chr1:2360324	[G/A]	chr1	2360324	Cc01_g01510:179	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	50.0%	2	GG	AA	NN	NN
-chr1:2360326	[G/A]	chr1	2360326	Cc01_g01510:181	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	50.0%	2	GG	AA	NN	NN
-chr1:2360328	[C/A]	chr1	2360328	Cc01_g01510:183	exon	NON_SYNONYMOUS_CODING	gaC/gaA	D/E	50.0%	2	CC	AA	NN	NN
-chr1:2361074	[C/T]	chr1	2361074	Cc01_g01510:929	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	16.7%	3	CC	CC	NN	CT
-chr1:2361629	[A/G]	chr1	2361629	Cc01_g01510:1263	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	50.0%	2	AA	NN	NN	GG
-chr1:2361636	[T/C]	chr1	2361636	Cc01_g01510:1270	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	50.0%	2	TT	NN	NN	CC
-chr1:2361659	[G/A]	chr1	2361659	Cc01_g01510:1293	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	50.0%	2	GG	NN	NN	AA
-chr1:2361716	[G/A]	chr1	2361716	Cc01_g01510:1350	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	50.0%	2	GG	NN	NN	AA
-chr1:2383654	[G/A]	chr1	2383654	Cc01_g01520:42	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	GA	GG	GG
-chr1:2383674	[T/C]	chr1	2383674	Cc01_g01520:62	exon	NON_SYNONYMOUS_CODING	aTc/aCc	I/T	25.0%	4	TT	CC	TT	TT
-chr1:2383681	[C/T]	chr1	2383681	Cc01_g01520:69	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	25.0%	4	CC	TT	CC	CC
-chr1:2383712	[G/A]	chr1	2383712	Cc01_g01520:100	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	GG	GG	GG	GA
-chr1:2383714	[T/C]	chr1	2383714	Cc01_g01520:102	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	TT	TT	TT	TC
-chr1:2383758	[T/C]	chr1	2383758	Cc01_g01520:146	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	25.0%	4	TT	CC	CC	CC
-chr1:2383785	[A/G]	chr1	2383785	Cc01_g01520:173	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	25.0%	4	AA	GG	AA	AA
-chr1:2383795	[C/A]	chr1	2383795	Cc01_g01520:183	exon	NON_SYNONYMOUS_CODING	aaC/aaA	N/K	50.0%	4	CC	AA	CC	AA
-chr1:2383839	[G/A]	chr1	2383839	Cc01_g01520:227	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	25.0%	4	GG	GG	AA	GG
-chr1:2383851	[A/T]	chr1	2383851	Cc01_g01520:239	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	12.5%	4	AA	AT	AA	AA
-chr1:2383866	[C/T]	chr1	2383866	Cc01_g01520:254	exon	NON_SYNONYMOUS_CODING	gCc/gTc	A/V	12.5%	4	CC	CT	CC	CC
-chr1:2383874	[T/A]	chr1	2383874	Cc01_g01520:262	exon	NON_SYNONYMOUS_CODING	Tgc/Agc	C/S	12.5%	4	TT	TA	TT	TT
-chr1:2383920	[G/T]	chr1	2383920	Cc01_g01520:308	exon	NON_SYNONYMOUS_CODING	cGa/cTa	R/L	25.0%	4	GG	GG	TT	GG
-chr1:2383927	[T/C]	chr1	2383927	Cc01_g01520:315	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	25.0%	4	TT	CC	TT	TT
-chr1:2384077	[T/G]	chr1	2384077	Cc01_g01520:465	exon	NON_SYNONYMOUS_CODING	agT/agG	S/R	25.0%	4	TT	TT	TT	GG
-chr1:2384181	[A/G]	chr1	2384181	Cc01_g01520:569	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	12.5%	4	AA	AA	AA	AG
-chr1:2384200	[C/T]	chr1	2384200	Cc01_g01520:588	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	25.0%	4	CC	CC	TT	CC
-chr1:2384756	[T/G]	chr1	2384756	Cc01_g01520:1041	exon	NON_SYNONYMOUS_CODING	agT/agG	S/R	12.5%	4	TT	TG	TT	TT
-chr1:2385308	[T/C]	chr1	2385308	Cc01_g01520:1470	exon	SYNONYMOUS_CODING	acT/acC	T/T	12.5%	4	TT	TC	TT	TT
-chr1:2409054	[C/A]	chr1	2409054	Cc01_g01530:78	exon	SYNONYMOUS_CODING	gtC/gtA	V/V	25.0%	4	CC	AA	CC	CC
-chr1:2409092	[T/C]	chr1	2409092	Cc01_g01530:116	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	25.0%	4	TT	CC	TT	TT
-chr1:2409231	[A/C]	chr1	2409231	Cc01_g01530:255	exon	SYNONYMOUS_CODING	tcA/tcC	S/S	16.7%	3	AA	AC	NN	AA
-chr1:2409249	[C/T]	chr1	2409249	Cc01_g01530:273	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	50.0%	3	CC	CT	NN	TT
-chr1:2409678	[A/G]	chr1	2409678	Cc01_g01530:702	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	16.7%	3	AA	NN	AA	AG
-chr1:2409702	[T/C]	chr1	2409702	Cc01_g01530:726	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	37.5%	4	TT	TC	CC	CC
-chr1:2409721	[T/A]	chr1	2409721	Cc01_g01530:745	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	12.5%	4	TT	TT	TT	TA
-chr1:2409726	[C/T]	chr1	2409726	Cc01_g01530:750	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	CC	CC	CC	CT
-chr1:2425980	[A/G]	chr1	2425980	Cc01_g01540:231	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	AA	GG	AG	AA
-chr1:2426360	[G/A]	chr1	2426360	Cc01_g01540:397	exon	NON_SYNONYMOUS_CODING	Ggt/Agt	G/S	37.5%	4	GG	AA	GA	GG
-chr1:2426489	[T/C]	chr1	2426489	Cc01_g01540:526	exon	NON_SYNONYMOUS_CODING	Ttt/Ctt	F/L	12.5%	4	TT	TC	TT	TT
-chr1:2427186	[G/A]	chr1	2427186	Cc01_g01540:843	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	GG	GA	GG	GG
-chr1:2427440	[T/C]	chr1	2427440	Cc01_g01540:936	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	37.5%	4	TT	CC	TC	TT
-chr1:2428201	[A/G]	chr1	2428201	Cc01_g01540:1375	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	37.5%	4	AA	GG	AG	AA
-chr1:2428270	[A/G]	chr1	2428270	Cc01_g01540:1444	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	12.5%	4	AA	AA	AG	AA
-chr1:2429289	[T/A]	chr1	2429289	Cc01_g01540:1547	exon	NON_SYNONYMOUS_CODING	aTg/aAg	M/K	12.5%	4	TT	TA	TT	TT
-chr1:2431687	[G/A]	chr1	2431687	Cc01_g01540:1638	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	GG	GG	GA	GG
-chr1:2432530	[C/T]	chr1	2432530	Cc01_g01540:1850	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	CC	CC	CT	CC
-chr1:2432737	[A/G]	chr1	2432737	Cc01_g01540:1942	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	12.5%	4	AA	AA	AG	AA
-chr1:2433099	[T/C]	chr1	2433099	Cc01_g01540:2141	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	12.5%	4	TT	TT	TC	TT
-chr1:2434119	[T/A]	chr1	2434119	Cc01_g01540:2374	exon	NON_SYNONYMOUS_CODING	Tct/Act	S/T	12.5%	4	TT	TA	TT	TT
-chr1:2434512	[A/G]	chr1	2434512	Cc01_g01540:2553	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	AA	AG	AA	AA
-chr1:2436532	[A/G]	chr1	2436532	Cc01_g01550:172	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	12.5%	4	AA	AG	AA	AA
-chr1:2436544	[G/A]	chr1	2436544	Cc01_g01550:184	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	12.5%	4	GG	AG	GG	GG
-chr1:2436558	[G/A]	chr1	2436558	Cc01_g01550:198	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	GG	AA	GG	GG
-chr1:2436572	[G/A]	chr1	2436572	Cc01_g01550:212	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	12.5%	4	GG	GA	GG	GG
-chr1:2439858	[T/C]	chr1	2439858	Cc01_g01550:505	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	25.0%	4	TT	TC	TT	TC
-chr1:2440047	[T/C]	chr1	2440047	Cc01_g01550:597	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	TC	TT	TT
-chr1:2440153	[C/G]	chr1	2440153	Cc01_g01550:703	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	25.0%	4	CC	CG	CC	CG
-chr1:2440191	[A/G]	chr1	2440191	Cc01_g01550:741	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	AA	AA	AA	AG
-chr1:2440206	[A/G]	chr1	2440206	Cc01_g01550:756	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	25.0%	4	AA	AG	AA	AG
-chr1:2444991	[C/G]	chr1	2444991	Cc01_g01560:39	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	25.0%	4	CC	CC	GG	CC
-chr1:2445037	[C/T]	chr1	2445037	Cc01_g01560:85	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	CC	CC	CC	CT
-chr1:2445130	[G/A]	chr1	2445130	Cc01_g01560:178	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	GG	GG	GG	GA
-chr1:2445144	[G/C]	chr1	2445144	Cc01_g01560:192	exon	SYNONYMOUS_CODING	tcG/tcC	S/S	25.0%	4	GG	CC	CC	CC
-chr1:2445153	[C/T]	chr1	2445153	Cc01_g01560:201	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	37.5%	4	CC	CT	CC	TT
-chr1:2445246	[G/A]	chr1	2445246	Cc01_g01560:294	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	37.5%	4	GG	GA	GG	AA
-chr1:2445335	[G/T]	chr1	2445335	Cc01_g01560:383	exon	NON_SYNONYMOUS_CODING	aGt/aTt	S/I	25.0%	4	GG	TT	TT	TT
-chr1:2445435	[T/C]	chr1	2445435	Cc01_g01560:483	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	TT	CC	CC	CC
-chr1:2445449	[C/G]	chr1	2445449	Cc01_g01560:497	exon	NON_SYNONYMOUS_CODING	aCc/aGc	T/S	16.7%	3	CC	CG	CC	NN
-chr1:2445473	[A/G]	chr1	2445473	Cc01_g01560:521	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	16.7%	3	AA	AA	AG	NN
-chr1:2445488	[G/A]	chr1	2445488	Cc01_g01560:536	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	33.3%	3	GG	GG	AA	NN
-chr1:2445537	[A/T]	chr1	2445537	Cc01_g01560:585	exon	SYNONYMOUS_CODING	atA/atT	I/I	16.7%	3	AA	AT	AA	NN
-chr1:2445552	[C/G]	chr1	2445552	Cc01_g01560:600	exon	SYNONYMOUS_CODING	ctC/ctG	L/L	25.0%	4	CC	CC	GG	CC
-chr1:2445610	[G/C]	chr1	2445610	Cc01_g01560:658	exon	NON_SYNONYMOUS_CODING	Gtt/Ctt	V/L	12.5%	4	GG	GC	GG	GG
-chr1:2445684	[G/A]	chr1	2445684	Cc01_g01560:732	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	25.0%	4	GG	AA	AA	AA
-chr1:2445697	[C/G]	chr1	2445697	Cc01_g01560:745	exon	NON_SYNONYMOUS_CODING	Ctt/Gtt	L/V	37.5%	4	CC	CG	CC	GG
-chr1:2445722	[T/G]	chr1	2445722	Cc01_g01560:770	exon	NON_SYNONYMOUS_CODING	gTa/gGa	V/G	37.5%	4	TT	TG	TT	GG
-chr1:2445747	[A/T]	chr1	2445747	Cc01_g01560:795	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	12.5%	4	AA	TA	AA	AA
-chr1:2445750	[T/C]	chr1	2445750	Cc01_g01560:798	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	TT	TT	TT	CC
-chr1:2445796	[A/T]	chr1	2445796	Cc01_g01560:844	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	37.5%	4	AA	AT	AA	TT
-chr1:2445815	[A/G]	chr1	2445815	Cc01_g01560:863	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	16.7%	3	AA	AG	AA	NN
-chr1:2445816	[G/A]	chr1	2445816	Cc01_g01560:864	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	16.7%	3	GG	AG	GG	NN
-chr1:2445827	[G/T]	chr1	2445827	Cc01_g01560:875	exon	NON_SYNONYMOUS_CODING	aGg/aTg	R/M	16.7%	3	GG	GT	GG	NN
-chr1:2483851	[A/G]	chr1	2483851	Cc01_g01570:110	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	50.0%	2	AA	GG	NN	NN
-chr1:2483849	[A/G]	chr1	2483849	Cc01_g01570:112	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	50.0%	2	AA	GG	NN	NN
-chr1:2483845	[A/G]	chr1	2483845	Cc01_g01570:116	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	50.0%	2	AA	GG	NN	NN
-chr1:2524880	[C/T]	chr1	2524880	Cc01_g01600:173	exon	NON_SYNONYMOUS_CODING	aGc/aAc	S/N	12.5%	4	CC	CT	CC	CC
-chr1:2523795	[C/T]	chr1	2523795	Cc01_g01600:1189	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	CC	CC	CT	CC
-chr1:2523742	[G/A]	chr1	2523742	Cc01_g01600:1242	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	16.7%	3	GG	NN	GG	GA
-chr1:2522662	[T/C]	chr1	2522662	Cc01_g01600:2133	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	25.0%	4	TT	TT	CC	TT
-chr1:2522423	[T/A]	chr1	2522423	Cc01_g01600:2279	exon	NON_SYNONYMOUS_CODING	gAt/gTt	D/V	12.5%	4	TT	TT	TT	TA
-chr1:2522420	[A/G]	chr1	2522420	Cc01_g01600:2282	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	AA	AG	AA	AA
-chr1:2522274	[T/C]	chr1	2522274	Cc01_g01600:2428	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	37.5%	4	TT	CC	TT	TC
-chr1:2522265	[A/G]	chr1	2522265	Cc01_g01600:2437	exon	NON_SYNONYMOUS_CODING	Tcc/Ccc	S/P	16.7%	3	AA	NN	AA	GA
-chr1:2522182	[G/C]	chr1	2522182	Cc01_g01600:2439	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	33.3%	3	GG	NN	CC	GG
-chr1:2522124	[G/A]	chr1	2522124	Cc01_g01600:2497	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	25.0%	4	GG	AA	GG	GG
-chr1:2522105	[T/C]	chr1	2522105	Cc01_g01600:2516	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	12.5%	4	TT	TT	TT	TC
-chr1:2522103	[C/T]	chr1	2522103	Cc01_g01600:2518	exon	NON_SYNONYMOUS_CODING	Gta/Ata	V/I	12.5%	4	CC	CC	CT	CC
-chr1:2522070	[G/A]	chr1	2522070	Cc01_g01600:2551	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	25.0%	4	GG	AA	GG	GG
-chr1:2522006	[C/A]	chr1	2522006	Cc01_g01600:2615	exon	NON_SYNONYMOUS_CODING	cGg/cTg	R/L	12.5%	4	CC	CC	CC	CA
-chr1:2521969	[T/C]	chr1	2521969	Cc01_g01600:2652	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	12.5%	4	TT	TT	TT	TC
-chr1:2521892	[T/C]	chr1	2521892	Cc01_g01600:2729	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	25.0%	4	TT	CC	TT	TT
-chr1:2521826	[G/A]	chr1	2521826	Cc01_g01600:2795	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	37.5%	4	GG	GG	AA	GA
-chr1:2521810	[G/C]	chr1	2521810	Cc01_g01600:2811	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	12.5%	4	GG	GG	GG	GC
-chr1:2521773	[A/G]	chr1	2521773	Cc01_g01600:2848	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	25.0%	4	AA	GG	GG	GG
-chr1:2521725	[G/C]	chr1	2521725	Cc01_g01600:2896	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	50.0%	4	GG	CC	GC	GC
-chr1:2521724	[T/A]	chr1	2521724	Cc01_g01600:2897	exon	NON_SYNONYMOUS_CODING	cAg/cTg	Q/L	12.5%	4	TT	TA	TT	TT
-chr1:2521694	[C/A]	chr1	2521694	Cc01_g01600:2927	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	12.5%	4	CC	AC	CC	CC
-chr1:2521672	[T/C]	chr1	2521672	Cc01_g01600:2949	exon	SYNONYMOUS_CODING	ggA/ggG	G/G	12.5%	4	TT	TT	CT	TT
-chr1:2521665	[G/A]	chr1	2521665	Cc01_g01600:2956	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	37.5%	4	GG	GA	GA	GA
-chr1:2521659	[T/C]	chr1	2521659	Cc01_g01600:2962	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	12.5%	4	TT	TC	TT	TT
-chr1:2521567	[C/T]	chr1	2521567	Cc01_g01600:3054	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	12.5%	4	CC	CC	CT	CC
-chr1:2521560	[A/T]	chr1	2521560	Cc01_g01600:3061	exon	NON_SYNONYMOUS_CODING	Tat/Aat	Y/N	12.5%	4	AA	AA	AA	AT
-chr1:2521545	[G/A]	chr1	2521545	Cc01_g01600:3076	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	12.5%	4	GG	GA	GG	GG
-chr1:2521544	[C/G]	chr1	2521544	Cc01_g01600:3077	exon	NON_SYNONYMOUS_CODING	cGt/cCt	R/P	12.5%	4	CC	CC	CG	CC
-chr1:2521538	[G/A]	chr1	2521538	Cc01_g01600:3083	exon	NON_SYNONYMOUS_CODING	aCg/aTg	T/M	12.5%	4	GG	GG	GA	GG
-chr1:2521522	[G/A]	chr1	2521522	Cc01_g01600:3099	exon	SYNONYMOUS_CODING	caC/caT	H/H	12.5%	4	GG	GG	AG	GG
-chr1:2521518	[G/A]	chr1	2521518	Cc01_g01600:3103	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	12.5%	4	GG	GG	AG	GG
-chr1:2521434	[C/T]	chr1	2521434	Cc01_g01600:3187	exon	NON_SYNONYMOUS_CODING	Gcg/Acg	A/T	12.5%	4	CC	CC	CC	CT
-chr1:2521424	[T/C]	chr1	2521424	Cc01_g01600:3197	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	12.5%	4	TT	TT	TT	TC
-chr1:2521409	[A/C]	chr1	2521409	Cc01_g01600:3212	exon	NON_SYNONYMOUS_CODING	tTg/tGg	L/W	37.5%	4	AA	AA	CC	CA
-chr1:2521377	[C/A]	chr1	2521377	Cc01_g01600:3244	exon	NON_SYNONYMOUS_CODING	Gta/Tta	V/L	25.0%	4	CC	CA	CC	CA
-chr1:2521375	[T/C]	chr1	2521375	Cc01_g01600:3246	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	25.0%	4	TT	TC	TT	CT
-chr1:2521230	[G/A]	chr1	2521230	Cc01_g01600:3301	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	GG	GA	AA	GG
-chr1:2520587	[T/C]	chr1	2520587	Cc01_g01600:3322	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	25.0%	4	TT	CC	CC	CC
-chr1:2520583	[C/T]	chr1	2520583	Cc01_g01600:3326	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	CC	CT	CC	CC
-chr1:2520561	[A/G]	chr1	2520561	Cc01_g01600:3348	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	AA	AA	AA	AG
-chr1:2520556	[G/T]	chr1	2520556	Cc01_g01600:3353	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	25.0%	4	GG	TT	TT	TT
-chr1:2520547	[A/G]	chr1	2520547	Cc01_g01600:3362	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	25.0%	4	AA	GG	GG	GG
-chr1:2520537	[T/C]	chr1	2520537	Cc01_g01600:3372	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	TT	TT	TC	TC
-chr1:2520525	[C/T]	chr1	2520525	Cc01_g01600:3384	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	CC	CC	CT	CC
-chr1:2520511	[A/G]	chr1	2520511	Cc01_g01600:3398	exon	NON_SYNONYMOUS_CODING	cTt/cCt	L/P	25.0%	4	AA	GG	GG	GG
-chr1:2526140	[A/T]	chr1	2526140	Cc01_g01610:233	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	25.0%	4	AA	AA	TT	AA
-chr1:2528701	[G/C]	chr1	2528701	Cc01_g01610:265	exon	NON_SYNONYMOUS_CODING	Ggg/Cgg	G/R	33.3%	3	GG	GG	NN	CC
-chr1:2528783	[T/C]	chr1	2528783	Cc01_g01610:347	exon	NON_SYNONYMOUS_CODING	gTc/gCc	V/A	12.5%	4	TT	TT	TT	TC
-chr1:2528803	[T/C]	chr1	2528803	Cc01_g01610:367	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	25.0%	4	TT	TT	TT	CC
-chr1:2528813	[T/C]	chr1	2528813	Cc01_g01610:377	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	12.5%	4	TT	TT	TC	TT
-chr1:2528941	[T/G]	chr1	2528941	Cc01_g01610:433	exon	NON_SYNONYMOUS_CODING	Tac/Gac	Y/D	50.0%	2	TT	NN	NN	GG
-chr1:2528952	[C/G]	chr1	2528952	Cc01_g01610:444	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	25.0%	4	CC	CG	CC	CG
-chr1:2529568	[A/G]	chr1	2529568	Cc01_g01610:557	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	50.0%	2	AA	NN	NN	GG
-chr1:2530078	[A/G]	chr1	2530078	Cc01_g01610:1067	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	37.5%	4	AA	AG	AG	AG
-chr1:2551182	[G/A]	chr1	2551182	Cc01_g01620:26	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	25.0%	4	GG	AA	GG	GG
-chr1:2551151	[G/T]	chr1	2551151	Cc01_g01620:57	exon	SYNONYMOUS_CODING	ctC/ctA	L/L	33.3%	3	GG	TT	NN	GG
-chr1:2551113	[C/T]	chr1	2551113	Cc01_g01620:95	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	37.5%	4	CC	TT	CC	CT
-chr1:2551100	[G/A]	chr1	2551100	Cc01_g01620:108	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	25.0%	4	GG	AA	GG	GG
-chr1:2551069	[T/A]	chr1	2551069	Cc01_g01620:139	exon	NON_SYNONYMOUS_CODING	Agc/Tgc	S/C	25.0%	4	TT	AA	TT	TT
-chr1:2551068	[C/A]	chr1	2551068	Cc01_g01620:140	exon	NON_SYNONYMOUS_CODING	aGc/aTc	S/I	25.0%	4	CC	AA	CC	CC
-chr1:2551000	[T/A]	chr1	2551000	Cc01_g01620:208	exon	NON_SYNONYMOUS_CODING	Agt/Tgt	S/C	12.5%	4	TT	TT	TT	TA
-chr1:2550995	[T/C]	chr1	2550995	Cc01_g01620:213	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	TT	TT	TT	TC
-chr1:2550979	[G/A]	chr1	2550979	Cc01_g01620:229	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	GG	GG	GG	GA
-chr1:2550929	[G/C]	chr1	2550929	Cc01_g01620:279	exon	NON_SYNONYMOUS_CODING	caC/caG	H/Q	12.5%	4	GG	GG	GG	CG
-chr1:2550905	[G/A]	chr1	2550905	Cc01_g01620:303	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	37.5%	4	GG	AA	GG	GA
-chr1:2550878	[T/C]	chr1	2550878	Cc01_g01620:330	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	12.5%	4	TT	TT	TT	TC
-chr1:2550853	[G/A]	chr1	2550853	Cc01_g01620:355	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	33.3%	3	GG	AA	NN	AA
-chr1:2550817	[C/T]	chr1	2550817	Cc01_g01620:391	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	12.5%	4	CC	CC	CC	CT
-chr1:2550788	[A/G]	chr1	2550788	Cc01_g01620:420	exon	SYNONYMOUS_CODING	caT/caC	H/H	37.5%	4	AA	GG	AA	AG
-chr1:2550718	[C/A]	chr1	2550718	Cc01_g01620:490	exon	NON_SYNONYMOUS_CODING	Gtc/Ttc	V/F	33.3%	3	CC	AA	NN	AA
-chr1:2550703	[A/G]	chr1	2550703	Cc01_g01620:505	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	33.3%	3	AA	AA	NN	GG
-chr1:2550656	[A/C]	chr1	2550656	Cc01_g01620:552	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	12.5%	4	AA	AC	AA	AA
-chr1:2550608	[A/G]	chr1	2550608	Cc01_g01620:600	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	50.0%	3	AA	GG	NN	AG
-chr1:2550457	[A/C]	chr1	2550457	Cc01_g01620:751	exon	NON_SYNONYMOUS_CODING	Tgt/Ggt	C/G	33.3%	3	AA	CC	AA	NN
-chr1:2550455	[A/T]	chr1	2550455	Cc01_g01620:753	exon	STOP_GAINED	tgT/tgA	C/1	33.3%	3	AA	TT	AA	NN
-chr1:2550410	[G/A]	chr1	2550410	Cc01_g01620:798	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	33.3%	3	GG	AA	NN	AA
-chr1:2550352	[A/C]	chr1	2550352	Cc01_g01620:856	exon	STOP_LOST	Taa/Gaa	2/E	33.3%	3	AA	CC	AA	NN
-chr1:2565722	[C/G]	chr1	2565722	Cc01_g01630:400	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	12.5%	4	CC	CG	CC	CC
-chr1:2565615	[C/T]	chr1	2565615	Cc01_g01630:437	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	12.5%	4	CC	TC	CC	CC
-chr1:2558672	[A/G]	chr1	2558672	Cc01_g01630:759	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	AA	AA	AA	AG
-chr1:2558633	[T/C]	chr1	2558633	Cc01_g01630:798	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	TT	TT	TC	CT
-chr1:2558434	[T/C]	chr1	2558434	Cc01_g01630:859	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	37.5%	4	TT	TC	CT	CT
-chr1:2558347	[C/A]	chr1	2558347	Cc01_g01630:946	exon	NON_SYNONYMOUS_CODING	Gca/Tca	A/S	12.5%	4	CC	CA	CC	CC
-chr1:2558280	[T/G]	chr1	2558280	Cc01_g01630:1013	exon	NON_SYNONYMOUS_CODING	cAt/cCt	H/P	12.5%	4	TT	TG	TT	TT
-chr1:2558276	[G/A]	chr1	2558276	Cc01_g01630:1017	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	GG	GA	GG	GG
-chr1:2558203	[G/A]	chr1	2558203	Cc01_g01630:1090	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	12.5%	4	GG	GA	GG	GG
-chr1:2558132	[G/C]	chr1	2558132	Cc01_g01630:1161	exon	SYNONYMOUS_CODING	acC/acG	T/T	12.5%	4	GG	GC	GG	GG
-chr1:2558129	[G/A]	chr1	2558129	Cc01_g01630:1164	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	GG	GA	GG	GG
-chr1:2558028	[G/A]	chr1	2558028	Cc01_g01630:1265	exon	NON_SYNONYMOUS_CODING	cCa/cTa	P/L	12.5%	4	GG	GA	GG	GG
-chr1:2557954	[G/C]	chr1	2557954	Cc01_g01630:1339	exon	NON_SYNONYMOUS_CODING	Cca/Gca	P/A	12.5%	4	GG	GC	GG	GG
-chr1:2557932	[A/T]	chr1	2557932	Cc01_g01630:1361	exon	NON_SYNONYMOUS_CODING	aTa/aAa	I/K	12.5%	4	AA	AT	AA	AA
-chr1:2557907	[G/A]	chr1	2557907	Cc01_g01630:1386	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	GG	GA	GG	GG
-chr1:2557619	[T/C]	chr1	2557619	Cc01_g01630:1575	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	12.5%	4	TT	TC	TT	TT
-chr1:2557277	[T/C]	chr1	2557277	Cc01_g01630:1917	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	12.5%	4	TT	TC	TT	TT
-chr1:2557173	[A/G]	chr1	2557173	Cc01_g01630:2021	exon	NON_SYNONYMOUS_CODING	cTg/cCg	L/P	12.5%	4	AA	AG	AA	AA
-chr1:2557145	[T/C]	chr1	2557145	Cc01_g01630:2049	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	TT	TC	TT	TT
-chr1:2557074	[C/A]	chr1	2557074	Cc01_g01630:2120	exon	NON_SYNONYMOUS_CODING	gGa/gTa	G/V	12.5%	4	CC	CA	CC	CC
-chr1:2557055	[G/A]	chr1	2557055	Cc01_g01630:2139	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	12.5%	4	GG	GA	GG	GG
-chr1:2557019	[T/C]	chr1	2557019	Cc01_g01630:2175	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	TT	TT	TC	TT
-chr1:2557016	[A/G]	chr1	2557016	Cc01_g01630:2178	exon	SYNONYMOUS_CODING	acT/acC	T/T	12.5%	4	AA	AG	AA	AA
-chr1:2610598	[G/T]	chr1	2610598	Cc01_g01650:233	exon	NON_SYNONYMOUS_CODING	gGt/gTt	G/V	12.5%	4	GG	GT	GG	GG
-chr1:2611238	[T/C]	chr1	2611238	Cc01_g01650:279	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TC	TT	TT
-chr1:2612873	[T/C]	chr1	2612873	Cc01_g01650:375	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	TT	TC	TT	TT
-chr1:2612964	[C/T]	chr1	2612964	Cc01_g01650:466	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	12.5%	4	CC	CC	CC	CT
-chr1:2613791	[G/C]	chr1	2613791	Cc01_g01650:835	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	12.5%	4	GG	GG	GG	GC
-chr1:2613877	[G/A]	chr1	2613877	Cc01_g01650:921	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	GG	GG	GG	GA
-chr1:2613943	[C/T]	chr1	2613943	Cc01_g01650:987	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	CC	CC	CT	CC
-chr1:2615356	[A/T]	chr1	2615356	Cc01_g01650:1179	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	12.5%	4	AA	AA	AT	AA
-chr1:2618568	[T/C]	chr1	2618568	Cc01_g01650:1693	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	TT	TC	TT	TT
-chr1:2618665	[C/T]	chr1	2618665	Cc01_g01650:1790	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	12.5%	4	CC	CC	CT	CC
-chr1:2618850	[C/T]	chr1	2618850	Cc01_g01650:1886	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	12.5%	4	CC	CC	CC	CT
-chr1:2618880	[A/G]	chr1	2618880	Cc01_g01650:1916	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	12.5%	4	AA	AA	AG	AA
-chr1:2619302	[A/G]	chr1	2619302	Cc01_g01650:2224	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	12.5%	4	AA	AG	AA	AA
-chr1:2619373	[C/T]	chr1	2619373	Cc01_g01650:2295	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CT	CC	CC
-chr1:2622083	[C/T]	chr1	2622083	Cc01_g01650:2580	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	CC	CT	CC	CC
-chr1:2622084	[A/C]	chr1	2622084	Cc01_g01650:2581	exon	NON_SYNONYMOUS_CODING	Aac/Cac	N/H	12.5%	4	AA	AC	AA	AA
-chr1:2622099	[C/G]	chr1	2622099	Cc01_g01650:2596	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	12.5%	4	CC	GC	CC	CC
-chr1:2623353	[A/C]	chr1	2623353	Cc01_g01650:2974	exon	SYNONYMOUS_CODING	Agg/Cgg	R/R	12.5%	4	AA	AA	AA	AC
-chr1:2624213	[G/T]	chr1	2624213	Cc01_g01650:3039	exon	NON_SYNONYMOUS_CODING	gaG/gaT	E/D	25.0%	4	GG	GT	GG	TG
-chr1:2624222	[T/A]	chr1	2624222	Cc01_g01650:3048	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	25.0%	4	TT	TA	TT	AT
-chr1:2624249	[T/C]	chr1	2624249	Cc01_g01650:3075	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	TT	TC	TT	TT
-chr1:2624263	[T/A]	chr1	2624263	Cc01_g01650:3089	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	12.5%	4	TT	TA	TT	TT
-chr1:2624270	[T/A]	chr1	2624270	Cc01_g01650:3096	exon	SYNONYMOUS_CODING	tcT/tcA	S/S	12.5%	4	TT	TA	TT	TT
-chr1:2624289	[G/T]	chr1	2624289	Cc01_g01650:3115	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	GG	GG	GG	TG
-chr1:2624433	[C/T]	chr1	2624433	Cc01_g01650:3173	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	12.5%	4	CC	CC	CC	CT
-chr1:2668103	[C/G]	chr1	2668103	Cc01_g01670:315	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	25.0%	4	CC	GG	GG	GG
-chr1:2668636	[A/G]	chr1	2668636	Cc01_g01670:848	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	25.0%	4	AA	AA	AA	GG
-chr1:2668660	[G/A]	chr1	2668660	Cc01_g01670:872	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	GG	GA	GG	GG
-chr1:2668692	[T/C]	chr1	2668692	Cc01_g01670:904	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	33.3%	3	TT	CC	NN	TT
-chr1:2668715	[T/G]	chr1	2668715	Cc01_g01670:927	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	33.3%	3	TT	NN	TT	GG
-chr1:2668739	[T/A]	chr1	2668739	Cc01_g01670:951	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	50.0%	2	TT	NN	AA	NN
-chr1:2668764	[A/T]	chr1	2668764	Cc01_g01670:976	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	50.0%	2	AA	NN	TT	NN
-chr1:2668782	[C/T]	chr1	2668782	Cc01_g01670:994	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	33.3%	3	CC	NN	TT	TT
-chr1:2668811	[G/A]	chr1	2668811	Cc01_g01670:1023	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	33.3%	3	GG	NN	AA	AA
-chr1:2669258	[A/C]	chr1	2669258	Cc01_g01670:1470	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	33.3%	3	AA	NN	CC	CC
-chr1:2669279	[T/A]	chr1	2669279	Cc01_g01670:1491	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	50.0%	2	TT	NN	AA	NN
-chr1:2669349	[A/G]	chr1	2669349	Cc01_g01670:1519	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	33.3%	3	AA	NN	GG	AA
-chr1:2669357	[T/A]	chr1	2669357	Cc01_g01670:1527	exon	SYNONYMOUS_CODING	cgT/cgA	R/R	33.3%	3	TT	NN	AA	AA
-chr1:2669424	[A/G]	chr1	2669424	Cc01_g01670:1594	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	33.3%	3	AA	NN	GG	GG
-chr1:2669466	[G/T]	chr1	2669466	Cc01_g01670:1636	exon	NON_SYNONYMOUS_CODING	Gcc/Tcc	A/S	33.3%	3	GG	NN	TT	GG
-chr1:2669497	[A/G]	chr1	2669497	Cc01_g01670:1667	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	33.3%	3	AA	NN	GG	AA
-chr1:2669523	[T/C]	chr1	2669523	Cc01_g01670:1693	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	12.5%	4	TT	TC	TT	TT
-chr1:2669527	[G/T]	chr1	2669527	Cc01_g01670:1697	exon	NON_SYNONYMOUS_CODING	tGc/tTc	C/F	25.0%	4	GG	GG	TT	GG
-chr1:2669572	[G/A]	chr1	2669572	Cc01_g01670:1742	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	GG	GG	AA	GG
-chr1:2669581	[C/A]	chr1	2669581	Cc01_g01670:1751	exon	NON_SYNONYMOUS_CODING	aCg/aAg	T/K	25.0%	4	CC	CC	AA	CC
-chr1:2669627	[T/C]	chr1	2669627	Cc01_g01670:1797	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	25.0%	4	TT	CC	CC	CC
-chr1:2669629	[A/G]	chr1	2669629	Cc01_g01670:1799	exon	NON_SYNONYMOUS_CODING	gAc/gGc	D/G	50.0%	4	AA	GG	GG	AA
-chr1:2669742	[A/C]	chr1	2669742	Cc01_g01670:1912	exon	NON_SYNONYMOUS_CODING	Aca/Cca	T/P	25.0%	4	AA	CC	CC	CC
-chr1:2669750	[T/C]	chr1	2669750	Cc01_g01670:1920	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	25.0%	4	TT	CC	TT	TT
-chr1:2669752	[A/T]	chr1	2669752	Cc01_g01670:1922	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	25.0%	4	AA	TT	AA	AA
-chr1:2669754	[G/A]	chr1	2669754	Cc01_g01670:1924	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	4	GG	AA	GG	AA
-chr1:2669766	[G/T]	chr1	2669766	Cc01_g01670:1936	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	50.0%	4	GG	GG	TT	TT
-chr1:2669787	[A/G]	chr1	2669787	Cc01_g01670:1957	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	AA	GG	AA	AA
-chr1:2669788	[T/C]	chr1	2669788	Cc01_g01670:1958	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	25.0%	4	TT	CC	CC	CC
-chr1:2669790	[C/A]	chr1	2669790	Cc01_g01670:1960	exon	NON_SYNONYMOUS_CODING	Cta/Ata	L/I	33.3%	3	CC	AA	NN	AA
-chr1:2669868	[C/T]	chr1	2669868	Cc01_g01670:2038	exon	NON_SYNONYMOUS_CODING	Ccg/Tcg	P/S	33.3%	3	CC	TT	NN	CC
-chr1:2670063	[C/T]	chr1	2670063	Cc01_g01670:2233	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	33.3%	3	CC	NN	CC	TT
-chr1:2670072	[C/T]	chr1	2670072	Cc01_g01670:2242	exon	STOP_GAINED	Cga/Tga	R/8	25.0%	4	CC	CC	CC	TT
-chr1:2670078	[G/A]	chr1	2670078	Cc01_g01670:2248	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	GG	AA	GG	GG
-chr1:2670084	[T/A]	chr1	2670084	Cc01_g01670:2254	exon	NON_SYNONYMOUS_CODING	Tta/Ata	L/I	50.0%	4	TT	AA	AA	TT
-chr1:2670086	[A/G]	chr1	2670086	Cc01_g01670:2256	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	33.3%	3	AA	GG	GG	NN
-chr1:2672520	[A/G]	chr1	2672520	Cc01_g01670:2295	exon	SYNONYMOUS_CODING	agA/agG	R/R	33.3%	3	AA	AA	NN	GG
-chr1:2672522	[C/G]	chr1	2672522	Cc01_g01670:2297	exon	NON_SYNONYMOUS_CODING	aCa/aGa	T/R	33.3%	3	CC	CC	NN	GG
-chr1:2672529	[A/T]	chr1	2672529	Cc01_g01670:2304	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	33.3%	3	AA	AA	NN	TT
-chr1:2672531	[T/C]	chr1	2672531	Cc01_g01670:2306	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	33.3%	3	TT	TT	NN	CC
-chr1:2672554	[T/A]	chr1	2672554	Cc01_g01670:2329	exon	NON_SYNONYMOUS_CODING	Tat/Aat	Y/N	33.3%	3	TT	TT	NN	AA
-chr1:2672699	[C/T]	chr1	2672699	Cc01_g01670:2474	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	25.0%	2	CC	CT	NN	NN
-chr1:2672995	[T/C]	chr1	2672995	Cc01_g01670:2770	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	50.0%	2	TT	CC	NN	NN
-chr1:2672999	[C/T]	chr1	2672999	Cc01_g01670:2774	exon	NON_SYNONYMOUS_CODING	tCc/tTc	S/F	25.0%	2	CC	CT	NN	NN
-chr1:2673033	[A/G]	chr1	2673033	Cc01_g01670:2808	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	37.5%	4	AA	AG	AA	GG
-chr1:2673073	[A/T]	chr1	2673073	Cc01_g01670:2848	exon	NON_SYNONYMOUS_CODING	Atc/Ttc	I/F	33.3%	3	AA	TT	TT	NN
-chr1:2673080	[T/C]	chr1	2673080	Cc01_g01670:2855	exon	NON_SYNONYMOUS_CODING	tTa/tCa	L/S	33.3%	3	TT	CC	TT	NN
-chr1:2673111	[G/T]	chr1	2673111	Cc01_g01670:2886	exon	NON_SYNONYMOUS_CODING	agG/agT	R/S	25.0%	4	GG	GG	TT	GG
-chr1:2673117	[A/T]	chr1	2673117	Cc01_g01670:2892	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	25.0%	4	AA	AA	AA	TT
-chr1:2673163	[T/G]	chr1	2673163	Cc01_g01670:2938	exon	NON_SYNONYMOUS_CODING	Ttc/Gtc	F/V	25.0%	4	TT	TT	GG	TT
-chr1:2673186	[G/C]	chr1	2673186	Cc01_g01670:2961	exon	NON_SYNONYMOUS_CODING	atG/atC	M/I	33.3%	3	GG	GG	NN	CC
-chr1:2673191	[G/A]	chr1	2673191	Cc01_g01670:2966	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	25.0%	2	GG	GA	NN	NN
-chr1:2673238	[C/G]	chr1	2673238	Cc01_g01670:3013	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	25.0%	2	CC	CG	NN	NN
-chr1:2673525	[G/A]	chr1	2673525	Cc01_g01670:3300	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	4	GG	GA	GG	GA
-chr1:2673526	[G/T]	chr1	2673526	Cc01_g01670:3301	exon	STOP_GAINED	Gag/Tag	E/1	25.0%	4	GG	GT	GG	GT
-chr1:2673538	[T/G]	chr1	2673538	Cc01_g01670:3313	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	50.0%	4	TT	TG	GG	TG
-chr1:2673541	[C/T]	chr1	2673541	Cc01_g01670:3316	exon	NON_SYNONYMOUS_CODING	Ccg/Tcg	P/S	25.0%	4	CC	TC	CC	CT
-chr1:2673542	[C/T]	chr1	2673542	Cc01_g01670:3317	exon	NON_SYNONYMOUS_CODING	cCg/cTg	P/L	25.0%	4	CC	TC	CC	CT
-chr1:2673543	[G/T]	chr1	2673543	Cc01_g01670:3318	exon	SYNONYMOUS_CODING	ccG/ccT	P/P	25.0%	4	GG	TG	GG	GT
-chr1:2674163	[G/A]	chr1	2674163	Cc01_g01670:3319	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	37.5%	4	GG	AG	GA	GA
-chr1:2674174	[G/C]	chr1	2674174	Cc01_g01670:3330	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	37.5%	4	GG	CG	GC	GC
-chr1:2674189	[A/C]	chr1	2674189	Cc01_g01670:3345	exon	SYNONYMOUS_CODING	ggA/ggC	G/G	25.0%	4	AA	CA	AA	AC
-chr1:2674276	[C/T]	chr1	2674276	Cc01_g01680:15	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CT	CC	CC
-chr1:2674294	[G/A]	chr1	2674294	Cc01_g01680:33	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	4	GG	AA	AA	AA
-chr1:2674295	[C/G]	chr1	2674295	Cc01_g01680:34	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	25.0%	4	CC	GG	GG	GG
-chr1:2674297	[G/T]	chr1	2674297	Cc01_g01680:36	exon	NON_SYNONYMOUS_CODING	caG/caT	Q/H	25.0%	4	GG	GG	GG	TT
-chr1:2674941	[A/G]	chr1	2674941	Cc01_g01680:48	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	AA	AA	AG	AA
-chr1:2674945	[C/T]	chr1	2674945	Cc01_g01680:52	exon	NON_SYNONYMOUS_CODING	Cct/Tct	P/S	12.5%	4	CC	CC	TC	CC
-chr1:2674962	[G/A]	chr1	2674962	Cc01_g01680:69	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	12.5%	4	GG	GG	GA	GG
-chr1:2674964	[G/T]	chr1	2674964	Cc01_g01680:71	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	37.5%	4	GG	GT	GG	TT
-chr1:2674973	[T/A]	chr1	2674973	Cc01_g01680:80	exon	STOP_GAINED	tTg/tAg	L/7	37.5%	4	TT	TA	AA	AA
-chr1:2674983	[G/T]	chr1	2674983	Cc01_g01680:90	exon	NON_SYNONYMOUS_CODING	ttG/ttT	L/F	25.0%	4	GG	TT	TT	TT
-chr1:2675001	[T/C]	chr1	2675001	Cc01_g01680:108	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	25.0%	2	TT	TC	NN	NN
-chr1:2675015	[T/A]	chr1	2675015	Cc01_g01680:122	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	16.7%	3	TT	TA	NN	TT
-chr1:2675040	[T/A]	chr1	2675040	Cc01_g01680:147	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	33.3%	3	TT	AA	NN	AA
-chr1:2675043	[C/T]	chr1	2675043	Cc01_g01680:150	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	33.3%	3	CC	TT	NN	TT
-chr1:2675048	[G/A]	chr1	2675048	Cc01_g01680:155	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	16.7%	3	GG	AG	NN	GG
-chr1:2675053	[A/T]	chr1	2675053	Cc01_g01680:160	exon	NON_SYNONYMOUS_CODING	Att/Ttt	I/F	50.0%	3	AA	AT	NN	TT
-chr1:2732265	[A/G]	chr1	2732265	Cc01_g01700:720	exon	SYNONYMOUS_CODING	acA/acG	T/T	25.0%	2	AA	NN	NN	AG
-chr1:2836390	[A/T]	chr1	2836390	Cc01_g01710:126	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	50.0%	2	AA	TT	NN	NN
-chr1:2836415	[G/C]	chr1	2836415	Cc01_g01710:151	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	25.0%	2	GG	GC	NN	NN
-chr1:2836420	[G/C]	chr1	2836420	Cc01_g01710:156	exon	SYNONYMOUS_CODING	gcG/gcC	A/A	50.0%	2	GG	CC	NN	NN
-chr1:2836423	[C/T]	chr1	2836423	Cc01_g01710:159	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	25.0%	2	CC	CT	NN	NN
-chr1:2836441	[C/A]	chr1	2836441	Cc01_g01710:177	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	33.3%	3	CC	AA	CC	NN
-chr1:2836445	[G/A]	chr1	2836445	Cc01_g01710:181	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	16.7%	3	GG	GA	GG	NN
-chr1:2836460	[G/A]	chr1	2836460	Cc01_g01710:196	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	33.3%	3	GG	AA	GG	NN
-chr1:2836484	[A/G]	chr1	2836484	Cc01_g01710:220	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	16.7%	3	AA	AG	AA	NN
-chr1:2836488	[C/T]	chr1	2836488	Cc01_g01710:224	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	16.7%	3	CC	CT	CC	NN
-chr1:2836561	[A/G]	chr1	2836561	Cc01_g01710:297	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	50.0%	2	AA	GG	NN	NN
-chr1:2837031	[G/A]	chr1	2837031	Cc01_g01720:58	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	50.0%	2	GG	AA	NN	NN
-chr1:2837037	[A/G]	chr1	2837037	Cc01_g01720:64	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	50.0%	2	AA	GG	NN	NN
-chr1:2837164	[A/G]	chr1	2837164	Cc01_g01720:191	exon	NON_SYNONYMOUS_CODING	gAa/gGa	E/G	25.0%	4	AA	AA	AA	GG
-chr1:2837166	[A/G]	chr1	2837166	Cc01_g01720:193	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	25.0%	4	AA	GG	AA	AA
-chr1:2837171	[A/G]	chr1	2837171	Cc01_g01720:198	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	25.0%	4	AA	GG	AA	AA
-chr1:2837187	[G/C]	chr1	2837187	Cc01_g01720:214	exon	NON_SYNONYMOUS_CODING	Gtc/Ctc	V/L	50.0%	4	GG	GG	CC	CC
-chr1:2837200	[T/G]	chr1	2837200	Cc01_g01720:227	exon	NON_SYNONYMOUS_CODING	cTg/cGg	L/R	37.5%	4	TT	TT	TG	GG
-chr1:2837207	[A/G]	chr1	2837207	Cc01_g01720:234	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	GG	AA	AA
-chr1:2837244	[G/A]	chr1	2837244	Cc01_g01720:271	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	25.0%	4	GG	GG	GA	GA
-chr1:2837245	[A/G]	chr1	2837245	Cc01_g01720:272	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	25.0%	4	AA	GG	GG	GG
-chr1:2837246	[T/C]	chr1	2837246	Cc01_g01720:273	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	37.5%	4	TT	TT	CC	TC
-chr1:2837248	[G/A]	chr1	2837248	Cc01_g01720:275	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	37.5%	4	GG	GG	AA	GA
-chr1:2837259	[T/C]	chr1	2837259	Cc01_g01720:286	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	37.5%	4	TT	CC	TT	CT
-chr1:2837266	[A/G]	chr1	2837266	Cc01_g01720:293	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	37.5%	4	AA	GG	AA	GA
-chr1:2837271	[C/T]	chr1	2837271	Cc01_g01720:298	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	37.5%	4	CC	CC	TT	CT
-chr1:2837287	[G/T]	chr1	2837287	Cc01_g01720:314	exon	NON_SYNONYMOUS_CODING	tGg/tTg	W/L	33.3%	3	GG	TT	NN	GG
-chr1:2837295	[T/C]	chr1	2837295	Cc01_g01720:322	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	33.3%	3	TT	CC	NN	CC
-chr1:2837310	[A/C]	chr1	2837310	Cc01_g01720:337	exon	NON_SYNONYMOUS_CODING	Att/Ctt	I/L	50.0%	3	AA	AC	NN	CC
-chr1:2837316	[G/A]	chr1	2837316	Cc01_g01720:343	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	50.0%	3	GG	GA	NN	AA
-chr1:2837318	[G/C]	chr1	2837318	Cc01_g01720:345	exon	SYNONYMOUS_CODING	ggG/ggC	G/G	33.3%	3	GG	GG	NN	CC
-chr1:2837319	[G/C]	chr1	2837319	Cc01_g01720:346	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	33.3%	3	GG	GG	NN	CC
-chr1:2837348	[A/G]	chr1	2837348	Cc01_g01720:375	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	33.3%	3	AA	AG	NN	AG
-chr1:2837391	[G/A]	chr1	2837391	Cc01_g01720:418	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	50.0%	3	GG	GA	NN	AA
-chr1:2837393	[A/T]	chr1	2837393	Cc01_g01720:420	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	16.7%	3	AA	TA	NN	AA
-chr1:2837420	[C/T]	chr1	2837420	Cc01_g01720:447	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	50.0%	3	CC	CT	NN	TT
-chr1:2837423	[T/G]	chr1	2837423	Cc01_g01720:450	exon	NON_SYNONYMOUS_CODING	aaT/aaG	N/K	33.3%	3	TT	GG	NN	GG
-chr1:2837425	[T/G]	chr1	2837425	Cc01_g01720:452	exon	NON_SYNONYMOUS_CODING	gTa/gGa	V/G	33.3%	3	TT	GG	NN	GG
-chr1:2837433	[A/G]	chr1	2837433	Cc01_g01720:460	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	33.3%	3	AA	GG	NN	GG
-chr1:2837480	[T/C]	chr1	2837480	Cc01_g01720:507	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	33.3%	3	TT	CC	NN	CC
-chr1:2837519	[G/A]	chr1	2837519	Cc01_g01720:546	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	33.3%	3	GG	AA	NN	AA
-chr1:2837526	[G/T]	chr1	2837526	Cc01_g01720:553	exon	NON_SYNONYMOUS_CODING	Gca/Tca	A/S	33.3%	3	GG	TT	NN	TT
-chr1:2837537	[G/A]	chr1	2837537	Cc01_g01720:564	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	33.3%	3	GG	AA	NN	AA
-chr1:2837615	[T/C]	chr1	2837615	Cc01_g01720:642	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	50.0%	2	TT	NN	CC	NN
-chr1:2837629	[T/A]	chr1	2837629	Cc01_g01720:656	exon	NON_SYNONYMOUS_CODING	cTa/cAa	L/Q	50.0%	2	TT	NN	AA	NN
-chr1:2837640	[A/G]	chr1	2837640	Cc01_g01720:667	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	50.0%	2	AA	NN	GG	NN
-chr1:2901565	[C/A]	chr1	2901565	Cc01_g01730:118	exon	NON_SYNONYMOUS_CODING	Cac/Aac	H/N	12.5%	4	CC	CA	CC	CC
-chr1:2901573	[A/T]	chr1	2901573	Cc01_g01730:126	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	16.7%	3	AA	AT	NN	AA
-chr1:2901666	[T/C]	chr1	2901666	Cc01_g01730:219	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	16.7%	3	TT	TC	NN	TT
-chr1:2902604	[C/T]	chr1	2902604	Cc01_g01730:618	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	50.0%	3	CC	CT	NN	TT
-chr1:2902609	[A/G]	chr1	2902609	Cc01_g01730:623	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	50.0%	3	AA	AG	NN	GG
-chr1:2902632	[G/A]	chr1	2902632	Cc01_g01730:646	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	33.3%	3	GG	AA	NN	AA
-chr1:2902646	[A/C]	chr1	2902646	Cc01_g01730:660	exon	NON_SYNONYMOUS_CODING	caA/caC	Q/H	33.3%	3	AA	CC	NN	CC
-chr1:2902650	[G/A]	chr1	2902650	Cc01_g01730:664	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	33.3%	3	GG	AA	NN	AA
-chr1:2902664	[T/C]	chr1	2902664	Cc01_g01730:678	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	33.3%	3	TT	CC	NN	CC
-chr1:2902673	[T/G]	chr1	2902673	Cc01_g01730:687	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	33.3%	3	TT	GG	NN	GG
-chr1:2902849	[T/G]	chr1	2902849	Cc01_g01730:863	exon	NON_SYNONYMOUS_CODING	aTa/aGa	I/R	25.0%	2	TT	NN	NN	TG
-chr1:2902856	[G/C]	chr1	2902856	Cc01_g01730:870	exon	SYNONYMOUS_CODING	ggG/ggC	G/G	50.0%	2	GG	NN	NN	CC
-chr1:2902865	[G/A]	chr1	2902865	Cc01_g01730:879	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	33.3%	3	GG	GG	NN	AA
-chr1:2902892	[A/G]	chr1	2902892	Cc01_g01730:906	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	50.0%	2	AA	GG	NN	NN
-chr1:2903083	[G/A]	chr1	2903083	Cc01_g01730:1097	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	33.3%	3	GG	AA	NN	AA
-chr1:2903094	[G/A]	chr1	2903094	Cc01_g01730:1108	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	33.3%	3	GG	AA	NN	AA
-chr1:2903117	[A/G]	chr1	2903117	Cc01_g01730:1131	exon	SYNONYMOUS_CODING	agA/agG	R/R	25.0%	4	AA	AA	GG	AA
-chr1:2903173	[T/G]	chr1	2903173	Cc01_g01730:1187	exon	NON_SYNONYMOUS_CODING	aTc/aGc	I/S	25.0%	4	TT	GG	GG	GG
-chr1:2903230	[C/G]	chr1	2903230	Cc01_g01730:1244	exon	NON_SYNONYMOUS_CODING	aCa/aGa	T/R	16.7%	3	CC	NN	CC	CG
-chr1:2903240	[A/G]	chr1	2903240	Cc01_g01730:1254	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	GG	AA	AA
-chr1:2903273	[A/G]	chr1	2903273	Cc01_g01730:1287	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AG	AA	AA
-chr1:2903283	[G/A]	chr1	2903283	Cc01_g01730:1297	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	GG	GA	GG	GG
-chr1:2903292	[G/A]	chr1	2903292	Cc01_g01730:1306	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	GG	AG	GG	GG
-chr1:2903341	[A/G]	chr1	2903341	Cc01_g01730:1355	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	50.0%	2	AA	GG	NN	NN
-chr1:2903558	[C/T]	chr1	2903558	Cc01_g01730:1572	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	50.0%	2	CC	TT	NN	NN
-chr1:2903571	[C/T]	chr1	2903571	Cc01_g01730:1585	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	50.0%	2	CC	TT	NN	NN
-chr1:2903610	[G/A]	chr1	2903610	Cc01_g01730:1624	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	50.0%	2	GG	AA	NN	NN
-chr1:2903621	[T/C]	chr1	2903621	Cc01_g01730:1635	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	50.0%	2	TT	CC	NN	NN
-chr1:2903627	[T/G]	chr1	2903627	Cc01_g01730:1641	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	33.3%	3	TT	GG	TT	NN
-chr1:2903770	[G/A]	chr1	2903770	Cc01_g01730:1784	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	50.0%	2	GG	NN	AA	NN
-chr1:2903814	[G/A]	chr1	2903814	Cc01_g01730:1828	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	33.3%	3	GG	NN	AA	GG
-chr1:2903816	[G/T]	chr1	2903816	Cc01_g01730:1830	exon	NON_SYNONYMOUS_CODING	gaG/gaT	E/D	33.3%	3	GG	NN	GG	TT
-chr1:2903820	[G/T]	chr1	2903820	Cc01_g01730:1834	exon	NON_SYNONYMOUS_CODING	Gta/Tta	V/L	33.3%	3	GG	NN	TT	GG
-chr1:2903823	[A/G]	chr1	2903823	Cc01_g01730:1837	exon	NON_SYNONYMOUS_CODING	Aga/Gga	R/G	33.3%	3	AA	NN	AA	GG
-chr1:2904055	[G/T]	chr1	2904055	Cc01_g01730:1910	exon	NON_SYNONYMOUS_CODING	aGg/aTg	R/M	50.0%	2	GG	TT	NN	NN
-chr1:2904064	[A/G]	chr1	2904064	Cc01_g01730:1919	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	50.0%	2	AA	GG	NN	NN
-chr1:2904368	[T/C]	chr1	2904368	Cc01_g01730:2163	exon	SYNONYMOUS_CODING	acT/acC	T/T	50.0%	2	TT	NN	CC	NN
-chr1:2904423	[C/T]	chr1	2904423	Cc01_g01730:2218	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	50.0%	3	CC	CT	TT	NN
-chr1:2986926	[T/C]	chr1	2986926	Cc01_g01750:549	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	50.0%	2	TT	CC	NN	NN
-chr1:2986947	[A/C]	chr1	2986947	Cc01_g01750:570	exon	SYNONYMOUS_CODING	acA/acC	T/T	25.0%	2	AA	AC	NN	NN
-chr1:2988225	[A/G]	chr1	2988225	Cc01_g01750:1848	exon	SYNONYMOUS_CODING	cgA/cgG	R/R	50.0%	2	AA	GG	NN	NN
-chr1:2988245	[A/G]	chr1	2988245	Cc01_g01750:1868	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	50.0%	2	AA	GG	NN	NN
-chr1:2989009	[G/A]	chr1	2989009	Cc01_g01750:2542	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	50.0%	2	GG	AA	NN	NN
-chr1:2989157	[G/T]	chr1	2989157	Cc01_g01750:2690	exon	NON_SYNONYMOUS_CODING	aGt/aTt	S/I	50.0%	2	GG	NN	NN	TT
-chr1:2989172	[A/G]	chr1	2989172	Cc01_g01750:2705	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	50.0%	2	AA	NN	NN	GG
-chr1:2989569	[T/C]	chr1	2989569	Cc01_g01750:3021	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	33.3%	3	TT	NN	CC	CC
-chr1:2989571	[T/G]	chr1	2989571	Cc01_g01750:3023	exon	NON_SYNONYMOUS_CODING	tTg/tGg	L/W	25.0%	4	TT	GG	GG	GG
-chr1:2989664	[A/G]	chr1	2989664	Cc01_g01750:3116	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	33.3%	3	AA	GG	NN	GG
-chr1:2989678	[G/C]	chr1	2989678	Cc01_g01750:3130	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	33.3%	3	GG	CC	NN	CC
-chr1:2989702	[G/A]	chr1	2989702	Cc01_g01750:3154	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	16.7%	3	GG	GA	NN	GG
-chr1:2989705	[A/G]	chr1	2989705	Cc01_g01750:3157	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	50.0%	4	AA	GG	GG	AA
-chr1:2989708	[G/A]	chr1	2989708	Cc01_g01750:3160	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	12.5%	4	GG	GG	GG	GA
-chr1:2989742	[A/G]	chr1	2989742	Cc01_g01750:3194	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	37.5%	4	AA	AG	AG	AG
-chr1:2989743	[A/T]	chr1	2989743	Cc01_g01750:3195	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	37.5%	4	AA	TA	TA	TA
-chr1:2989751	[G/A]	chr1	2989751	Cc01_g01750:3203	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	12.5%	4	GG	GG	AG	GG
-chr1:2989752	[G/T]	chr1	2989752	Cc01_g01750:3204	exon	SYNONYMOUS_CODING	cgG/cgT	R/R	12.5%	4	GG	GG	TG	GG
-chr1:2989766	[G/A]	chr1	2989766	Cc01_g01750:3218	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	50.0%	4	GG	AA	GA	AG
-chr1:2989770	[A/G]	chr1	2989770	Cc01_g01750:3222	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	AA	GG	AA	GA
-chr1:2989771	[C/T]	chr1	2989771	Cc01_g01750:3223	exon	STOP_GAINED	Cga/Tga	R/5	12.5%	4	CC	CC	CT	CC
-chr1:2989797	[C/T]	chr1	2989797	Cc01_g01750:3249	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	CC	CC	CC	CT
-chr1:2989804	[T/G]	chr1	2989804	Cc01_g01750:3256	exon	STOP_LOST	Tag/Gag	1/E	50.0%	2	TT	GG	NN	NN
-chr1:2996368	[A/C]	chr1	2996368	Cc01_g01760:9	exon	SYNONYMOUS_CODING	cgA/cgC	R/R	33.3%	3	AA	CC	NN	CC
-chr1:2996399	[G/A]	chr1	2996399	Cc01_g01760:40	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	33.3%	3	GG	GA	NN	GA
-chr1:2996415	[G/A]	chr1	2996415	Cc01_g01760:56	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	16.7%	3	GG	GG	NN	AG
-chr1:2996419	[A/G]	chr1	2996419	Cc01_g01760:60	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	16.7%	3	AA	AA	NN	AG
-chr1:2996421	[A/G]	chr1	2996421	Cc01_g01760:62	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	33.3%	3	AA	GG	NN	GG
-chr1:2996436	[G/T]	chr1	2996436	Cc01_g01760:77	exon	NON_SYNONYMOUS_CODING	aGa/aTa	R/I	25.0%	4	GG	GG	GG	TT
-chr1:2997079	[G/A]	chr1	2997079	Cc01_g01760:118	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	25.0%	4	GG	GA	GG	GA
-chr1:2997084	[T/C]	chr1	2997084	Cc01_g01760:123	exon	SYNONYMOUS_CODING	agT/agC	S/S	50.0%	4	TT	CC	TT	CC
-chr1:2997085	[A/C]	chr1	2997085	Cc01_g01760:124	exon	NON_SYNONYMOUS_CODING	Agt/Cgt	S/R	25.0%	4	AA	AA	CC	AA
-chr1:2997097	[G/C]	chr1	2997097	Cc01_g01760:136	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	25.0%	4	GG	CG	GG	CG
-chr1:2997102	[A/T]	chr1	2997102	Cc01_g01760:141	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	12.5%	4	AA	AA	AA	AT
-chr1:2997106	[A/G]	chr1	2997106	Cc01_g01760:145	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	12.5%	4	AA	AG	AA	AA
-chr1:2997108	[T/C]	chr1	2997108	Cc01_g01760:147	exon	SYNONYMOUS_CODING	atT/atC	I/I	50.0%	4	TT	CC	TT	CC
-chr1:2997111	[T/C]	chr1	2997111	Cc01_g01760:150	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	TT	TT	TT	TC
-chr1:2997112	[G/A]	chr1	2997112	Cc01_g01760:151	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	12.5%	4	GG	GG	GG	GA
-chr1:2997122	[T/A]	chr1	2997122	Cc01_g01760:161	exon	NON_SYNONYMOUS_CODING	cTa/cAa	L/Q	25.0%	4	TT	TA	TT	AT
-chr1:2997125	[C/T]	chr1	2997125	Cc01_g01760:164	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	12.5%	4	CC	CC	CT	CC
-chr1:2997133	[A/G]	chr1	2997133	Cc01_g01760:172	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	37.5%	4	AA	AG	GA	AG
-chr1:2997137	[G/A]	chr1	2997137	Cc01_g01760:176	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	12.5%	4	GG	GG	GA	GG
-chr1:2997152	[T/C]	chr1	2997152	Cc01_g01760:191	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	12.5%	4	TT	TT	CT	TT
-chr1:2997154	[G/C]	chr1	2997154	Cc01_g01760:193	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	25.0%	4	GG	CG	GG	GC
-chr1:2997157	[A/G]	chr1	2997157	Cc01_g01760:196	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	25.0%	4	AA	GA	AA	AG
-chr1:2997163	[G/C]	chr1	2997163	Cc01_g01760:202	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	50.0%	4	GG	CC	CG	GC
-chr1:2997173	[C/T]	chr1	2997173	Cc01_g01760:212	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	CC	CC	CT	CC
-chr1:2997174	[T/G]	chr1	2997174	Cc01_g01760:213	exon	SYNONYMOUS_CODING	gcT/gcG	A/A	12.5%	4	TT	TT	TG	TT
-chr1:2997191	[C/T]	chr1	2997191	Cc01_g01760:230	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	12.5%	4	CC	CC	CC	TC
-chr1:2997196	[T/C]	chr1	2997196	Cc01_g01760:235	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	37.5%	4	TT	TC	CT	CT
-chr1:2997204	[A/G]	chr1	2997204	Cc01_g01760:243	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	AA	AG	GA	AG
-chr1:2997206	[G/A]	chr1	2997206	Cc01_g01760:245	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	25.0%	4	GG	AA	AA	AA
-chr1:2997213	[C/G]	chr1	2997213	Cc01_g01760:252	exon	NON_SYNONYMOUS_CODING	agC/agG	S/R	37.5%	4	CC	GC	GC	CG
-chr1:2997215	[C/T]	chr1	2997215	Cc01_g01760:254	exon	NON_SYNONYMOUS_CODING	tCa/tTa	S/L	37.5%	4	CC	CT	TC	TC
-chr1:2997227	[T/G]	chr1	2997227	Cc01_g01760:266	exon	NON_SYNONYMOUS_CODING	tTg/tGg	L/W	25.0%	4	TT	TT	TG	GT
-chr1:2997231	[C/T]	chr1	2997231	Cc01_g01760:270	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	12.5%	4	CC	CT	CC	CC
-chr1:2997233	[G/C]	chr1	2997233	Cc01_g01760:272	exon	NON_SYNONYMOUS_CODING	aGa/aCa	R/T	25.0%	4	GG	GG	GC	CG
-chr1:2997243	[T/A]	chr1	2997243	Cc01_g01760:282	exon	SYNONYMOUS_CODING	atT/atA	I/I	25.0%	4	TT	AA	AA	AA
-chr1:2997247	[C/G]	chr1	2997247	Cc01_g01760:286	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	12.5%	4	CC	CG	CC	CC
-chr1:2997250	[C/T]	chr1	2997250	Cc01_g01760:289	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	12.5%	4	CC	CC	TC	CC
-chr1:2997252	[T/C]	chr1	2997252	Cc01_g01760:291	exon	SYNONYMOUS_CODING	caT/caC	H/H	25.0%	4	TT	TT	TC	CT
-chr1:2997275	[C/A]	chr1	2997275	Cc01_g01760:314	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	12.5%	4	CC	CA	CC	CC
-chr1:2997294	[G/T]	chr1	2997294	Cc01_g01760:333	exon	STOP_LOST	taG/taT	1/Y	25.0%	4	GG	GG	GG	TT
-chr1:3052579	[G/A]	chr1	3052579	Cc01_g01770:91	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	50.0%	2	GG	NN	NN	AA
-chr1:3052586	[C/T]	chr1	3052586	Cc01_g01770:98	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	33.3%	3	CC	NN	TT	TT
-chr1:3052603	[G/A]	chr1	3052603	Cc01_g01770:115	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	50.0%	2	GG	NN	NN	AA
-chr1:3052725	[G/A]	chr1	3052725	Cc01_g01770:237	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	50.0%	4	GG	AA	GA	GA
-chr1:3052735	[C/A]	chr1	3052735	Cc01_g01770:247	exon	NON_SYNONYMOUS_CODING	Cac/Aac	H/N	25.0%	4	CC	AA	AA	AA
-chr1:3052737	[C/A]	chr1	3052737	Cc01_g01770:249	exon	NON_SYNONYMOUS_CODING	caC/caA	H/Q	12.5%	4	CC	CC	CC	CA
-chr1:3052781	[T/C]	chr1	3052781	Cc01_g01770:293	exon	NON_SYNONYMOUS_CODING	aTc/aCc	I/T	33.3%	3	TT	NN	CC	TT
-chr1:3052796	[G/A]	chr1	3052796	Cc01_g01770:308	exon	NON_SYNONYMOUS_CODING	tGc/tAc	C/Y	50.0%	2	GG	NN	AA	NN
-chr1:3052819	[G/A]	chr1	3052819	Cc01_g01770:331	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	16.7%	3	GG	GG	GA	NN
-chr1:3052820	[C/A]	chr1	3052820	Cc01_g01770:332	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	16.7%	3	CC	CC	CA	NN
-chr1:3052827	[T/C]	chr1	3052827	Cc01_g01770:339	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	33.3%	3	TT	CC	TT	NN
-chr1:3052878	[C/G]	chr1	3052878	Cc01_g01770:390	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	33.3%	3	CC	GG	GG	NN
-chr1:3053184	[T/A]	chr1	3053184	Cc01_g01770:696	exon	NON_SYNONYMOUS_CODING	caT/caA	H/Q	16.7%	3	TT	NN	TA	TT
-chr1:3053253	[T/C]	chr1	3053253	Cc01_g01770:765	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	TT	CC	CC	CC
-chr1:3053284	[A/G]	chr1	3053284	Cc01_g01770:796	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	50.0%	4	AA	AA	GG	GG
-chr1:3053300	[A/G]	chr1	3053300	Cc01_g01770:812	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	50.0%	4	AA	AA	GG	GG
-chr1:3053448	[T/A]	chr1	3053448	Cc01_g01770:886	exon	NON_SYNONYMOUS_CODING	Tct/Act	S/T	50.0%	2	TT	NN	NN	AA
-chr1:3053505	[C/T]	chr1	3053505	Cc01_g01770:943	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	33.3%	3	CC	TT	TT	NN
-chr1:3053568	[T/C]	chr1	3053568	Cc01_g01770:1006	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	TT	TT	TC	TT
-chr1:3053590	[A/C]	chr1	3053590	Cc01_g01770:1028	exon	NON_SYNONYMOUS_CODING	gAt/gCt	D/A	50.0%	4	AA	AC	CA	CC
-chr1:3053591	[T/C]	chr1	3053591	Cc01_g01770:1029	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	12.5%	4	TT	CT	TT	TT
-chr1:3053592	[T/G]	chr1	3053592	Cc01_g01770:1030	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	50.0%	4	TT	TG	GT	GG
-chr1:3053593	[A/G]	chr1	3053593	Cc01_g01770:1031	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	50.0%	4	AA	AG	GA	GG
-chr1:3053596	[A/C]	chr1	3053596	Cc01_g01770:1034	exon	NON_SYNONYMOUS_CODING	gAa/gCa	E/A	12.5%	4	AA	AA	AC	AA
-chr1:3053597	[A/C]	chr1	3053597	Cc01_g01770:1035	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	37.5%	4	AA	AA	CA	CC
-chr1:3053608	[G/A]	chr1	3053608	Cc01_g01770:1046	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	12.5%	4	GG	GG	GA	GG
-chr1:3053622	[A/C]	chr1	3053622	Cc01_g01770:1060	exon	NON_SYNONYMOUS_CODING	Atg/Ctg	M/L	16.7%	3	AA	NN	CA	AA
-chr1:3053627	[C/T]	chr1	3053627	Cc01_g01770:1065	exon	SYNONYMOUS_CODING	agC/agT	S/S	33.3%	3	CC	NN	CC	TT
-chr1:3053887	[T/C]	chr1	3053887	Cc01_g01770:1325	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	50.0%	2	TT	NN	NN	CC
-chr1:3054011	[A/G]	chr1	3054011	Cc01_g01770:1449	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	16.7%	3	AA	AA	AG	NN
-chr1:3054042	[G/A]	chr1	3054042	Cc01_g01770:1480	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	33.3%	3	GG	AA	GG	NN
-chr1:3054054	[G/T]	chr1	3054054	Cc01_g01770:1492	exon	NON_SYNONYMOUS_CODING	Gta/Tta	V/L	25.0%	4	GG	TT	GG	GG
-chr1:3054055	[T/A]	chr1	3054055	Cc01_g01770:1493	exon	NON_SYNONYMOUS_CODING	gTa/gAa	V/E	37.5%	4	TT	TT	TA	AA
-chr1:3054103	[C/T]	chr1	3054103	Cc01_g01770:1541	exon	NON_SYNONYMOUS_CODING	tCc/tTc	S/F	25.0%	4	CC	CC	TT	CC
-chr1:3054112	[T/G]	chr1	3054112	Cc01_g01770:1550	exon	NON_SYNONYMOUS_CODING	aTt/aGt	I/S	33.3%	3	TT	NN	GG	TT
-chr1:3054118	[T/C]	chr1	3054118	Cc01_g01770:1556	exon	NON_SYNONYMOUS_CODING	tTt/tCt	F/S	33.3%	3	TT	NN	CC	TT
-chr1:3054218	[G/T]	chr1	3054218	Cc01_g01770:1605	exon	SYNONYMOUS_CODING	ggG/ggT	G/G	50.0%	2	GG	NN	NN	TT
-chr1:3054264	[C/T]	chr1	3054264	Cc01_g01770:1651	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	50.0%	2	CC	TT	NN	NN
-chr1:3054265	[G/A]	chr1	3054265	Cc01_g01770:1652	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	50.0%	2	GG	AA	NN	NN
-chr1:3054271	[G/T]	chr1	3054271	Cc01_g01770:1658	exon	NON_SYNONYMOUS_CODING	aGg/aTg	R/M	50.0%	2	GG	TT	NN	NN
-chr1:3054274	[T/A]	chr1	3054274	Cc01_g01770:1661	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	50.0%	2	TT	AA	NN	NN
-chr1:3054279	[G/A]	chr1	3054279	Cc01_g01770:1666	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	33.3%	3	GG	AA	GG	NN
-chr1:3054354	[G/A]	chr1	3054354	Cc01_g01770:1741	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	12.5%	4	GG	GG	GA	GG
-chr1:3054370	[A/G]	chr1	3054370	Cc01_g01770:1757	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	33.3%	3	AA	GG	AA	NN
-chr1:3054389	[G/A]	chr1	3054389	Cc01_g01770:1776	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	33.3%	3	GG	AA	GG	NN
-chr1:3054402	[C/G]	chr1	3054402	Cc01_g01770:1789	exon	NON_SYNONYMOUS_CODING	Cca/Gca	P/A	33.3%	3	CC	CC	GG	NN
-chr1:3054406	[G/A]	chr1	3054406	Cc01_g01770:1793	exon	NON_SYNONYMOUS_CODING	tGc/tAc	C/Y	33.3%	3	GG	GG	AA	NN
-chr1:3054411	[T/G]	chr1	3054411	Cc01_g01770:1798	exon	NON_SYNONYMOUS_CODING	Tgt/Ggt	C/G	33.3%	3	TT	TT	GG	NN
-chr1:3054417	[A/T]	chr1	3054417	Cc01_g01770:1804	exon	NON_SYNONYMOUS_CODING	Agt/Tgt	S/C	33.3%	3	AA	AA	TT	NN
-chr1:3054423	[C/G]	chr1	3054423	Cc01_g01770:1810	exon	NON_SYNONYMOUS_CODING	Cac/Gac	H/D	33.3%	3	CC	CC	NN	GG
-chr1:3054432	[A/T]	chr1	3054432	Cc01_g01770:1819	exon	NON_SYNONYMOUS_CODING	Aat/Tat	N/Y	16.7%	3	AA	AT	NN	AA
-chr1:3054439	[A/G]	chr1	3054439	Cc01_g01770:1826	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	16.7%	3	AA	AG	NN	AA
-chr1:3054447	[A/T]	chr1	3054447	Cc01_g01770:1834	exon	NON_SYNONYMOUS_CODING	Aca/Tca	T/S	33.3%	3	AA	AA	NN	TT
-chr1:3054480	[G/A]	chr1	3054480	Cc01_g01770:1867	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	33.3%	3	GG	AA	NN	GG
-chr1:3054501	[C/T]	chr1	3054501	Cc01_g01770:1888	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	33.3%	3	CC	TT	NN	CC
-chr1:3054566	[C/G]	chr1	3054566	Cc01_g01770:1953	exon	SYNONYMOUS_CODING	acC/acG	T/T	33.3%	3	CC	CC	NN	GG
-chr1:3054570	[A/C]	chr1	3054570	Cc01_g01770:1957	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	33.3%	3	AA	AA	NN	CC
-chr1:3054575	[G/C]	chr1	3054575	Cc01_g01770:1962	exon	NON_SYNONYMOUS_CODING	agG/agC	R/S	16.7%	3	GG	GC	NN	GG
-chr1:3054596	[A/G]	chr1	3054596	Cc01_g01770:1983	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	50.0%	3	AA	AG	NN	GG
-chr1:3054734	[C/G]	chr1	3054734	Cc01_g01770:2121	exon	SYNONYMOUS_CODING	ccC/ccG	P/P	12.5%	4	CC	CG	CC	CC
-chr1:3054743	[A/G]	chr1	3054743	Cc01_g01770:2130	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	12.5%	4	AA	AG	AA	AA
-chr1:3054746	[A/G]	chr1	3054746	Cc01_g01770:2133	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	12.5%	4	AA	AG	AA	AA
-chr1:3054764	[G/C]	chr1	3054764	Cc01_g01770:2151	exon	NON_SYNONYMOUS_CODING	caG/caC	Q/H	25.0%	4	GG	GG	GG	CC
-chr1:3054783	[C/A]	chr1	3054783	Cc01_g01770:2170	exon	NON_SYNONYMOUS_CODING	Caa/Aaa	Q/K	25.0%	4	CC	CC	CC	AA
-chr1:3054800	[A/T]	chr1	3054800	Cc01_g01770:2187	exon	NON_SYNONYMOUS_CODING	gaA/gaT	E/D	25.0%	4	AA	AA	AA	TT
-chr1:3054820	[A/G]	chr1	3054820	Cc01_g01770:2207	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	12.5%	4	AA	AG	AA	AA
-chr1:3054956	[A/C]	chr1	3054956	Cc01_g01770:2238	exon	SYNONYMOUS_CODING	cgA/cgC	R/R	50.0%	2	AA	NN	NN	CC
-chr1:3054966	[T/C]	chr1	3054966	Cc01_g01770:2248	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	33.3%	3	TT	NN	CC	CC
-chr1:3054968	[A/G]	chr1	3054968	Cc01_g01770:2250	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	33.3%	3	AA	NN	GG	GG
-chr1:3054987	[C/G]	chr1	3054987	Cc01_g01770:2269	exon	NON_SYNONYMOUS_CODING	Cca/Gca	P/A	25.0%	4	CC	CC	CC	GG
-chr1:3055134	[T/C]	chr1	3055134	Cc01_g01770:2416	exon	NON_SYNONYMOUS_CODING	Tcc/Ccc	S/P	25.0%	4	TT	TT	CC	TT
-chr1:3055136	[C/T]	chr1	3055136	Cc01_g01770:2418	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	CC	CT	CC	CC
-chr1:3055137	[G/A]	chr1	3055137	Cc01_g01770:2419	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	GG	GG	GA	GG
-chr1:3055144	[C/A]	chr1	3055144	Cc01_g01770:2426	exon	NON_SYNONYMOUS_CODING	gCc/gAc	A/D	25.0%	4	CC	CC	AA	CC
-chr1:3055154	[C/A]	chr1	3055154	Cc01_g01770:2436	exon	SYNONYMOUS_CODING	cgC/cgA	R/R	25.0%	4	CC	CA	CC	CA
-chr1:3055178	[A/G]	chr1	3055178	Cc01_g01770:2460	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	37.5%	4	AA	AG	GG	AA
-chr1:3055254	[T/G]	chr1	3055254	Cc01_g01770:2470	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	25.0%	4	TT	GT	TG	TT
-chr1:3055255	[A/T]	chr1	3055255	Cc01_g01770:2471	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	12.5%	4	AA	AT	AA	AA
-chr1:3055257	[T/C]	chr1	3055257	Cc01_g01770:2473	exon	NON_SYNONYMOUS_CODING	Ttt/Ctt	F/L	25.0%	4	TT	TC	TC	TT
-chr1:3055258	[T/C]	chr1	3055258	Cc01_g01770:2474	exon	NON_SYNONYMOUS_CODING	tTt/tCt	F/S	25.0%	4	TT	TC	TC	TT
-chr1:3055259	[T/G]	chr1	3055259	Cc01_g01770:2475	exon	NON_SYNONYMOUS_CODING	ttT/ttG	F/L	12.5%	4	TT	TT	TG	TT
-chr1:3076176	[T/C]	chr1	3076176	Cc01_g01770:2481	exon	SYNONYMOUS_CODING	agT/agC	S/S	37.5%	4	TT	CT	CC	CC
-chr1:3076177	[G/A]	chr1	3076177	Cc01_g01770:2482	exon	NON_SYNONYMOUS_CODING	Ggt/Agt	G/S	37.5%	4	GG	GA	GG	AA
-chr1:3076201	[A/G]	chr1	3076201	Cc01_g01770:2506	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	12.5%	4	AA	AG	AA	AA
-chr1:3076211	[A/T]	chr1	3076211	Cc01_g01770:2516	exon	NON_SYNONYMOUS_CODING	cAa/cTa	Q/L	12.5%	4	AA	AA	AT	AA
-chr1:3076217	[C/T]	chr1	3076217	Cc01_g01770:2522	exon	NON_SYNONYMOUS_CODING	tCa/tTa	S/L	37.5%	4	CC	TC	CT	CT
-chr1:3076219	[G/A]	chr1	3076219	Cc01_g01770:2524	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	25.0%	4	GG	GA	AG	GG
-chr1:3076221	[C/T]	chr1	3076221	Cc01_g01770:2526	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	37.5%	4	CC	TT	CT	TT
-chr1:3076224	[A/G]	chr1	3076224	Cc01_g01770:2529	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	AA	AG	GA	AA
-chr1:3076239	[G/A]	chr1	3076239	Cc01_g01770:2544	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	GG	GA	GG	GA
-chr1:3076622	[T/G]	chr1	3076622	Cc01_g01770:2572	exon	NON_SYNONYMOUS_CODING	Tct/Gct	S/A	12.5%	4	TT	TT	GT	TT
-chr1:3080563	[C/T]	chr1	3080563	Cc01_g01780:14	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	50.0%	2	CC	TT	NN	NN
-chr1:3080566	[T/A]	chr1	3080566	Cc01_g01780:17	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	50.0%	2	TT	AA	NN	NN
-chr1:3080588	[T/C]	chr1	3080588	Cc01_g01780:39	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	33.3%	3	TT	TT	CC	NN
-chr1:3080607	[C/T]	chr1	3080607	Cc01_g01780:58	exon	NON_SYNONYMOUS_CODING	Cgc/Tgc	R/C	37.5%	4	CC	CT	TT	TT
-chr1:3080619	[G/A]	chr1	3080619	Cc01_g01780:70	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	37.5%	4	GG	GA	AA	AA
-chr1:3080771	[T/C]	chr1	3080771	Cc01_g01780:138	exon	SYNONYMOUS_CODING	atT/atC	I/I	25.0%	4	TT	TT	TT	CC
-chr1:3080777	[A/G]	chr1	3080777	Cc01_g01780:144	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	AA	AG	AA	AA
-chr1:3080789	[T/C]	chr1	3080789	Cc01_g01780:156	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	25.0%	4	TT	TC	TT	TC
-chr1:3080803	[T/A]	chr1	3080803	Cc01_g01780:170	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	25.0%	4	TT	TA	TT	TA
-chr1:3080819	[C/A]	chr1	3080819	Cc01_g01780:186	exon	SYNONYMOUS_CODING	tcC/tcA	S/S	12.5%	4	CC	CC	CC	AC
-chr1:3080919	[C/A]	chr1	3080919	Cc01_g01780:200	exon	NON_SYNONYMOUS_CODING	gCt/gAt	A/D	25.0%	4	CC	AA	CC	CC
-chr1:3080921	[C/T]	chr1	3080921	Cc01_g01780:202	exon	NON_SYNONYMOUS_CODING	Ccc/Tcc	P/S	37.5%	4	CC	CC	TT	TC
-chr1:3080927	[C/G]	chr1	3080927	Cc01_g01780:208	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	25.0%	4	CC	CC	CG	CG
-chr1:3080944	[G/A]	chr1	3080944	Cc01_g01780:225	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	37.5%	4	GG	AA	AA	GA
-chr1:3080947	[A/G]	chr1	3080947	Cc01_g01780:228	exon	SYNONYMOUS_CODING	acA/acG	T/T	37.5%	4	AA	AA	GG	AG
-chr1:3080956	[T/A]	chr1	3080956	Cc01_g01780:237	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	4	TT	AA	AA	AA
-chr1:3081805	[A/T]	chr1	3081805	Cc01_g01780:415	exon	STOP_GAINED	Aga/Tga	R/9	50.0%	3	AA	TT	NN	AT
-chr1:3081884	[T/A]	chr1	3081884	Cc01_g01780:494	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	25.0%	4	TT	TA	TA	TT
-chr1:3081885	[T/A]	chr1	3081885	Cc01_g01780:495	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	37.5%	4	TT	AT	TT	AA
-chr1:3081886	[T/A]	chr1	3081886	Cc01_g01780:496	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	25.0%	4	TT	TA	TA	TT
-chr1:3081887	[T/A]	chr1	3081887	Cc01_g01780:497	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	12.5%	4	TT	TT	TT	TA
-chr1:3081888	[T/A]	chr1	3081888	Cc01_g01780:498	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	12.5%	4	TT	TA	TT	TT
-chr1:3100066	[G/C]	chr1	3100066	Cc01_g01790:442	exon	NON_SYNONYMOUS_CODING	Cga/Gga	R/G	37.5%	4	GG	GC	GG	CC
-chr1:3100063	[C/T]	chr1	3100063	Cc01_g01790:445	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	37.5%	4	CC	CT	CC	TT
-chr1:3099861	[T/C]	chr1	3099861	Cc01_g01790:647	exon	NON_SYNONYMOUS_CODING	gAt/gGt	D/G	16.7%	3	TT	TC	TT	NN
-chr1:3099819	[A/G]	chr1	3099819	Cc01_g01790:689	exon	NON_SYNONYMOUS_CODING	tTc/tCc	F/S	16.7%	3	AA	AG	AA	NN
-chr1:3099817	[A/G]	chr1	3099817	Cc01_g01790:691	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	16.7%	3	AA	AG	AA	NN
-chr1:3099361	[C/T]	chr1	3099361	Cc01_g01790:921	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	50.0%	2	CC	NN	NN	TT
-chr1:3099178	[C/T]	chr1	3099178	Cc01_g01790:1104	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	33.3%	3	CC	NN	TT	CC
-chr1:3098863	[C/T]	chr1	3098863	Cc01_g01790:1419	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	50.0%	2	CC	NN	TT	NN
-chr1:3098710	[T/G]	chr1	3098710	Cc01_g01790:1572	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	33.3%	3	TT	NN	GG	TT
-chr1:3098694	[C/T]	chr1	3098694	Cc01_g01790:1588	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	CC	CC	TT	CC
-chr1:3098670	[C/T]	chr1	3098670	Cc01_g01790:1612	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	25.0%	4	CC	CC	CC	TT
-chr1:3098669	[A/T]	chr1	3098669	Cc01_g01790:1613	exon	NON_SYNONYMOUS_CODING	gTg/gAg	V/E	25.0%	4	AA	AA	AA	TT
-chr1:3098646	[G/A]	chr1	3098646	Cc01_g01790:1636	exon	NON_SYNONYMOUS_CODING	Cgg/Tgg	R/W	33.3%	3	GG	NN	GG	AA
-chr1:3098643	[C/T]	chr1	3098643	Cc01_g01790:1639	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	33.3%	3	CC	NN	TT	CC
-chr1:3098575	[T/A]	chr1	3098575	Cc01_g01790:1707	exon	SYNONYMOUS_CODING	gtA/gtT	V/V	33.3%	3	TT	TT	NN	AA
-chr1:3098545	[C/T]	chr1	3098545	Cc01_g01790:1737	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	2	CC	NN	NN	CT
-chr1:3098445	[T/G]	chr1	3098445	Cc01_g01790:1837	exon	NON_SYNONYMOUS_CODING	Agt/Cgt	S/R	33.3%	3	TT	GG	TT	NN
-chr1:3098439	[A/C]	chr1	3098439	Cc01_g01790:1843	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	33.3%	3	AA	AC	AC	NN
-chr1:3098433	[C/T]	chr1	3098433	Cc01_g01790:1849	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	16.7%	3	CC	CC	TC	NN
-chr1:3098416	[A/G]	chr1	3098416	Cc01_g01790:1866	exon	SYNONYMOUS_CODING	atT/atC	I/I	16.7%	3	AA	AA	GA	NN
-chr1:3098249	[T/G]	chr1	3098249	Cc01_g01790:1982	exon	NON_SYNONYMOUS_CODING	cAa/cCa	Q/P	50.0%	2	TT	NN	GG	NN
-chr1:3098236	[T/G]	chr1	3098236	Cc01_g01790:1995	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	25.0%	4	TT	TG	TG	TT
-chr1:3098217	[T/C]	chr1	3098217	Cc01_g01790:2014	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	25.0%	4	TT	TT	TT	CC
-chr1:3098210	[C/A]	chr1	3098210	Cc01_g01790:2021	exon	NON_SYNONYMOUS_CODING	aGg/aTg	R/M	25.0%	4	CC	AC	AC	CC
-chr1:3098185	[G/T]	chr1	3098185	Cc01_g01790:2046	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	25.0%	4	GG	GG	GG	TT
-chr1:3098182	[C/T]	chr1	3098182	Cc01_g01790:2049	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	37.5%	4	CC	CC	TC	TT
-chr1:3098175	[C/T]	chr1	3098175	Cc01_g01790:2056	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	25.0%	4	CC	CC	TC	CT
-chr1:3098148	[A/G]	chr1	3098148	Cc01_g01790:2083	exon	NON_SYNONYMOUS_CODING	Tac/Cac	Y/H	25.0%	4	AA	GG	GG	GG
-chr1:3098140	[C/G]	chr1	3098140	Cc01_g01790:2091	exon	NON_SYNONYMOUS_CODING	caG/caC	Q/H	25.0%	4	CC	CC	GC	CG
-chr1:3098133	[C/A]	chr1	3098133	Cc01_g01790:2098	exon	NON_SYNONYMOUS_CODING	Gat/Tat	D/Y	37.5%	4	CC	AA	CA	CC
-chr1:3098100	[T/C]	chr1	3098100	Cc01_g01790:2131	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	25.0%	4	TT	TT	TC	TC
-chr1:3098097	[C/T]	chr1	3098097	Cc01_g01790:2134	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	12.5%	4	CC	CC	CC	TC
-chr1:3098083	[C/G]	chr1	3098083	Cc01_g01790:2148	exon	NON_SYNONYMOUS_CODING	gaG/gaC	E/D	12.5%	4	CC	CC	CG	CC
-chr1:3098073	[G/C]	chr1	3098073	Cc01_g01790:2158	exon	NON_SYNONYMOUS_CODING	Cac/Gac	H/D	37.5%	4	GG	CC	CG	GG
-chr1:3098015	[T/C]	chr1	3098015	Cc01_g01790:2216	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	50.0%	2	TT	NN	NN	CC
-chr1:3097800	[C/T]	chr1	3097800	Cc01_g01790:2431	exon	NON_SYNONYMOUS_CODING	Gcg/Acg	A/T	50.0%	2	CC	NN	NN	TT
-chr1:3130398	[G/A]	chr1	3130398	Cc01_g01800:5	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	37.5%	4	GG	GA	GA	GA
-chr1:3130394	[G/A]	chr1	3130394	Cc01_g01800:9	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	GG	GG	AG	GG
-chr1:3130389	[G/A]	chr1	3130389	Cc01_g01800:14	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	37.5%	4	GG	AG	GA	AG
-chr1:3130367	[A/G]	chr1	3130367	Cc01_g01800:36	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	37.5%	4	AA	GA	AG	GA
-chr1:3130332	[C/T]	chr1	3130332	Cc01_g01800:71	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	12.5%	4	CC	CC	TC	CC
-chr1:3130320	[A/G]	chr1	3130320	Cc01_g01800:83	exon	NON_SYNONYMOUS_CODING	gTt/gCt	V/A	12.5%	4	AA	GA	AA	AA
-chr1:3130313	[C/T]	chr1	3130313	Cc01_g01800:90	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	25.0%	4	CC	TT	TT	TT
-chr1:3130268	[G/C]	chr1	3130268	Cc01_g01800:135	exon	NON_SYNONYMOUS_CODING	atC/atG	I/M	37.5%	4	GG	CC	GC	GG
-chr1:3130244	[G/A]	chr1	3130244	Cc01_g01800:159	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	12.5%	4	GG	GG	GG	GA
-chr1:3130238	[G/T]	chr1	3130238	Cc01_g01800:165	exon	NON_SYNONYMOUS_CODING	aaC/aaA	N/K	37.5%	4	GG	TT	GT	GG
-chr1:3130227	[T/C]	chr1	3130227	Cc01_g01800:176	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	50.0%	4	TT	CC	TC	TC
-chr1:3130205	[T/C]	chr1	3130205	Cc01_g01800:198	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	37.5%	4	TT	CC	TC	TT
-chr1:3130073	[A/C]	chr1	3130073	Cc01_g01800:276	exon	NON_SYNONYMOUS_CODING	aaT/aaG	N/K	33.3%	3	AA	CC	CC	NN
-chr1:3130016	[G/T]	chr1	3130016	Cc01_g01800:333	exon	SYNONYMOUS_CODING	ctC/ctA	L/L	50.0%	3	GG	NN	TT	GT
-chr1:3129989	[G/C]	chr1	3129989	Cc01_g01800:360	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	12.5%	4	GG	GC	GG	GG
-chr1:3129968	[G/C]	chr1	3129968	Cc01_g01800:381	exon	NON_SYNONYMOUS_CODING	caC/caG	H/Q	12.5%	4	GG	GG	GC	GG
-chr1:3129955	[C/T]	chr1	3129955	Cc01_g01800:394	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	37.5%	4	CC	TT	TC	CC
-chr1:3129939	[G/C]	chr1	3129939	Cc01_g01800:410	exon	NON_SYNONYMOUS_CODING	aCg/aGg	T/R	12.5%	4	GG	GG	GG	GC
-chr1:3129936	[G/A]	chr1	3129936	Cc01_g01800:413	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	12.5%	4	GG	GG	GG	GA
-chr1:3129931	[T/G]	chr1	3129931	Cc01_g01800:418	exon	SYNONYMOUS_CODING	Aga/Cga	R/R	12.5%	4	TT	TT	TT	TG
-chr1:3129930	[C/T]	chr1	3129930	Cc01_g01800:419	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	12.5%	4	CC	CC	CC	TC
-chr1:3129911	[A/G]	chr1	3129911	Cc01_g01800:438	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	12.5%	4	AA	AA	AA	GA
-chr1:3129147	[T/C]	chr1	3129147	Cc01_g01800:481	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	50.0%	2	TT	CC	NN	NN
-chr1:3129110	[C/T]	chr1	3129110	Cc01_g01800:518	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	50.0%	2	CC	TT	NN	NN
-chr1:3129103	[G/A]	chr1	3129103	Cc01_g01800:525	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	50.0%	2	GG	AA	NN	NN
-chr1:3128596	[C/T]	chr1	3128596	Cc01_g01800:1032	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	33.3%	3	CC	NN	TT	CC
-chr1:3128592	[T/C]	chr1	3128592	Cc01_g01800:1036	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	33.3%	3	TT	NN	CC	TT
-chr1:3128555	[A/G]	chr1	3128555	Cc01_g01800:1073	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	16.7%	3	AA	NN	AG	AA
-chr1:3128551	[T/C]	chr1	3128551	Cc01_g01800:1077	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	16.7%	3	TT	NN	TC	TT
-chr1:3128512	[A/C]	chr1	3128512	Cc01_g01800:1116	exon	NON_SYNONYMOUS_CODING	gaT/gaG	D/E	33.3%	3	AA	NN	CC	CC
-chr1:3128013	[A/T]	chr1	3128013	Cc01_g01800:1525	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	33.3%	3	AA	NN	TT	AA
-chr1:3127995	[T/A]	chr1	3127995	Cc01_g01800:1543	exon	NON_SYNONYMOUS_CODING	Aat/Tat	N/Y	33.3%	3	TT	NN	TT	AA
-chr1:3127863	[C/T]	chr1	3127863	Cc01_g01800:1675	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	33.3%	3	CC	NN	TT	CC
-chr1:3127784	[G/T]	chr1	3127784	Cc01_g01800:1754	exon	NON_SYNONYMOUS_CODING	cCg/cAg	P/Q	33.3%	3	GG	NN	GG	TT
-chr1:3127444	[C/G]	chr1	3127444	Cc01_g01800:2094	exon	NON_SYNONYMOUS_CODING	caG/caC	Q/H	50.0%	2	CC	NN	NN	GG
-chr1:3127440	[C/A]	chr1	3127440	Cc01_g01800:2098	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	33.3%	3	CC	NN	CC	AA
-chr1:3127337	[C/T]	chr1	3127337	Cc01_g01800:2201	exon	NON_SYNONYMOUS_CODING	gGa/gAa	G/E	33.3%	3	CC	TT	CC	NN
-chr1:3127308	[G/A]	chr1	3127308	Cc01_g01800:2230	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	50.0%	3	GG	GA	AA	NN
-chr1:3127296	[T/C]	chr1	3127296	Cc01_g01800:2242	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	33.3%	3	TT	CC	CC	NN
-chr1:3127276	[C/T]	chr1	3127276	Cc01_g01800:2262	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	33.3%	3	CC	CC	TT	NN
-chr1:3127267	[C/T]	chr1	3127267	Cc01_g01800:2271	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	33.3%	3	CC	TT	TT	NN
-chr1:3127260	[A/C]	chr1	3127260	Cc01_g01800:2278	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	33.3%	3	AA	CC	AA	NN
-chr1:3127254	[T/G]	chr1	3127254	Cc01_g01800:2284	exon	SYNONYMOUS_CODING	Agg/Cgg	R/R	50.0%	2	TT	NN	GG	NN
-chr1:3127253	[C/T]	chr1	3127253	Cc01_g01800:2285	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	33.3%	3	CC	TT	TT	NN
-chr1:3127252	[C/T]	chr1	3127252	Cc01_g01800:2286	exon	SYNONYMOUS_CODING	agG/agA	R/R	33.3%	3	CC	TT	TT	NN
-chr1:3127234	[G/A]	chr1	3127234	Cc01_g01800:2304	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	25.0%	2	GG	NN	GA	NN
-chr1:3127034	[G/A]	chr1	3127034	Cc01_g01800:2411	exon	NON_SYNONYMOUS_CODING	gCa/gTa	A/V	50.0%	2	GG	AA	NN	NN
-chr1:3127033	[T/A]	chr1	3127033	Cc01_g01800:2412	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	50.0%	2	TT	AA	NN	NN
-chr1:3126983	[A/G]	chr1	3126983	Cc01_g01800:2462	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	25.0%	4	AA	AA	AA	GG
-chr1:3126979	[A/G]	chr1	3126979	Cc01_g01800:2466	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	AA	GG	AA	AA
-chr1:3126953	[A/C]	chr1	3126953	Cc01_g01800:2492	exon	NON_SYNONYMOUS_CODING	cTc/cGc	L/R	33.3%	3	AA	NN	AA	CC
-chr1:3126937	[G/T]	chr1	3126937	Cc01_g01800:2508	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	33.3%	3	GG	NN	GG	TT
-chr1:3126913	[C/T]	chr1	3126913	Cc01_g01800:2532	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	16.7%	3	CC	NN	CT	CC
-chr1:3126816	[G/A]	chr1	3126816	Cc01_g01800:2569	exon	NON_SYNONYMOUS_CODING	Cac/Tac	H/Y	33.3%	3	GG	NN	GG	AA
-chr1:3126795	[C/T]	chr1	3126795	Cc01_g01800:2590	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	CC	CC	CC	TT
-chr1:3126780	[A/T]	chr1	3126780	Cc01_g01800:2605	exon	NON_SYNONYMOUS_CODING	Tcg/Acg	S/T	25.0%	4	AA	AA	AA	TT
-chr1:3126751	[G/A]	chr1	3126751	Cc01_g01800:2634	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	33.3%	3	GG	AA	AA	NN
-chr1:3126700	[G/T]	chr1	3126700	Cc01_g01800:2685	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	50.0%	4	GG	TT	GG	TT
-chr1:3126699	[G/A]	chr1	3126699	Cc01_g01800:2686	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	25.0%	4	GG	GA	GG	GA
-chr1:3126690	[C/G]	chr1	3126690	Cc01_g01800:2695	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	50.0%	4	CC	GG	CC	GG
-chr1:3126637	[A/G]	chr1	3126637	Cc01_g01800:2748	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	50.0%	4	AA	GG	AA	GG
-chr1:3126626	[C/T]	chr1	3126626	Cc01_g01800:2759	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	33.3%	3	CC	TT	CC	NN
-chr1:3126612	[G/A]	chr1	3126612	Cc01_g01800:2773	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	33.3%	3	GG	AA	GG	NN
-chr1:3126600	[A/T]	chr1	3126600	Cc01_g01800:2785	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	33.3%	3	AA	TT	AA	NN
-chr1:3126553	[T/A]	chr1	3126553	Cc01_g01800:2832	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	33.3%	3	TT	TT	AA	NN
-chr1:3126547	[G/T]	chr1	3126547	Cc01_g01800:2838	exon	SYNONYMOUS_CODING	ctC/ctA	L/L	33.3%	3	GG	GG	TT	NN
-chr1:3126532	[T/A]	chr1	3126532	Cc01_g01800:2853	exon	NON_SYNONYMOUS_CODING	ttA/ttT	L/F	33.3%	3	TT	TT	AA	NN
-chr1:3126528	[T/C]	chr1	3126528	Cc01_g01800:2857	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	33.3%	3	TT	CC	TT	NN
-chr1:3126526	[T/A]	chr1	3126526	Cc01_g01800:2859	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	25.0%	4	TT	TT	TT	AA
-chr1:3126503	[C/T]	chr1	3126503	Cc01_g01800:2882	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	12.5%	4	CC	CC	CT	CC
-chr1:3126400	[T/C]	chr1	3126400	Cc01_g01800:2985	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	33.3%	3	TT	CC	TT	NN
-chr1:3126397	[C/T]	chr1	3126397	Cc01_g01800:2988	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	CC	TT	TT	TT
-chr1:3126364	[G/T]	chr1	3126364	Cc01_g01800:3021	exon	SYNONYMOUS_CODING	cgC/cgA	R/R	50.0%	4	GG	TT	GG	TT
-chr1:3126267	[A/G]	chr1	3126267	Cc01_g01800:3118	exon	NON_SYNONYMOUS_CODING	Tcg/Ccg	S/P	33.3%	3	AA	GG	GG	NN
-chr1:3126189	[T/C]	chr1	3126189	Cc01_g01800:3196	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	50.0%	2	TT	NN	CC	NN
-chr1:3126120	[T/G]	chr1	3126120	Cc01_g01800:3265	exon	SYNONYMOUS_CODING	Aga/Cga	R/R	33.3%	3	TT	GG	GG	NN
-chr1:3148320	[G/C]	chr1	3148320	Cc01_g01810:19	exon	NON_SYNONYMOUS_CODING	Cat/Gat	H/D	25.0%	4	GG	CC	CC	CC
-chr1:3148319	[T/G]	chr1	3148319	Cc01_g01810:20	exon	NON_SYNONYMOUS_CODING	cAt/cCt	H/P	12.5%	4	TT	TT	TT	TG
-chr1:3148309	[A/T]	chr1	3148309	Cc01_g01810:30	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	25.0%	4	AA	TT	TT	TT
-chr1:3148308	[A/C]	chr1	3148308	Cc01_g01810:31	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	25.0%	4	AA	CC	CC	CC
-chr1:3148305	[G/A]	chr1	3148305	Cc01_g01810:34	exon	NON_SYNONYMOUS_CODING	Cat/Tat	H/Y	25.0%	4	GG	AA	AA	AA
-chr1:3148268	[G/T]	chr1	3148268	Cc01_g01810:71	exon	NON_SYNONYMOUS_CODING	aCg/aAg	T/K	12.5%	4	GG	GG	GT	GG
-chr1:3148255	[A/T]	chr1	3148255	Cc01_g01810:84	exon	SYNONYMOUS_CODING	acT/acA	T/T	12.5%	4	AA	AA	AT	AA
-chr1:3148238	[A/G]	chr1	3148238	Cc01_g01810:101	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	37.5%	4	AA	GG	GA	GG
-chr1:3148222	[G/C]	chr1	3148222	Cc01_g01810:117	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	12.5%	4	GG	GG	CG	GG
-chr1:3148212	[A/G]	chr1	3148212	Cc01_g01810:127	exon	NON_SYNONYMOUS_CODING	Tgt/Cgt	C/R	12.5%	4	AA	AG	AA	AA
-chr1:3148211	[C/T]	chr1	3148211	Cc01_g01810:128	exon	NON_SYNONYMOUS_CODING	tGt/tAt	C/Y	37.5%	4	CC	TT	TC	TT
-chr1:3148184	[T/C]	chr1	3148184	Cc01_g01810:155	exon	NON_SYNONYMOUS_CODING	tAc/tGc	Y/C	12.5%	4	TT	CT	TT	TT
-chr1:3148162	[G/A]	chr1	3148162	Cc01_g01810:177	exon	SYNONYMOUS_CODING	agC/agT	S/S	12.5%	4	GG	AG	GG	GG
-chr1:3148147	[C/T]	chr1	3148147	Cc01_g01810:192	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	CC	TT	TT	TT
-chr1:3148104	[T/C]	chr1	3148104	Cc01_g01810:202	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	12.5%	4	TT	TT	TC	TT
-chr1:3148094	[G/T]	chr1	3148094	Cc01_g01810:212	exon	STOP_GAINED	tCa/tAa	S/1	12.5%	4	GG	GG	GG	GT
-chr1:3148091	[G/T]	chr1	3148091	Cc01_g01810:215	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	12.5%	4	GG	GG	GG	GT
-chr1:3191460	[A/G]	chr1	3191460	Cc01_g01820:313	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	25.0%	4	AA	GG	AA	AA
-chr1:3191468	[T/G]	chr1	3191468	Cc01_g01820:321	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	12.5%	4	TT	TG	TT	TT
-chr1:3191469	[G/A]	chr1	3191469	Cc01_g01820:322	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	25.0%	4	GG	AA	AA	AA
-chr1:3191497	[A/G]	chr1	3191497	Cc01_g01820:350	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	12.5%	4	AA	AA	AA	AG
-chr1:3191499	[G/A]	chr1	3191499	Cc01_g01820:352	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	12.5%	4	GG	GG	GG	GA
-chr1:3191505	[C/G]	chr1	3191505	Cc01_g01820:358	exon	NON_SYNONYMOUS_CODING	Cta/Gta	L/V	25.0%	4	CC	CC	CC	GG
-chr1:3191507	[A/G]	chr1	3191507	Cc01_g01820:360	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	37.5%	4	AA	GA	AA	GG
-chr1:3191521	[C/A]	chr1	3191521	Cc01_g01820:374	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	12.5%	4	CC	CC	CA	CC
-chr1:3191526	[G/T]	chr1	3191526	Cc01_g01820:379	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	12.5%	4	GG	GG	GT	GG
-chr1:3191552	[T/C]	chr1	3191552	Cc01_g01820:405	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	37.5%	4	TT	CC	CC	TC
-chr1:3191561	[A/G]	chr1	3191561	Cc01_g01820:414	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AA	AA	GA
-chr1:3191576	[T/C]	chr1	3191576	Cc01_g01820:429	exon	SYNONYMOUS_CODING	acT/acC	T/T	25.0%	4	TT	TT	TC	TC
-chr1:3191774	[T/C]	chr1	3191774	Cc01_g01820:627	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	12.5%	4	TT	TC	TT	TT
-chr1:3191801	[A/G]	chr1	3191801	Cc01_g01820:654	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	AA	AA	AA	AG
-chr1:3191814	[A/G]	chr1	3191814	Cc01_g01820:667	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	12.5%	4	AA	AA	AA	AG
-chr1:3191835	[G/A]	chr1	3191835	Cc01_g01820:688	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	12.5%	4	GG	GG	GG	AG
-chr1:3191836	[G/A]	chr1	3191836	Cc01_g01820:689	exon	NON_SYNONYMOUS_CODING	gGa/gAa	G/E	12.5%	4	GG	GG	GA	GG
-chr1:3191840	[A/G]	chr1	3191840	Cc01_g01820:693	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	AA	AA	AG	AA
-chr1:3191846	[A/C]	chr1	3191846	Cc01_g01820:699	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	12.5%	4	AA	AA	AC	AA
-chr1:3191856	[C/A]	chr1	3191856	Cc01_g01820:709	exon	SYNONYMOUS_CODING	Cgg/Agg	R/R	25.0%	4	CC	CA	CC	AC
-chr1:3191872	[G/A]	chr1	3191872	Cc01_g01820:725	exon	NON_SYNONYMOUS_CODING	gGa/gAa	G/E	25.0%	4	GG	GA	GG	AG
-chr1:3191876	[A/C]	chr1	3191876	Cc01_g01820:729	exon	NON_SYNONYMOUS_CODING	gaA/gaC	E/D	25.0%	4	AA	AC	AA	CA
-chr1:3191881	[A/G]	chr1	3191881	Cc01_g01820:734	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	25.0%	4	AA	AG	AG	AA
-chr1:3191888	[A/C]	chr1	3191888	Cc01_g01820:741	exon	NON_SYNONYMOUS_CODING	caA/caC	Q/H	12.5%	4	AA	AA	CA	AA
-chr1:3191897	[G/A]	chr1	3191897	Cc01_g01820:750	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	12.5%	4	GG	GG	GG	GA
-chr1:3191902	[A/G]	chr1	3191902	Cc01_g01820:755	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	12.5%	4	AA	AA	AA	AG
-chr1:3191903	[G/A]	chr1	3191903	Cc01_g01820:756	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	GG	GG	GG	GA
-chr1:3191912	[T/A]	chr1	3191912	Cc01_g01820:765	exon	SYNONYMOUS_CODING	ctT/ctA	L/L	50.0%	4	TT	TT	AA	AA
-chr1:3192960	[A/G]	chr1	3192960	Cc01_g01820:1688	exon	NON_SYNONYMOUS_CODING	cAt/cGt	H/R	50.0%	2	AA	NN	GG	NN
-chr1:3192995	[G/T]	chr1	3192995	Cc01_g01820:1723	exon	NON_SYNONYMOUS_CODING	Ggc/Tgc	G/C	25.0%	2	GG	NN	GT	NN
-chr1:3193034	[T/A]	chr1	3193034	Cc01_g01820:1762	exon	NON_SYNONYMOUS_CODING	Tgg/Agg	W/R	50.0%	3	TT	AA	TA	NN
-chr1:3193036	[G/T]	chr1	3193036	Cc01_g01820:1764	exon	NON_SYNONYMOUS_CODING	tgG/tgT	W/C	50.0%	3	GG	TT	GT	NN
-chr1:3193095	[A/G]	chr1	3193095	Cc01_g01820:1823	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	25.0%	2	AA	NN	NN	AG
-chr1:3193128	[G/A]	chr1	3193128	Cc01_g01820:1856	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	33.3%	3	GG	AA	GG	NN
-chr1:3193178	[T/C]	chr1	3193178	Cc01_g01820:1906	exon	NON_SYNONYMOUS_CODING	Tgc/Cgc	C/R	33.3%	3	TT	CC	TT	NN
-chr1:3193205	[G/A]	chr1	3193205	Cc01_g01820:1933	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	33.3%	3	GG	AA	GG	NN
-chr1:3193208	[C/G]	chr1	3193208	Cc01_g01820:1936	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	33.3%	3	CC	GG	GG	NN
-chr1:3193232	[G/A]	chr1	3193232	Cc01_g01820:1960	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	33.3%	3	GG	AA	GG	NN
-chr1:3193249	[T/A]	chr1	3193249	Cc01_g01820:1977	exon	NON_SYNONYMOUS_CODING	ttT/ttA	F/L	33.3%	3	TT	AA	TT	NN
-chr1:3193250	[A/G]	chr1	3193250	Cc01_g01820:1978	exon	NON_SYNONYMOUS_CODING	Agg/Ggg	R/G	33.3%	3	AA	GG	AA	NN
-chr1:3193251	[G/A]	chr1	3193251	Cc01_g01820:1979	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	33.3%	3	GG	AA	GG	NN
-chr1:3193257	[A/T]	chr1	3193257	Cc01_g01820:1985	exon	NON_SYNONYMOUS_CODING	cAa/cTa	Q/L	33.3%	3	AA	TT	AA	NN
-chr1:3193258	[A/T]	chr1	3193258	Cc01_g01820:1986	exon	NON_SYNONYMOUS_CODING	caA/caT	Q/H	33.3%	3	AA	TT	AA	NN
-chr1:3193262	[G/A]	chr1	3193262	Cc01_g01820:1990	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	33.3%	3	GG	AA	GG	NN
-chr1:3193330	[T/C]	chr1	3193330	Cc01_g01820:2058	exon	SYNONYMOUS_CODING	caT/caC	H/H	50.0%	2	TT	NN	CC	NN
-chr1:3193551	[A/C]	chr1	3193551	Cc01_g01820:2279	exon	NON_SYNONYMOUS_CODING	tAt/tCt	Y/S	50.0%	4	AA	CC	AA	CC
-chr1:3193556	[A/G]	chr1	3193556	Cc01_g01820:2284	exon	NON_SYNONYMOUS_CODING	Acc/Gcc	T/A	25.0%	4	AA	AA	AA	GG
-chr1:3193561	[T/C]	chr1	3193561	Cc01_g01820:2289	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	25.0%	4	TT	TT	TT	CC
-chr1:3193565	[C/A]	chr1	3193565	Cc01_g01820:2293	exon	NON_SYNONYMOUS_CODING	Cag/Aag	Q/K	25.0%	4	CC	AA	CC	CC
-chr1:3193580	[A/T]	chr1	3193580	Cc01_g01820:2308	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	25.0%	4	AA	AA	AA	TT
-chr1:3193581	[C/T]	chr1	3193581	Cc01_g01820:2309	exon	NON_SYNONYMOUS_CODING	aCt/aTt	T/I	25.0%	4	CC	CC	CC	TT
-chr1:3193590	[G/A]	chr1	3193590	Cc01_g01820:2318	exon	NON_SYNONYMOUS_CODING	gGc/gAc	G/D	25.0%	4	GG	AA	GG	GG
-chr1:3193598	[G/A]	chr1	3193598	Cc01_g01820:2326	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	25.0%	4	GG	AA	GG	GG
-chr1:3193621	[A/G]	chr1	3193621	Cc01_g01820:2349	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	33.3%	3	AA	NN	AA	GG
-chr1:3193623	[G/A]	chr1	3193623	Cc01_g01820:2351	exon	NON_SYNONYMOUS_CODING	cGa/cAa	R/Q	33.3%	3	GG	NN	GG	AA
-chr1:3193638	[T/C]	chr1	3193638	Cc01_g01820:2366	exon	NON_SYNONYMOUS_CODING	tTg/tCg	L/S	33.3%	3	TT	NN	TT	CC
-chr1:3193642	[G/T]	chr1	3193642	Cc01_g01820:2370	exon	NON_SYNONYMOUS_CODING	gaG/gaT	E/D	12.5%	4	GG	GG	GT	GG
-chr1:3193647	[A/T]	chr1	3193647	Cc01_g01820:2375	exon	NON_SYNONYMOUS_CODING	gAa/gTa	E/V	37.5%	4	AA	TT	AT	AA
-chr1:3193825	[G/T]	chr1	3193825	Cc01_g01820:2553	exon	SYNONYMOUS_CODING	tcG/tcT	S/S	16.7%	3	GG	GG	GT	NN
-chr1:3193843	[A/G]	chr1	3193843	Cc01_g01820:2571	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	33.3%	3	AA	GG	AA	NN
-chr1:3193848	[A/G]	chr1	3193848	Cc01_g01820:2576	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	33.3%	3	AA	AG	AG	NN
-chr1:3193868	[G/A]	chr1	3193868	Cc01_g01820:2596	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	16.7%	3	GG	GA	GG	NN
-chr1:3193975	[T/C]	chr1	3193975	Cc01_g01820:2703	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	33.3%	3	TT	NN	TT	CC
-chr1:3194001	[G/A]	chr1	3194001	Cc01_g01820:2729	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	33.3%	3	GG	NN	GG	AA
-chr1:3197392	[A/G]	chr1	3197392	Cc01_g01830:128	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	12.5%	4	AA	AG	AA	AA
-chr1:3197403	[C/T]	chr1	3197403	Cc01_g01830:139	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	37.5%	4	CC	CT	TT	CC
-chr1:3197417	[A/G]	chr1	3197417	Cc01_g01830:153	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	50.0%	4	AA	AG	GG	AG
-chr1:3197423	[A/G]	chr1	3197423	Cc01_g01830:159	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	AA	AG	AA	AG
-chr1:3197426	[A/G]	chr1	3197426	Cc01_g01830:162	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	25.0%	4	AA	AG	AA	AG
-chr1:3197433	[T/A]	chr1	3197433	Cc01_g01830:169	exon	NON_SYNONYMOUS_CODING	Ttg/Atg	L/M	50.0%	4	TT	TA	AA	TA
-chr1:3197457	[T/C]	chr1	3197457	Cc01_g01830:193	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	25.0%	4	TT	CT	TT	CT
-chr1:3197458	[C/T]	chr1	3197458	Cc01_g01830:194	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	12.5%	4	CC	CC	CT	CC
-chr1:3197465	[T/G]	chr1	3197465	Cc01_g01830:201	exon	SYNONYMOUS_CODING	gcT/gcG	A/A	25.0%	4	TT	TT	TG	TG
-chr1:3197474	[C/T]	chr1	3197474	Cc01_g01830:210	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	37.5%	4	CC	CT	TC	CT
-chr1:3197478	[T/C]	chr1	3197478	Cc01_g01830:214	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	12.5%	4	TT	TT	TC	TT
-chr1:3197482	[T/C]	chr1	3197482	Cc01_g01830:218	exon	NON_SYNONYMOUS_CODING	cTa/cCa	L/P	37.5%	4	TT	CT	TC	CT
-chr1:3197490	[G/A]	chr1	3197490	Cc01_g01830:226	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	GG	GG	GA	GG
-chr1:3197494	[T/C]	chr1	3197494	Cc01_g01830:230	exon	NON_SYNONYMOUS_CODING	aTc/aCc	I/T	12.5%	4	TT	CT	TT	TT
-chr1:3197498	[C/T]	chr1	3197498	Cc01_g01830:234	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	12.5%	4	CC	TC	CC	CC
-chr1:3197500	[T/C]	chr1	3197500	Cc01_g01830:236	exon	NON_SYNONYMOUS_CODING	cTt/cCt	L/P	25.0%	4	TT	CT	TC	TT
-chr1:3197504	[C/T]	chr1	3197504	Cc01_g01830:240	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CC	CT	CC
-chr1:3197513	[G/T]	chr1	3197513	Cc01_g01830:249	exon	SYNONYMOUS_CODING	gtG/gtT	V/V	12.5%	4	GG	GG	GT	GG
-chr1:3197514	[C/A]	chr1	3197514	Cc01_g01830:250	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	25.0%	4	CC	CA	AC	CC
-chr1:3197516	[T/G]	chr1	3197516	Cc01_g01830:252	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	25.0%	4	TT	GT	TG	TT
-chr1:3197529	[G/A]	chr1	3197529	Cc01_g01830:265	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	50.0%	4	GG	GA	GA	AA
-chr1:3197531	[C/T]	chr1	3197531	Cc01_g01830:267	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	CC	CC	CC	CT
-chr1:3197533	[A/T]	chr1	3197533	Cc01_g01830:269	exon	NON_SYNONYMOUS_CODING	gAt/gTt	D/V	12.5%	4	AA	AA	AA	AT
-chr1:3197544	[T/G]	chr1	3197544	Cc01_g01830:280	exon	NON_SYNONYMOUS_CODING	Tgt/Ggt	C/G	12.5%	4	TT	TT	TT	GT
-chr1:3197558	[C/T]	chr1	3197558	Cc01_g01830:294	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	CC	CC	CT	CC
-chr1:3293623	[C/T]	chr1	3293623	Cc01_g01840:150	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	33.3%	3	CC	TT	NN	TT
-chr1:3293672	[A/C]	chr1	3293672	Cc01_g01840:199	exon	NON_SYNONYMOUS_CODING	Aag/Cag	K/Q	12.5%	4	AA	AA	AC	AA
-chr1:3293717	[G/A]	chr1	3293717	Cc01_g01840:244	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	GG	GG	GA	GG
-chr1:3294121	[G/C]	chr1	3294121	Cc01_g01840:555	exon	NON_SYNONYMOUS_CODING	aaG/aaC	K/N	25.0%	4	GG	CC	GG	GG
-chr1:3294122	[A/C]	chr1	3294122	Cc01_g01840:556	exon	NON_SYNONYMOUS_CODING	Aag/Cag	K/Q	25.0%	4	AA	AA	CC	AA
-chr1:3294138	[T/A]	chr1	3294138	Cc01_g01840:572	exon	NON_SYNONYMOUS_CODING	cTc/cAc	L/H	33.3%	3	TT	TT	AA	NN
-chr1:3294175	[A/G]	chr1	3294175	Cc01_g01840:609	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	16.7%	3	AA	AA	NN	AG
-chr1:3294278	[G/A]	chr1	3294278	Cc01_g01840:655	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	33.3%	3	GG	AA	NN	AA
-chr1:3294351	[C/T]	chr1	3294351	Cc01_g01840:728	exon	NON_SYNONYMOUS_CODING	tCa/tTa	S/L	25.0%	4	CC	CC	TT	CC
-chr1:3294386	[A/G]	chr1	3294386	Cc01_g01840:763	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	33.3%	3	AA	GG	NN	GG
-chr1:3294489	[G/T]	chr1	3294489	Cc01_g01840:866	exon	NON_SYNONYMOUS_CODING	cGa/cTa	R/L	25.0%	4	GG	TT	TT	TT
-chr1:3294543	[C/T]	chr1	3294543	Cc01_g01840:920	exon	NON_SYNONYMOUS_CODING	tCt/tTt	S/F	12.5%	4	CC	CT	CC	CC
-chr1:3295343	[G/C]	chr1	3295343	Cc01_g01840:1501	exon	NON_SYNONYMOUS_CODING	Gaa/Caa	E/Q	33.3%	3	GG	CC	GG	NN
-chr1:3295400	[G/A]	chr1	3295400	Cc01_g01840:1558	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	37.5%	4	GG	GA	GG	AA
-chr1:3295407	[C/A]	chr1	3295407	Cc01_g01840:1565	exon	NON_SYNONYMOUS_CODING	gCt/gAt	A/D	25.0%	4	CC	CC	AA	CC
-chr1:3295410	[T/A]	chr1	3295410	Cc01_g01840:1568	exon	NON_SYNONYMOUS_CODING	gTt/gAt	V/D	25.0%	4	TT	TT	TT	AA
-chr1:3295411	[T/G]	chr1	3295411	Cc01_g01840:1569	exon	SYNONYMOUS_CODING	gtT/gtG	V/V	50.0%	4	TT	GG	TT	GG
-chr1:3295423	[G/T]	chr1	3295423	Cc01_g01840:1581	exon	SYNONYMOUS_CODING	ccG/ccT	P/P	12.5%	4	GG	TG	GG	GG
-chr1:3295466	[G/A]	chr1	3295466	Cc01_g01840:1624	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	33.3%	3	GG	AA	NN	AA
-chr1:3295709	[T/C]	chr1	3295709	Cc01_g01840:1867	exon	NON_SYNONYMOUS_CODING	Tgt/Cgt	C/R	50.0%	2	TT	NN	NN	CC
-chr1:3295750	[A/G]	chr1	3295750	Cc01_g01840:1908	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	50.0%	2	AA	NN	NN	GG
-chr1:3295781	[G/A]	chr1	3295781	Cc01_g01840:1939	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	16.7%	3	GG	GG	NN	GA
-chr1:3295793	[T/A]	chr1	3295793	Cc01_g01840:1951	exon	NON_SYNONYMOUS_CODING	Tgg/Agg	W/R	25.0%	4	TT	TT	TT	AA
-chr1:3295794	[G/A]	chr1	3295794	Cc01_g01840:1952	exon	STOP_GAINED	tGg/tAg	W/1	50.0%	4	GG	AA	GG	AA
-chr1:3295796	[T/G]	chr1	3295796	Cc01_g01840:1954	exon	NON_SYNONYMOUS_CODING	Tat/Gat	Y/D	33.3%	3	TT	TT	NN	GG
-chr1:3295811	[C/G]	chr1	3295811	Cc01_g01840:1969	exon	NON_SYNONYMOUS_CODING	Caa/Gaa	Q/E	37.5%	4	CC	CG	CC	GG
-chr1:3295832	[G/C]	chr1	3295832	Cc01_g01840:1990	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	50.0%	3	GG	CC	NN	GC
-chr1:3295834	[T/A]	chr1	3295834	Cc01_g01840:1992	exon	NON_SYNONYMOUS_CODING	gaT/gaA	D/E	50.0%	3	TT	AA	NN	TA
-chr1:3295846	[A/G]	chr1	3295846	Cc01_g01840:2004	exon	SYNONYMOUS_CODING	acA/acG	T/T	33.3%	3	AA	AG	NN	GA
-chr1:3295852	[T/C]	chr1	3295852	Cc01_g01840:2010	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	33.3%	3	TT	CC	NN	CC
-chr1:3295877	[T/A]	chr1	3295877	Cc01_g01840:2035	exon	NON_SYNONYMOUS_CODING	Tac/Aac	Y/N	33.3%	3	TT	TT	AA	NN
-chr1:3295893	[G/A]	chr1	3295893	Cc01_g01840:2051	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	33.3%	3	GG	NN	AA	GG
-chr1:3323377	[T/C]	chr1	3323377	Cc01_g01850:669	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	12.5%	4	TT	TT	TT	TC
-chr1:3323201	[C/T]	chr1	3323201	Cc01_g01850:845	exon	NON_SYNONYMOUS_CODING	aGc/aAc	S/N	16.7%	3	CC	CT	NN	CC
-chr1:3337218	[C/A]	chr1	3337218	Cc01_g01860:15	exon	SYNONYMOUS_CODING	acG/acT	T/T	12.5%	4	CC	CA	CC	CC
-chr1:3337216	[G/A]	chr1	3337216	Cc01_g01860:17	exon	NON_SYNONYMOUS_CODING	tCg/tTg	S/L	12.5%	4	GG	GG	GG	GA
-chr1:3337209	[G/C]	chr1	3337209	Cc01_g01860:24	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	12.5%	4	GG	GG	GC	GG
-chr1:3337191	[C/T]	chr1	3337191	Cc01_g01860:42	exon	SYNONYMOUS_CODING	ctG/ctA	L/L	37.5%	4	CC	TT	TC	CC
-chr1:3337176	[G/T]	chr1	3337176	Cc01_g01860:57	exon	SYNONYMOUS_CODING	ctC/ctA	L/L	50.0%	4	GG	TT	TT	GG
-chr1:3337167	[C/T]	chr1	3337167	Cc01_g01860:66	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	37.5%	4	CC	TT	TC	CC
-chr1:3337129	[C/T]	chr1	3337129	Cc01_g01860:104	exon	NON_SYNONYMOUS_CODING	aGa/aAa	R/K	25.0%	4	CC	TT	TT	TT
-chr1:3336284	[G/A]	chr1	3336284	Cc01_g01860:213	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	GG	GG	GA	GG
-chr1:3336266	[G/A]	chr1	3336266	Cc01_g01860:231	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	50.0%	4	GG	GA	GA	AA
-chr1:3336239	[T/C]	chr1	3336239	Cc01_g01860:258	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	50.0%	4	TT	TC	CC	TC
-chr1:3333450	[A/T]	chr1	3333450	Cc01_g01860:400	exon	NON_SYNONYMOUS_CODING	Tta/Ata	L/I	12.5%	4	AA	AA	AT	AA
-chr1:3333413	[G/C]	chr1	3333413	Cc01_g01860:437	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	12.5%	4	GG	GC	GG	GG
-chr1:3333326	[G/A]	chr1	3333326	Cc01_g01860:524	exon	NON_SYNONYMOUS_CODING	tCa/tTa	S/L	12.5%	4	GG	GG	GG	GA
-chr1:3333322	[T/C]	chr1	3333322	Cc01_g01860:528	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	12.5%	4	TT	TT	TC	TT
-chr1:3333297	[C/T]	chr1	3333297	Cc01_g01860:553	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	12.5%	4	CC	CC	TC	CC
-chr1:3333229	[G/A]	chr1	3333229	Cc01_g01860:621	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	25.0%	4	GG	GA	GG	GA
-chr1:3333223	[C/T]	chr1	3333223	Cc01_g01860:627	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	CC	CC	CT	CC
-chr1:3332599	[C/T]	chr1	3332599	Cc01_g01860:669	exon	SYNONYMOUS_CODING	acG/acA	T/T	12.5%	4	CC	CC	CT	CC
-chr1:3332597	[C/G]	chr1	3332597	Cc01_g01860:671	exon	NON_SYNONYMOUS_CODING	cGa/cCa	R/P	12.5%	4	CC	CC	GC	CC
-chr1:3332395	[T/C]	chr1	3332395	Cc01_g01860:775	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	12.5%	4	TT	TT	TC	TT
-chr1:3332371	[G/C]	chr1	3332371	Cc01_g01860:799	exon	NON_SYNONYMOUS_CODING	Cag/Gag	Q/E	12.5%	4	GG	GG	CG	GG
-chr1:3332350	[T/C]	chr1	3332350	Cc01_g01860:820	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	25.0%	4	TT	CC	TT	TT
-chr1:3332348	[T/C]	chr1	3332348	Cc01_g01860:822	exon	SYNONYMOUS_CODING	acA/acG	T/T	37.5%	4	TT	CC	CC	TC
-chr1:3332316	[A/G]	chr1	3332316	Cc01_g01860:854	exon	NON_SYNONYMOUS_CODING	cTa/cCa	L/P	12.5%	4	AA	AG	AA	AA
-chr1:3332250	[A/G]	chr1	3332250	Cc01_g01860:920	exon	NON_SYNONYMOUS_CODING	cTt/cCt	L/P	12.5%	4	AA	AA	AA	AG
-chr1:3332219	[G/A]	chr1	3332219	Cc01_g01860:951	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	12.5%	4	GG	GA	GG	GG
-chr1:3332209	[T/C]	chr1	3332209	Cc01_g01860:961	exon	NON_SYNONYMOUS_CODING	Act/Gct	T/A	37.5%	4	TT	CC	CC	TC
-chr1:3338434	[G/T]	chr1	3338434	Cc01_g01870:20	exon	NON_SYNONYMOUS_CODING	cGa/cTa	R/L	16.7%	3	GG	GG	GT	NN
-chr1:3338449	[A/G]	chr1	3338449	Cc01_g01870:35	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	25.0%	2	AA	NN	AG	NN
-chr1:3338455	[C/G]	chr1	3338455	Cc01_g01870:41	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	50.0%	2	CC	NN	GG	NN
-chr1:3338489	[T/G]	chr1	3338489	Cc01_g01870:75	exon	SYNONYMOUS_CODING	gcT/gcG	A/A	16.7%	3	TT	TT	TG	NN
-chr1:3338523	[A/G]	chr1	3338523	Cc01_g01870:109	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	25.0%	2	AA	NN	AG	NN
-chr1:3338527	[C/G]	chr1	3338527	Cc01_g01870:113	exon	NON_SYNONYMOUS_CODING	cCg/cGg	P/R	25.0%	2	CC	NN	CG	NN
-chr1:3338584	[C/A]	chr1	3338584	Cc01_g01870:170	exon	NON_SYNONYMOUS_CODING	cCg/cAg	P/Q	25.0%	4	CC	CC	AA	CC
-chr1:3338618	[G/A]	chr1	3338618	Cc01_g01870:204	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	25.0%	4	GG	GG	AA	GG
-chr1:3338682	[A/G]	chr1	3338682	Cc01_g01870:268	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	12.5%	4	AA	AG	AA	AA
-chr1:3340569	[G/C]	chr1	3340569	Cc01_g01870:341	exon	NON_SYNONYMOUS_CODING	gGt/gCt	G/A	12.5%	4	GG	GG	GC	GG
-chr1:3340586	[C/A]	chr1	3340586	Cc01_g01870:358	exon	NON_SYNONYMOUS_CODING	Caa/Aaa	Q/K	25.0%	4	CC	CA	CA	CC
-chr1:3340636	[A/T]	chr1	3340636	Cc01_g01870:408	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	25.0%	4	AA	AT	AT	AA
-chr1:3341154	[G/A]	chr1	3341154	Cc01_g01870:609	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	GG	AA	GG	GG
-chr1:3341373	[A/G]	chr1	3341373	Cc01_g01870:828	exon	SYNONYMOUS_CODING	acA/acG	T/T	25.0%	4	AA	AG	AG	AA
-chr1:3341763	[C/A]	chr1	3341763	Cc01_g01870:1039	exon	NON_SYNONYMOUS_CODING	Cta/Ata	L/I	25.0%	4	CC	CA	CA	CC
-chr1:3341885	[T/G]	chr1	3341885	Cc01_g01870:1161	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	25.0%	4	TT	TT	GG	TT
-chr1:3341925	[G/T]	chr1	3341925	Cc01_g01870:1201	exon	NON_SYNONYMOUS_CODING	Gcc/Tcc	A/S	25.0%	4	GG	GG	TT	GG
-chr1:3341957	[C/T]	chr1	3341957	Cc01_g01870:1233	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	CC	CC	CT	CC
-chr1:3342026	[A/G]	chr1	3342026	Cc01_g01870:1302	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	25.0%	4	AA	AA	GG	AA
-chr1:3342047	[T/C]	chr1	3342047	Cc01_g01870:1323	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	12.5%	4	TT	TT	TC	TT
-chr1:3342053	[G/A]	chr1	3342053	Cc01_g01870:1329	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	25.0%	4	GG	GG	AA	GG
-chr1:3342122	[T/G]	chr1	3342122	Cc01_g01870:1398	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	25.0%	4	TT	TG	TG	TT
-chr1:3342260	[C/G]	chr1	3342260	Cc01_g01870:1441	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	12.5%	4	CC	CC	CG	CC
-chr1:3342603	[G/A]	chr1	3342603	Cc01_g01870:1728	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	16.7%	3	GG	GG	GA	NN
-chr1:3342762	[T/C]	chr1	3342762	Cc01_g01870:1887	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	25.0%	4	TT	TC	TC	TT
-chr1:3342780	[C/T]	chr1	3342780	Cc01_g01870:1905	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	12.5%	4	CC	CC	TC	CC
-chr1:3342870	[C/T]	chr1	3342870	Cc01_g01870:1995	exon	SYNONYMOUS_CODING	ggC/ggT	G/G	25.0%	4	CC	CT	CT	CC
-chr1:3342879	[T/C]	chr1	3342879	Cc01_g01870:2004	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	12.5%	4	TT	TT	TC	TT
-chr1:3342996	[C/T]	chr1	3342996	Cc01_g01870:2121	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	33.3%	3	CC	CT	CT	NN
-chr1:3342999	[A/T]	chr1	3342999	Cc01_g01870:2124	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	33.3%	3	AA	AT	AT	NN
-chr1:3343053	[T/A]	chr1	3343053	Cc01_g01870:2178	exon	SYNONYMOUS_CODING	gcT/gcA	A/A	16.7%	3	TT	TT	TA	NN
-chr1:3343056	[T/C]	chr1	3343056	Cc01_g01870:2181	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	16.7%	3	TT	TT	TC	NN
-chr1:3343080	[C/T]	chr1	3343080	Cc01_g01870:2205	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	16.7%	3	CC	NN	CT	CC
-chr1:3343146	[T/C]	chr1	3343146	Cc01_g01870:2271	exon	SYNONYMOUS_CODING	cgT/cgC	R/R	16.7%	3	TT	NN	TC	TT
-chr1:3343149	[C/T]	chr1	3343149	Cc01_g01870:2274	exon	SYNONYMOUS_CODING	tgC/tgT	C/C	16.7%	3	CC	NN	CT	CC
-chr1:3343251	[C/T]	chr1	3343251	Cc01_g01870:2376	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	12.5%	4	CC	CC	CT	CC
-chr1:3343348	[G/A]	chr1	3343348	Cc01_g01870:2473	exon	NON_SYNONYMOUS_CODING	Gca/Aca	A/T	25.0%	4	GG	GG	AA	GG
-chr1:3343425	[A/T]	chr1	3343425	Cc01_g01870:2550	exon	SYNONYMOUS_CODING	acA/acT	T/T	16.7%	3	AA	NN	AT	AA
-chr1:3343449	[A/G]	chr1	3343449	Cc01_g01870:2574	exon	SYNONYMOUS_CODING	tcA/tcG	S/S	16.7%	3	AA	NN	AG	AA
-chr1:3343557	[G/A]	chr1	3343557	Cc01_g01870:2682	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	2	GG	NN	GA	NN
-chr1:3343584	[G/C]	chr1	3343584	Cc01_g01870:2709	exon	NON_SYNONYMOUS_CODING	ttG/ttC	L/F	12.5%	4	GG	GG	GC	GG
-chr1:3343605	[T/C]	chr1	3343605	Cc01_g01870:2730	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	TT	TT	TC	TT
-chr1:3343713	[G/A]	chr1	3343713	Cc01_g01870:2838	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	GG	GG	GA	GG
-chr1:3343793	[A/G]	chr1	3343793	Cc01_g01870:2918	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	33.3%	3	AA	NN	GG	AA
-chr1:3343946	[T/A]	chr1	3343946	Cc01_g01870:3071	exon	NON_SYNONYMOUS_CODING	tTt/tAt	F/Y	12.5%	4	TT	TT	TA	TT
-chr1:3343980	[T/A]	chr1	3343980	Cc01_g01870:3105	exon	SYNONYMOUS_CODING	ctT/ctA	L/L	12.5%	4	TT	TT	TA	TT
-chr1:3344061	[T/C]	chr1	3344061	Cc01_g01870:3186	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	TT	TT	TC	TT
-chr1:3344094	[C/G]	chr1	3344094	Cc01_g01870:3219	exon	SYNONYMOUS_CODING	ctC/ctG	L/L	25.0%	4	CC	CC	GG	CC
-chr1:3344225	[A/C]	chr1	3344225	Cc01_g01870:3350	exon	NON_SYNONYMOUS_CODING	aAc/aCc	N/T	25.0%	4	AA	AC	AC	AA
-chr1:3344291	[A/G]	chr1	3344291	Cc01_g01870:3416	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	25.0%	4	AA	AG	AG	AA
-chr1:3344304	[A/G]	chr1	3344304	Cc01_g01870:3429	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	25.0%	4	AA	AG	AG	AA
-chr1:3344335	[A/T]	chr1	3344335	Cc01_g01870:3460	exon	NON_SYNONYMOUS_CODING	Act/Tct	T/S	12.5%	4	AA	AA	AT	AA
-chr1:3344340	[A/G]	chr1	3344340	Cc01_g01870:3465	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	AA	AA	AG	AA
-chr1:3344367	[G/A]	chr1	3344367	Cc01_g01870:3492	exon	NON_SYNONYMOUS_CODING	atG/atA	M/I	12.5%	4	GG	GG	GA	GG
-chr1:3344610	[A/G]	chr1	3344610	Cc01_g01870:3646	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	25.0%	4	AA	AG	AG	AA
-chr1:3344615	[C/T]	chr1	3344615	Cc01_g01870:3651	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	25.0%	4	CC	CT	CT	CC
-chr1:3344705	[T/C]	chr1	3344705	Cc01_g01870:3741	exon	SYNONYMOUS_CODING	agT/agC	S/S	50.0%	4	TT	CC	CC	TT
-chr1:3344765	[C/T]	chr1	3344765	Cc01_g01870:3801	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	25.0%	4	CC	CT	CT	CC
-chr1:3344998	[C/G]	chr1	3344998	Cc01_g01870:3928	exon	NON_SYNONYMOUS_CODING	Cta/Gta	L/V	25.0%	4	CC	CC	GG	CC
-chr1:3345023	[C/G]	chr1	3345023	Cc01_g01870:3953	exon	NON_SYNONYMOUS_CODING	aCt/aGt	T/S	12.5%	4	CC	CC	CG	CC
-chr1:3345239	[G/A]	chr1	3345239	Cc01_g01870:4077	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	37.5%	4	GG	GA	AA	GG
-chr1:3345251	[G/A]	chr1	3345251	Cc01_g01870:4089	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	12.5%	4	GG	GG	GA	GG
-chr1:3345257	[A/G]	chr1	3345257	Cc01_g01870:4095	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	12.5%	4	AA	AA	AG	AA
-chr1:3345539	[A/G]	chr1	3345539	Cc01_g01870:4290	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	AA	AA	GG	AA
-chr1:3346036	[G/A]	chr1	3346036	Cc01_g01870:4488	exon	SYNONYMOUS_CODING	acG/acA	T/T	12.5%	4	GG	GA	GG	GG
-chr1:3346713	[T/C]	chr1	3346713	Cc01_g01870:4716	exon	SYNONYMOUS_CODING	cgT/cgC	R/R	25.0%	4	TT	TC	TC	TT
-chr1:3346848	[C/T]	chr1	3346848	Cc01_g01870:4851	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	25.0%	4	CC	CT	CT	CC
-chr1:3346851	[T/G]	chr1	3346851	Cc01_g01870:4854	exon	SYNONYMOUS_CODING	cgT/cgG	R/R	12.5%	4	TT	TT	TG	TT
-chr1:3346917	[G/A]	chr1	3346917	Cc01_g01870:4920	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	33.3%	3	GG	GA	GA	NN
-chr1:3346920	[T/G]	chr1	3346920	Cc01_g01870:4923	exon	SYNONYMOUS_CODING	ctT/ctG	L/L	16.7%	3	TT	TT	GT	NN
-chr1:3347106	[T/C]	chr1	3347106	Cc01_g01870:5109	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	25.0%	4	TT	TC	TC	TT
-chr1:3347181	[C/A]	chr1	3347181	Cc01_g01870:5184	exon	SYNONYMOUS_CODING	acC/acA	T/T	25.0%	4	CC	CA	CA	CC
-chr1:3347198	[T/C]	chr1	3347198	Cc01_g01870:5201	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	12.5%	4	TT	TT	TC	TT
-chr1:3347363	[C/T]	chr1	3347363	Cc01_g01870:5280	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	25.0%	4	CC	CT	CT	CC
-chr1:3347553	[A/G]	chr1	3347553	Cc01_g01870:5361	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	12.5%	4	AA	AA	AG	AA
-chr1:3347739	[C/T]	chr1	3347739	Cc01_g01870:5547	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CC	CT	CC
-chr1:3347754	[A/G]	chr1	3347754	Cc01_g01870:5562	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AA	AG	AA
-chr1:3347884	[T/C]	chr1	3347884	Cc01_g01870:5616	exon	SYNONYMOUS_CODING	cgT/cgC	R/R	12.5%	4	TT	TT	TC	TT
-chr1:3347890	[A/C]	chr1	3347890	Cc01_g01870:5622	exon	SYNONYMOUS_CODING	ggA/ggC	G/G	12.5%	4	AA	AA	AC	AA
-chr1:3348120	[T/A]	chr1	3348120	Cc01_g01870:5852	exon	NON_SYNONYMOUS_CODING	gTc/gAc	V/D	25.0%	4	TT	AA	AA	AA
-chr1:3348121	[C/A]	chr1	3348121	Cc01_g01870:5853	exon	SYNONYMOUS_CODING	gtC/gtA	V/V	25.0%	4	CC	AA	AA	AA
-chr1:3348167	[A/G]	chr1	3348167	Cc01_g01870:5899	exon	NON_SYNONYMOUS_CODING	Att/Gtt	I/V	12.5%	4	AA	AA	AG	AA
-chr1:3348225	[A/G]	chr1	3348225	Cc01_g01870:5957	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	12.5%	4	AA	AG	AA	AA
-chr1:3348593	[G/A]	chr1	3348593	Cc01_g01870:6109	exon	NON_SYNONYMOUS_CODING	Gtg/Atg	V/M	12.5%	4	GG	GG	GG	GA
-chr1:3348598	[C/T]	chr1	3348598	Cc01_g01870:6114	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	CC	CT	CC	CC
-chr1:3348607	[G/A]	chr1	3348607	Cc01_g01870:6123	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	GG	GG	GA	GG
-chr1:3348689	[G/T]	chr1	3348689	Cc01_g01870:6205	exon	NON_SYNONYMOUS_CODING	Gtt/Ttt	V/F	12.5%	4	GG	GG	GT	GG
-chr1:3348691	[T/C]	chr1	3348691	Cc01_g01870:6207	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	TT	TC	TC	TT
-chr1:3348799	[C/T]	chr1	3348799	Cc01_g01870:6219	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	25.0%	4	CC	CT	CT	CC
-chr1:3348886	[T/C]	chr1	3348886	Cc01_g01870:6306	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	TT	TT	TC	TT
-chr1:3348950	[T/C]	chr1	3348950	Cc01_g01870:6370	exon	NON_SYNONYMOUS_CODING	Tat/Cat	Y/H	12.5%	4	TT	TT	TC	TT
-chr1:3349098	[C/A]	chr1	3349098	Cc01_g01870:6441	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	12.5%	4	CC	CC	CA	CC
-chr1:3349159	[A/T]	chr1	3349159	Cc01_g01870:6502	exon	NON_SYNONYMOUS_CODING	Atg/Ttg	M/L	12.5%	4	AA	AA	AT	AA
-chr1:3349258	[T/C]	chr1	3349258	Cc01_g01870:6601	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	12.5%	4	TT	TT	TC	TT
-chr1:3349275	[T/C]	chr1	3349275	Cc01_g01870:6618	exon	SYNONYMOUS_CODING	caT/caC	H/H	12.5%	4	TT	TT	TC	TT
-chr1:3349309	[A/G]	chr1	3349309	Cc01_g01870:6652	exon	NON_SYNONYMOUS_CODING	Atg/Gtg	M/V	25.0%	4	AA	AA	AA	GG
-chr1:3349550	[A/G]	chr1	3349550	Cc01_g01870:6731	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	12.5%	4	AA	AA	AA	AG
-chr1:3349635	[A/G]	chr1	3349635	Cc01_g01870:6816	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	37.5%	4	AA	AG	GG	AA
-chr1:3349684	[A/C]	chr1	3349684	Cc01_g01870:6865	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	25.0%	4	AA	AC	AC	AA
-chr1:3349692	[T/C]	chr1	3349692	Cc01_g01870:6873	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	12.5%	4	TT	TT	TC	TT
-chr1:3349701	[G/A]	chr1	3349701	Cc01_g01870:6882	exon	SYNONYMOUS_CODING	acG/acA	T/T	25.0%	4	GG	GG	GA	GA
-chr1:3349725	[T/C]	chr1	3349725	Cc01_g01870:6906	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	TT	TT	TC	TT
-chr1:3349872	[T/A]	chr1	3349872	Cc01_g01870:6942	exon	SYNONYMOUS_CODING	ccT/ccA	P/P	25.0%	4	TT	TA	TA	TT
-chr1:3349938	[A/G]	chr1	3349938	Cc01_g01870:7008	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	12.5%	4	AA	AA	AG	AA
-chr1:3349953	[T/G]	chr1	3349953	Cc01_g01870:7023	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	12.5%	4	TT	TT	TG	TT
-chr1:3349955	[A/G]	chr1	3349955	Cc01_g01870:7025	exon	NON_SYNONYMOUS_CODING	aAg/aGg	K/R	12.5%	4	AA	AA	AG	AA
-chr1:3349959	[C/G]	chr1	3349959	Cc01_g01870:7029	exon	NON_SYNONYMOUS_CODING	gaC/gaG	D/E	25.0%	4	CC	GG	GG	GG
-chr1:3349968	[T/C]	chr1	3349968	Cc01_g01870:7038	exon	SYNONYMOUS_CODING	caT/caC	H/H	25.0%	4	TT	CC	TT	TT
-chr1:3350026	[A/G]	chr1	3350026	Cc01_g01870:7096	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	37.5%	4	AA	AG	GG	AA
-chr1:3350040	[C/T]	chr1	3350040	Cc01_g01870:7110	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	12.5%	4	CC	CT	CC	CC
-chr1:3362501	[A/T]	chr1	3362501	Cc01_g01900:15	exon	SYNONYMOUS_CODING	atT/atA	I/I	33.3%	3	AA	NN	TT	TT
-chr1:3362493	[G/C]	chr1	3362493	Cc01_g01900:23	exon	STOP_GAINED	tCa/tGa	S8*	25.0%	4	GG	CC	CC	CC
-chr1:3362488	[C/T]	chr1	3362488	Cc01_g01900:28	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	25.0%	4	CC	TT	TT	TT
-chr1:3362464	[C/G]	chr1	3362464	Cc01_g01900:52	exon	NON_SYNONYMOUS_CODING	Gtc/Ctc	V/L	25.0%	4	CC	GG	GG	GG
-chr1:3362461	[C/G]	chr1	3362461	Cc01_g01900:55	exon	NON_SYNONYMOUS_CODING	Gat/Cat	D/H	25.0%	4	CC	GG	GG	GG
-chr1:3362423	[T/G]	chr1	3362423	Cc01_g01900:93	exon	NON_SYNONYMOUS_CODING	aaA/aaC	K/N	50.0%	4	TT	TT	GG	GG
-chr1:3383330	[A/T]	chr1	3383330	Cc01_g01910:149	exon	NON_SYNONYMOUS_CODING	aTc/aAc	I/N	50.0%	2	AA	TT	NN	NN
-chr1:3383254	[C/T]	chr1	3383254	Cc01_g01910:225	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	50.0%	2	CC	NN	NN	TT
-chr1:3383250	[A/C]	chr1	3383250	Cc01_g01910:229	exon	NON_SYNONYMOUS_CODING	Tca/Gca	S/A	50.0%	2	AA	NN	NN	CC
-chr1:3383240	[T/G]	chr1	3383240	Cc01_g01910:239	exon	NON_SYNONYMOUS_CODING	cAa/cCa	Q/P	50.0%	2	TT	NN	NN	GG
-chr1:3543339	[T/C]	chr1	3543339	Cc01_g01950:133	exon	NON_SYNONYMOUS_CODING	Tcc/Ccc	S/P	37.5%	4	TT	CC	TT	TC
-chr1:3543344	[T/C]	chr1	3543344	Cc01_g01950:138	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	12.5%	4	TT	TC	TT	TT
-chr1:3543798	[C/T]	chr1	3543798	Cc01_g01950:592	exon	SYNONYMOUS_CODING	Ctg/Ttg	L/L	12.5%	4	CC	CT	CC	CC
-chr1:3544052	[T/C]	chr1	3544052	Cc01_g01950:846	exon	SYNONYMOUS_CODING	caT/caC	H/H	12.5%	4	TT	TC	TT	TT
-chr1:3563539	[T/A]	chr1	3563539	Cc01_g01960:208	exon	NON_SYNONYMOUS_CODING	Tgg/Agg	W/R	33.3%	3	TT	AA	TT	NN
-chr1:3563667	[G/A]	chr1	3563667	Cc01_g01960:336	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	16.7%	3	GG	GG	NN	GA
-chr1:3563754	[G/C]	chr1	3563754	Cc01_g01960:423	exon	SYNONYMOUS_CODING	acG/acC	T/T	25.0%	4	GG	GC	GG	GC
-chr1:3563771	[A/G]	chr1	3563771	Cc01_g01960:440	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	50.0%	4	AA	GG	AG	AG
-chr1:3563793	[T/C]	chr1	3563793	Cc01_g01960:462	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	25.0%	4	TT	TC	TC	TT
-chr1:3574473	[G/C]	chr1	3574473	Cc01_g01970:51	exon	SYNONYMOUS_CODING	gcC/gcG	A/A	33.3%	3	GG	NN	CC	GG
-chr1:3574458	[A/G]	chr1	3574458	Cc01_g01970:66	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	33.3%	3	AA	NN	AA	GG
-chr1:3574326	[A/T]	chr1	3574326	Cc01_g01970:198	exon	NON_SYNONYMOUS_CODING	aaT/aaA	N/K	33.3%	3	AA	NN	TT	TT
-chr1:3574296	[A/G]	chr1	3574296	Cc01_g01970:228	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	33.3%	3	AA	NN	AA	GG
-chr1:3574115	[T/C]	chr1	3574115	Cc01_g01970:409	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	33.3%	3	TT	NN	CC	CC
-chr1:3574063	[G/A]	chr1	3574063	Cc01_g01970:461	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	25.0%	4	GG	GG	AA	GG
-chr1:3574027	[A/T]	chr1	3574027	Cc01_g01970:497	exon	NON_SYNONYMOUS_CODING	gTt/gAt	V/D	33.3%	3	AA	NN	AA	TT
-chr1:3573800	[C/T]	chr1	3573800	Cc01_g01970:724	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	CC	TT	TT	TT
-chr1:3573759	[A/G]	chr1	3573759	Cc01_g01970:765	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	33.3%	3	AA	NN	AA	GG
-chr1:3573736	[C/T]	chr1	3573736	Cc01_g01970:788	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	50.0%	4	CC	TT	CC	TT
-chr1:3573699	[G/C]	chr1	3573699	Cc01_g01970:825	exon	NON_SYNONYMOUS_CODING	ttC/ttG	F/L	25.0%	4	GG	GG	CC	GG
-chr1:3573693	[A/G]	chr1	3573693	Cc01_g01970:831	exon	SYNONYMOUS_CODING	gtT/gtC	V/V	50.0%	4	AA	GG	AA	GG
-chr1:3573559	[A/T]	chr1	3573559	Cc01_g01970:965	exon	NON_SYNONYMOUS_CODING	gTt/gAt	V/D	33.3%	3	AA	NN	AA	TT
-chr1:3573509	[A/T]	chr1	3573509	Cc01_g01970:1015	exon	NON_SYNONYMOUS_CODING	Ttt/Att	F/I	33.3%	3	AA	NN	AA	TT
-chr1:3573370	[C/T]	chr1	3573370	Cc01_g01970:1053	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	33.3%	3	CC	NN	CC	TT
-chr1:3573336	[C/A]	chr1	3573336	Cc01_g01970:1087	exon	NON_SYNONYMOUS_CODING	Ggc/Tgc	G/C	50.0%	4	CC	AA	CC	AA
-chr1:3573271	[C/G]	chr1	3573271	Cc01_g01970:1152	exon	SYNONYMOUS_CODING	ggG/ggC	G/G	33.3%	3	CC	NN	GG	CC
-chr1:3573239	[G/C]	chr1	3573239	Cc01_g01970:1184	exon	NON_SYNONYMOUS_CODING	tCg/tGg	S/W	33.3%	3	GG	NN	CC	CC
-chr1:3573098	[G/T]	chr1	3573098	Cc01_g01970:1251	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	50.0%	4	GG	TT	GG	TT
-chr1:3573097	[T/G]	chr1	3573097	Cc01_g01970:1252	exon	NON_SYNONYMOUS_CODING	Ata/Cta	I/L	50.0%	4	TT	GG	TT	GG
-chr1:3572965	[G/A]	chr1	3572965	Cc01_g01970:1384	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	33.3%	3	GG	NN	AA	AA
-chr1:3572931	[A/G]	chr1	3572931	Cc01_g01970:1418	exon	NON_SYNONYMOUS_CODING	tTa/tCa	L/S	33.3%	3	AA	NN	GG	GG
-chr1:3572899	[T/C]	chr1	3572899	Cc01_g01970:1450	exon	NON_SYNONYMOUS_CODING	Ata/Gta	I/V	25.0%	4	TT	CC	CC	CC
-chr1:3572885	[C/G]	chr1	3572885	Cc01_g01970:1464	exon	SYNONYMOUS_CODING	gcG/gcC	A/A	25.0%	4	CC	GG	GG	GG
-chr1:3572859	[C/T]	chr1	3572859	Cc01_g01970:1490	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	25.0%	4	CC	TT	TT	TT
-chr1:3572854	[G/T]	chr1	3572854	Cc01_g01970:1495	exon	NON_SYNONYMOUS_CODING	Ctc/Atc	L/I	25.0%	4	GG	TT	TT	TT
-chr1:3572835	[T/A]	chr1	3572835	Cc01_g01970:1514	exon	NON_SYNONYMOUS_CODING	aAg/aTg	K/M	25.0%	4	TT	TT	AA	TT
-chr1:3649364	[A/T]	chr1	3649364	Cc01_g01980:156	exon	SYNONYMOUS_CODING	tcA/tcT	S/S	12.5%	4	AA	AA	AA	AT
-chr1:3649391	[C/T]	chr1	3649391	Cc01_g01980:183	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CC	CC	CT
-chr1:3649422	[C/G]	chr1	3649422	Cc01_g01980:214	exon	NON_SYNONYMOUS_CODING	Cgc/Ggc	R/G	25.0%	4	CC	GG	CC	CC
-chr1:3649490	[G/A]	chr1	3649490	Cc01_g01980:282	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	GG	AA	GG	GG
-chr1:3649502	[T/C]	chr1	3649502	Cc01_g01980:294	exon	SYNONYMOUS_CODING	gcT/gcC	A/A	37.5%	4	TT	CC	TC	CC
-chr1:3649727	[T/C]	chr1	3649727	Cc01_g01980:519	exon	SYNONYMOUS_CODING	tgT/tgC	C/C	12.5%	4	TT	TC	TT	TT
-chr1:3649746	[G/T]	chr1	3649746	Cc01_g01980:538	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	25.0%	4	GG	TT	TT	TT
-chr1:3661555	[G/C]	chr1	3661555	Cc01_g01990:23	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	33.3%	3	GG	CC	GG	NN
-chr1:3661523	[T/C]	chr1	3661523	Cc01_g01990:55	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	33.3%	3	TT	CC	CC	NN
-chr1:3661511	[C/G]	chr1	3661511	Cc01_g01990:67	exon	NON_SYNONYMOUS_CODING	Gtt/Ctt	V/L	33.3%	3	CC	GG	NN	CC
-chr1:3661507	[A/C]	chr1	3661507	Cc01_g01990:71	exon	NON_SYNONYMOUS_CODING	cTg/cGg	L/R	33.3%	3	AA	CC	NN	AA
-chr1:3661453	[T/C]	chr1	3661453	Cc01_g01990:125	exon	NON_SYNONYMOUS_CODING	aAa/aGa	K/R	25.0%	4	TT	CC	TT	TT
-chr1:3661403	[A/T]	chr1	3661403	Cc01_g01990:175	exon	NON_SYNONYMOUS_CODING	Tgg/Agg	W/R	33.3%	3	AA	TT	AA	NN
-chr1:3661345	[G/T]	chr1	3661345	Cc01_g01990:233	exon	NON_SYNONYMOUS_CODING	tCt/tAt	S/Y	33.3%	3	GG	GG	NN	TT
-chr1:3661344	[A/G]	chr1	3661344	Cc01_g01990:234	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	16.7%	3	AA	AG	NN	AA
-chr1:3660894	[T/C]	chr1	3660894	Cc01_g01990:273	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	33.3%	3	TT	CC	NN	TT
-chr1:3660770	[C/T]	chr1	3660770	Cc01_g01990:319	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	33.3%	3	CC	NN	TT	CC
-chr1:3660756	[A/C]	chr1	3660756	Cc01_g01990:333	exon	NON_SYNONYMOUS_CODING	caT/caG	H/Q	25.0%	4	AA	CC	AA	AA
-chr1:3660584	[T/C]	chr1	3660584	Cc01_g01990:379	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	25.0%	4	TT	TT	TT	CC
-chr1:3660566	[G/A]	chr1	3660566	Cc01_g01990:397	exon	NON_SYNONYMOUS_CODING	Cca/Tca	P/S	37.5%	4	GG	GA	AA	GG
-chr1:3660548	[C/T]	chr1	3660548	Cc01_g01990:415	exon	NON_SYNONYMOUS_CODING	Gga/Aga	G/R	37.5%	4	CC	CT	TT	CC
-chr1:3660530	[C/T]	chr1	3660530	Cc01_g01990:433	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	25.0%	4	CC	TT	TT	TT
-chr1:3660529	[C/A]	chr1	3660529	Cc01_g01990:434	exon	NON_SYNONYMOUS_CODING	gGc/gTc	G/V	50.0%	4	CC	AA	AA	CC
-chr1:3660523	[C/T]	chr1	3660523	Cc01_g01990:440	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	50.0%	4	CC	TT	TT	CC
-chr1:3660509	[T/C]	chr1	3660509	Cc01_g01990:454	exon	NON_SYNONYMOUS_CODING	Aat/Gat	N/D	25.0%	4	TT	CC	TT	TT
-chr1:3660489	[T/G]	chr1	3660489	Cc01_g01990:474	exon	SYNONYMOUS_CODING	gcA/gcC	A/A	50.0%	4	TT	GG	GG	TT
-chr1:3660392	[T/G]	chr1	3660392	Cc01_g01990:571	exon	NON_SYNONYMOUS_CODING	Aaa/Caa	K/Q	25.0%	4	TT	GG	GG	GG
-chr1:3660382	[T/A]	chr1	3660382	Cc01_g01990:581	exon	NON_SYNONYMOUS_CODING	aAa/aTa	K/I	25.0%	4	TT	AA	TT	TT
-chr1:3660368	[T/C]	chr1	3660368	Cc01_g01990:595	exon	NON_SYNONYMOUS_CODING	Agt/Ggt	S/G	25.0%	4	TT	CC	CC	CC
-chr1:3663378	[T/A]	chr1	3663378	Cc01_g02000:123	exon	SYNONYMOUS_CODING	tcA/tcT	S/S	12.5%	4	TT	TA	TT	TT
-chr1:3663363	[C/T]	chr1	3663363	Cc01_g02000:138	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	12.5%	4	CC	TC	CC	CC
-chr1:3663324	[G/A]	chr1	3663324	Cc01_g02000:177	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	GG	AG	GG	GG
-chr1:3663323	[C/T]	chr1	3663323	Cc01_g02000:178	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	12.5%	4	CC	CC	CT	CC
-chr1:3663308	[A/T]	chr1	3663308	Cc01_g02000:193	exon	STOP_LOST	Tag/Aag	6/K	37.5%	4	AA	TT	AT	AA
-chr1:3704574	[A/T]	chr1	3704574	Cc01_g02010:179	exon	NON_SYNONYMOUS_CODING	cTg/cAg	L/Q	25.0%	4	AA	TT	TT	TT
-chr1:3704558	[T/A]	chr1	3704558	Cc01_g02010:195	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	12.5%	4	TT	TT	TA	TT
-chr1:3704537	[A/G]	chr1	3704537	Cc01_g02010:216	exon	SYNONYMOUS_CODING	caT/caC	H/H	12.5%	4	AA	AA	AG	AA
-chr1:3704524	[A/T]	chr1	3704524	Cc01_g02010:229	exon	NON_SYNONYMOUS_CODING	Tat/Aat	Y/N	12.5%	4	AA	AA	AA	AT
-chr1:3704520	[G/C]	chr1	3704520	Cc01_g02010:233	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	12.5%	4	GG	GG	GC	GG
-chr1:3704494	[C/T]	chr1	3704494	Cc01_g02010:259	exon	NON_SYNONYMOUS_CODING	Gcc/Acc	A/T	25.0%	4	CC	TT	TT	TT
-chr1:3702641	[A/T]	chr1	3702641	Cc01_g02010:350	exon	NON_SYNONYMOUS_CODING	cTt/cAt	L/H	12.5%	4	AA	AT	AA	AA
-chr1:3702616	[T/A]	chr1	3702616	Cc01_g02010:375	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	12.5%	4	TT	TA	TT	TT
-chr1:3702601	[T/C]	chr1	3702601	Cc01_g02010:390	exon	SYNONYMOUS_CODING	agA/agG	R/R	12.5%	4	TT	TT	TT	TC
-chr1:3702599	[T/A]	chr1	3702599	Cc01_g02010:392	exon	NON_SYNONYMOUS_CODING	cAa/cTa	Q/L	12.5%	4	TT	TT	TT	AT
-chr1:3702582	[C/T]	chr1	3702582	Cc01_g02010:409	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	CC	TC	CC	CC
-chr1:3702367	[T/C]	chr1	3702367	Cc01_g02010:534	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	25.0%	4	TT	TT	TT	CC
-chr1:3702346	[A/T]	chr1	3702346	Cc01_g02010:555	exon	SYNONYMOUS_CODING	tcT/tcA	S/S	12.5%	4	AA	AA	AT	AA
-chr1:3702331	[G/A]	chr1	3702331	Cc01_g02010:570	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	37.5%	4	GG	GA	AA	GG
-chr1:3702283	[G/A]	chr1	3702283	Cc01_g02010:618	exon	SYNONYMOUS_CODING	agC/agT	S/S	25.0%	4	GG	AA	AA	AA
-chr1:3702270	[A/G]	chr1	3702270	Cc01_g02010:631	exon	NON_SYNONYMOUS_CODING	Tgg/Cgg	W/R	12.5%	4	AA	AG	AA	AA
-chr1:3702235	[A/G]	chr1	3702235	Cc01_g02010:666	exon	SYNONYMOUS_CODING	agT/agC	S/S	12.5%	4	AA	GA	AA	AA
-chr1:3702233	[T/C]	chr1	3702233	Cc01_g02010:668	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	37.5%	4	TT	TC	CC	TT
-chr1:3702222	[T/G]	chr1	3702222	Cc01_g02010:679	exon	SYNONYMOUS_CODING	Aga/Cga	R/R	12.5%	4	TT	TT	TT	TG
-chr1:3702218	[T/C]	chr1	3702218	Cc01_g02010:683	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	12.5%	4	TT	TT	TT	CT
-chr1:3701396	[C/T]	chr1	3701396	Cc01_g02010:708	exon	SYNONYMOUS_CODING	gtG/gtA	V/V	12.5%	4	CC	CC	CC	CT
-chr1:3701386	[A/G]	chr1	3701386	Cc01_g02010:718	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	25.0%	4	AA	AA	AA	GG
-chr1:3701243	[T/C]	chr1	3701243	Cc01_g02010:861	exon	SYNONYMOUS_CODING	gcA/gcG	A/A	12.5%	4	TT	TT	TC	TT
-chr1:3701240	[G/A]	chr1	3701240	Cc01_g02010:864	exon	SYNONYMOUS_CODING	acC/acT	T/T	25.0%	4	GG	GG	GG	AA
-chr1:3701237	[C/T]	chr1	3701237	Cc01_g02010:867	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	12.5%	4	CC	CC	CT	CC
-chr1:3700510	[C/T]	chr1	3700510	Cc01_g02010:931	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	16.7%	3	CC	CC	CT	NN
-chr1:3699429	[C/T]	chr1	3699429	Cc01_g02010:1020	exon	SYNONYMOUS_CODING	agG/agA	R/R	25.0%	4	CC	CC	CC	TT
-chr1:3699397	[G/C]	chr1	3699397	Cc01_g02010:1052	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	16.7%	3	GG	GG	GC	NN
-chr1:3699002	[C/A]	chr1	3699002	Cc01_g02010:1192	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	37.5%	4	CC	CA	CC	AA
-chr1:3698979	[A/G]	chr1	3698979	Cc01_g02010:1215	exon	SYNONYMOUS_CODING	caT/caC	H/H	12.5%	4	AA	AA	AA	AG
-chr1:3698964	[T/C]	chr1	3698964	Cc01_g02010:1230	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	TT	TT	TC	TT
-chr1:3698934	[C/T]	chr1	3698934	Cc01_g02010:1260	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	50.0%	4	CC	CT	CT	TT
-chr1:3698922	[C/T]	chr1	3698922	Cc01_g02010:1272	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	25.0%	4	CC	CC	CC	TT
-chr1:3698901	[C/T]	chr1	3698901	Cc01_g02010:1293	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	37.5%	4	CC	CC	CT	TT
-chr1:3698886	[A/G]	chr1	3698886	Cc01_g02010:1308	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	AA	AA	AG	AA
-chr1:3698880	[T/C]	chr1	3698880	Cc01_g02010:1314	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TC	TT
-chr1:3698871	[T/A]	chr1	3698871	Cc01_g02010:1323	exon	SYNONYMOUS_CODING	ctA/ctT	L/L	25.0%	4	TT	TT	TT	AA
-chr1:3698841	[T/A]	chr1	3698841	Cc01_g02010:1353	exon	NON_SYNONYMOUS_CODING	ttA/ttT	L/F	25.0%	4	TT	AA	AA	AA
-chr1:3698450	[C/T]	chr1	3698450	Cc01_g02010:1477	exon	NON_SYNONYMOUS_CODING	Gct/Act	A/T	12.5%	4	CC	CC	CT	CC
-chr1:3698412	[G/A]	chr1	3698412	Cc01_g02010:1515	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	25.0%	4	GG	GG	GG	AA
-chr1:3698398	[T/A]	chr1	3698398	Cc01_g02010:1529	exon	NON_SYNONYMOUS_CODING	tAc/tTc	Y/F	12.5%	4	TT	TA	TT	TT
-chr1:3698247	[A/G]	chr1	3698247	Cc01_g02010:1680	exon	SYNONYMOUS_CODING	taT/taC	Y/Y	25.0%	4	AA	AA	AA	GG
-chr1:3697989	[T/C]	chr1	3697989	Cc01_g02010:1692	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	12.5%	4	TT	TT	TC	TT
-chr1:3696904	[A/T]	chr1	3696904	Cc01_g02010:1866	exon	NON_SYNONYMOUS_CODING	caT/caA	H/Q	50.0%	2	AA	NN	TT	NN
-chr1:3696445	[A/G]	chr1	3696445	Cc01_g02010:1945	exon	NON_SYNONYMOUS_CODING	Tat/Cat	Y/H	25.0%	4	AA	AA	AA	GG
-chr1:3696441	[C/T]	chr1	3696441	Cc01_g02010:1949	exon	NON_SYNONYMOUS_CODING	gGt/gAt	G/D	25.0%	4	CC	TT	TT	TT
-chr1:3696389	[C/T]	chr1	3696389	Cc01_g02010:2001	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	37.5%	4	CC	CC	CT	TT
-chr1:3696380	[C/T]	chr1	3696380	Cc01_g02010:2010	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	25.0%	4	CC	TT	TT	TT
-chr1:3696362	[T/C]	chr1	3696362	Cc01_g02010:2028	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	25.0%	4	TT	TT	TT	CC
-chr1:3696314	[T/G]	chr1	3696314	Cc01_g02010:2076	exon	SYNONYMOUS_CODING	tcA/tcC	S/S	25.0%	4	TT	TT	TT	GG
-chr1:3696312	[C/G]	chr1	3696312	Cc01_g02010:2078	exon	NON_SYNONYMOUS_CODING	aGa/aCa	R/T	37.5%	4	CC	GG	CG	CC
-chr1:3695395	[A/G]	chr1	3695395	Cc01_g02010:2114	exon	NON_SYNONYMOUS_CODING	gTa/gCa	V/A	12.5%	4	AA	AA	AA	AG
-chr1:3695358	[T/C]	chr1	3695358	Cc01_g02010:2151	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TT	CT
-chr1:3695350	[T/C]	chr1	3695350	Cc01_g02010:2159	exon	NON_SYNONYMOUS_CODING	aAc/aGc	N/S	50.0%	4	TT	CC	CC	TT
-chr1:3695299	[G/A]	chr1	3695299	Cc01_g02010:2210	exon	NON_SYNONYMOUS_CODING	aCa/aTa	T/I	25.0%	4	GG	GG	GG	AA
-chr1:3725796	[T/C]	chr1	3725796	Cc01_g02020:642	exon	SYNONYMOUS_CODING	atT/atC	I/I	16.7%	3	TT	NN	TT	TC
-chr1:3725964	[A/G]	chr1	3725964	Cc01_g02020:810	exon	NON_SYNONYMOUS_CODING	atA/atG	I/M	33.3%	3	AA	NN	GG	GG
-chr1:3727454	[C/T]	chr1	3727454	Cc01_g02020:1724	exon	NON_SYNONYMOUS_CODING	gCc/gTc	A/V	50.0%	2	CC	NN	NN	TT
-chr1:3727458	[A/T]	chr1	3727458	Cc01_g02020:1728	exon	NON_SYNONYMOUS_CODING	aaA/aaT	K/N	50.0%	2	AA	NN	NN	TT
-chr1:3727501	[G/A]	chr1	3727501	Cc01_g02020:1771	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	37.5%	4	GG	AA	AA	GA
-chr1:3727517	[T/C]	chr1	3727517	Cc01_g02020:1787	exon	NON_SYNONYMOUS_CODING	aTt/aCt	I/T	12.5%	4	TT	TT	TT	TC
-chr1:3727787	[T/A]	chr1	3727787	Cc01_g02020:2057	exon	NON_SYNONYMOUS_CODING	tTc/tAc	F/Y	33.3%	3	TT	NN	AA	TT
-chr1:3727789	[A/G]	chr1	3727789	Cc01_g02020:2059	exon	NON_SYNONYMOUS_CODING	Aag/Gag	K/E	50.0%	2	AA	NN	NN	GG
-chr1:3727802	[T/G]	chr1	3727802	Cc01_g02020:2072	exon	NON_SYNONYMOUS_CODING	tTg/tGg	L/W	50.0%	2	TT	NN	NN	GG
-chr1:3727809	[C/T]	chr1	3727809	Cc01_g02020:2079	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	50.0%	2	CC	NN	NN	TT
-chr1:3727827	[T/C]	chr1	3727827	Cc01_g02020:2097	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	50.0%	2	TT	NN	NN	CC
-chr1:3727876	[T/G]	chr1	3727876	Cc01_g02020:2146	exon	NON_SYNONYMOUS_CODING	Tac/Gac	Y/D	50.0%	2	TT	NN	NN	GG
-chr1:3727959	[G/A]	chr1	3727959	Cc01_g02020:2229	exon	SYNONYMOUS_CODING	acG/acA	T/T	25.0%	2	GG	NN	NN	GA
-chr1:3727969	[T/C]	chr1	3727969	Cc01_g02020:2239	exon	NON_SYNONYMOUS_CODING	Tca/Cca	S/P	33.3%	3	TT	TT	NN	CC
-chr1:3728011	[C/T]	chr1	3728011	Cc01_g02020:2281	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	25.0%	2	CC	NN	NN	CT
-chr1:3728022	[C/T]	chr1	3728022	Cc01_g02020:2292	exon	SYNONYMOUS_CODING	ttC/ttT	F/F	25.0%	2	CC	NN	NN	CT
-chr1:3728064	[G/A]	chr1	3728064	Cc01_g02020:2334	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	50.0%	2	GG	NN	NN	AA
-chr1:3728080	[T/A]	chr1	3728080	Cc01_g02020:2350	exon	NON_SYNONYMOUS_CODING	Ttc/Atc	F/I	50.0%	2	TT	NN	NN	AA
-chr1:3740570	[G/A]	chr1	3740570	Cc01_g02030:19	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	33.3%	3	GG	AA	AA	NN
-chr1:3740594	[G/A]	chr1	3740594	Cc01_g02030:43	exon	NON_SYNONYMOUS_CODING	Gac/Aac	D/N	33.3%	3	GG	AA	GG	NN
-chr1:3740608	[G/T]	chr1	3740608	Cc01_g02030:57	exon	SYNONYMOUS_CODING	tcG/tcT	S/S	50.0%	2	GG	TT	NN	NN
-chr1:3740686	[G/A]	chr1	3740686	Cc01_g02030:135	exon	SYNONYMOUS_CODING	gaG/gaA	E/E	25.0%	4	GG	AA	GG	GG
-chr1:3740718	[C/T]	chr1	3740718	Cc01_g02030:167	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	12.5%	4	CC	CT	CC	CC
-chr1:3740764	[C/T]	chr1	3740764	Cc01_g02030:213	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	33.3%	3	CC	NN	TT	CC
-chr1:3740817	[C/A]	chr1	3740817	Cc01_g02030:266	exon	NON_SYNONYMOUS_CODING	gCa/gAa	A/E	33.3%	3	CC	NN	AA	CC
-chr1:3750735	[C/T]	chr1	3750735	Cc01_g02040:6	exon	SYNONYMOUS_CODING	ggG/ggA	G/G	25.0%	4	CC	CT	CC	CT
-chr1:3750711	[C/G]	chr1	3750711	Cc01_g02040:30	exon	SYNONYMOUS_CODING	gtG/gtC	V/V	12.5%	4	CC	CG	CC	CC
-chr1:3750587	[C/T]	chr1	3750587	Cc01_g02040:154	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	12.5%	4	CC	CC	CC	CT
-chr1:3750577	[C/T]	chr1	3750577	Cc01_g02040:164	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	12.5%	4	CC	CT	CC	CC
-chr1:3750569	[T/C]	chr1	3750569	Cc01_g02040:172	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	12.5%	4	TT	TT	TT	TC
-chr1:3750546	[T/A]	chr1	3750546	Cc01_g02040:195	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	12.5%	4	TT	TT	TA	TT
-chr1:3750522	[A/G]	chr1	3750522	Cc01_g02040:219	exon	SYNONYMOUS_CODING	caT/caC	H/H	50.0%	4	AA	AA	GG	GG
-chr1:3750505	[G/C]	chr1	3750505	Cc01_g02040:236	exon	NON_SYNONYMOUS_CODING	tCt/tGt	S/C	12.5%	4	GG	GG	GC	GG
-chr1:3748656	[T/C]	chr1	3748656	Cc01_g02040:302	exon	NON_SYNONYMOUS_CODING	cAg/cGg	Q/R	50.0%	2	TT	NN	NN	CC
-chr1:3748610	[C/T]	chr1	3748610	Cc01_g02040:348	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	12.5%	4	CC	CC	CC	CT
-chr1:3748546	[C/T]	chr1	3748546	Cc01_g02040:412	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	CC	CC	CT	CC
-chr1:3748306	[A/G]	chr1	3748306	Cc01_g02040:562	exon	SYNONYMOUS_CODING	Ttg/Ctg	L/L	12.5%	4	AA	AA	AA	AG
-chr1:3748282	[C/T]	chr1	3748282	Cc01_g02040:586	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	25.0%	4	CC	TT	TT	TT
-chr1:3748213	[T/C]	chr1	3748213	Cc01_g02040:655	exon	NON_SYNONYMOUS_CODING	Aac/Gac	N/D	25.0%	4	TT	TT	TT	CC
-chr1:3748170	[A/C]	chr1	3748170	Cc01_g02040:698	exon	NON_SYNONYMOUS_CODING	cTa/cGa	L/R	12.5%	4	AA	AA	AA	AC
-chr1:3747303	[G/A]	chr1	3747303	Cc01_g02040:777	exon	SYNONYMOUS_CODING	gcC/gcT	A/A	12.5%	4	GG	GG	GA	GG
-chr1:3747255	[G/A]	chr1	3747255	Cc01_g02040:825	exon	SYNONYMOUS_CODING	gtC/gtT	V/V	25.0%	4	GG	AA	AA	AA
-chr1:3747226	[T/G]	chr1	3747226	Cc01_g02040:854	exon	NON_SYNONYMOUS_CODING	cAg/cCg	Q/P	12.5%	4	TT	TT	TT	TG
-chr1:3745743	[G/A]	chr1	3745743	Cc01_g02040:1024	exon	NON_SYNONYMOUS_CODING	Cgc/Tgc	R/C	50.0%	4	GG	GG	AA	AA
-chr1:3745742	[C/T]	chr1	3745742	Cc01_g02040:1025	exon	NON_SYNONYMOUS_CODING	cGc/cAc	R/H	25.0%	4	CC	TT	CC	CC
-chr1:3745322	[A/T]	chr1	3745322	Cc01_g02040:1191	exon	SYNONYMOUS_CODING	atT/atA	I/I	12.5%	4	AA	AA	AA	AT
-chr1:3745225	[G/T]	chr1	3745225	Cc01_g02040:1288	exon	NON_SYNONYMOUS_CODING	Ctc/Atc	L/I	12.5%	4	GG	GG	GG	GT
-chr1:3745223	[G/A]	chr1	3745223	Cc01_g02040:1290	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	12.5%	4	GG	GG	GG	AG
-chr1:3745208	[T/C]	chr1	3745208	Cc01_g02040:1305	exon	SYNONYMOUS_CODING	ctA/ctG	L/L	50.0%	4	TT	CC	TT	CC
-chr1:3745196	[T/C]	chr1	3745196	Cc01_g02040:1317	exon	SYNONYMOUS_CODING	acA/acG	T/T	25.0%	4	TT	TT	TC	CT
-chr1:3745187	[T/A]	chr1	3745187	Cc01_g02040:1326	exon	SYNONYMOUS_CODING	ctA/ctT	L/L	12.5%	4	TT	TT	TT	TA
-chr1:3745165	[G/A]	chr1	3745165	Cc01_g02040:1348	exon	NON_SYNONYMOUS_CODING	Cgt/Tgt	R/C	12.5%	4	GG	GG	GG	AG
-chr1:3745164	[C/T]	chr1	3745164	Cc01_g02040:1349	exon	NON_SYNONYMOUS_CODING	cGt/cAt	R/H	12.5%	4	CC	CC	CT	CC
-chr1:3744647	[G/C]	chr1	3744647	Cc01_g02040:1598	exon	NON_SYNONYMOUS_CODING	cCt/cGt	P/R	12.5%	4	GG	GG	GG	GC
-chr1:3744596	[C/T]	chr1	3744596	Cc01_g02040:1649	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	CC	CC	CC	CT
-chr1:3744575	[T/C]	chr1	3744575	Cc01_g02040:1670	exon	NON_SYNONYMOUS_CODING	aAt/aGt	N/S	12.5%	4	TT	TT	TC	TT
-chr1:3744299	[T/A]	chr1	3744299	Cc01_g02040:1698	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	12.5%	4	TT	TT	TA	TT
-chr1:3742967	[T/C]	chr1	3742967	Cc01_g02040:1935	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	12.5%	4	TT	TT	TC	TT
-chr1:3742922	[G/A]	chr1	3742922	Cc01_g02040:1980	exon	SYNONYMOUS_CODING	agC/agT	S/S	37.5%	4	GG	AA	GG	GA
-chr1:3742793	[C/T]	chr1	3742793	Cc01_g02040:2109	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	50.0%	4	CC	TT	TT	CC
-chr1:3741865	[T/G]	chr1	3741865	Cc01_g02040:2131	exon	NON_SYNONYMOUS_CODING	Att/Ctt	I/L	12.5%	4	TT	TG	TT	TT
-chr1:3741857	[A/G]	chr1	3741857	Cc01_g02040:2139	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	12.5%	4	AA	AA	AA	AG
-chr1:3741842	[T/C]	chr1	3741842	Cc01_g02040:2154	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	TT	TT	TT	TC
-chr1:3741793	[C/T]	chr1	3741793	Cc01_g02040:2203	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	CC	CC	CC	CT
-chr1:3759622	[T/A]	chr1	3759622	Cc01_g02050:54	exon	SYNONYMOUS_CODING	ggT/ggA	G/G	25.0%	4	TT	TT	TA	TA
-chr1:3762484	[A/G]	chr1	3762484	Cc01_g02050:82	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	12.5%	4	AA	AA	AA	AG
-chr1:3762723	[A/G]	chr1	3762723	Cc01_g02050:202	exon	NON_SYNONYMOUS_CODING	Aca/Gca	T/A	12.5%	4	AA	AA	AA	AG
-chr1:3762755	[A/G]	chr1	3762755	Cc01_g02050:234	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	GG	GG	GG
-chr1:3762781	[A/C]	chr1	3762781	Cc01_g02050:260	exon	NON_SYNONYMOUS_CODING	gAg/gCg	E/A	12.5%	4	AA	AA	AC	AA
-chr1:3762848	[G/A]	chr1	3762848	Cc01_g02050:327	exon	SYNONYMOUS_CODING	acG/acA	T/T	37.5%	4	GG	AA	GG	GA
-chr1:3763034	[A/G]	chr1	3763034	Cc01_g02050:411	exon	SYNONYMOUS_CODING	ccA/ccG	P/P	25.0%	4	AA	GG	AA	AA
-chr1:3763038	[C/A]	chr1	3763038	Cc01_g02050:415	exon	NON_SYNONYMOUS_CODING	Cta/Ata	L/I	25.0%	4	CC	AA	CC	CC
-chr1:3763049	[G/A]	chr1	3763049	Cc01_g02050:426	exon	SYNONYMOUS_CODING	caG/caA	Q/Q	25.0%	4	GG	AA	GG	GG
-chr1:3763055	[A/T]	chr1	3763055	Cc01_g02050:432	exon	SYNONYMOUS_CODING	ccA/ccT	P/P	37.5%	4	AA	AA	TT	AT
-chr1:3763064	[A/G]	chr1	3763064	Cc01_g02050:441	exon	SYNONYMOUS_CODING	acA/acG	T/T	25.0%	4	AA	GG	AA	AA
-chr1:3763079	[G/A]	chr1	3763079	Cc01_g02050:456	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	37.5%	4	GG	GG	AA	GA
-chr1:3766634	[T/G]	chr1	3766634	Cc01_g02060:471	exon	SYNONYMOUS_CODING	ccT/ccG	P/P	33.3%	3	TT	GG	NN	TT
-chr1:3766695	[T/C]	chr1	3766695	Cc01_g02060:532	exon	SYNONYMOUS_CODING	Tta/Cta	L/L	33.3%	3	TT	NN	TT	CC
-chr1:3920385	[G/T]	chr1	3920385	Cc01_g02110:211	exon	NON_SYNONYMOUS_CODING	Gca/Tca	A/S	50.0%	2	GG	NN	TT	NN
-chr1:3920402	[T/C]	chr1	3920402	Cc01_g02110:228	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	50.0%	2	TT	NN	CC	NN
-chr1:3923592	[A/T]	chr1	3923592	Cc01_g02120:176	exon	NON_SYNONYMOUS_CODING	gAg/gTg	E/V	12.5%	4	AA	AA	AA	AT
-chr1:3923713	[C/T]	chr1	3923713	Cc01_g02120:207	exon	SYNONYMOUS_CODING	ccC/ccT	P/P	12.5%	4	CC	CC	CT	CC
-chr1:3923759	[C/T]	chr1	3923759	Cc01_g02120:253	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	12.5%	4	CC	CC	CT	CC
-chr1:3923905	[C/T]	chr1	3923905	Cc01_g02120:399	exon	SYNONYMOUS_CODING	tcC/tcT	S/S	50.0%	4	CC	TT	CT	CT
-chr1:3923938	[T/A]	chr1	3923938	Cc01_g02120:432	exon	SYNONYMOUS_CODING	cgT/cgA	R/R	12.5%	4	TT	TA	TT	TT
-chr1:3923947	[C/T]	chr1	3923947	Cc01_g02120:441	exon	SYNONYMOUS_CODING	gaC/gaT	D/D	50.0%	4	CC	TT	CT	CT
-chr1:3924037	[G/A]	chr1	3924037	Cc01_g02120:531	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	12.5%	4	GG	GG	GA	GG
-chr1:3924086	[C/T]	chr1	3924086	Cc01_g02120:580	exon	NON_SYNONYMOUS_CODING	Cct/Tct	P/S	12.5%	4	CC	CT	CC	CC
-chr1:3924307	[T/C]	chr1	3924307	Cc01_g02120:801	exon	SYNONYMOUS_CODING	tcT/tcC	S/S	12.5%	4	TT	TC	TT	TT
-chr1:3924337	[G/A]	chr1	3924337	Cc01_g02120:831	exon	SYNONYMOUS_CODING	tcG/tcA	S/S	25.0%	4	GG	AA	AA	AA
-chr1:3924341	[C/G]	chr1	3924341	Cc01_g02120:835	exon	NON_SYNONYMOUS_CODING	Cct/Gct	P/A	12.5%	4	CC	CC	CG	CC
-chr1:3924368	[C/A]	chr1	3924368	Cc01_g02120:862	exon	NON_SYNONYMOUS_CODING	Cct/Act	P/T	12.5%	4	CC	AC	CC	CC
-chr1:3924378	[A/G]	chr1	3924378	Cc01_g02120:872	exon	NON_SYNONYMOUS_CODING	cAc/cGc	H/R	12.5%	4	AA	AG	AA	AA
-chr1:3924397	[G/A]	chr1	3924397	Cc01_g02120:891	exon	SYNONYMOUS_CODING	ttG/ttA	L/L	12.5%	4	GG	GA	GG	GG
-chr1:3924554	[A/C]	chr1	3924554	Cc01_g02120:1048	exon	SYNONYMOUS_CODING	Agg/Cgg	R/R	12.5%	4	AA	AC	AA	AA
-chr1:3924566	[T/C]	chr1	3924566	Cc01_g02120:1060	exon	NON_SYNONYMOUS_CODING	Tct/Cct	S/P	12.5%	4	TT	TT	TT	TC
-chr1:3924571	[C/A]	chr1	3924571	Cc01_g02120:1065	exon	SYNONYMOUS_CODING	ccC/ccA	P/P	12.5%	4	CC	CA	CC	CC
-chr1:3924632	[G/T]	chr1	3924632	Cc01_g02120:1126	exon	NON_SYNONYMOUS_CODING	Gct/Tct	A/S	12.5%	4	GG	TG	GG	GG
-chr1:3924644	[G/A]	chr1	3924644	Cc01_g02120:1138	exon	NON_SYNONYMOUS_CODING	Gag/Aag	E/K	12.5%	4	GG	GA	GG	GG
-chr1:3924648	[A/C]	chr1	3924648	Cc01_g02120:1142	exon	NON_SYNONYMOUS_CODING	gAg/gCg	E/A	12.5%	4	AA	AA	AC	AA
-chr1:3924703	[A/G]	chr1	3924703	Cc01_g02120:1197	exon	SYNONYMOUS_CODING	gaA/gaG	E/E	12.5%	4	AA	AG	AA	AA
-chr1:3924857	[G/C]	chr1	3924857	Cc01_g02120:1351	exon	NON_SYNONYMOUS_CODING	Gag/Cag	E/Q	12.5%	4	GG	GC	GG	GG
-chr1:3924860	[G/A]	chr1	3924860	Cc01_g02120:1354	exon	NON_SYNONYMOUS_CODING	Ggc/Agc	G/S	12.5%	4	GG	AG	GG	GG
-chr1:3924877	[A/C]	chr1	3924877	Cc01_g02120:1371	exon	SYNONYMOUS_CODING	ccA/ccC	P/P	12.5%	4	AA	CA	AA	AA
-chr1:3925027	[T/C]	chr1	3925027	Cc01_g02120:1521	exon	SYNONYMOUS_CODING	ggT/ggC	G/G	12.5%	4	TT	TC	TT	TT
-chr1:3925086	[C/T]	chr1	3925086	Cc01_g02120:1580	exon	NON_SYNONYMOUS_CODING	gCg/gTg	A/V	12.5%	4	CC	TC	CC	CC
-chr1:3925308	[G/A]	chr1	3925308	Cc01_g02120:1650	exon	SYNONYMOUS_CODING	aaG/aaA	K/K	37.5%	4	GG	GA	GA	GA
-chr1:3925317	[T/C]	chr1	3925317	Cc01_g02120:1659	exon	SYNONYMOUS_CODING	ttT/ttC	F/F	37.5%	4	TT	TC	TC	TC
-chr1:3925320	[G/T]	chr1	3925320	Cc01_g02120:1662	exon	NON_SYNONYMOUS_CODING	aaG/aaT	K/N	37.5%	4	GG	GT	GT	GT
-chr1:3925346	[A/G]	chr1	3925346	Cc01_g02120:1688	exon	NON_SYNONYMOUS_CODING	gAg/gGg	E/G	25.0%	4	AA	AG	AA	AG
-chr1:3930848	[G/T]	chr1	3930848	Cc01_g02130:14	exon	NON_SYNONYMOUS_CODING	tGc/tTc	C/F	12.5%	4	GG	GT	GG	GG
-chr1:3930877	[G/T]	chr1	3930877	Cc01_g02130:43	exon	NON_SYNONYMOUS_CODING	Ggt/Tgt	G/C	12.5%	4	GG	GG	GG	GT
-chr1:3930883	[G/T]	chr1	3930883	Cc01_g02130:49	exon	NON_SYNONYMOUS_CODING	Gta/Tta	V/L	50.0%	4	GG	TT	GT	GT
-chr1:3930897	[T/A]	chr1	3930897	Cc01_g02130:63	exon	SYNONYMOUS_CODING	gtT/gtA	V/V	12.5%	4	TT	TA	TT	TT
-chr1:3931056	[C/T]	chr1	3931056	Cc01_g02130:222	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	25.0%	4	CC	CT	CT	CC
-chr1:3931087	[C/A]	chr1	3931087	Cc01_g02130:253	exon	SYNONYMOUS_CODING	Cga/Aga	R/R	37.5%	4	CC	AA	CA	CC
-chr1:3931218	[A/G]	chr1	3931218	Cc01_g02130:267	exon	SYNONYMOUS_CODING	agA/agG	R/R	25.0%	4	AA	GA	AA	AG
-chr1:3931281	[T/C]	chr1	3931281	Cc01_g02130:330	exon	SYNONYMOUS_CODING	gaT/gaC	D/D	50.0%	4	TT	CC	TC	CT
-chr1:3931307	[C/T]	chr1	3931307	Cc01_g02130:356	exon	NON_SYNONYMOUS_CODING	gCt/gTt	A/V	50.0%	4	CC	TT	CT	TC
-chr1:3932233	[C/T]	chr1	3932233	Cc01_g02130:381	exon	SYNONYMOUS_CODING	acC/acT	T/T	37.5%	4	CC	CT	CT	CT
-chr1:3932286	[G/A]	chr1	3932286	Cc01_g02130:434	exon	NON_SYNONYMOUS_CODING	cGg/cAg	R/Q	37.5%	4	GG	GA	GA	GA
-chr1:3932490	[A/G]	chr1	3932490	Cc01_g02130:492	exon	SYNONYMOUS_CODING	aaA/aaG	K/K	12.5%	4	AA	AA	AA	GA
-chr1:3933113	[G/T]	chr1	3933113	Cc01_g02130:592	exon	NON_SYNONYMOUS_CODING	Gtg/Ttg	V/L	12.5%	4	GG	GT	GG	GG
-chr1:3933131	[G/A]	chr1	3933131	Cc01_g02130:610	exon	NON_SYNONYMOUS_CODING	Gaa/Aaa	E/K	25.0%	4	GG	GG	GA	GA
-chr1:3933913	[C/T]	chr1	3933913	Cc01_g02130:645	exon	SYNONYMOUS_CODING	taC/taT	Y/Y	50.0%	4	CC	TT	CT	CT
-chr1:3933970	[T/C]	chr1	3933970	Cc01_g02130:702	exon	SYNONYMOUS_CODING	ctT/ctC	L/L	25.0%	4	TT	TC	TC	TT
-chr1:3933994	[C/T]	chr1	3933994	Cc01_g02130:726	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	12.5%	4	CC	CC	CC	CT
-chr1:3934095	[A/G]	chr1	3934095	Cc01_g02130:733	exon	NON_SYNONYMOUS_CODING	Aaa/Gaa	K/E	25.0%	4	AA	AG	AG	AA
-chr1:3934103	[C/T]	chr1	3934103	Cc01_g02130:741	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	CC	CC	CC	TC
-chr1:3934155	[G/A]	chr1	3934155	Cc01_g02130:793	exon	NON_SYNONYMOUS_CODING	Ggg/Agg	G/R	25.0%	4	GG	AG	GG	GA
-chr1:3935070	[A/G]	chr1	3935070	Cc01_g02130:858	exon	SYNONYMOUS_CODING	gtA/gtG	V/V	25.0%	4	AA	AG	AG	AA
-chr1:3935127	[A/G]	chr1	3935127	Cc01_g02130:915	exon	SYNONYMOUS_CODING	ttA/ttG	L/L	37.5%	4	AA	GG	AG	GG
-chr1:3935145	[A/T]	chr1	3935145	Cc01_g02130:933	exon	SYNONYMOUS_CODING	ctA/ctT	L/L	25.0%	4	AA	AT	AT	AA
-chr1:3935149	[G/C]	chr1	3935149	Cc01_g02130:937	exon	NON_SYNONYMOUS_CODING	Gct/Cct	A/P	12.5%	4	GG	GG	GG	GC
-chr1:3935722	[A/C]	chr1	3935722	Cc01_g02130:949	exon	SYNONYMOUS_CODING	Aga/Cga	R/R	25.0%	4	AA	AC	AC	AA
-chr1:3935742	[A/G]	chr1	3935742	Cc01_g02130:969	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	25.0%	4	AA	AG	AG	AA
-chr1:3935757	[G/A]	chr1	3935757	Cc01_g02130:984	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	GG	GG	GG	AG
-chr1:3935791	[T/G]	chr1	3935791	Cc01_g02130:1018	exon	NON_SYNONYMOUS_CODING	Tct/Gct	S/A	37.5%	4	TT	GG	TG	GG
-chr1:3935805	[T/G]	chr1	3935805	Cc01_g02130:1032	exon	SYNONYMOUS_CODING	gtT/gtG	V/V	12.5%	4	TT	TT	TT	TG
-chr1:3935956	[A/C]	chr1	3935956	Cc01_g02130:1061	exon	NON_SYNONYMOUS_CODING	gAt/gCt	D/A	12.5%	4	AA	AA	AA	AC
-chr1:3935975	[G/A]	chr1	3935975	Cc01_g02130:1080	exon	SYNONYMOUS_CODING	gcG/gcA	A/A	12.5%	4	GG	GG	GG	GA
-chr1:3936792	[A/G]	chr1	3936792	Cc01_g02130:1125	exon	SYNONYMOUS_CODING	acA/acG	T/T	12.5%	4	AA	AA	AA	AG
-chr1:3936831	[A/G]	chr1	3936831	Cc01_g02130:1164	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	50.0%	4	AA	AG	AG	GG
-chr1:3936971	[G/C]	chr1	3936971	Cc01_g02130:1222	exon	NON_SYNONYMOUS_CODING	Gtt/Ctt	V/L	37.5%	4	GG	CC	GC	CC
-chr1:3942733	[G/A]	chr1	3942733	Cc01_g02140:62	exon	NON_SYNONYMOUS_CODING	cCc/cTc	P/L	25.0%	4	GG	AA	GG	GG
-chr1:3942723	[T/A]	chr1	3942723	Cc01_g02140:72	exon	SYNONYMOUS_CODING	gcA/gcT	A/A	25.0%	4	TT	AA	TT	TT
-chr1:3940926	[G/A]	chr1	3940926	Cc01_g02140:213	exon	SYNONYMOUS_CODING	ctC/ctT	L/L	12.5%	4	GG	GG	GA	GG
-chr1:3940777	[C/A]	chr1	3940777	Cc01_g02140:362	exon	NON_SYNONYMOUS_CODING	aGt/aTt	S/I	25.0%	4	CC	AA	CC	CC
-chr1:3940686	[A/G]	chr1	3940686	Cc01_g02140:453	exon	SYNONYMOUS_CODING	aaT/aaC	N/N	12.5%	4	AA	AG	AA	AA
-chr1:3940475	[A/G]	chr1	3940475	Cc01_g02140:664	exon	NON_SYNONYMOUS_CODING	Ttc/Ctc	F/L	12.5%	4	AA	AA	AA	AG
-chr1:3940287	[C/T]	chr1	3940287	Cc01_g02140:852	exon	SYNONYMOUS_CODING	acG/acA	T/T	25.0%	4	CC	TT	CC	CC
-chr1:3940278	[G/A]	chr1	3940278	Cc01_g02140:861	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	25.0%	4	GG	AA	GG	GG
-chr1:3940190	[T/C]	chr1	3940190	Cc01_g02140:949	exon	NON_SYNONYMOUS_CODING	Atc/Gtc	I/V	12.5%	4	TT	TT	TC	TT
-chr1:3940062	[G/A]	chr1	3940062	Cc01_g02140:1077	exon	SYNONYMOUS_CODING	aaC/aaT	N/N	37.5%	4	GG	AA	GA	AA
-chr1:3939962	[C/A]	chr1	3939962	Cc01_g02140:1177	exon	NON_SYNONYMOUS_CODING	Gcc/Tcc	A/S	12.5%	4	CC	CA	CC	CC
-chr1:3939959	[G/T]	chr1	3939959	Cc01_g02140:1180	exon	NON_SYNONYMOUS_CODING	Ctt/Att	L/I	25.0%	4	GG	TT	GG	GG
-chr1:3939916	[C/T]	chr1	3939916	Cc01_g02140:1223	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	25.0%	4	CC	TT	CC	CC
-chr1:3938977	[G/C]	chr1	3938977	Cc01_g02140:1335	exon	SYNONYMOUS_CODING	tcC/tcG	S/S	12.5%	4	GG	GC	GG	GG
-chr1:3938798	[T/G]	chr1	3938798	Cc01_g02140:1369	exon	NON_SYNONYMOUS_CODING	Agt/Cgt	S/R	37.5%	4	TT	GG	TG	TT
-chr1:3938797	[C/G]	chr1	3938797	Cc01_g02140:1370	exon	NON_SYNONYMOUS_CODING	aGt/aCt	S/T	12.5%	4	CC	CC	CC	CG
-chr1:3938792	[G/A]	chr1	3938792	Cc01_g02140:1375	exon	SYNONYMOUS_CODING	Cta/Tta	L/L	12.5%	4	GG	GG	GG	AG
-chr1:3938784	[C/T]	chr1	3938784	Cc01_g02140:1383	exon	SYNONYMOUS_CODING	ccG/ccA	P/P	25.0%	4	CC	TC	CT	CC
-chr1:3938738	[C/T]	chr1	3938738	Cc01_g02140:1429	exon	NON_SYNONYMOUS_CODING	Gtt/Att	V/I	12.5%	4	CC	CC	CT	CC
-chr1:3938734	[T/C]	chr1	3938734	Cc01_g02140:1433	exon	NON_SYNONYMOUS_CODING	cAa/cGa	Q/R	25.0%	4	TT	TT	TC	CT
-chr1:3938731	[A/G]	chr1	3938731	Cc01_g02140:1436	exon	NON_SYNONYMOUS_CODING	gTg/gCg	V/A	12.5%	4	AA	AA	AG	AA
-chr1:3938674	[C/T]	chr1	3938674	Cc01_g02140:1493	exon	NON_SYNONYMOUS_CODING	aGt/aAt	S/N	12.5%	4	CC	CC	CT	CC
-chr1:3950327	[A/C]	chr1	3950327	Cc01_g02150:300	exon	NON_SYNONYMOUS_CODING	caT/caG	H/Q	37.5%	4	AA	CC	AC	AA
-chr1:3949508	[G/T]	chr1	3949508	Cc01_g02150:438	exon	SYNONYMOUS_CODING	tcC/tcA	S/S	12.5%	4	GG	GT	GG	GG
-chr1:3949500	[T/C]	chr1	3949500	Cc01_g02150:446	exon	NON_SYNONYMOUS_CODING	tAt/tGt	Y/C	12.5%	4	TT	TT	TC	TT
-chr1:3949478	[G/A]	chr1	3949478	Cc01_g02150:468	exon	SYNONYMOUS_CODING	cgC/cgT	R/R	12.5%	4	GG	GG	GA	GG
-chr1:3949470	[C/T]	chr1	3949470	Cc01_g02150:476	exon	NON_SYNONYMOUS_CODING	aGg/aAg	R/K	25.0%	4	CC	TT	CC	CC
-chr1:3949465	[C/G]	chr1	3949465	Cc01_g02150:481	exon	NON_SYNONYMOUS_CODING	Ggt/Cgt	G/R	37.5%	4	CC	GG	CG	CC
-chr1:3949086	[C/T]	chr1	3949086	Cc01_g02150:541	exon	NON_SYNONYMOUS_CODING	Gtc/Atc	V/I	12.5%	4	CC	CC	CT	CC
-chr1:3967535	[C/T]	chr1	3967535	Cc01_g02160:57	exon	SYNONYMOUS_CODING	cgG/cgA	R/R	12.5%	4	CC	CT	CC	CC
-chr1:3967530	[A/T]	chr1	3967530	Cc01_g02160:62	exon	NON_SYNONYMOUS_CODING	cTg/cAg	L/Q	12.5%	4	AA	AA	AA	AT
-chr1:3967524	[G/A]	chr1	3967524	Cc01_g02160:68	exon	NON_SYNONYMOUS_CODING	cCa/cTa	P/L	37.5%	4	GG	AG	GA	AG
-chr1:3967512	[A/G]	chr1	3967512	Cc01_g02160:80	exon	NON_SYNONYMOUS_CODING	aTa/aCa	I/T	12.5%	4	AA	AA	AG	AA
-chr1:3967435	[A/G]	chr1	3967435	Cc01_g02160:157	exon	NON_SYNONYMOUS_CODING	Tcc/Ccc	S/P	25.0%	4	AA	AG	AA	AG
-chr1:3967421	[G/A]	chr1	3967421	Cc01_g02160:171	exon	SYNONYMOUS_CODING	acC/acT	T/T	12.5%	4	GG	AG	GG	GG
-chr1:3967412	[A/C]	chr1	3967412	Cc01_g02160:180	exon	STOP_GAINED	taT/taG	Y/0	37.5%	4	AA	AC	AC	AC
-chr1:3967382	[A/G]	chr1	3967382	Cc01_g02160:210	exon	SYNONYMOUS_CODING	ccT/ccC	P/P	25.0%	4	AA	GA	GA	AA
-chr1:3967354	[G/T]	chr1	3967354	Cc01_g02160:238	exon	NON_SYNONYMOUS_CODING	Caa/Aaa	Q/K	12.5%	4	GG	GG	GG	GT
-chr1:3967352	[T/C]	chr1	3967352	Cc01_g02160:240	exon	SYNONYMOUS_CODING	caA/caG	Q/Q	37.5%	4	TT	CC	CT	CC
-chr1:3967310	[G/C]	chr1	3967310	Cc01_g02160:282	exon	NON_SYNONYMOUS_CODING	atC/atG	I/M	37.5%	4	GG	GC	GC	GC
-chr1:3967300	[C/T]	chr1	3967300	Cc01_g02160:292	exon	NON_SYNONYMOUS_CODING	Gat/Aat	D/N	12.5%	4	CC	CC	CC	TC
-chr1:3967295	[G/A]	chr1	3967295	Cc01_g02160:297	exon	SYNONYMOUS_CODING	atC/atT	I/I	12.5%	4	GG	GG	GA	GG
-chr1:3966909	[T/A]	chr1	3966909	Cc01_g02160:683	exon	NON_SYNONYMOUS_CODING	tAt/tTt	Y/F	12.5%	4	TT	TA	TT	TT
-chr1:3966784	[G/A]	chr1	3966784	Cc01_g02160:808	exon	NON_SYNONYMOUS_CODING	Ctt/Ttt	L/F	16.7%	3	GG	NN	GA	GG
diff -r 420b57c3c185 -r feb40a9a8eae SNP_density/test-data/result.txt
--- a/SNP_density/test-data/result.txt	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-Chromosome	Position	SNPs
-chr1	200000	355
-chr1	400000	228
-chr1	600000	63
-chr1	800000	191
-chr1	1000000	88
-chr1	1200000	90
-chr1	1400000	190
-chr1	1600000	267
-chr1	1800000	226
-chr1	2000000	163
-chr1	2200000	357
-chr1	2400000	132
-chr1	2600000	158
-chr1	2800000	104
-chr1	3000000	146
-chr1	3200000	331
-chr1	3400000	181
-chr1	3600000	36
-chr1	3800000	167
-chr1	4000000	110
diff -r 420b57c3c185 -r feb40a9a8eae SNP_density/test-data/result_bysample.txt
--- a/SNP_density/test-data/result_bysample.txt	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-Chromosome	BA58	BA59	BD54
-chr1	220	197	225
-chr1	130	119	133
-chr1	43	43	40
-chr1	139	167	141
-chr1	62	72	78
-chr1	35	76	38
-chr1	98	123	82
-chr1	133	205	135
-chr1	94	141	151
-chr1	112	116	117
-chr1	228	238	204
-chr1	86	95	96
-chr1	60	106	82
-chr1	60	74	64
-chr1	106	112	115
-chr1	199	220	228
-chr1	151	94	64
-chr1	18	32	27
-chr1	87	90	100
-chr1	54	75	47
diff -r 420b57c3c185 -r feb40a9a8eae VCF2Hapmap/VCF2FastaAndHapmap.pl
--- a/VCF2Hapmap/VCF2FastaAndHapmap.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,525 +0,0 @@
-
-#!/usr/bin/perl
-
-use strict;
-use Getopt::Long;
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-
-where <args> are:
-
-    -v, --vcf          <VCF input>
-    -o, --out          <Output basename>
-      
-<opts> are:
-
-    -r, --reference    <Reference fasta file>
-    -g, --gff          <GFF input file to create alignments of genes>
-~;
-$usage .= "\n";
-
-my ($input,$out,$reference,$gff);
-
-
-
-GetOptions(
-	"vcf=s"          => \$input,
-	"out=s"          => \$out,
-	"reference=s"    => \$reference,
-	"gff=s"          => \$gff
-);
-
-
-die $usage
-  if ( !$input || !$out);
- 
-if ($gff && !$reference)
-{
-	die "You must provide a Fasta reference file when providing GFF annotation\n";
-}
-
- 
-my %ref_sequences;  
-if ($reference)
-{
-	my $id;
-	my $sequence = "";
-	open(my $R,$reference) or die "cannot open file: $reference";
-	while(<$R>)
-	{
-		my $line =$_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		if ($line =~ />([^\s]+)/){
-			$ref_sequences{$id} = $sequence;
-			$id=$1;$sequence="";
-		}
-		else
-		{
-			$sequence .= $line;
-		}
-	}
-	close($R);
-	$ref_sequences{$id} = $sequence;
-}
-
-
-my %chr_of_gene;
-my %ann;
-if ($gff)
-{
-	open(my $G,$gff) or die "cannot open file: $gff";
-	while(<$G>)
-	{
-		my $line =$_;
-		$line =~s/\n//g;
-		$line =~s/\r//g;
-		my @i = split(/\t/,$line);
-		my $chr = $i[0];
-		my $feature = $i[2];
-		my $strand = $i[6];
-		my $start = $i[3];
-		my $stop = $i[4];
-		my $inf = $i[8];
-		if ($feature eq 'gene')
-		{
-			 if ($inf =~/Name=([\w\-\.]+)[;\s]*/){$inf = $1;}
-			$ann{$inf}{"start"}=$start;
-			$ann{$inf}{"stop"}=$stop;
-			$ann{$inf}{"strand"}=$strand;
-			$chr_of_gene{$inf} = $chr;
-		}
-	}
-	close($G);
-}
-
-
-
-my %IUPAC =
-(
-        '[A/G]'=> "R",
-        '[G/A]'=> "R",
-        '[C/T]'=> "Y",
-        '[T/C]'=> "Y",
-        '[T/G]'=> "K",
-        '[G/T]'=> "K",
-        '[C/G]'=> "S",
-        '[G/C]'=> "S",
-        '[A/T]'=> "W",
-        '[T/A]'=> "W",
-        '[A/C]'=> "M",
-        '[C/A]'=> "M",
-        '[C/A/T]'=> "H",
-        '[A/T/C]'=> "H",
-        '[A/C/T]'=> "H",
-        '[C/T/A]'=> "H",
-        '[T/C/A]'=> "H",
-        '[T/A/C]'=> "H",
-        '[C/A/G]'=> "V",
-        '[A/G/C]'=> "V",
-        '[A/C/G]'=> "V",
-        '[C/G/A]'=> "V",
-        '[G/C/A]'=> "V",
-        '[G/A/C]'=> "V",
-        '[C/T/G]'=> "B",
-        '[T/G/C]'=> "B",
-        '[T/C/G]'=> "B",
-        '[C/G/T]'=> "B",
-        '[G/C/T]'=> "B",
-        '[G/T/C]'=> "B",
-        '[T/A/G]'=> "D",
-        '[A/G/T]'=> "D",
-        '[A/T/G]'=> "D",
-        '[T/G/A]'=> "D",
-        '[G/T/A]'=> "D",
-        '[G/A/T]'=> "D",
-);
-
-my %snps_of_gene;
-my %snps_of_gene2;
-my %indiv_order;
-my $indiv_list;
-my %genotyping_infos;
-my $num_line = 0;
-my $genename_rank_in_snpeff = 4;
-
-my $find_annotations = `grep -c 'EFF=' $input`;
-
-open(my $HAPMAP,">$out.hapmap");
-print $HAPMAP "rs#	alleles	chrom	pos	gene	feature	effect	codon_change	amino_acid_change	MAF	missing_data";
-open(my $VCF,$input);
-while(<$VCF>)
-{
-	my $line = $_;
-	chomp($line);
-	my @infos = split(/\t/,$line);
-	
-	if (/^##INFO=\<ID=EFF/ && /Amino_Acid_length \| Gene_Name \| Transcript_BioType \| Gene_Coding/)
-	{
-		$genename_rank_in_snpeff = 8;
-	}
-
-	if (scalar @infos > 9)
-	{
-		if (/#CHROM/)
-		{
-			for (my $j=9;$j<=$#infos;$j++)
-			{
-				my $individu = $infos[$j];
-				$indiv_list .= "	$individu";
-				$indiv_order{$j} = $individu;
-			}
-			print $HAPMAP "$indiv_list\n";
-		}
-		elsif (!/^#/)
-		{
-			$num_line++;
-
-			my $chromosome = $infos[0];
-			my $chromosome_position = $infos[1];
-			my $ref_allele = $infos[3];
-			my $alt_allele = $infos[4];
-                    	
-			if ($ref_allele =~/\w\w+/)
-			{
-				$ref_allele = "A";
-				$alt_allele = "T";
-			}
-			elsif ($alt_allele =~/\w\w+/)
-			{
-				$ref_allele = "T";
-				$alt_allele = "A";
-			}
-			
-			my $info = $infos[7];
-			my $is_in_exon = "#";
-			my $is_synonyme = "#";
-			my $gene;
-			if ($find_annotations > 1)
-			{
-				$gene = "intergenic";
-			}
-			else
-			{
-				$gene = $chromosome;
-			}
-			my $modif_codon = "#";
-			my $modif_aa = "#";
-			my $geneposition;
-			if ($info =~/EFF=(.*)/)
-			{
-					my @annotations = split(",",$1);
-					foreach my $annotation(@annotations)
-					{
-						my ($syn, $additional) = split(/\(/,$annotation);
-
-						if ($syn =~/STREAM/){next;}
-
-						$is_in_exon = "exon";
-						if ($syn =~/UTR/)
-						{
-							$is_in_exon = $syn;
-						}
-						else
-						{
-							$is_synonyme = $syn;
-						}
-						my @infos_additional = split(/\|/,$additional);
-						$gene = $infos_additional[$genename_rank_in_snpeff];
-						$modif_codon = $infos_additional[2];
-						$modif_aa = $infos_additional[3];
-						
-						if ($syn =~/INTERGENIC/)
-						{
-							$is_synonyme = "#";
-							$gene = "intergenic";
-							$is_in_exon = "#";
-						}
-						elsif ($syn =~/SYNONYM/)
-						{
-							$is_in_exon = "exon";
-						}
-						elsif ($syn =~/INTRON/ or $syn =~/SPLICE_SITE_DONOR/)
-						{
-							$is_in_exon = "intron";
-							$is_synonyme = "#";
-						}
-						
-						
-						if ($modif_aa =~/(\w)(\d+)$/)
-						{
-							$modif_aa = "$1/$1";
-						}
-						elsif ($modif_aa =~/(\w)(\d+)(\w)/)
-						{
-							$modif_aa = "$1/$3";
-						}
-						if ($infos_additional[8] =~/Exon/)
-						{
-							$is_in_exon = "exon";
-						}
-						
-						if (!$modif_aa){$modif_aa="#";}
-						if (!$modif_codon){$modif_codon="#";}
-					}
-			}
-			$gene =~s/\.\d//g;
-			if ($ann{$gene}{"start"})
-			{
-				my $strand = $ann{$gene}{"strand"};
-				if ($strand eq '-')
-				{
-					$geneposition = $ann{$gene}{"stop"} - $chromosome_position;
-				}
-				else
-				{
-					$geneposition = $chromosome_position - $ann{$gene}{"start"};
-				}
-			}
-			#if ($info =~/GenePos=(\d+);/)
-			#{
-			#	$geneposition = $1;
-			#}
-			my $ratio_missing_data;
-			my $snp_frequency;
-			my $genotyping = "";
-			
-			if (2 > 1)
-			{
-				
-				$genotyping_infos{"ref"} = "$ref_allele$ref_allele";
-				
-				my %alleles_found;
-				my $nb_readable_ind = 0;
-				for (my $i = 9;$i <= $#infos;$i++)
-				{
-					my $dnasample = $indiv_order{$i};
-					my @infos_alleles = split(":",$infos[$i]);
-					my $genotype = $infos_alleles[0];
-					$genotype =~s/0/$ref_allele/g;
-
-					if ($alt_allele =~/,/)
-					{
-						my @alt_alleles = split(",",$alt_allele);
-						my $num_all = 1;
-						foreach my $alt_al(@alt_alleles)
-						{
-							$genotype =~s/$num_all/$alt_al/g;
-							$num_all++;
-						}
-					}
-					else
-					{
-						$genotype =~s/1/$alt_allele/g;
-					}
-					if ($genotype eq '.'){$genotype = "./.";}
-					$genotype =~s/\./N/g;
-					if ($genotype !~/N\/N/)
-					{
-						$nb_readable_ind++;
-					}
-					my @alleles;
-					if ($genotype =~/\//)
-					{
-						@alleles = split(/\//,$genotype);
-					}
-					else
-					{
-						@alleles = split(/\|/,$genotype);
-					}
-					$genotyping .= join("",@alleles) . "	";
-					$genotyping_infos{$dnasample} = join("",@alleles);
-					
-					foreach my $al(@alleles)
-					{
-						if ($al ne 'N'){$alleles_found{$al}++;}
-					}	
-				}
-				chop($genotyping);
-				
-				$snp_frequency = 0;
-					
-				my $max = 0;
-				my $min = 10000000;
-				my $total = 0;
-				foreach my $al(keys(%alleles_found))
-				{
-					my $nb = $alleles_found{$al};
-					$total+= $nb;
-					if ($nb > $max)
-					{
-						$max = $nb;
-					}
-					if ($nb < $min)
-					{
-						$min = $nb;
-					}
-				}
-				if ($total > 0)
-				{
-					$snp_frequency = sprintf("%.1f",($min/$total)*100);
-				}
-				
-				$ratio_missing_data = 100 - ($nb_readable_ind / ($#infos - 8)) * 100;
-				$ratio_missing_data = sprintf("%.1f",$ratio_missing_data);
-
-				foreach my $dna(keys(%genotyping_infos))
-				{
-					$snps_of_gene{$gene}{$geneposition}{$dna} = $genotyping_infos{$dna};
-				}
-			}
-			my $snp_type = "[$ref_allele/$alt_allele]";
-			$snps_of_gene2{$chromosome}{$chromosome_position} = $snp_type;
-			#print $HAPMAP "$chromosome:$chromosome_position\t$snp_type\t$chromosome\t$chromosome_position\t$gene:$geneposition\t$is_in_exon\t$is_synonyme\t$modif_codon\t$modif_aa\t$snp_frequency%\t$nb_readable_ind\t$genotyping\n";
-			print $HAPMAP "$chromosome:$chromosome_position\t$ref_allele/$alt_allele\t$chromosome\t$chromosome_position\t$gene:$geneposition\t$is_in_exon\t$is_synonyme\t$modif_codon\t$modif_aa\t$snp_frequency%\t$ratio_missing_data%\t$genotyping\n";
-		}
-	}
-}
-close($VCF);
-close($HAPMAP);
-
-
-if (!$reference){exit;}
-
-#################################################################
-# generate flanking sequences for Illumina VeraCode technology
-#################################################################
-open(my $FLANKING,">$out.flanking.txt");
-foreach my $seq(keys(%ref_sequences))
-{
-                        if ($snps_of_gene2{$seq})
-                        {
-                                my $refhash = $snps_of_gene2{$seq};
-                                my %hashreal = %$refhash;
-
-                                # create consensus
-                                my $refseq = $ref_sequences{$seq};
-                                my $consensus = "";
-                                my $previous = 0;
-                                foreach my $pos(sort {$a<=>$b} keys(%hashreal))
-                                {
-                                        my $length = $pos - $previous - 1;
-                                        $consensus .= substr($refseq,$previous,$length);
-                                        my $iupac_code = $IUPAC{$snps_of_gene2{$seq}{$pos}};
-                                        $consensus .= $iupac_code;
-                                        $previous = $pos;
-                                }
-                                my $length = length($refseq) - $previous;
-                                $consensus .= substr($refseq,$previous,$length);
-
-                                foreach my $pos(sort {$a<=>$b} keys(%hashreal))
-                                {
-                                        my $snp_name = "$seq-$pos";
-                                        my $flanking_length = 60;
-                                        my $length = $flanking_length;
-                                        my $start = $pos - $flanking_length - 1;
-                                        if ($pos <= $flanking_length)
-                                        {
-                                                $length = $pos - 1;
-                                                $start = 0;
-                                        }
-                                        my $sequence = substr($consensus,$start,$length);
-				
-                                        $sequence .= $snps_of_gene2{$seq}{$pos};
-                                        $sequence .= substr($consensus,$pos,$flanking_length);
-                                        print $FLANKING "$snp_name,$sequence,0,0,0,Project_name,0,diploid,Other,Forward\n";
-                                }
-                        }
-	}
-
-	close($FLANKING);
-
-	if (!$gff){exit;}
-
-	my @individuals_list = split(/\t/,$indiv_list);
-	if ((scalar @individuals_list * scalar keys(%snps_of_gene)) > 800000)
-	{
-		print "Sorry, too many sequences to manage ...\n";
-		exit;
-	}
-
-	open(my $ALIGN_EGGLIB,">$out.gene_alignment.fas");
-	my %alignments_ind;
-	foreach my $seq(keys(%snps_of_gene))
-	{
-		if ($snps_of_gene{$seq})
-		{
-			my $refhash = $snps_of_gene{$seq};
-			my %hashreal = %$refhash;
-
-			# get flanking sequences
-			my %flanking5;
-			my $start = $ann{$seq}{"start"};
-			my $stop = $ann{$seq}{"stop"};
-			my $strand = $ann{$seq}{"strand"};
-			my $genelength = $stop - $start+1;
-			my $chr = $chr_of_gene{$seq};
-		my $refseq = substr($ref_sequences{$chr},$start-1,$genelength);
-		if ($strand eq '-')
-		{
-			$refseq =~ tr /atcgATCG/tagcTAGC/; $refseq = reverse($refseq);
-		}	
-		#print "$seq $chr $start $stop $refseq \n";
-		my $previous = 0;
-		foreach my $pos(sort {$a<=>$b} keys(%hashreal))
-		{
-			my $length = $pos - $previous - 1;
-			$flanking5{$pos} = substr($refseq,$previous,$length);
-			$previous = $pos;
-		}
-		my $length = length($refseq) - $previous;
-		my $flanking3 = substr($refseq,$previous,$length);
-		foreach my $ind(@individuals_list)
-		{
-			my $nb_missing_data_for_this_individual = 0;
-			if ($ind)
-			{
-                                                my $alignment_for_ind = "";
-                                                my $seq_without_underscore = $seq;
-                                                $seq_without_underscore =~s/_//g;
-                                                $alignment_for_ind .= ">$seq_without_underscore" . "_$ind" . "_1\n";
-                                                foreach my $pos(sort {$a<=>$b} keys(%hashreal))
-                                                {
-                                                        $alignment_for_ind .= $flanking5{$pos};
-                                                        my $geno = $snps_of_gene{$seq}{$pos}{$ind};
-                                                        $geno =~s/N/?/g;
-                                                        if ($geno =~/\?/){$nb_missing_data_for_this_individual++;}
-                                                        my @alleles = split("",$geno);
-                                                        $alignment_for_ind .= $alleles[0];
-                                                        if ($alleles[0] eq $alleles[1])
-                                                        {
-                                                                $alignments_ind{$ind} .= $alleles[1];
-                                                        }
-                                                        else
-                                                        {
-                                                                my $snp_type = "[" . $alleles[0] . "/" . $alleles[1] . "]";
-                                                                $alignments_ind{$ind} .= $IUPAC{$snp_type};
-                                                        }
-                                                }
-                                                $alignment_for_ind .= $flanking3;
-						$alignment_for_ind .= "\n";
-			
-			
-                                                $alignment_for_ind .= ">$seq_without_underscore" . "_$ind" . "_2\n";
-                                                foreach my $pos(sort {$a<=>$b} keys(%hashreal))
-                                                {
-                                                        $alignment_for_ind .= $flanking5{$pos};
-                                                        my $geno = $snps_of_gene{$seq}{$pos}{$ind};
-                                                        $geno =~s/N/?/g;
-                                                        my @alleles = split("",$geno);
-                                                        $alignment_for_ind .= $alleles[1];
-                                                }
-                                                $alignment_for_ind .= $flanking3;
-						$alignment_for_ind .= "\n";
-                                                if (keys(%hashreal) != $nb_missing_data_for_this_individual)
-                                                {
-                                                        print $ALIGN_EGGLIB $alignment_for_ind;
-                                                }
-			}
-		}
-	}
-}
-close($ALIGN_EGGLIB);
-
-
-
diff -r 420b57c3c185 -r feb40a9a8eae VCF2Hapmap/vcf2FastaAndHapmap.sh
--- a/VCF2Hapmap/vcf2FastaAndHapmap.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-#!/bin/bash
-
-tool_path=$(dirname $0)
-
-
-
-filein=$1
-fileout_label=$2
-fileout=$3
-option=$4
-
-option_text=''
-
-
-if [ "$option" != "none" ]
-then fileout_seq=$5 
-	fileout_fa1=$6 
-	filefasta=$7
-	if [ "$option" == "fasta_gff" ]
-		then filegff=$8
-	fi
-fi
-
-if [ "$option" == "fasta" ]
-then option_text="--reference $filefasta"
-fi
-
-if [ "$option" == "fasta_gff" ]
-then option_text="--reference $filefasta --gff $filegff"
-fi
-
-
-perl $tool_path/VCF2FastaAndHapmap.pl --vcf $filein --out $fileout_label $option_text
-
-
-cp  $fileout_label.hapmap $fileout ; rm $fileout_label.hapmap
-
-if [ "$option" == "fasta_gff" ]
-then cp  $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; cp  $fileout_label.gene_alignment.fas $fileout_fa1 ; rm $fileout_label.gene_alignment.fas ;
-fi
-
-if [ "$option" == "fasta" ]
-then cp  $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ;
-fi
-
diff -r 420b57c3c185 -r feb40a9a8eae VCF2Hapmap/vcf2FastaAndHapmap.xml
--- a/VCF2Hapmap/vcf2FastaAndHapmap.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,251 +0,0 @@
-<tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="1.1.0">
-    
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
-    <description> Convert VCF to Hapmap  </description>
-    
-    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
-    <requirements>
-        <requirement type="binary">perl</requirement>
-    </requirements>
-    
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
-    
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="bash">
-	vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt 
-	#if str( $optional.file_opt ) != "none":
-		$fileout_seq $fileout_fa1 $filefasta 
-		#if str( $optional.file_opt ) == "fasta_gff":
-		$filegff
-		#end if
-	#end if
-    </command>
-     
-    <!-- [REQUIRED] Input files and tool parameters -->
-    <inputs>
-	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
-	<param name="fileout_label" type="text" value="input" optional="false" label="Output file basename"/>
-	<conditional name="optional" >
-	    <param name="file_opt" type="select" label="Optional files" >
-	    	<option value="none" selected="true">No</option>
-	    	<option value="fasta">Fasta</option>
-            	<option value="fasta_gff">Fasta and GFF</option>
-            </param>
-	    <when value="none" />
-            <when value="fasta">
-		<param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
-            </when>
-	    <when value="fasta_gff">
-		<param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
-		<param name="filegff" type="data" format="gff" optional="false" label="GFF file input" help="VCF file must be annotated" />
-            </when>
-        </conditional>
-    </inputs>
-    
-    <!-- [REQUIRED] Output files -->
-    <outputs>
-	<data name="fileout" format="txt" label="${fileout_label}.hapmap" />
-	<data name="fileout_seq" format="txt" label="${fileout_label}.flanking.txt">
-		<filter>(optional['file_opt'] != 'none')</filter>
-	</data>
-	<data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas">
-		<filter>(optional['file_opt'] == 'fasta_gff')</filter>
-	</data>
-    </outputs>
-    
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-        <test>
-         <param name="filein" value="sample.vcf" />
-         <param name="otpional.file_opt" value="none" />
-         <output name="fileout" file="result1.hapmap" />
-        </test>
-	<test>
-         <param name="filein" value="sample.vcf" />
-	 <param name="otpional.file_opt" value="fasta" />
-         <param name="filefasta" value="reference.fa" />
-         <output name="fileout" file="result2.hapmap" />
-         <output name="fileout_seq" file="result2.flanking.txt" />
-         <output name="fileout_fa1" file="result2.gene_alignment.fas" />
-        </test>
-    </tests>
-    
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
-    <help>
-
-
-.. class:: infomark
-
-**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
-
- | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
-.. class:: infomark
-
-**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. 
-
-.. class:: infomark
-
-**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr 
-
----------------------------------------------------
-
-=======================
-VCF to Hapmap
-=======================
-
------------
-Description
------------
-
-  | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided.
-  | Furthermore it also creates fasta alignment of genes if GFF annotation is provided 
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ========================== =======
-Name            output file(s)             format 
-=============== ========================== =======
-VCFtools Filter VCF file		   VCF
-=============== ========================== =======
-
-
-**Downstream tool**
-
-=============== ========================== ===========
-Name            input file(s)              format 
-=============== ========================== ===========
-SNP density	Hapmap file 	 	   tabular
-=============== ========================== ===========
-
-
-----------
-Input file
-----------
-
-VCF file
-	VCF file with all SNPs
-
-----------
-Parameters
-----------
-
-Output file basename
-	Prefix for the output VCF file
-
-Optional files
-        To add additional files fasta file and GFF file.
-
-------------
-Output files
-------------
-
-Hapmap file 
-	Hapmap converted file
-
-Additional files 
-	If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-VCF file
----------
-
-::
-
-	#fileformat=VCFv4.1
-	#FILTER=&lt;ID=LowQual,Description="Low quality">
-	#FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-	[...]
-	CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CATB1
-	chr1	2209	.	G	T	213.84	.	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)	GT:AD:DP:GQ:PL	1/1:0,7:7:18:242,18,0
-
-Fasta file
-----------
-
-
-::
-
-	>chr1
-	CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT
-
-Parameters
-==========
-
-Output name -> input
-
-Optional files -> Fasta
-
-
-Output files
-============
-
-input.hapmap
-------------
-
-::
-
-        rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panelLSID	QCcode	CATB1
-	chr1:2209	G/T	chr1	2209	+	NA	NA	NA	NA	NA	NA	GG	TT
-	chr1:2232	A/C	chr1	2232	+	NA	NA	NA	NA	NA	NA	AA	CC
-
-input.flanking.txt
-------------------
-
-::
-
-	chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward
-	chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward
-
-input.gene_alignment.fas
-------------------------
-
-::
-
-	>chr1_CATB1_1
-	TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT
-
-	
-    </help>
-
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	}</citation>
-
-    </citations>
-    
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae check_gwas_inputs/CheckGWASInputs.pl
--- a/check_gwas_inputs/CheckGWASInputs.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,184 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -h, --hapmap       <Hapmap input file>
-    -t, --trait        <Trait input file>
-    -o, --out          <Output base name>
-~;
-$usage .= "\n";
-
-my ($hapmap,$trait,$out);
-
-
-GetOptions(
-        "trait=s"      => \$trait,
-        "out=s"        => \$out,
-        "hapmap=s"     => \$hapmap
-);
-
-
-die $usage
-  if ( !$trait || !$out || !$hapmap);
-  
-my %inds;
-
-#######################################
-# get individuals in trait file
-#######################################
-my %traits;
-my $head_trait = `head -1 $trait`;
-open(my $T,$trait);
-<$T>;
-while(<$T>)
-{
-	my @infos = split(/\t/,$_);
-	my $ind = $infos[0];
-	$inds{$ind}++;
-	$traits{$ind} = $_;
-}
-close($T);
-my $nb_ind_trait = scalar keys(%traits);
-
-#######################################
-# get individuals in hapmap file
-#######################################
-my $line_ind = `head -1 $hapmap`;
-chomp($line_ind);
-my @infos = split(/\t/,$line_ind);
-for (my $i = 11; $i <= $#infos; $i++)
-{
-	my $ind = $infos[$i];
-	$inds{$ind}++;
-}
-my $nb_ind_hapmap = scalar @infos - 11;
-
-#################################################################
-# create trait output by keeping individuals found in both files
-#################################################################
-open(my $O,">$out.trait");
-print $O $head_trait;
-my $nb_common = 0;
-foreach my $ind(keys(%inds))
-{
-	my $nb_found = $inds{$ind};
-	if ($nb_found == 2)
-	{
-		$nb_common++;
-		print $O $traits{$ind};
-	}
-}
-close($O);
-
-
-#####################################################################
-# create hapmap output after keeping individuals found in both files
-# and removing monomorphic positions
-#####################################################################
-open(my $O2,">$out.hapmap");
-my $numline = 0;
-my %genotypes;
-my %columns_to_keep;
-my $nb_monomorphic = 0;
-my $not_biallelic = 0;
-my $diff_variation = 0;
-open(my $H,$hapmap);
-while(<$H>)
-{
-	$numline++;
-	my $line = $_;
-	$line =~s/\n//g;
-	$line =~s/\r//g;
-	my @infos = split(/\t/,$line);
-	if ($numline == 1)
-	{
-		my @titles;
-		for (my $i = 0; $i <= 10; $i++)
-		{
-			my $title = $infos[$i];
-			push(@titles,$title);
-		}
-		print $O2 join("\t",@titles);
-		for (my $i = 11; $i <= $#infos; $i++)
-		{
-			my $ind = $infos[$i];
-			my $nb_found = $inds{$ind};
-			if ($nb_found == 2)
-			{
-				print $O2 "	$ind";
-				$columns_to_keep{$i} = 1;
-			}
-		}
-		print $O2 "\n";
-	}
-	else
-	{
-		my $to_be_printed = "";
-		my $variation = $infos[1];
-        for (my $i = 0; $i <= 10; $i++)
-		{
-			my $title = $infos[$i];
-			$to_be_printed .= "$title	";
-		}
-		my %letters;
-		for (my $i = 11; $i <= $#infos; $i++)
-		{
-			if ($columns_to_keep{$i})
-			{
-				my $genotype = $infos[$i];
-				if ($genotype ne 'NN')
-				{
-					my ($allele1,$allele2) = split(//,$genotype);
-					$letters{$allele1}=1;
-					$letters{$allele2}=1;
-				}
-				$to_be_printed .= "$genotype	";
-			}
-		}
-		chop($to_be_printed);
-		
-		my $variation_obs = join("/",sort keys(%letters));
-		
-		# print only if polymorphic
-		if (scalar keys(%letters) < 2)
-		{
-			$nb_monomorphic++;
-		}
-		elsif (scalar keys(%letters) > 2)
-		{
-			$not_biallelic++;
-		}
-		else
-		{
-			if ($variation ne $variation_obs)
-			{
-				$to_be_printed =~s/$variation/$variation_obs/;
-				$diff_variation++;
-			}
-			
-			print $O2 $to_be_printed . "\n";
-		}
-	}
-}
-close($H);
-close($O2);
-
-print "==============================================\n";
-print "Individuals\n";
-print "==============================================\n";
-print "Individuals in hapmap file: $nb_ind_hapmap\n";
-print "Individuals in trait file: $nb_ind_trait\n";
-print "Individuals found in both files: $nb_common\n";
-print "==============================================\n";
-print "Markers\n";
-print "==============================================\n";
-print "Discarded markers:\n";
-print "Monomorphic: $nb_monomorphic\n";
-print "Not biallelic: $not_biallelic\n";
-print "Modified markers:\n";
-print "Difference in variation: $diff_variation\n";
-
diff -r 420b57c3c185 -r feb40a9a8eae check_gwas_inputs/CheckGWASInputs.sh
--- a/check_gwas_inputs/CheckGWASInputs.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-#!/bin/bash
-hapmap=$1
-trait=$2
-out_hapmap=$3
-out_trait=$4
-stats=$5
-
-directory=`dirname $0`
-mkdir tmpdir$$
-#cp -rf $input tmpdir$$/input
- 
-perl $directory/CheckGWASInputs.pl -h $hapmap -t $trait -o tmpdir$$/out >>$stats 2>&1
-
-mv tmpdir$$/out.hapmap $out_hapmap
-mv tmpdir$$/out.trait $out_trait
-
-
diff -r 420b57c3c185 -r feb40a9a8eae check_gwas_inputs/CheckGWASInputs.xml
--- a/check_gwas_inputs/CheckGWASInputs.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,184 +0,0 @@
-<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0">
-	<description>checks concordance between input files for GWAS analysis</description>
-	<command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
-    </command>
-	<inputs>
-		<param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
-		<param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="out_hapmap" label="Hapmap output"/>
-		<data format="txt" name="out_trait" label="Trait output"/>
-		<data format="txt" name="stats" label="Logfile and statistics"/>
-	</outputs>
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-	<help>
-	
-        <![CDATA[
-
-
-.. class:: infomark
-
-**Authors** South Green
-
-  | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
-.. class:: infomark
-
-**Galaxy integration** South Green.
-
----------------------------------------------------
-
-
-===============
-CheckGWASInputs
-===============
-
------------
-Description
------------
-
-  | CheckGWASInputs checks concordance between input files for GWAS analysis.
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ====================== ===========
-Name            output file(s)         format 
-=============== ====================== ===========
-VCF to Hapmap   Hapmap file	       hapmap
-=============== ====================== ===========
-
-
-
-
-----------
-Input file
-----------
-
-Hapmap file
-	Allelic file in Hapmap format
-
-Trait file
-	Phenotypic file
-
-------------
-Output files
-------------
-
-Hapmap output
-
-Trait output
-
-Logfile and statistics
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-Hapmap file
------------
-
-::
-	
-	rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panel	QCcode	Ind1	Ind2
-	SNP1	A/T	1	3102	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
-	SNP2	A/T	1	4648	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
-
-Trait file
-----------
-
-::
-	
-	<Trait>	Test
-	Ind1	-2.9985936006411
-	Ind2	-2.68669426456267
-
-Output files
-============
-
-Hapmap output
--------------
-
-::
-
-        rs#     alleles chrom   pos     strand  assembly#       center  protLSID        assayLSID       panel   QCcode  Ind1    Ind2    Ind3    Ind4
-        SNP1    A/T     1       3102    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      AA
-        SNP2    A/T     1       4648    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      TT
-	
-
-Trait output
-------------
-
-::
-
-        <Trait> Test
-        Ind429  -26.2142525264157
-        Ind373  12.0306115988504
-        Ind81   1.98118654229534
-
-Logfile and statistics
-----------------------
-
-::
-
-
-        ==============================================
-        Individuals
-        ==============================================
-        Individuals in hapmap file: 500
-        Individuals in trait file: 500
-        Individuals found in both files: 500
-        ==============================================
-        Markers
-        ==============================================
-        Discarded markers:
-        Monomorphic: 0
-        Not biallelic: 0
-        Modified markers:
-        Difference in variation: 0
-
-        ]]>
-
-	
-	</help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae check_gwas_inputs/CheckGWASInputs.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_gwas_inputs/CheckGWASInputs.xml~	Fri Jul 10 10:38:11 2015 -0400
@@ -0,0 +1,184 @@
+<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0">
+	<description>checks concordance between input files for GWAS analysis</description>
+	<command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
+    </command>
+	<inputs>
+		<param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
+		<param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
+	</inputs>
+	<outputs>
+		<data format="txt" name="out_hapmap" label="Hapmap output"/>
+		<data format="txt" name="out_trait" label="Trait output"/>
+		<data format="txt" name="stats" label="Logfile and statistics"/>
+	</outputs>
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    
+    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
+    <tests>
+        <!-- [HELP] Test files have to be in the ~/test-data directory -->
+        <!-- [HELP] Multiple tests can be defined with different parameters -->
+<!--
+        <test>
+        </test>
+-->
+    </tests>
+	<help>
+	
+        <![CDATA[
+
+
+.. class:: infomark
+
+**Authors** South Green
+
+  | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
+
+.. class:: infomark
+
+**Galaxy integration** South Green.
+
+---------------------------------------------------
+
+
+===============
+CheckGWASInputs
+===============
+
+-----------
+Description
+-----------
+
+  | CheckGWASInputs checks concordance between input files for GWAS analysis.
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tool**
+
+=============== ====================== ===========
+Name            output file(s)         format 
+=============== ====================== ===========
+VCF to Hapmap   Hapmap file	       hapmap
+=============== ====================== ===========
+
+
+
+
+----------
+Input file
+----------
+
+Hapmap file
+	Allelic file in Hapmap format
+
+Trait file
+	Phenotypic file
+
+------------
+Output files
+------------
+
+Hapmap output
+
+Trait output
+
+Logfile and statistics
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+Hapmap file
+-----------
+
+::
+	
+	rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panel	QCcode	Ind1	Ind2
+	SNP1	A/T	1	3102	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
+	SNP2	A/T	1	4648	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
+
+Trait file
+----------
+
+::
+	
+	<Trait>	Test
+	Ind1	-2.9985936006411
+	Ind2	-2.68669426456267
+
+Output files
+============
+
+Hapmap output
+-------------
+
+::
+
+        rs#     alleles chrom   pos     strand  assembly#       center  protLSID        assayLSID       panel   QCcode  Ind1    Ind2    Ind3    Ind4
+        SNP1    A/T     1       3102    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      AA
+        SNP2    A/T     1       4648    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      TT
+	
+
+Trait output
+------------
+
+::
+
+        <Trait> Test
+        Ind429  -26.2142525264157
+        Ind373  12.0306115988504
+        Ind81   1.98118654229534
+
+Logfile and statistics
+----------------------
+
+::
+
+
+        ==============================================
+        Individuals
+        ==============================================
+        Individuals in hapmap file: 500
+        Individuals in trait file: 500
+        Individuals found in both files: 500
+        ==============================================
+        Markers
+        ==============================================
+        Discarded markers:
+        Monomorphic: 0
+        Not biallelic: 0
+        Modified markers:
+        Difference in variation: 0
+
+        ]]>
+
+	
+	</help>
+    <citations>
+        <!-- [HELP] As DOI or BibTex entry -->
+    	<citation type="bibtex">@article{Dereeper03062015,
+author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
+title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
+year = {2015}, 
+doi = {10.1093/nar/gkv351}, 
+abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
+URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
+eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
+journal = {Nucleic Acids Research} 
+}
+
+    	</citation>
+
+    </citations>
+</tool>
diff -r 420b57c3c185 -r feb40a9a8eae egglib/CalculateDiversityIndexes.pl
--- a/egglib/CalculateDiversityIndexes.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-use Bio::SeqIO;
-
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -i, --input         <FASTA input>
-    -o, --output        <output filename>
-    -d, --directory     <directory of egglib package>
-~;
-$usage .= "\n";
-
-my ($infile,$outfile,$dir_exe);
-
-
-GetOptions(
-	"input=s"    => \$infile,
-	"output=s"   => \$outfile,
-	"directory=s"=> \$dir_exe
-);
-
-
-die $usage
-  if ( !$infile || !$outfile || !$dir_exe);
-  
-
-my $EGGSTATS_EXE = "$dir_exe/egglib-2.1.5/bin/eggstats";
-
-my %gene_alignments;
-my $in  = Bio::SeqIO->new(-file => $infile , '-format' => 'Fasta');
-while ( my $seq = $in->next_seq() ) 
-{
-	my $id = $seq -> id();
-	my $sequence = $seq -> seq();
-	my ($gene,$ind,$num_allele) = split("_",$id);
-	$gene_alignments{$gene}.= ">$id\n$sequence\n";
-}
-
-open(OUT,">$outfile");
-foreach my $gene(keys(%gene_alignments))
-{
-	open(F,">$gene.egglib_input.fa");
-	print F $gene_alignments{$gene};
-	close(F);
-	
-	my $results_egglib = `$EGGSTATS_EXE $gene.egglib_input.fa`;
-
-	# parse Seqlib output
-	if ($results_egglib)
-	{
-		my %egglig_stats;
-		my @eggstats = split(/^/,$results_egglib);
-		foreach my $eggstat(@eggstats)
-		{
-			my ($desc,$value) = split(/: /,$eggstat);
-			chomp($value);
-			$egglig_stats{$desc} = $value;
-		}
-		print OUT "$gene;";
-		print OUT $egglig_stats{"Total number of sequences"} . ";";
-		print OUT $egglig_stats{"Total number of sites"} . ";";
-		print OUT $egglig_stats{"Number of analyzed sites"} . ";";
-		print OUT $egglig_stats{"S"} . ";";
-		print OUT $egglig_stats{"thetaW"} . ";";
-		print OUT $egglig_stats{"Pi"} . ";";
-		print OUT $egglig_stats{"D"} . ";";
-		print OUT $egglig_stats{"number of haplotypes"} . ";";
-		print OUT $egglig_stats{"haplotypes diversity"} . ";";
-		print OUT $egglig_stats{"Fay and Wu H"} . ";";
-		print OUT $egglig_stats{"Fst"} . ";";
-		print OUT $egglig_stats{"Snn"} . ";";
-		print OUT "\n";
-		unlink("$gene.egglib_input.fa");
-	}
-}
-close(OUT);
-
diff -r 420b57c3c185 -r feb40a9a8eae egglib/CalculateDiversityIndexes.sh
--- a/egglib/CalculateDiversityIndexes.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#!/bin/bash
-input=$1
-output=$2
-log=$3
-
-directory=`dirname $0`
- 
-perl $directory/CalculateDiversityIndexes.pl -i $input -o $output -d $directory >>$log 2>&1
-
-
-
diff -r 420b57c3c185 -r feb40a9a8eae egglib/CalculateDiversityIndexes.xml
--- a/egglib/CalculateDiversityIndexes.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,175 +0,0 @@
-<tool id="calculate_diversity" name="Diversity by gene" version="2.1.6">
-	<description>calculates various diversity indexes with EggLib.</description>
-	<command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log
-    </command>
-	<inputs>
-		<param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="output" label="Diversity"/>
-		<data format="txt" name="log" label="Logfile"/>
-	</outputs>
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-	<help>
-	
-
-
-.. class:: infomark
-
-**Authors** EggLib_
-
-.. _EggLib: http://egglib.sourceforge.net/
-
-  | "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27.
-
-.. class:: infomark
-
-**Galaxy integration** South Green.
-
-.. class:: infomark
-
-**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
----------------------------------------------------
-
-
-
-==================
-Diversity by genes
-==================
-
------------
-Description
------------
-
-  | Provides various diversity indexes using EggLib library.
-  | For further informations, please visite the EggLib website_.
-
-.. _website: http://egglib.sourceforge.net/
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ====================== ===========
-Name            output file(s)         format 
-=============== ====================== ===========
-VCF to Hapmap   Fasta alignment        fasta
-=============== ====================== ===========
-
-
-
-----------
-Input file
-----------
-
-Fasta file
-	Fasta alignment
-
-
-
-------------
-Output files
-------------
-
-Diversity
-
-Log file
-
-
-------------
-Dependencies
-------------
-EggLib 
-	version 2.1.5
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-Fasta file
-----------
-
-::
-	
-	>LOCOs11g09160_AZUCENA_1
-	ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
-	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
-	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
-	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
-	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
-	>LOCOs11g09160_AZUCENA_2
-	ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
-	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
-	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
-	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
-	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
-	>LOCOs11g09160_BULUPANDAK_1
-	ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
-	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
-	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
-	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
-	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
-	>LOCOs11g09160_BULUPANDAK_2
-	ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA
-	CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG
-	GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT
-	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
-	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
-	>LOCOs07g23169_AZUCENA_1
-	ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA
-	GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA
-	TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC
-
-Output files
-============
-
-Diversity
----------
-
-::
-
-	LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1;
-	LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1;
-
-
-	</help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/bin/eggstats
Binary file egglib/egglib-2.1.5/bin/eggstats has changed
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,378 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_ALIGN_HPP
-#define EGGLIB_ALIGN_HPP
-
-#include "Container.hpp"
-#include "CharMatrix.hpp"
-#include <vector>
-
-/** \mainpage Summary
- * 
- * This is the automatically-generated reference manual of the C++
- * egglib-cpp library. The library is presented as several modules, but
- * note that they are only used to structure the documentation.
- * 
- * There is a single namespace (egglib) in which all classes are
- * defined. See an example of programming with egglib-cpp in the
- * EggLib package main documentation. Use "Modules" or "Classes" above
- * to navigate in the library reference manual.
- * 
- */
-
-
-/** \defgroup core core
- *
- * \brief Central core of the C++ library of Egglib
- *
- * Data storage classes, parsers/formatters and tools, plus exception
- * types.
- * 
- */
-
-namespace egglib {
-
-
-   /** \brief Handles a sequence alignment
-    *
-    * \ingroup core
-    * 
-    * Creation from a file or string stream should be performed using
-    * the class Fasta. Align objects can be created by deep copy from
-    * both Align and Container type. In the latter case, the length are
-    * artificially equalized by "?" characters. Align objects can be
-    * created from a DataMatrix object (and all the way arround) using
-    * the specific class DMAConverter.
-    *
-    * Sequences are represented by two strings (name and sequence) and
-    * an integer (group) that can be accessed or modified by index.The
-    * order of sequences is guaranteed to be conserved, as if Align was
-    * a list of triplets (name, sequence, group).
-    *
-    * The data matrix is implemented as continuous array (char**) and
-    * allows efficient access and modification of data. For very large
-    * data matrices you might claim immediately the required memory
-    * using the constructor Align(unsigned int, char**).
-    * 
-    */
-    class Align : public Container, public CharMatrix {
-        public:
-        
-           /** \brief Creates an empty alignment
-            * 
-            */
-            Align();
-
-
-           /** \brief Creates an alignment from a data matrix.
-            * 
-            * Allows you to create an object from data stored in a char*
-            * array. The array's dimensions must be passed to the
-            * constructor, and as a result there is not need to
-            * terminate each sequence by a NULL character.
-            * 
-            * \param number_of_sequences the number of sequences (the
-            * length of the first dimension of the array).
-            * 
-            * \param alignment_length the length of sequences (the
-            * length of all lines of the array).
-            * 
-            * \param cstring_array the pointer to the data matrix.
-            * 
-            */
-            Align(unsigned int number_of_sequences, unsigned int alignment_length, char const * const * const cstring_array);
-
-
-            /** \brief Creates an alignment with given dimensions
-             * 
-             * Allows you to allocate directly a data matrix of a given
-             * size. Names are empty strings, groups 0, and all
-             * characters are ?.
-             * 
-            * \param number_of_sequences the number of sequences (the
-            * length of the first dimension of the array).
-            * 
-            * \param alignment_length the length of sequences (the
-            * length of all lines of the array).
-            * 
-            */
-            Align(unsigned int number_of_sequences, unsigned int alignment_length);
-
-
-           /** \brief Copy constructor
-            * 
-            */
-            Align(const Align& align);
-
-
-           /** \brief Copy constructor accepting a Container object
-            * 
-            * All but the longest sequences are padded with ? to match
-            * the longest sequence's length.
-            * 
-            */
-            Align(const Container& container);
-
-
-           /** \brief Copy operator
-            * 
-            */
-            Align& operator=(const Align& align);
-
-
-           /** \brief Copy operator accepting a Container object
-            * 
-            * All but the longest sequences are padded with ? to match
-            * the longest sequence's length.
-            * 
-            */
-            Align& operator=(const Container& container);
-
-
-           /** \brief Destructor
-            * 
-            */
-            virtual ~Align();
-
-
-           /** \brief Adds a sequence
-            *
-            * If the object already contains at least one sequence, the
-            * new sequence must have the same length. Otherwise, a
-            * EggUnalignedError is raised.
-            *
-            * \param name the name of the sequence.
-            * \param sequence the sequence string.
-            * \param group the group index of the sequence.
-            * \return The new number of sequences.
-            * 
-            */
-            virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0);
-
-
-           /** \brief Removes a position (column) of the alignment
-            *
-            * \param pos the position to remove in the alignment.
-            * \return The new length of the alignment.
-            *
-            */
-            virtual unsigned int removePosition(unsigned int pos);
-
-
-           /** \brief Removes a sequence from the alignment
-            *
-            * \param pos the index of the sequence to remove.
-            * \return The new number of sequences.
-            * 
-            */
-            virtual unsigned int remove(unsigned int pos);
-
-
-           /** \brief Replace a sequence string
-            * 
-            * The new sequence must have the same length than the
-            * alignment. Otherwise, a EggUnalignedError is raised.
-            * 
-            * \param seq the index of the sequence to change.
-            * \param sequence the new sequence.
-            * 
-            */
-            virtual void sequence(unsigned int seq, const char* sequence);
-
-
-           /** \brief Gets the name of a given sequence
-            * 
-            * \param pos the index of the sequence.
-            * 
-            * \return The sequence string for that particular sequence.
-            * 
-            */
-            virtual inline const char* sequence(unsigned int pos) const { return Container::sequence(pos); }
-            
-            
-           /** \brief Alignment length
-            * 
-            * Returns 0 if the alignment is empty.
-            * 
-            */
-            virtual  unsigned int ls() const;
-
-
-           /** \brief Length of a given sequence
-            * 
-            * Calling this function is exactly the same as calling ls()
-            * (without arguments), regardless of the index provided,
-            * except that an exception is thrown if the index is out of
-            * bounds. Provided for compatibility with Container.
-            * 
-            * \param pos the index of the sequence.
-            * \return the length of the alignment.
-            * 
-            */
-            virtual unsigned int ls(unsigned int pos) const;
-
-
-           /** \brief Fast and unsecure accessor
-            * 
-            * This accessor doesn't perform out-of-bound checking!
-            * 
-            * \param s the index of the sequence (line).
-            * \param p the position in the alignment (column).
-            * \return The character at the given position.
-            * 
-            */
-            inline char character(unsigned int s, unsigned int p) const { return sequences[s][p]; }
-
-
-           /** \brief Gets a nucleotide
-            * 
-            * This modifier does perform out-of-bound checking.
-            * The specified position must exist.
-            * 
-            * \param sequence the index of the sequence (line).
-            * \param position the position in the alignment (column).
-            * \return the character at the given position.
-            * 
-            */
-            virtual char get(unsigned int sequence, unsigned int position) const;
-
-
-           /** \brief Sets a matrix position to a new character
-            * 
-            * This modifier does perform out-of-bound checking.
-            * The specified position must exist.
-            * 
-            * \param sequence the index of the sequence (line).
-            * \param position the position in the alignment (column).
-            * \param ch the new character value.
-            */
-            virtual void set(unsigned int sequence, unsigned position, char ch);
-
-
-           /** \brief Reverse a given column in binary data
-            *
-            * The specified column must contain only "0" ans "1" characters.
-            * "0" is replaced by "1" and all the way around
-            * 
-            */
-            void binSwitch(unsigned int pos);
-
-
-           /** \brief Extracts specified positions (columns) of the alignment
-            *
-            * All the specified sites are extracted in the specified
-            * order. This function is suitable for bootstrap (resample
-            * allowing redrawing the same site) and permutations.
-            * 
-            * This function doesn't perform out-of-bound checking.
-            * 
-            * \param list_of_sites a vector containing alignment
-            * positions.
-            * 
-            * \return A copy of the object containing the specified
-            * set of positions.
-            * 
-            */
-            Align vslice(std::vector<unsigned int> list_of_sites);
-
-
-           /** \brief Extracts a range of positions (columns)
-            * 
-            * \param a the first position.
-            * 
-            * \param b the index immediately passed the last sequence to
-            * extract.
-            * 
-            * \return A copy of the object containing the specified
-            * range of sequences.
-            * 
-            * Positions a to b-1 are extracted, provided that the
-            * indices fit in the current length of sequences. To extract
-            * all sequences, use align.vslice(0, align.ls()).
-            * 
-            * Note: invalid ranges will be silently supported. If
-            * a>=ls or b<=a, an empty object is returned. If b>ns,
-            * ls will be substituted to a.
-            */
-            Align vslice(unsigned int a, unsigned int b);
-
-
-           /** \brief Deletes all the content of the object
-            * 
-            */
-            virtual void clear();
-
-
-           /** \brief Same as ns()
-            * 
-            */
-            inline unsigned int numberOfSequences() const {
-                return _ns;
-            }
-
-
-           /** \brief Same as ls()
-            * 
-            */
-            inline unsigned int numberOfSites() const {
-                return _ls;
-            }
-
-
-           /** \brief Gets a group label (insecure)
-            * 
-            */
-            inline unsigned int populationLabel(unsigned int sequenceIndex) const {
-                return groups[sequenceIndex];
-            }
-            
-            
-           /** \brief Just return the passed value
-            *
-            */
-            inline double sitePosition(unsigned int position) const {
-                return (double) position;
-            }
-
-
-        protected:
-        
-            /// This function is not available for alignments
-            virtual void appendSequence(unsigned int pos, const char* sequence) {}
-
-            // Initializer (creates a valid empty alignment)
-            virtual void init();
-        
-            // Makes a deep copy of the specified data matrix - if cstring_array is NULL, then ignores it and pads with ?'s
-            virtual void setFromSource(unsigned int number_of_sequences, unsigned int alignment_length, const char* const * const cstring_array);
-
-            // Copies from a Container
-            virtual void copyObject(const Container&);
-            
-            // Copies from an Align
-            virtual void copyObject(const Align&);
-            
-            // Alignment length
-            unsigned int _ls;
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,300 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_ARG_HPP
-#define EGGLIB_ARG_HPP
-
-
-#include "Current.hpp"
-#include "Edge.hpp"
-#include <string>
-
-
-/** \defgroup coalesce coalesce
- *
- * \brief Coalescent simulator
- *
- * The set of classes implements a three-scale coalescent simulator with
- * recombination, and a flexible mutation model. The main classes are
- * Controller (the starting point for generating genealogies), ParamSet
- * (that centralizes parameter specification), the Change hierarchy
- * (that implements demographic change specifications), Arg (ancestral
- * recombination graph; the result of generation a genealogy) and
- * Mutator (that generates genotype data from an ARG).
- * 
- */
-
-
-namespace egglib {
-    
-    class Random;
-
-   /** \brief Ancestral recombination graph
-    *
-    * \ingroup coalesce
-    * 
-    * This class stores the ARG (genealogical information). It is
-    * progressively built by appropriate (especially regarding to the
-    * timing) calls to coal() and recomb() methods. Then it can be
-    * used by a mutator class to generates data, or it can also
-    * generate newick trees (one tree by non-recombining segment).
-    *
-    */
-    class Arg {
-
-        public:
-        
-           /** \brief Default constructor
-            *
-            * Creates a null, useless, object.
-            *
-            */
-            Arg();
-
-            
-           /** \brief Object initialization
-            * 
-            * \param current address of the Current instance used by
-            * the simulator.
-            * 
-            * \param numberOfSegments number of recombining segments.
-            * 
-            */
-            void set(Current* current, unsigned int numberOfSegments);
-
-            
-           /** \brief Object reset method
-            * 
-            * This method doesn't reset all parameters (the number of
-            * segments and associated tables are retained, as well as
-            * the Edge object pool).
-            * 
-            * \param current address of the Current instance used by
-            * the simulator.
-            * 
-            */
-            void reset(Current* current);
-
-
-           /** \brief Standard constructor
-            * 
-            * \param current address of the Current instance used by
-            * the simulator.
-            * 
-            * \param numberOfSegments number of recombining segments
-            *
-            */
-            Arg(Current* current, unsigned int numberOfSegments);
-
-            
-           /** \brief Destructor
-            * 
-            * Clears all Edge instances referenced in the object.
-            * 
-            */
-            virtual ~Arg();
-            
-
-           /** \brief Gets the current value of the time counter
-            * 
-            */ 
-            double time() const;
-            
-
-           /** \brief Increments the time counter
-            * 
-            */
-            void addTime(double increment);
-            
-
-           /** \brief Performs a coalescence event
-            * 
-            * For this version, the two lineages to coalesce are
-            * predefined.
-            * 
-            * \param incr increment of the time counter.
-            * \param pop index of the population.
-            * \param index1 first lineage to coalesce.
-            * \param index2 second lineage to coalesce.
-            * 
-            */ 
-            void coalescence(double incr, unsigned int pop, unsigned int index1, unsigned int index2);
-
-
-           /** \brief Performs a coalescence event
-            * 
-            * For this version, the two lineages to coalesce are
-            * randomly picked in the given population
-            * 
-            * \param incr increment of the time counter.
-            * \param pop index of the population.
-            * \param random pointer to simulator's random generator
-            * instance.
-            * 
-            */ 
-            void coalescence(double incr, unsigned int pop, Random* random);
-
-
-           /** \brief Performs a recombination event
-            * 
-            * \param incr increment of the time counter.
-            * \param random pointer to simulator's random generator
-            * instance.
-            * 
-            */
-            void recombination(double incr, Random* random);
-            
-
-           /** \brief Places a mutation
-            * 
-            * \param segment index of the segment affected.
-            * 
-            * \param treePosition a random number placed on the
-            * interval defined by the tree length at this position.
-            * 
-            * \return the concerned Edge's address.
-            * 
-            * \todo why this is not encapsulated?
-            * 
-            * Another nerve-taking point: calling this method assume 
-            * that all Edge of have previously undergone a call of
-            * branchLength(position) with intervalPosition - what 
-            * should be done by the called (that is, Mutator) through
-            * my (Arg's) treeLength of something. BEWARE WHEN MODIFYING
-            * (enhancements should be directed to Edge in my view) 
-            * 
-            */
-            Edge* mute(unsigned int segment, double treePosition);
-
-            
-           /** \brief Age of the uMRCA
-            * 
-            * The uMRCA is the ultimate Most Recent Common Ancestor,
-            * that is the point where the last segment finds its most
-            * recent common ancestor. This member will have a meaningful
-            * value only if the coalescent process is completed.
-            * 
-            */
-            inline double ageUltimateMRCA() const {
-                return _time;
-            }
-            
-
-           /** \brief Age of the MRCA for a given segment
-            * 
-            * The MRCA is the Most Recent Common Ancestor, that is the
-            * point where the coalescent process is over (all lineages
-            * have coalesced). This member will have a meaningful
-            * value only if the coalescent process is completed.
-            * 
-            * Note that the value is cached; it is computed only one
-            * upon first call and no again, even if the Arg is modified<
-            * 
-            */
-            inline double ageMRCA(unsigned int segmentIndex) {
-                return _MRCA[segmentIndex]->bottom;
-            }
-
-           /** \brief  MRCA for each segment
-            * 
-            * The MRCA is the Most Recent Common Ancestor, that is the
-            * point where the coalescent process is over (all lineages
-            * have coalesced). This member will have a meaningful
-            * value only if the coalescent process is completed.
-            * 
-            * Note that the value is cached; it is computed only one
-            * upon first call and no again, even if the Arg is modified
-            * 
-            */
-            inline const Edge* MRCA(unsigned int segmentIndex) {
-                return _MRCA[segmentIndex];
-            }
-
-            /// Ultimate MRCA
-            
-            inline const Edge* uMRCA() {
-                return edges[numberOfEdges-1];
-            }
-            
-            
-            /// the number of recombining segments
-            unsigned int numberOfSegments;
-
-           /** \brief Formats the newick-formatted tree for a segment
-            * 
-            */
-            std::string newick(unsigned int segment);
-            
-
-            /// Number of initial lineages
-            unsigned int numberOfSamples;
-
-
-           /** \brief Total tree length (summed over all segments)
-            * 
-            */
-            double totalLength;
-
-           /** \brief Segment-specific tree length
-            * 
-            */
-            double* segmentLengths;
-
-            /// Current number of Edges in the tree (including the MRCA node)
-            unsigned int numberOfEdges;
-
-            /// Total number of recombination events that occurred
-            unsigned int numberOfRecombinationEvents;
-           
-            /// Set the number of actual sites in all branches
-            void set_actualNumberOfSites(unsigned int actualNumberOfSites);
-           
-            
-        private:
-        
-            /// Copy constructor not available
-            Arg(const Arg&) { }
-            
-            /// Assignment operator not available
-            Arg& operator=(const Arg&) { return *this; }
-
-            void init_stable_parameters();
-            void init_variable_parameters();
-            void clear();
-            void addEdge(Edge*);
-            std::string rnewick(Edge* edge, unsigned int segment, double cache);
-
-            Current* current;
-            double _time;
-            Edge** edges;
-            
-            void findMRCA(unsigned int segmentIndex);
-            void computeTotalLength();
-            void computeSegmentLength(unsigned int segmentIndex);
-
-            unsigned int* numberOfEdgesPerSegment;
-            Edge** _MRCA;
-            
-            EdgePool edgePool;
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/BaseDiversity.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/BaseDiversity.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,169 +0,0 @@
-/*
-    Copyright 2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_BASEDIVERSITY_HPP
-#define EGGLIB_BASEDIVERSITY_HPP
-
-#include "CharMatrix.hpp"
-#include "SitePolymorphism.hpp"
-#include <string>
-
-/** \defgroup polymorphism polymorphism
- *
- * \brief Diversity analyses
- *
- * Two classes are contained in this module: NucleotideDiversity, that
- * performs site-centered polymorphism analyses, and HaplotypeDiversity,
- * that performs haplotype-centered analyses. The detection of
- * polymorphic sites is common to both, through the base class
- * BaseDiversity. However this phase must be repeated when stats from
- * the two classes are needed. To reduce the computational burden, the
- * function reserve() can be use, that directly allocates needed memory
- * when the eventual number of polymorphic sites is known prior to
- * analysis (even if not precisely). For both classes, a set of
- * statistics are computed immediately upon load of a data set. For
- * NucleotideDiversity, additional statistics are computed per group
- * upon use of the corresponding accessors. This number of operations
- * performed several times is strictly limited. This is particularly
- * useful when different statistics are needed for a given alignment.
- * However, this system allows not computing unnecessary statistics to
- * a certain extend.
- * 
- */
-
-namespace egglib {
-
-    /** \brief Base class of diversity classes
-    *
-    * Mutualizes the analysis of polymorphic sites through the method
-    * importSites() and related accessors.
-    * 
-    * \ingroup polymorphism
-    *
-    */
-    class BaseDiversity {
-    
-        public:
-    
-           /** \brief Constructor
-            * 
-            */ 
-            BaseDiversity();
-            
-           /** \brief Destructor
-            * 
-            */ 
-            virtual ~BaseDiversity();
-            
-           /** \brief Reserve sufficient memory for a given number of
-            * polymorphic sites.
-            * 
-            * This method makes importSite function faster when you
-            * already know how many polymorphic sites to expect, since
-            * the necessary memory will be allocated prior the screening
-            * of data. It is possible to use reserve() even if with a
-            * number of sites that is not matching what importSites()
-            * will find.
-            * 
-            * \param numberOfSites a strictly positive integer.
-            * 
-            */
-            virtual void reserve(unsigned int numberOfSites);
-
-            /// Gets a site
-            const SitePolymorphism* get_site(unsigned int index) const;
-
-            /// Gets a site position
-            unsigned int get_position(unsigned int index) const;
-
-           /** \brief Predefined mapping string for DNA data
-            * 
-            */
-            static const std::string dnaMapping;
-
-
-           /** \brief Predefined mapping string for RNA data
-            * 
-            */
-            static const std::string rnaMapping;
-
-
-           /** \brief Predefined mapping string for amino acid data
-            * 
-            */
-            static const std::string aaMapping;
-
-
-            /// Clears and re-initializes object
-            virtual void reset();
-
-
-        protected:
-    
-            virtual void init();
-            virtual void clear();
-    
-            // 
-            void importSites(CharMatrix& data, bool allowMultipleMutations,
-                double minimumExploitableData, unsigned int ignoreFrequency,
-                std::string characterMapping, bool useZeroAsAncestral,
-                bool ignoreOutgroup);
-
-            // 
-            void analyzeSite(CharMatrix& data, unsigned int index, double maxMissingData, bool ignoreOutgroup); // analyzes a site, adds a Site to the Site container if the site is polymorphic
-            unsigned int getPopIndex(unsigned int label) const;  // returns v_npop if not found
-            
-            SitePolymorphism** v_sites;  // holder of polymorphic site addresses
-            bool* v_orientables;         // stores whether the sites are orientable or not
-            unsigned int* v_sitePositions;   // stores position of sites
-
-            unsigned int  v_reserved;
-            unsigned int  v_ns;       // maximum number of sequences analyzed (max of sites' ns)
-            unsigned int  v_S;        // number of polymorphic sites
-            unsigned int  v_So;       // number of orientable sites
-            unsigned int  v_eta;      // number of mutation (whatever multiple)
-            double        v_nseff;    // average number of analyzed sequence
-            unsigned int  v_lseff;    // number of analyzed sites
-            double        v_nseffo;   // average number of analyzed sequences for analyzes with outgroup
-            unsigned int  v_lseffo;   // number of analyzed sites for analyzes with outgroup
-            unsigned int  v_npop;     // number of populations
-            unsigned int *v_popLabel; // label of each pop
-
-            // options
-            bool          p_allowMultipleMutations;
-            double        p_minimumExploitableData;
-            std::string   p_characterMapping;
-            unsigned int  p_pos_sep_mapping;
-            bool          p_useZeroAsAncestral;
-            unsigned int  p_ignoreFrequency;
-
-
-    
-        private:
-            
-            BaseDiversity(const BaseDiversity& source) { }
-            
-            BaseDiversity& operator=(const BaseDiversity& source) {
-                return *this;
-            }
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/ChangeTypes.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/ChangeTypes.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,428 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_CHANGETYPES_HPP
-#define EGGLIB_CHANGETYPES_HPP
-
-#include "ParamSet.hpp"
-#include "Controller.hpp"
-
-namespace egglib {
-
-/**********************************************************************/
-
-   /** \brief Pure virtual base class for parameter changes
-    *
-    * \ingroup coalesce
-    *
-    */
-    class Change {
-        public:
-    
-           /** \brief Default constructor
-            *
-            * The default date is 0.
-            *
-            */
-            Change();
-            
-           /** \brief Standard constructor
-            *
-            * \param date the event date.
-            *
-            */
-            Change(double date);
-
-            /// Gets the event date value
-            double date() const;
-            
-            /// Sets the event date value
-            void date(double value);
-            
-           /** \brief Applies the event
-            *
-            * \param paramSet the ParamSet instance to which the Change
-            * instance is attached.
-            * \param controller the Controller instance of the
-            * simulation.
-            *
-            */
-            virtual void apply(ParamSet* paramSet, Controller* controller) const = 0;
-        
-        protected:
-            double _date;
-    
-    };
-
-/**********************************************************************/
-
-   /** \brief Pure virtual base class for single parameter changes
-    *
-    * \ingroup coalesce
-    *
-    */
-    class SingleParamChange : public Change {
-        public:
-    
-           /** \brief Default constructor
-            *
-            * The default date is 0., the default parameter value is 0.
-            *
-            */
-            SingleParamChange();
-            
-           /** \brief Standard constructor
-            *
-            * \param date the event date.
-            * \param value the parameter value.
-            *
-            */
-            SingleParamChange(double date, double value);
-
-            /// Gets the parameter value
-            double value() const;
-            
-            /// Sets the parameter value
-            void value(double value);
-
-        protected:
-            double _value;
-
-    };
-
-/**********************************************************************/
-
-   /** \brief Single parameter changes applied to a single population
-    *
-    * \ingroup coalesce
-    *
-    */
-    class PopulationParamChange : public SingleParamChange {
-        public:
-
-           /** \brief Default constructor
-            *
-            * The default date is 0., the default parameter value is 0.,
-            * the  default population is 0
-            *
-            */
-            PopulationParamChange();
-            
-           /** \brief Standard constructor
-            *
-            * \param date the event date.
-            * \param population the population index.
-            * \param value the parameter value.
-            *
-            */
-            PopulationParamChange(double date, unsigned int population, double value);
-
-            /// Gets the population index
-            unsigned int population() const;
-            
-            /// Sets the population index
-            void population(unsigned int value);
-    
-        protected:
-        
-            unsigned int _population;
-
-    };
-
-            
-/**********************************************************************/
-    
-   /** \brief Bottleneck event
-    *
-    * \ingroup coalesce
-    * 
-    * The bottleneck parameter is its strength, corresponding to an
-    * amount of time where time is locked and only coalescences are
-    * allowed (resulting in a given - and random - number of
-    * instantaneous coalescence with branches).
-    *
-    */
-    class Bottleneck : public SingleParamChange {
-        public:
-            Bottleneck(double date, double param) : SingleParamChange(date, param) {}
-            void apply(ParamSet* paramSet, Controller* controller) const;
-    };
-
-/**********************************************************************/
-    
-   /** \brief Population-specific bottleneck event
-    *
-    * \ingroup coalesce
-    *
-    */
-    class PopulationBottleneck : public PopulationParamChange {
-        public:
-            PopulationBottleneck(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {}
-            void apply(ParamSet* paramSet, Controller* controller) const;
-    };
-
-
-/**********************************************************************/
-    
-   /** \brief Change of the size of all populations
-    *
-    * The parameter is the new size (applied to all populations)
-    *
-    * \ingroup coalesce
-    *
-    */
-    class AllPopulationSizeChange : public SingleParamChange {
-        public:
-            AllPopulationSizeChange(double date, double value) : SingleParamChange(date, value) {}
-            void apply(ParamSet* paramSet, Controller* controller) const; 
-    };
-    
-    
-/**********************************************************************/
-    
-   /** \brief Change of a single population size
-    *
-    * \ingroup coalesce
-    *
-    */
-    class SinglePopulationSizeChange : public PopulationParamChange {
-        public:
-            SinglePopulationSizeChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {}
-            void apply(ParamSet* paramSet, Controller* controller) const;    
-    };
-    
-
-    
-/**********************************************************************/
-    
-   /** \brief Change of the growth rate of all populations
-    *
-    * The parameter is the new rate (applied to all populations)
-    *
-    * \ingroup coalesce
-    *
-    */
-    class GrowthRateChange : public SingleParamChange {
-        public:
-            GrowthRateChange(double date, double value) : SingleParamChange(date, value) {}
-            void apply(ParamSet* paramSet, Controller* controller) const;
-    };
-    
-    
-/**********************************************************************/
-    
-   /** \brief Change of a single population's growth rate
-    *
-    * \ingroup coalesce
-    *
-    */
-    class PopulationGrowthRateChange : public PopulationParamChange {
-        public:
-            PopulationGrowthRateChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {}
-            void apply(ParamSet* paramSet, Controller* controller) const;
-    };
-    
-/**********************************************************************/
-    
-   /** \brief Change of the selfing rate
-    *
-    * The parameter is the new rate
-    *
-    * \ingroup coalesce
-    *
-    */
-    class SelfingRateChange : public SingleParamChange {
-        public:
-            SelfingRateChange(double date, double value) : SingleParamChange(date, value) {}
-            void apply(ParamSet* paramSet, Controller* controller) const;
-    };
-    
-/**********************************************************************/
-    
-   /** \brief Fusion of two populations
-    *
-    * \ingroup coalesce
-    *
-    */
-    class PopulationFusion : public Change {
-        public:
-           /** \brief Default constructor
-            *
-            * The default date is 0., the default mother is 0, the
-            * default daughter is 0.
-            *
-            */
-            PopulationFusion();
-
-           /** \brief Standard constructor
-            *
-            * \param date the date of the event.
-            * \param mother first population to merge.
-            * \param daughter second population to merge.
-            *
-            * A time date, all the lineages from the daughter population
-            * are moved to the mother population and all mutation rates
-            * to the daughter population are cancelled. This functions
-            * emulates a population split (forward in time).
-            *
-            */
-            PopulationFusion(double date, unsigned int mother, unsigned int daughter);
-            
-            void apply(ParamSet* paramSet, Controller* controller) const;
-        
-            /// Sets the daughter population
-            void daughter(unsigned int);
-            
-            /// Gets the daughter population
-            unsigned int daughter() const;
-            
-            /// Sets the mother population
-            void mother(unsigned int);
-            
-            /// Gets the mother population
-            unsigned int mother() const;
-        
-        protected:
-            unsigned int _mother;
-            unsigned int _daughter;
-    };    
-    
-    
-/**********************************************************************/
-    
-   /** \brief Split of a population
-    *
-    * \ingroup coalesce
-    *
-    */
-    class PopulationSplit : public Change {
-        public:
-           /** \brief Default constructor
-            *
-            * The default date is 0., the default population is 0, the
-            * default probability is 0.5.
-            *
-            */
-            PopulationSplit();
-
-           /** \brief Standard constructor
-            *
-            * A the time given by date, the specified population is
-            * split in two. An additional population (whose index is
-            * incremented from the current total number of population)
-            * is created and lineages are randomly picked and moved to
-            * the new population. The parameter proba gives the
-            * probability that a lineage from the population number pop
-            * moves instantly to the new population. If proba is 0,
-            * the program emulates the creation of an empty population
-            * (thinking forward in time, this is a population
-            * extinction). In general, forward in time, this is a
-            * population fusion.
-            * 
-            * \param date the date of the event.
-            * \param pop population index.
-            * \param proba the probability that lineages move to the
-            * new population.
-            *
-            */
-            PopulationSplit(double date, unsigned int pop, double proba);
-            
-            void apply(ParamSet* paramSet, Controller* controller) const;
-            
-            /// Gets the population index
-            unsigned int population() const;
-            
-            /// Sets the population index
-            void population(unsigned int);
-            
-            /// Gets the probability of instant migration
-            double probability() const;
-
-            /// Sets the probability of instant migration
-            void probability(double);
-            
-        protected:
-            unsigned int _population;
-            double _probability;
-    };
-
-/**********************************************************************/
-
-   /** \brief Change of the migration rate of all population pairs
-    *
-    * The parameter is the new rate (applied to all population pairs)
-    *
-    * \ingroup coalesce
-    *
-    */
-    class AllMigrationRateChange : public SingleParamChange {
-        public:
-        AllMigrationRateChange(double date, double value) : SingleParamChange(date, value) {}
-        void apply(ParamSet* paramSet, Controller* controller) const;
-    };
-
-/**********************************************************************/
-    
-   /** \brief Change of a single migration rate
-    *
-    * \ingroup coalesce
-    *
-    */
-    class SingleMigrationRateChange : public SingleParamChange {
-        public:
-           /** \brief Default constructor
-            *
-            * The default date is 0., the default parameter value is 0.,
-            * the  default source population is 0, the default
-            * destination population 1.
-            *
-            */
-            SingleMigrationRateChange();
-
-           /** \brief Standard constructor
-            *
-            * \param date the date of the event.
-            * \param source index of the source population.
-            * \param dest index of the destination population.
-            * \param migr new value of the pairwise migration rate.
-            *
-            */
-            SingleMigrationRateChange(double date, unsigned int source, unsigned int dest, double migr);
-            
-            /// Gets the source population index
-            unsigned source() const;
-            
-            /// Sets the source population index
-            void source(unsigned int);
-
-            /// Gets the dest population index
-            unsigned dest() const;
-            
-            /// Sets the dest population index
-            void dest(unsigned int);
-
-            void apply(ParamSet* paramSet, Controller* controller) const;
-        
-        protected:
-            unsigned int _source;
-            unsigned int _dest;
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/CharMatrix.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/CharMatrix.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-/*
-    Copyright 2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_CHARMATRIX_HPP
-#define EGGLIB_CHARMATRIX_HPP
-
-
-namespace egglib {
-
-    /** \brief Interface for classes usable as a square matrix of characters
-    *
-    * \ingroup core
-    *
-    */
-    class CharMatrix {
-    
-    public:
-    
-        /** \brief Gets number of rows or sequences
-         * 
-         */
-        virtual unsigned int numberOfSequences() const = 0;
-
-
-        /** \brief Gets number of columns or sites
-         * 
-         */
-        virtual unsigned int numberOfSites() const = 0;
-        
-        
-        /** \brief Gets the character at a given position
-         * 
-         * The accessor should be "fast" and does not guarantee to
-         * perform out-of-bounds checks
-         * 
-         */
-        virtual char character(unsigned int sequence, unsigned int site) const = 0;
-        
-        
-       /** \brief Gets population index
-        * 
-        */
-        virtual unsigned int populationLabel(unsigned int row) const = 0;
-        
-        
-       /** \brief Get site position
-        * 
-        */
-        virtual double sitePosition(unsigned int column) const = 0;
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Consensus.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Consensus.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,421 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_CONSENSUS_HPP
-#define EGGLIB_CONSENSUS_HPP
-
-#include "Align.hpp"
-#include <sstream>
-#include <string>
-#include <vector>
-
-namespace egglib {
-
-   /** \brief Generates consensus sequences
-    *
-    * \ingroup polymorphism
-    * 
-    *
-    * A consensus is generated when two sequences have the same name, 
-    * ignoring everything after the first separator character (by
-    * default, "_"). Hence, the names "foo", "foo_goo" and "foo_third"
-    * will be treated as identical and the root will be "foo". The root
-    * will be used to name the resulting sequence. Note that the
-    * class works only for DNA sequences.
-    *
-    * Symbol convention:
-    *     - A: adenosine
-    *     - C: cytosine
-    *     - G: guanine
-    *     - T: thymine
-    *     - M: A or C
-    *     - R: A or G
-    *     - W: A or T (weak)
-    *     - S: C or G (strong)
-    *     - Y: C or T
-    *     - K: G or T
-    *     - B: C or G or T(not A)
-    *     - D: A or G or T (not C)
-    *     - H: A or C or T (not G)
-    *     - V: A or C or G (not T)
-    *     - N: A or C or G or T
-    *     - ?: nonsequenced position
-    * 
-    * Other symbols will be treated as ? (lowercase are supported).
-    * 
-    * Rigorous (alias liberal or strong) mode:
-    *    - If two characters are the same, it is retained whatever it is
-    * (A + A = A)
-    * - Otherwise:
-    *        - If one is the missing character (?) the other is retained
-    * whatever it is (A + ? = A).
-    *             - If characters are consistent, that is one contains
-    * more information, that one is retained (A + M = A).
-    *             - If characters are not consistent, the closest 
-    * generic symbol is retained (A + C = M).
-    *    .
-    *     Note that the feedback of inconsistent characters in the
-    * outcome is not garanteed.
-    *     In fact, (A + A + G) will result in R (as expected) but (A +
-    * G + A) will result in A, masking the problem.
-    *     However, the position will indeed be counted as inconsistent.
-    *  
-    * Not rigorous (conservative/weak) mode:
-    *     - If two characters are the same, it is retained whatever it
-    * is (A + A = A).
-    *     - Otherwise:
-    *        - If one is ? the other is retained whatever it is (A + ?
-    * = A).
-    *        - Otherwise an inconsistent character (by default, Z) is
-    * retained (A + C = Z).
-    * 
-    * Iterative process of consensus:
-    *     - Each sequence is taken in turn.
-    *     - Each pair involving the focus sequence is processed and a
-    * consensus is generated.
-    *     - When all pair have been processsed, the consensus already
-    * generated are themselves iteratively processed until only one
-    * remains.
-    *     - Note that at each time the last two are taken first.
-    * 
-    * A transparent interface gives access to the data for all steps of
-    * the consensus process, as vectors that covers all pairs (including
-    * intermediate steps of the iterative procedure described above) as
-    * well as singleton sequences. For the latter, the second name is
-    * not filled and all counts are set to 0. Note also that the name of
-    * such singleton sequence is shortened to the separator as well.
-    * 
-    */
-    class Consensus {
-       public:
-         /** \brief Constructor
-          * 
-          */
-          Consensus();
-          
-         /** \brief Destructor
-          * 
-          */
-          virtual ~Consensus() {}
-          
-          /// Sets the character interpreted as missing (default: ?)
-          void setMissing(char);
-          
-          /// Sets the character used to point to disagreements (default: Z)
-          void setDisagreement(char);
-          
-          /// Checks all the characters
-          bool check_sequences(Align& align);
-          
-         /** \brief Reduces the sequence alignment by making consensus sequences
-          * 
-          * \param align the original alignment.
-          * 
-          * \param separator the character used to separated the root
-          * name of sequences to the variable part, as in (for the
-          * default value: "sequence_read1".
-          * 
-          * \param rigorous consensus mode.
-          * 
-          * \return An Align instance with duplicated sequences consensed.
-          * 
-          */
-          Align consensus(Align& align, char separator='_', bool rigorous=true);
-
-          /// First name of consensed pairs
-          const std::vector<std::string>& firstSequenceNames();
-
-          /// Second names of consensed pairs
-          const std::vector<std::string>& secondSequenceNames();
-          
-          /// Root names of consensed pairs
-          const std::vector<std::string>& roots();
-          
-          /// Number of consistent positions for all consensed pairs
-          const std::vector<int>& consistentPositions();
-
-          /// Number of complementary positions for all consensed pairs
-          const std::vector<int>& complementaryPositions();
-
-          /// Number of uninformative positions for all consensed pairs
-          const std::vector<int>& uninformativePositions();
-
-          /// Number of ambiguous positions for all consensed pairs
-          const std::vector<int>& ambiguousPositions();
-
-          /// Number of at least partially resolved ambiguities for all consensed pairs
-          const std::vector<int>& atLeastPartiallyResolvedAmbiguities();
-
-          /// Vector of inconsistent positions ofr all consensed pairs
-          const std::vector<std::vector<int> >& inconsistentPositions();
-
-
-       private:
-
-           /** \brief Copying this class is not allowed
-            * 
-            */
-            Consensus(const Consensus& source) { }
-            
-           /** \brief Copying this class is not allowed
-            * 
-            */
-            Consensus& operator=(const Consensus& source) { return *this; }
-            
-          // A private helper
-          class PairwiseConsensus;
-         
-          // report data
-          std::vector<std::string> t_firstSequenceNames;
-          std::vector<std::string> t_secondSequenceNames;
-          std::vector<std::string> t_roots;
-          std::vector<int> t_consistentPositions;
-          std::vector<int> t_complementaryPositions;
-          std::vector<int> t_uninformativePositions;
-          std::vector<int> t_ambiguousPositions;
-          std::vector<int> t_atLeastPartiallyResolvedAmbiguities;
-          std::vector<std::vector<int> > t_inconsistentPositions;
-
-          // Code for missing data (usually ?)
-          char MISSING;
-
-          // Code for disgrement
-          char DISAGREEMENT;
-
-          // Helper class managing a single pair
-          class PairwiseConsensus {
-              public:
-                 // Default object creation
-                 PairwiseConsensus();
-                 
-                 // Object destruction
-                 virtual ~PairwiseConsensus() {}
-                 
-                 // Usual object creation
-                 PairwiseConsensus(std::string, std::string);
-                 
-                 // Fills an object created with the default constructor
-                 void load(std::string,std::string);
-                 
-                 // Changes the MISSING character
-                 void setUndeterminedCharacter(char);
-                 
-                 // Changes the DISAGREEMENT character
-                 void setDisagreementCharacter(char);
-                 
-                 /* Uses the conservative mode of consensus
-                  * 
-                  * Tries to avoid to make decisions, and adds the
-                  * character set by DISAGREEMENT upon inconsistencies
-                  * 
-                  * return The number of inconsistencies.
-                  */
-                 int generateSoftConsensus();
-                 
-                 /* Strict mode of consensus
-                  * 
-                  * The number of inconsistencies.
-                  */
-                 int generateHardConsensus();
-                 
-                 // Two fully resolved (including gap) and identical characters
-                 int getConsistentPositions();
-
-                 // One informative (including gap) and one missing
-                 int getComplementaryPositions();
-
-                 // None missing, but different and incompatible
-                 int getInconsistentPositions();
-                 
-                 // Both are missing
-                 int getUninformativePositions();
-                 
-                 // Both identical or one missing, but not fully resolved
-                 int getAmbiguousPositions();
-                 
-                 // Different, not missing, complementary.
-                 int getAtLeastPartiallyResolvedAmbiguities();
-                 
-                 // Accessor
-                 int getThisInconsistentPosition(unsigned int);
-                 
-                 // Generates the consensus sequence
-                 std::string getConsensus();
-
-              private:
-              
-                inline bool isValid(char c) {
-                    switch (c) {
-                        case 'A': case 'a':
-                        case 'C': case 'c':
-                        case 'G': case 'g':
-                        case 'T': case 't': 
-                            return true;
-                        default:
-                            return false;
-                    }
-                }
-              
-                 // This initiates a series of embedded objects
-                 void setCharacterContainers();
-                 
-                 // The first sequence
-                 std::string seqA;
-                 
-                 // The second sequence
-                 std::string seqB;
-                 
-                 // The resulting consensus
-                 std::string cons;
-                 
-                 // The vecotr storing the inconsistent positions
-                 std::vector<int> posIncons;
-                 
-                 // The length of the sequences
-                 unsigned int ls;
-                 
-                 // Counter
-                 int cntConsistentPositions;
-                 
-                 // Counter
-                 int cntComplementaryPositions;
-                 
-                 // Counter
-                 int cntAmbiguousPositions;
-                 
-                 // Counter
-                 int cntInconsistentPositions;
-                 
-                 // Counter
-                 int cntUninformativePositions;
-                 
-                 // Counter
-                 int cntAtLeastPartiallyResolvedAmbiguities;
-
-                 // Code for missing data (usually ?)
-                 char MISSING;
-
-                 // Code for disgrement
-                 char DISAGREEMENT;
-     
-            public:
-                // This class manages relationships different symbols
-                class CharacterContainer {
-                      public:
-                         // Default value: @
-                         CharacterContainer();
-                         
-                         // Initiates to a given symbol
-                         CharacterContainer(const char&);
-                         
-                         // Assignment operator
-                         CharacterContainer& operator=(const char&);
-                         
-                         // Sets the symbol
-                         void setValue(char);
-                         
-                         // Set the descendants
-                         void setSons(std::vector<CharacterContainer>);
-                         
-                         // Tests whether the symbol is the same
-                         bool is(CharacterContainer);
-                         
-                         // Tests if the query is contained amongst the sons
-                         bool has(CharacterContainer);
-                         
-                         // Tests if the query is contained amongst the sons
-                         bool has(char);
-                         
-                         /* Tests whether the left character has the left one
-                          * Should be called on the N object only.
-                          */
-                         char lhas(CharacterContainer,CharacterContainer);
-                         
-                         /* Creates the object with the proper sons
-                          * Should be called on the N object only.
-                          */
-                         CharacterContainer init(char);
-                         
-                         // The symbol
-                         char value;
-                         
-                         // The descendants
-                         std::vector<CharacterContainer> sons;
-                  };
-
-             private:
-                  // Symbol ?
-                  CharacterContainer ccQ;
-                  
-                  // Symbol A
-                  CharacterContainer ccA;
-                  
-                  // Symbol C
-                  CharacterContainer ccC;
-                  
-                  // Symbol G
-                  CharacterContainer ccG;
-                  
-                  // Symbol T
-                  CharacterContainer ccT;
-                  
-                  // Symbol U
-                  CharacterContainer ccU;
-                  
-                  // Symbol M
-                  CharacterContainer ccM;
-                  
-                  // Symbol R
-                  CharacterContainer ccR;
-                  
-                  // Symbol W
-                  CharacterContainer ccW;
-                  
-                  // Symbol S
-                  CharacterContainer ccS;
-                  
-                  // Symbol Y
-                  CharacterContainer ccY;
-                  
-                  // Symbol K
-                  CharacterContainer ccK;
-                  
-                  // Symbol B
-                  CharacterContainer ccB;
-                  
-                  // Symbol D
-                  CharacterContainer ccD;
-                  
-                  // Symbol H
-                  CharacterContainer ccH;
-                  
-                  // Symbol V
-                  CharacterContainer ccV;
-                  
-                  // Symbol N
-                  CharacterContainer ccN;
-                  
-                  // Symbol -
-                  CharacterContainer ccGAP;
-          };
-    };
-}
-
-#endif
-
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,326 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-    
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_CONTAINER_HPP
-#define EGGLIB_CONTAINER_HPP
-
-
-namespace egglib {
-
-   /** \brief Handles a set of sequence alignment (aligned or not)
-    *
-    * \ingroup core
-    * 
-    * Creation from a file or string stream should be performed using
-    * the class Fasta.
-    *
-    * Sequences are represented by two strings (name and sequence) and
-    * an integer (group) that can be accessed or modified by index.The
-    * order of sequences is guaranteed to be conserved, as if Container
-    * was a list of triplets (name, sequence, group).
-    *
-    * The data matrix is implemented as continuous arrays (char**) and
-    * allows efficient access and modification of data. For very large
-    * data matrices you might claim immediately the required memory
-    * using the constructor Container(unsigned int, char**).
-    *
-    */
-    class Container {
-    
-        public:
-      
-          /** \brief Creates an empty object
-            * 
-            */
-            Container();
-        
-        
-           /** \brief Copy constructor
-            * 
-            */
-            Container(const Container& source);
-        
-        
-           /** \brief Assignment operator
-            * 
-            */
-            Container& operator= (const Container& source);
-
-
-           /** \brief Creates an object from a data matrix
-            * 
-            * Allows you to create an object from data stored in a char*
-            * array. The array's size must be passed to the constructor.
-            * Since sequences can have different lengths, you need to
-            * terminate each sequence by a NULL character. This constructor
-            * is dedicated to very performance-critical tasks. For usual
-            * tasks, using the default constructor and subsequently adding
-            * sequences with addSeq should be enough.
-            * 
-            * \param number_of_sequences the number of sequences (the length
-            * of the first dimension of the array).
-            * 
-            * \param cstring_array the pointer to the data matrix.
-            * 
-            */
-            Container(unsigned int number_of_sequences, char const* const* const cstring_array);
-
-
-           /** \brief Destructor
-            * 
-            */
-            virtual ~Container();
-
-        
-           /** \brief Clears all content of the object
-            * 
-            */
-            virtual void clear();
-
-
-           /** \brief Adds a sequence to the object
-            *
-            * \param name the name of the sequence, as a c-string.
-            * \param sequence the sequence string, as a c-string.
-            * \param group the group index of the sequence.
-            *
-            * \return The new number of sequences.
-            * 
-            */
-            virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0);
-    
-    
-           /** \brief Removes a sequence from the object
-            *
-            * \param pos the index of the sequence to remove.
-            * 
-            * \return The new number of sequences.
-            */
-            virtual unsigned int remove(unsigned int pos);
-
-
-           /** \brief Changes the name of a given sequence
-            * 
-            * \param pos the sequence index.
-            * \param name the new name as a C-like string.
-            * 
-            */
-            virtual void name(unsigned int pos, const char* name);
-
-
-           /** \brief Changes the sequence string of a given sequence
-            * 
-            * \param pos the sequence index.
-            * \param sequence the new sequence as a C-like string.
-            * 
-            */
-            virtual void sequence(unsigned int pos, const char* sequence);
-
-
-           /** \brief Appends a string to the a given sequence
-            * 
-            * \param pos the sequence index.
-            * \param sequence the sequence to append at the end of the
-            * current one.
-            * 
-            */
-            virtual void appendSequence(unsigned int pos, const char* sequence);
-
-
-           /** \brief Changes a character
-            * 
-            * \param sequence the sequence index.
-            * \param position the character index.
-            * \param ch the new character value.
-            * 
-            * The positions must fit in the current ranges.
-            * 
-            */
-            virtual void set(unsigned int sequence, unsigned position, char ch);
-
-
-           /** \brief Gets a given character
-            * 
-            * \param s the sequence index.
-            * \param p the character index.
-            * 
-            * \return the character value.
-            * 
-            * The positions must fit in the current ranges.
-            * 
-            */
-            virtual char get(unsigned int s, unsigned int p) const;
-
-
-           /** \brief Changes the group index of a given sequence
-            * 
-            * \param pos the sequence index.
-            * \param group the new group index value.
-            * 
-            */
-            virtual void group(unsigned int pos, unsigned int group);
-
-        
-           /** \brief Extracts a range of sequences
-            * 
-            * \param a the index of the first sequence.
-            * 
-            * \param b the index immediately passed the last sequence to
-            * extract.
-            * 
-            * \return A copy of the object containing the specified
-            * range of sequences.
-            * 
-            * Sequences a to b-1 are extracted, provided that the
-            * indices fit in the current number of sequences. To extract
-            * all sequences, use container.hslice(0, container.ns()).
-            * 
-            * Note: invalid ranges will be silently supported. If
-            * a>=ls or b<=a, an empty object is returned. If b>ns,
-            * ls will be substituted to a.
-            * 
-            */
-            Container hslice(unsigned int a, unsigned int b) const;
-
-
-           /** \brief Gets the number of sequences
-            * 
-            */
-            unsigned int ns() const;
-        
-        
-           /** \brief Gets the length of a given sequence
-            * 
-            * \param pos the index of the sequence.
-            * 
-            * \return The length of that particular sequence.
-            * 
-            */
-            virtual unsigned int ls(unsigned int pos) const ;
-        
-        
-           /** \brief Gets the name of the a given sequence
-            * 
-            * \param pos the index of the sequence.
-            * 
-            * \return The name of that particular sequence.
-            * 
-            */
-            virtual const char* name(unsigned int pos) const;
-
-        
-           /** \brief Gets the name of a given sequence
-            * 
-            * \param pos the index of the sequence.
-            * 
-            * \return The sequence string for that particular sequence.
-            * 
-            */
-            virtual const char* sequence(unsigned int pos) const;
-
-
-
-           /** \brief Gets the group index of a given sequence
-            * 
-            * \param pos the index of the sequence.
-            * 
-            * \return The group index of that particular sequence.
-            * 
-            */
-            virtual unsigned int group(unsigned int pos) const;
-        
-        
-           /** \brief Checks if all lengths are equal
-            * 
-            * Returns true if the length of all sequences are equal or
-            * if there is less thant two sequences.
-            * 
-            */
-            bool isEqual() const;
-
-
-           /** \brief Equalizes sequence lengths
-            *
-            * Extends sequences as need to ensure that all sequences
-            * have the same length.
-            *
-            * \param ch the character to use for padding.
-            * 
-            * \return The final length obtained, which is the length of
-            * the longest sequence before the operation.
-            * 
-            */
-            unsigned int equalize(char ch='?');
-
-        
-           /** \brief Finds a sequence by its name
-            * 
-            * Gets the position of the first sequence with the specified
-            * name.
-            * 
-            * \param string a sequence name.
-            * 
-            * \param strict if true, seeks an exact match. If false,
-            * compares only until the end of the requested name (for
-            * example: ATCFF will match ATCFF_01 if strict is false).
-            * 
-            * \return The lowest index where the name matches, -1 if no
-            * sequence has such name.
-            * 
-            */
-            int find(const char* string, bool strict=true) const;
-
-
-        protected:
-            // The number of sequences
-            unsigned int _ns;
-        
-            // The array of name lengths
-            unsigned int* lnames;
-    
-            // The array of names
-            char** names;
-        
-            // The array of sequences (as c-strings)
-            char** sequences;
-        
-            // The array of groups
-            unsigned int* groups;
-        
-            // Imports an array of c-strings
-            virtual void setFromSource(unsigned int number_of_sequences, const char* const* const cstring_array);
-        
-            // Constructor helper
-            virtual void copyObject(const Container&);
-        
-            // Constructor partial helper
-            virtual void getNamesAndGroups(const Container&);
-        
-        private:
-       
-            // The array of sequence lengths
-            unsigned int* lsequences;
-        
-            // Setup a valid empty object
-            virtual void init();
-    };
-}
-    
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_CONTROLLER_HPP
-#define EGGLIB_CONTROLLER_HPP
-
-#include "Current.hpp"
-#include "Arg.hpp"
-#include "ParamSet.hpp"
-
-namespace egglib {
-    
-    class Random;
-
-   /** \brief Controls a coalescent simulation
-    *
-    * \ingroup coalesce
-    * 
-    * This class generates the gene genealogy, based on the parameters
-    * stocked in a ParamSet object.
-    *
-    */
-    class Controller {
-
-        public:
-    
-           /** \brief Default constructor
-            *
-            * Uses a default ParamSet object that will not allow
-            * performing simulations.
-            *
-            */
-            Controller();
-
-           /** \brief Destructor
-            * 
-            */
-            ~Controller();
-            
-           /** \brief Standard constructor
-            * 
-            * \param paramSet a ParamSet object containing run
-            * parameters (it is taken as a reference and stored as this
-            * so it must not be modified during simulations).
-            * 
-            * \param random the address of the random number generator.
-            *
-            */
-            Controller(const ParamSet* paramSet, Random* random);
-            
-          /** \brief Reset for a new simulation
-           * 
-           * Object is reinitiliazed for a new simulation.
-           * 
-           */
-           void reset();
-            
-           /** \brief Increments the coalescent model
-            * 
-            * \return The number of lineages.
-            *
-            */
-            unsigned int step();
-            
-           /** \brief Gets the Ancestral Recombination Graph
-            * 
-            * \return The address of the ARG contained in the object.
-            * 
-            */
-            Arg* getArg();
-
-           /** \brief Applies a bottleneck to a given population
-            * 
-            * The bottleneck is applied following Galtier, Depaulis and
-            * Barton (Genetics, 2000): the general time counter is
-            * stopped, and coalescence events are performed during a
-            * time (of normal coalescent process) given by the parameter
-            * strength. All coalescent events are instantaneous.
-            * 
-            * \param populationIndex index of the population concerned
-            * by the event.
-            * 
-            * \param strength strength of the bottleneck given by a
-            * number of time units (2N generations times the size of
-            * the population).
-            * 
-            */
-            void bottleneck(unsigned int populationIndex, double strength);
-
-           /** \brief Migrate a complete population
-            * 
-            * Takes all the lineages currently present in the population
-            * source to the population dest.
-            * 
-            */
-            void moveAllLineages(unsigned int source, unsigned int dest);
-            
-           /** \brief Migrate a complete population
-            * 
-            * Takes all the lineages currently present in the population
-            * source to the population dest.
-            * 
-            * \param source source population.
-            * \param dest destination population.
-            * \param probability the probability that a lineage of
-            * source migrates to dest.
-            * 
-            */
-            void moveSomeLineages(unsigned int source, unsigned int dest, double probability);
-
-            /// Adds an empty population
-            void addPopulation();
-
-        private:
-        
-            /// The copy constructor is disabled
-            Controller(const Controller& source) {}
-            
-            /// The assignment operator is disabled
-            Controller& operator=(const Controller& source) {return *this;}
-
-            void diploids();
-            double getMigrationTime(double& migrationParameterDestination);
-            void getCoalescenceTime(double& destTime, unsigned int& destPopIndex);
-            double getCoalescenceTimeForPopulation(unsigned int populationIndex);
-            double getRecombinationTime() const;
-            void migrate(double migrationParameter);
-
-            const ParamSet* initialParamSet;
-            ParamSet paramSet;
-            Current current;
-            Arg arg;
-            
-            Random* random;
-
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Convert.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Convert.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,234 +0,0 @@
-/*
-    Copyright 2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_CONVERT_HPP
-#define EGGLIB_CONVERT_HPP
-
-
-#include "DataMatrix.hpp"
-#include "Align.hpp"
-#include "EggException.hpp"
-#include "Random.hpp"
-#include <string>
-
-#include "config.h"
-
-#ifdef HAVE_LIBBPP_SEQ
-#include <Bpp/Seq/Alphabet.all>
-#include <Bpp/Seq/Sequence.h>
-#include <Bpp/Seq/Container.all>
-#endif
-
-
-
-namespace egglib {
-
-
-   /** \brief Performs conversion between sequence holder types
-    *
-    * \ingroup core
-    * 
-    * Static methods of this class allows conversion between sequence
-    * holder types implying parametrizable modifications.
-    * 
-    */
-    class Convert {
-
-        public:
-        
-           /** \brief DataMatrix to Align conversion
-            * 
-            * By defaut, this method generates an Align instance
-            * containing only the polymorphic sites. The integers of
-            * the DataMatrix will be converted as follow: 0 to A, 1 to
-            * C, 2 to G and 3 to T. This behaviour can be largely
-            * modified using options.
-            * 
-            * \param dataMatrix DataMatrix instance.
-            * 
-            * \param length length of the desired alignment. Non-varying
-            * stretches of data will be introduced to reach the
-            * specified length. By default the positions of segregating
-            * sites will be determined from the positions given by the
-            * DataMatrix object. Those positions are expressed in a
-            * continuous range, and will be discretized. Mutations
-            * falling on the same site will be moved of one position
-            * left or right (always preserving the order of mutation
-            * sites). If positions are all zero (the default of the
-            * DataMatrix class) and if length is larger than the number
-            * of segregating sites, then all segregating sites will
-            * cluster on the left-hand side of the alignment.
-            * 
-            * \param random the address to a Random object allowing to 
-            * draw random numbers (for randomizing positions and/or
-            * non-varying states). If an address is provided but no
-            * random numbers are required, it is ignored. If no address
-            * if provided and random numbers are required, a Random
-            * instance is built internally.
-            * 
-            * \param randomizePositions if true, the positions specified
-            * in the DataMatrix objects are ignored and the positions of
-            * mutations are drawn randomly along the interval (only if
-            * the specified length is larger than the number of
-            * segregating sites). If randomizePositions and false and
-            * positions are not
-            * 
-            * \param enforceLength specify whether a
-            * EggRuntimeError should be thrown when the number of
-            * polymorphic sites is larger than the specified length. If
-            * false (the default) and in cases where the specified
-            * length is too short to harbor all polymorphic sites, the
-            * alignment length will be increased as needed.
-            * 
-            * \param randomizeNonVaryingStates if true, the stretches of
-            * conserved positions (between segregating sites) will be
-            * randomly drawn from the current symbol mapping. Otherwise,
-            * the symbol given by fixed will be used.
-            * 
-            * \param randomizeAlleles if true, alleles will be drawn
-            * randomly from the mapped characters. Note that if a
-            * genotype value is larger than the size of the mapping, it
-            * will be replaced by the character given by unknown,
-            * without randomization. In other words, with the mapping
-            * "ACGT", alleles 0, 1, 2 and 3 will be randomly assigned
-            * to these four characters, but larger and negative alleles
-            * will be assigned to the unknown character.
-            * 
-            * \param mapping a string given the character to assign to
-            * different character values read from the DataMatrix. If
-            * the read value is 0, the first character of the string
-            * will used, the the value is 1, the second character will
-            * be used, and so on. If the integer read is out of range
-            * (in particular, for any negative value), then the
-            * character given by unknown will be used. An empty string
-            * will always lead to alignments containing only the
-            * character given by unknown. The string "01" is suitable
-            * for binary data.
-            * 
-            * \param unknown the character to use if an integer genotype
-            * value is not mapped in the mapping string (that is, if
-            * the mapping string is too short).
-            * 
-            * \param nonVaryingState character to use for conserved
-            * stretches of data. It doesn't have to be included in the
-            * mapping. If randomizeNonVaryingState is true, this
-            * argument is ignored.
-            * 
-            * \return The resulting Align object.
-            * 
-            */
-            static Align align(
-                DataMatrix& dataMatrix,
-                unsigned int length=0,
-                Random* random=NULL,
-                bool randomizePositions=false,
-                bool randomizeNonVaryingStates=false,
-                bool randomizeAlleles=false,
-                bool enforceLength=false,
-                std::string mapping="ACGT",
-                char unknown='?',
-                char nonVaryingState='A'
-            );
-
-
-#ifdef HAVE_LIBBPP_SEQ
-
-            /** \brief Converts an alignment to the equivalent Bio++ type
-            *
-            * During conversion, name information is lost (arbitrary
-            * names are generated in order toprevent duplicate names).
-            * The object is attached to an alphabet matching the passed
-            * integer. The names are bare rank integers (starting at the
-            * value giving by *offset*).
-            *
-            * \param align the source alignment object.
-            * 
-            * \param alphabetID an integer indicating which alphabet to
-            * use:
-            *       - 1 for DNA
-            *       - 2 for RNA
-            *       - 3 for proteins
-            *       - 4 for standard codon
-            *       - 5 for vertebrate mitochondrial codon
-            *       - 6 for invertebrate mitochondrial codon
-            *       - 7 for echinoderm mitochondrial codon
-            *       .
-            * Other values will result in an exception.
-            * 
-            * \param outgroupFlag an integer indicating whether to
-            * include outgroup sequences:
-            *       - 0 use all sequences
-            *       - 1 use only sequences without 999 label (ingroup)
-            *       - 2 use only sequences with 999 label (outgroup)
-            *       .
-            * Other values will result in an exception.
-            * 
-            * \param offset enter an integer to shift the names of the
-            * resulting alignment (useful to merge alignment and ensure
-            * that names are not duplicated).
-            * 
-            * \return A Bio++ alignment.
-            * 
-            */
-            static bpp::AlignedSequenceContainer egglib2bpp(Align& align, unsigned int alphabetID, unsigned int outgroupFlag, unsigned int offset=0);
-
-#endif
-
-
-
-        protected:
-
-           /** \brief This class cannot be instantiated
-            * 
-            */
-            Convert() { }
-
-
-           /** \brief This class cannot be instantiated
-            * 
-            */
-            Convert(const Convert& source) { }
-
-
-           /** \brief This class cannot be instantiated
-            * 
-            */
-            Convert& operator=(const Convert& source) { return *this; }
-
-
-           /** \brief This class cannot be instantiated
-            * 
-            */
-            virtual ~Convert() { }
-
-#ifdef HAVE_LIBBPP_SEQ
-            static bpp::DNA dnaAlphabet;
-            static bpp::RNA rnaAlphabet;
-            static bpp::ProteicAlphabet proteicAlphabet;
-            static bpp::StandardCodonAlphabet standardCodonAlphabet;
-            static bpp::VertebrateMitochondrialCodonAlphabet vertebrateMitochondrialCodonAlphabet;
-            static bpp::InvertebrateMitochondrialCodonAlphabet invertebrateMitochondrialCodonAlphabet;
-            static bpp::EchinodermMitochondrialCodonAlphabet echinodermMitochondrialCodonAlphabet;
-#endif
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_CURRENT_HPP
-#define EGGLIB_CURRENT_HPP
-
-
-namespace egglib {
-
-    class Population;
-    class ParamSet;
-
-   /** \brief Represents the current set of populations
-    *
-    * \ingroup coalesce
-    * 
-    */
-    class Current {
-
-        public:
-
-           /** \brief Default constructor
-            * 
-            */
-            Current();
-            
-           /** \brief Standard constructor
-            *
-            * \param paramSet allows to initiate the correct structure
-            * of populations.
-            * 
-            */
-            Current(ParamSet* paramSet);
-
-           /** \brief Rebuilds the object
-            *
-            * \param paramSet allows to initiate the correct structure
-            * of populations.
-            * 
-            */
-            void reset(ParamSet* paramSet);
-            
-           /** \brief Destructor
-            * 
-            */
-            virtual ~Current();
-
-           /** \brief Copy constructor
-            * 
-            */
-            Current(const Current&);
-
-           /** \brief Assignment operator
-            * 
-            */
-            Current& operator=(const Current&);
-
-           /** \brief Gets the current number of populations
-            * 
-            */
-            unsigned int numberOfPopulations() const;
-
-            
-           /** \brief Adds an empty population to the system
-            *
-            */
-            void addPopulation();
-
-            
-           /** \brief Gets the number of lineages contained by a given
-            * population
-            * 
-            */
-            unsigned int populationNumberOfLineages(unsigned int populationIndex) const;
-
-            
-           /** \brief Provides access to a given population
-            * 
-            * The returned pointer can be used to modify the object.
-            * 
-            */
-            Population* population(unsigned int populationIndex);
-            
-            
-           /** \brief Total number of lineages
-            * 
-            */
-            unsigned int totalNumberOfLineages() const;
-
-
-           /** \brief Efficient number of lineages
-            * 
-            * This sums the number of covered segments of each lineage.
-            * 
-            */
-            unsigned int efficientNumberOfLineages() const;
-
-
-        private:
-
-            void setPopulationArray();
-            void copy(const Current&);
-            void clear();
-
-            unsigned int _numberOfPopulations;
-            unsigned int _numberOfSegments;
-            Population** populations;
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/DataMatrix.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/DataMatrix.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,219 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_DATAMATRIX_HPP
-#define EGGLIB_DATAMATRIX_HPP
-
-
-#include "CharMatrix.hpp"
-
-
-namespace egglib {
-
-    /** \brief Data table
-    *
-    * \ingroup core
-    *
-    * Holds a data matrix representing genotype data from simulations.
-    * Data are stored as integers, to each site is associated a
-    * position, and to each sequence is associated a group index (any
-    * integer labelling, for example, a subpopulation). Supports the
-    * CharMatrix interface with the condition that allele genotype
-    * datum is >=0 and <=9.
-    * 
-    */
-    class DataMatrix : public CharMatrix {
-    
-    public:
-    
-        /** \brief Default constructor
-         *
-         * The data table default dimensions are {0,0}
-         *
-         */
-        DataMatrix();
-
-
-        /** \brief Standard constructor
-         *
-         * The data table dimensions must be given.
-         * Each cell default default is 0, and each site position is 0..
-         *
-         * \param numberOfSequences number of lines of the data table.
-         * \param numberOfSites number of columns of the data table.
-         *
-         */
-        DataMatrix(unsigned int numberOfSequences, unsigned int numberOfSites);
-
-
-        /** \brief Copy constructor
-         * 
-         */
-        DataMatrix(const DataMatrix&);
-
-
-        /** \brief Copy constructor
-         * 
-         */
-        DataMatrix(const CharMatrix&);
-
-        
-        /** \brief Assignment operator
-         * 
-         */
-        virtual DataMatrix& operator=(const DataMatrix&);
-        
-        
-        /** \brief Assignment operator
-         * 
-         */
-        virtual DataMatrix& operator=(const CharMatrix&);
-
-
-        /** \brief Destructor
-         * 
-         */
-        virtual ~DataMatrix();
-        
-        
-        /** \brief Gets number of sites
-         * 
-         */
-        unsigned int numberOfSites() const;
-
-
-        /** \brief Gets number of sequences
-         * 
-         */
-        unsigned int numberOfSequences() const;
-        
-        
-        /** \brief Sets a value of the data table
-         * 
-         */
-        void set(unsigned int sequence, unsigned int site, int value);
-
-
-        /** \brief Gets a value from the data table
-         * 
-         */
-        int get(unsigned int sequence, unsigned int site) const;
-        
-        
-        /** \brief Faster and unsecure version of get
-         * 
-         */
-        inline int fget(unsigned int sequence, unsigned int site) const {
-            return dataMatrix[sequence][site];
-        }
-
-
-        /** \brief Sets the position of a site
-         * 
-         */
-        void sitePosition(unsigned int site, double value);
-
-
-        /** \brief Gets the position of a site
-         * 
-         */
-        double sitePosition(unsigned int site) const;
-
-
-        /** \brief Sets the group label of a sequence
-         * 
-         */
-        void populationLabel(unsigned int sequence, unsigned int value);
-
-
-        /** \brief Gets the group label of a sequence
-         * 
-         */
-        unsigned int populationLabel(unsigned int sequence) const;
-
-
-        /** \brief Removes all information from the object
-         * 
-         */
-        void clear();
-
-
-        /** \brief Resizes the data matrix
-         *
-         * \param newNumberOfSequences number of sequences (rows)
-         * \param newNumberOfSites number of sites (columns)
-         *
-         * If new values are larger, data already set is left unchanged.
-         * New data are set to zero.
-         *
-         */
-        void resize(unsigned int newNumberOfSequences, unsigned int newNumberOfSites);
-
-
-       /** \brief Shifts allele value
-        * 
-        * \param minimum the minimum allele value.
-        * 
-        * Shifts all alleles at all sites to ensure that alleles alleles
-        * are equal to or larger than minimum. The shifting is specific
-        * to each site.
-        * 
-        */
-        void shift(int minimum);
-
-        /** \brief Gets the character at a given position
-         * 
-         * An exception is generated if the allele value at this
-         * position is not >=0 and <=9. Not out-of-bound check is
-         * performed.
-         * 
-         */
-        char character(unsigned int sequence, unsigned int site) const;
-        
-
-
-    private:
-        
-        // Initializes to default values (for empty object)
-        void init();
-        
-        // Copies from a source object
-        virtual void copy(const CharMatrix&);
-
-        // Copies from a source object
-        virtual void copy(const DataMatrix&);
-        
-        // Number of lines of the data matrix
-        unsigned int _numberOfSequences;
-        
-        // Number of columns of the data matrix
-        unsigned int _numberOfSites;
-        
-        // Data matrix
-        int **dataMatrix;
-        
-        // Vector of site positions
-        double *positions;
-        
-        // Vector of group indices
-        unsigned int *groups;
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Edge.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Edge.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,331 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_EDGE_HPP
-#define EGGLIB_EDGE_HPP
-
-#include <vector>
-#include <climits>
-#include "EggException.hpp"
-
-namespace egglib {
-
-    class Random;
-
-    /** \brief Edge of the ancestral recombination graph
-    *
-    * \ingroup coalesce
-    *
-    * Each Edge instance provides access to its 0, 1 or 2 descendants
-    * (the former holds for a terminal node, the middle for the parent
-    * of a recombined node and the latter for the parent of a coalesced
-    * node (most classical node in the coalescent).The Edge also
-    * provides to the edge length. Note that the Edge instance must be
-    * understood as an ARG node and the branch above it (latter in the
-    * coalescence process). Edge instances also keep track of the list
-    * of descendants descending from this node (which may differ along
-    * recombining segment). Edge instances *must* be created through one
-    * of the "default" and "coalescence" constructors or through the 
-    * recombination method. Edge instances should never be copied but
-    * manipulated by references.
-    * 
-    */
-    class Edge {
-    
-        public:
-        
-            /// Destructor
-            virtual ~Edge();
-        
-           /** \brief Constructor
-            * 
-            * \param numberOfSegments the number of recombining segments
-            * (one for a non-recombining region).
-            * 
-            * Use the Pool, instead. Objects are delivered with a
-            * complete coverage.
-            * 
-            */ 
-            Edge(unsigned int numberOfSegments);
-
-
-            /// Restore object to `factory` state
-            void reset();
-
-
-           /** \brief Builds for internal node
-            * 
-            * \param date the date of creation of the edge.
-            * \param son1 first edge descending from this edge.
-            * \param son2 second edge descending from this edge.
-            * \param edgesPerSegments counts the current number of
-            * (non-coalesced lineages for each lineages); must have the
-            * appropriate size and will be updated.
-            * \param MRCA the list where to place the address of segment
-            * MRCA, if it occurs.
-            * \param totalLength the total length of the tree.
-            * \param segmentLengths the table of tree lengths per
-            * segment.
-            *
-            * Assumes the current object has the correct number of
-            * segments.
-            * 
-            */
-            void coalescence(double date, Edge* son1, Edge* son2,
-                        unsigned int* edgesPerSegments, Edge** MRCA,
-                        double& totalLength, double* segmentLengths);
-
-
-           /** \brief Generates a recombination event
-            * 
-            * \param date the date of the event.
-            * \param dest1 destination for the first resulting edge.
-            * \param dest2 destination for the second resulting edge.
-            * \param random pointer to the Random instance used by the 
-            * simulator.
-            * \param totalLength the total length of the tree.
-            * \param segmentLengths the table of tree lengths per
-            * segment.
-            * 
-            * dest1 and dest2 must be Edge address initialized with the
-            * appropriate number of segments.
-            * 
-            */
-            void recombination(double date,
-                        Edge* dest1, Edge* dest2, Random* random,
-                        double& totalLength, double* segmentLengths);
-
-
-           /** \brief Define this edge to be terminal
-            * 
-            * The edge have only non-covered segments
-            * 
-            */
-            void set_terminal(unsigned int leaf_index);
-            
-            /// Branch's raw length (doesn't take account segment coverage)
-            double length;
-
-            /// Number of covered segments
-            unsigned int coverage;
-            
-            /// Time position of the branch's bottom
-            double bottom;
-            
-            /// Time position of the branch's top
-            double top;
-            
-            /// Address of the  first son
-            Edge* son1;
-
-            /// Address of the second son
-            Edge* son2;
-
-            /// Number of sons (0, 1 or 2)
-            unsigned int numberOfSons;
-
-            /// Checks if a given segment is covered
-            inline bool segment(unsigned int segmentIndex) const {
-                //while(segments[segmentIndex]==0) segmentIndex--;
-                if (segments[segmentIndex]==0)  return false;
-                if (segments[segmentIndex]==UINT_MAX) return true;
-                return segbools[segmentIndex];
-            }
-
-            /// leaf index (0 for internal nodes)
-            inline unsigned int label() const {
-                return _label;
-            }
-
-            /// Number of mutations per segment
-            unsigned int* numberOfMutationsPerActualSite;
-
-            /// Sets the actual number of sites
-            void set_actualNumberOfSites(unsigned int actualNumberOfSites);
-
-
-        private:
-
-            unsigned int _label;
-
-            /// Default constructor is not available
-            Edge();
-
-            /// Copy constructor is not available
-            Edge(const Edge& edge) {}
-
-            /// Assignment operator is not available
-            Edge& operator=(const Edge& edge) { return *this; }
-
-            void init(unsigned int numberOfSegments);
-
-            unsigned int numberOfSegments;
-            unsigned int* segments;
-            bool* segbools;
-
-            /// complete the covered ranges with UINT_MAX's and the non-covered by 0's
-            inline void fill() {
-                coverage=0.;
-                unsigned int i=0,j;
-                while (i<numberOfSegments) {
-                    if (segbools[i]==true) {
-                        coverage += segments[i];
-                        for (j=1; j<segments[i]; j++) {
-                            segments[i+j] = UINT_MAX;
-                        }
-                    }
-                    i+=segments[i];
-                }
-            }
-
-
-
-            /// update containing Arg's branch lengths
-            inline void update_lengths(double& totalLength, double* segmentLengths) {
-                unsigned int i=0,j;
-                while (i<numberOfSegments) {
-                    if (segbools[i]==true) {
-                        totalLength += segments[i]*length;
-                        for (j=0; j<segments[i]; j++) {
-                            segmentLengths[i+j] += length;
-                        }
-                    }
-                    i+=segments[i];
-                }
-            }
-
-
-    };
-
-
-
-
-
-
-
-
-
-
-
-
-    /** \brief Pool of Edge objects
-    *
-    * \ingroup coalesce
-    *
-    * Holds a pool of Edge objects that can be recycled to spare the
-    * building burden. A construction time, a number of Edge objects
-    * equals to the predicted number of needed instances should be
-    * requested. The Edge's will be prebuilt immediately and delivered
-    * upon request. After use, the Edge's should be released. It is only
-    * possible to release the last issued Edge instance or all of them
-    * at once.
-    * 
-    */
-    class EdgePool {
-
-        public:
-        
-            /// Default constructor (nothing allocated)
-            EdgePool();
-
-
-            /// Destructor
-            virtual ~EdgePool();
-
-
-           /** \brief Configure pool
-            * 
-            * Pre-allocates a given number of Edge objects. The objects
-            * will be immediately available.
-            * 
-            * Data previously allocated (by a previous call of this
-            * function or by the deliver() method) will be lost so it
-            * can be required to use clear() before.
-            * 
-            * \param numberOfSegments the number of segments of the
-            * simulation; all Edge instances will use this value.
-            * 
-            * \param numberOfPreAllocated the number of Edge that should
-            * be kept ready for immediate use.
-            * 
-            */
-            void set(unsigned int numberOfSegments, unsigned numberOfPreAllocated);
-            
-            
-           /** \brief Frees internally stored memory
-            * 
-            * This invalidate all points that have been delivered
-            * previously. However, any previously set number of segments
-            * (0, by default) is retained.
-            * 
-            */
-            void clear();
-
-            
-           /** \brief Deliver an Edge
-            * 
-            * The object must not be freed by the client! This object is
-            * allocated on the heap if the cache is not large enough,
-            * only reset if it was previously released, or just delivered
-            * if it is one of the initially allocated instances.
-            * 
-            */
-            Edge* deliver();
-            
-            
-           /** \brief Release an Edge
-            * 
-            * Release the last delivered Edge. The instance is only
-            * cached for a potential future use; it is not freed nor
-            * reset immediately.  If no Edge's are in use, nothing is
-            * done.
-            * 
-            */
-            void releaseLast();
-
-            
-           /** \brief Release all Edge's
-            * 
-            * Release all delivered Edges. The instances are only
-            * cached for a potential future use; they are not freed nor
-            * reset immediately. If no Edge's are in use, nothing is
-            * done.
-            * 
-            */
-            void releaseAll();
-
-        private:
-        
-            /// Not available
-            EdgePool(const EdgePool& ep) {}
-            
-            /// Not available
-            EdgePool& operator=(const EdgePool& ep) { return *this; }
-
-            unsigned int numberOfSegments;
-            unsigned int used;
-            unsigned int released;
-            unsigned int ready;
-            Edge** cache;
-            
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/EggException.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/EggException.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-/*
-    Copyright 2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_EGGEXCEPTION_HPP
-#define EGGLIB_EGGEXCEPTION_HPP
-
-#include <string>
-#include <exception>
-
-namespace egglib {
-
-    /** \brief Base exception type for errors occurring in this library
-     *
-     * \ingroup core
-     *
-     */
-    class EggException : public std::exception {
-        public:
-            /// Constructor with empty error message
-            EggException();
-            /// Creates the exception
-            EggException(const char* message);
-            /// Destructor
-            ~EggException() throw() {}
-            /// Gets error message
-            virtual const char* what() const throw();
-            
-      protected:
-            std::string message;
-
-    };
-
-  
-    /** \brief Exception type for memory errors
-     *
-     * \ingroup core
-     *
-     */
-    class EggMemoryError : public EggException {
-        public:
-            /// Creates the exception
-            EggMemoryError();
-            /// Destructor
-            ~EggMemoryError() throw() {}
-    };
-
-
-    /** \brief Exception type for argument value errors
-     *
-     * \ingroup core
-     *
-     */
-    class EggArgumentValueError : public EggException {
-        public:
-            /// Creates the exception
-            EggArgumentValueError(const char* m );
-            /// Destructor
-            ~EggArgumentValueError() throw() {}
-    };
-    
-
-    /** \brief Exception type for runtime errors
-     * 
-     * Runtime error definition is rather large. Includes bugs as well
-     * as logical errors.
-     *
-     * \ingroup core
-     *
-     */
-    class EggRuntimeError : public EggException {
-        public:
-            /// Creates the exception
-            EggRuntimeError(const char* m );
-            /// Destructor
-            ~EggRuntimeError() throw() {}
-    };
-
-
-    /** \brief Exception type for file/string formatting errors
-     *
-     * \ingroup core
-     *
-     */
-    class EggFormatError : public EggException {
-        public:
-            /// Creates the exception
-            EggFormatError(const char* fileName, const char* expectedFormat, const char* m);
-            /// Destructor
-            ~EggFormatError() throw() {}
-            /// Gets the file name
-            std::string fileName() const;
-            /// Gets the expected format
-            std::string expectedFormat() const;
-            /// Formats a longer string
-            virtual const char* what_more() const;
-            
-        protected:
-            std::string fname;
-            std::string eformat;
-    };
-
-
-    /** \brief Exception type for errors while opening a file
-     * 
-     * \ingroup core
-     *
-     */
-    class EggOpenFileError : public EggException {
-        public:
-            /// Creates the exception
-            EggOpenFileError(const char* fileName );
-            /// Destructor
-            ~EggOpenFileError() throw() {}
-    };
-    
-    
-    /** \brief Exception type for unaligned sequences
-     * 
-     * \ingroup core
-     * 
-     */
-    class EggUnalignedError : public EggException {
-        public:
-           /** \brief Creates the exception
-            * 
-            */
-            EggUnalignedError();
-            
-           /** \brief Destructor
-            * 
-            */
-            ~EggUnalignedError() throw() {}
-    };
-
-   /** \brief Exception type for invalid character
-    * 
-    * \ingroup core
-    * 
-    */
-    class EggInvalidCharacterError : public EggException {
-        public:
-           /** \brief Creates the exception
-            * 
-            */
-            EggInvalidCharacterError(char c, unsigned int seqIndex, unsigned int posIndex);
-            
-           /** \brief Destructor
-            * 
-            */
-            ~EggInvalidCharacterError() throw() {}
-    };
-
-}
-
-
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/FStatistics.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/FStatistics.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,288 +0,0 @@
-/*
-    Copyright 2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_FSTATISTICS_HPP
-#define EGGLIB_FSTATISTICS_HPP
-
-
-
-namespace egglib {
-
-
-    /** \brief Computes Fis, Fst and Fit from diploid data
-    *
-    * The class requires loading data. Data are loaded by individual
-    * (two genotypes per individual). The analyses are cached: they are
-    * performed upon the first call to statistics accessors. The cache
-    * is emptied whenever a datum is loaded.
-    * 
-    * The computations are performed after Weir and Cockerham. The
-    * statistics F, theta and f are generalized for multiple alleles.
-    * To allow computation of multi-locus statistics, variance
-    * components are also available. The three components of the
-    * variance are Vpopulation (between-population), Vindividual
-    * (within-population, between-individual) and Vallele (within-
-    * individual). The formulas to compute the F-statistics are as
-    * follows:
-    *       - 1-F = Vallele/(Vpopulation+Vindividual+Vallele)
-    *       - theta = Vpopulation/(Vpopulation+Vindividual+Vallele)
-    *       - 1-f = Vallele/(Vindividual+Vallele).
-    * 
-    * \ingroup polymorphism
-    *
-    */
-    class FStatistics {
-    
-        public:
-    
-           /** \brief Constructor
-            * 
-            */ 
-            FStatistics();
-
-            
-           /** \brief Destructor
-            * 
-            */ 
-            virtual ~FStatistics();
-
-            
-           /** \brief Reserve sufficient memory for a given number of
-            * individuals.
-            * 
-            * This method makes the load function faster by allocating
-            * all required memory at once.
-            * 
-            * \param numberOfIndividuals a strictly positive integer.
-            * 
-            */
-            void reserve(unsigned int numberOfIndividuals);
-
-
-           /** \brief Loads the data for one individual
-            * 
-            * \param genotype1 an integer giving the first allele.
-            * \param genotype2 an integer giving the second allele.
-            * \param populationLabel an integer indication belonging to
-            * a population.
-            * 
-            * Genotypes and population labels are not required to be
-            * consecutive (both are labels, not indices). They are
-            * internally mapped to indices (the mapping can be obtained
-            * by accessors populationLabel and allele).
-            * 
-            * All genotypes are considered to be valid (no missing data).
-            * If statistics were computed previous to call to this
-            * function, all data will be erase.
-            * 
-            */
-            void loadIndividual(unsigned int genotype1,
-                    unsigned int genotype2, unsigned int populationLabel);
-
-
-           /** \brief Label of a population
-            * 
-            * The index corresponds to the local mapping of populations
-            * regardless of the ranking of population labels. (No out
-            * of bound checking.)
-            * 
-            */
-            unsigned int populationLabel(unsigned int populationIndex);
-
-
-           /** \brief Value of an allele
-            * 
-            * The index corresponds to the local mapping of alleles
-            * regardless of the ranking of allele values. (No out of
-            * bound checking.)
-            * 
-            */
-            unsigned int alleleValue(unsigned int alleleIndex);
-
-
-            /// First allele of a given individual (no checking)
-            unsigned int firstAllele(unsigned int individualIndex) const;
-
-            /// Second allele of a given individual (no checking)
-            unsigned int secondAllele(unsigned int individualIndex) const;
-
-            /// Population label of a given individual (no checking)
-            unsigned int individualLabel(unsigned int individualIndex) const;
-
-
-           /** \brief Number of alleles
-            * 
-            */
-            unsigned int numberOfAlleles();
-
-
-           /** \brief Number of populations
-            * 
-            */
-            unsigned int numberOfPopulations();
-
-
-           /** \brief Number of loaded genotypes
-            * 
-            */
-            unsigned int numberOfGenotypes() const;
-
-
-           /** \brief Absolute total allele frequency
-            * 
-            */
-            unsigned int alleleFrequencyTotal(unsigned int alleleIndex);
-            
-
-           /** \brief Absolute allele frequency in a population
-            * 
-            */
-            unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex);
-
-
-           /** \brief Absolute genotype frequency
-            * 
-            * Note that allele AB is considered different to BA (this
-            * means that values can be accessed both sides of the
-            * diagonal.
-            * 
-            */
-            unsigned int genotypeFrequencyTotal(unsigned int alleleIndex1, unsigned int alleleIndex2);
-
-
-           /** \brief Absolute genotype frequency in a population
-            * 
-            * Note that allele AB is considered different to BA (this
-            * means that values can be accessed both sides of the
-            * diagonal.
-            * 
-            */
-            unsigned int genotypeFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex1, unsigned int alleleIndex2);
-
-            
-           /** \brief Sample size of a population
-            * 
-            */
-            unsigned int populationFrequency(unsigned int populationIndex);
-
-
-           /** \brief Weir-Cockerham F-statistic
-            * 
-            * Note: equivalent to Fit.
-            * 
-            */
-            double F();
-
-
-           /** \brief Weir-Cockerham theta-statistic
-            * 
-            * Note: equivalent to Fst.
-            * 
-            */
-            double theta();
-
-
-           /** \brief Weir-Cockerham f-statistic
-            * 
-            * Note: equivalent to Fis.
-            * 
-            */
-            double f();
-            
-
-           /** \brief Between-population component of variance
-            * 
-            */
-            double Vpopulation();
-
-
-           /** \brief Within-population, between-individual component of variance
-            * 
-            */
-            double Vindividual();
-            
-            
-           /** \brief Within-individual component of variance
-            * 
-            */
-            double Vallele();
-
-
-        protected:
-    
-            bool d_flag;
-            void d_init();
-            void d_clear();
-            unsigned int  d_reserved;
-            unsigned int  d_numberOfGenotypes;
-            unsigned int *d_genotypes;
-            unsigned int *d_populationLabels;
-
-            bool s_flag;
-            void s_init();
-            void s_clear();
-            void s_compute();
-            void processPopulations();
-            void processAlleles();
-            unsigned int getPopulationIndex(unsigned int) const;
-            unsigned int getAlleleIndex(unsigned int) const;
-            unsigned int    s_numberOfAlleles;
-            unsigned int   *s_alleleValueMapping;
-            unsigned int    s_numberOfPopulations;
-            unsigned int   *s_populationLabelMapping;
-            unsigned int   *s_populationFrequencies;
-            unsigned int   *s_alleleFrequenciesTotal;
-            unsigned int  **s_alleleFrequenciesPerPopulation;
-            unsigned int  **s_genotypeFrequenciesTotal;
-            unsigned int ***s_genotypeFrequenciesPerPopulation;
-
-            bool w_flag;
-            void w_init();
-            void w_clear();
-            void w_compute();
-            double  w_F;
-            double  w_T;
-            double  w_f;
-            double *w_a;
-            double *w_b;
-            double *w_c;
-            double  w_nbar;
-            double  w_nc;
-            double *w_pbar;
-            double *w_ssquare;
-            double *w_hbar;
-            double  w_sum_a;
-            double  w_sum_b;
-            double  w_sum_c;
-            double  w_sum_abc;
-            double  w_sum_bc;
-
-    
-        private:
-            
-            FStatistics(const FStatistics& source) { }
-            
-            FStatistics& operator=(const FStatistics& source) {
-                return *this;
-            }
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Fasta.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Fasta.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,278 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_FASTA_HPP
-#define EGGLIB_FASTA_HPP
-
-#include <istream>
-#include <iostream>
-#include <string>
-#include "Container.hpp"
-
-namespace egglib {
-
-   /** \brief Fasta parser/formatted
-    *
-    * \ingroup core
-    *
-    * Reads a multifasta sequence file from a string, a stream or a file
-    * and returns a Container. See the description of the format below.
-    * Formats a fasta string from a sequence container object and places
-    * it in a string, a stream of a file. All methods are static and the
-    * class cannot be instantiated. The methods parsef and formatf will
-    * open the file for you while the others will read/write directly
-    * in a string.
-    * 
-    * Specifications of the fasta format:
-    * 
-    *    - The number of sequences is not limited.
-    * 
-    *    - Each sequence is preceded by a header limited to a single
-    *      line and starting by a ">" character.
-    * 
-    *    - The header length is not limited and all characters are
-    *      allowed but white spaces and special characters are
-    *      discouraged.
-    * 
-    *    - Group indices are specified by \@0, \@1, \@2...  strings
-    *      appearing at the end of the header string (just before the
-    *      carriage return). Note that group labels are ignored by
-    *      default.
-    * 
-    *    - Group indices are ignored unless specifically specified in a
-    *      parser's options.
-    * 
-    *    - The sequence itself continues on following lines until the
-    *      next ">" character or the end of the file.
-    * 
-    *    - White spaces, tab and carriage returns are allowed at any
-    *      position There is no limitation in length and different
-    *      sequences can have different lengths.
-    * 
-    *    - Although the standard is lower case characters, Fasta
-    *      assumes upper case characters and only supports lower case
-    *      characters (and converts them to upper case characters).
-    *      Information coded by change in case is lost.
-    *
-    */
-    class Fasta {
-
-      public:
-
-       /** \brief Imports a fasta file
-         *
-         * Imports the content of the file as is. Calls the method
-         * pase(std::istream*, bool) by creating its own istream.
-         *
-         * \param fname the name of a fasta file.
-         * 
-         * \param importGroupLabels if set to true, scan automatically
-         * for groups. The format is @ followed by an integer, placed
-         * at the end of the header string(sequences without labels
-         * will be treated as \@0).
-         * 
-         * \return A Container object containing the sequences.
-         * 
-         */
-        static Container parsef(const char* fname, bool importGroupLabels=false);
-
-
-       /** \brief Imports a fasta file
-         *
-         * Imports the content of the file as is. Calls the method
-         * pase(std::istream*, bool) by creating its own istream. This
-         * method expects a reference to a Container to which the
-         * sequences will be appended.
-         *
-         * \param fname the name of a fasta file.
-         * 
-         * \param container a Container instance, empty or not.
-         * 
-         * \param importGroupLabels if set to true, scan automatically
-         * for groups. The format is @ followed by an integer, placed
-         * at the end of the header string(sequences without labels
-         * will be treated as \@0).
-         * 
-         * \return Nothings: the new sequences are appended to the
-         * Container passed as argument.
-         * 
-         */
-        static void parsef(const char* fname, Container& container, bool importGroupLabels=false);
-
-
-       /** \brief Imports a fasta file
-         *
-         * Imports the content of the file as is. Calls the method
-         * pase(std::istream*, bool) by creating its own istream.
-         *
-         * \param str a string containing the data.
-         * 
-         * \param importGroupLabels if set to true, scan automatically
-         * for groups. The format is @ followed by an integer, placed
-         * at the end of the header string(sequences without labels
-         * will be treated as \@0).
-         * 
-         * \return A Container object containing the sequences.
-         * 
-         */
-        static Container parse(const std::string& str, bool importGroupLabels=false);
-
-
-       /** \brief Imports a fasta file
-         *
-         * Imports the content of the file as is. Calls the method
-         * pase(std::istream*, bool) by creating its own istream. This
-         * method expects a reference to a Container to which the
-         * sequences will be appended.
-         *
-         * \param str a string containing the data.
-         * 
-         * \param container a Container instance, empty or not.
-         * 
-         * \param importGroupLabels if set to true, scan automatically
-         * for groups. The format is @ followed by an integer, placed
-         * at the end of the header string(sequences without labels
-         * will be treated as \@0).
-         * 
-         * \return Nothing: new sequences are appended to the Container
-         * passed as argument.
-         * 
-         */
-        static void parse(const std::string& str, Container& container, bool importGroupLabels=false);
-
-
-       /** \brief Imports a fasta file from an open stream
-         *
-         * Imports the content of the file as is.
-         *
-         * \param stream an open stream (file or string) containing the
-         * data.
-         * 
-         * \param importGroupLabels if set to true, scan automatically
-         * for groups. The format is @ followed by an integer, placed
-         * at the end of the header string(sequences without labels
-         * will be treated as \@0).
-         * 
-         * \return A Container object containing the sequences.
-         * 
-         */
-        static Container parse(std::istream& stream, bool importGroupLabels=false);
-
-
-       /** \brief Imports a fasta file from an open stream
-         *
-         * Imports the content of the file as is. This
-         * method expects a reference to a Container to which the
-         * sequences will be appended.
-         *
-         * \param stream an open stream (file or string) containing the
-         * data.
-         * 
-         * \param container a Container instance, empty or not.
-         * 
-         * \param importGroupLabels if set to true, scan automatically
-         * for groups. The format is @ followed by an integer, placed
-         * at the end of the header string(sequences without labels
-         * will be treated as \@0).
-         * 
-         * \return Nothing: the new sequences are appended to the
-         * Container passed as argument.
-         * 
-         */
-        static void parse(std::istream& stream, Container& container, bool importGroupLabels=false);
-        
-        
-       /** \brief Export sequences as fasta
-        *
-        * \param fname the name of the file where to place the result.
-        * 
-        * \param container Container object to export.
-        * 
-        * \param exportGroupLabels if set to true, exports group
-        * indices as a \@x at the end of the sequence name, where x is
-        * the group index. Otherwise, this information is discarded.
-        * 
-        * \param lineLength the number of characters to place on a
-        * single line. If zero, no newlines are inserted within
-        * sequences.
-        * 
-        */
-        static void formatf(const char* fname, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50);
-
-
-       /** \brief Export sequences as fasta
-        *
-        * \param file an open stream.
-        * 
-        * \param container Container object to export.
-        * 
-        * \param exportGroupLabels if set to true, exports group
-        * indices as a \@x at the end of the sequence name, where x is
-        * the group index. Otherwise, this information is discarded.
-        * 
-        * \param lineLength the number of characters to place on a
-        * single line. If zero, no newlines are inserted within
-        * sequences.
-        * 
-        */
-        static void format(std::ostream& file, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50);
-
-
-       /** \brief Export sequences as fasta
-        * 
-        * This medod creates internally an ostringstream, calls the
-        * method format(ostream, container, bool) and returns the
-        * resulting string.
-        *
-        * \param container Container object to export.
-        * 
-        * \param exportGroupLabels if set to true, exports group
-        * indices as a \@x at the end of the sequence name, where x is
-        * the group index. Otherwise, this information is discarded.
-        * 
-        * \param lineLength the number of characters to place on a
-        * single line. If zero, no newlines are inserted within
-        * sequences.
-        * 
-        * \return The formatted string.
-        * 
-        */
-        static std::string format(const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50);
-
-          
-          
-      protected:
-        
-        /// This class cannot be instantiated
-        Fasta() { }
-        
-        /// This class cannot be instantiated
-        Fasta(const Fasta& source) { }
-        
-        /// This class cannot be or copied
-        Fasta& operator=(const Fasta& source) { return *this; }
-        
-        /// This class cannot be instantiated
-        virtual ~Fasta() { }
-
-        
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/HFStatistics.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/HFStatistics.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,227 +0,0 @@
-/*
-    Copyright 2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_HFSTATISTICS_HPP
-#define EGGLIB_HFSTATISTICS_HPP
-
-
-
-namespace egglib {
-
-
-    /** \brief Computes Fst and Fit from haploid data
-    *
-    * The class requires loading data. Data are loaded by haploid
-    * (one genotype per individual). The analyses are cached: they are
-    * performed upon the first call to statistics accessors. The cache
-    * is emptied whenever a datum is loaded.
-    * 
-    * The computations are performed after Weir and Cockerham. The
-    * statistic theta is generalized for multiple alleles. To allow
-    * computation of multi-locus statistics, variance components are
-    * also available. The two components of the variance are T1 and T2
-    * and theta is T1/T2 (from Weir 1996 "Genetic Data Analysis II",
-    * Sinauer associates, Sunderland MA).
-    * 
-    * \ingroup polymorphism
-    *
-    */
-    class HFStatistics {
-    
-        public:
-    
-           /** \brief Constructor
-            * 
-            */ 
-            HFStatistics();
-
-            
-           /** \brief Destructor
-            * 
-            */ 
-            virtual ~HFStatistics();
-
-            
-           /** \brief Reserve sufficient memory for a given number of
-            * individuals.
-            * 
-            * This method makes the load function faster by allocating
-            * all required memory at once.
-            * 
-            * \param numberOfIndividuals a strictly positive integer.
-            * 
-            */
-            void reserve(unsigned int numberOfIndividuals);
-
-
-           /** \brief Loads the data for one individual
-            * 
-            * \param genotype an integer giving the allele.
-            * \param populationLabel an integer indication belonging to
-            * a population.
-            * 
-            * Genotypes and population labels are not required to be
-            * consecutive (both are labels, not indices). They are
-            * internally mapped to indices (the mapping can be obtained
-            * by accessors populationLabel and allele).
-            * 
-            * All genotypes are considered to be valid (no missing data).
-            * If statistics were computed previous to call to this
-            * function, all data will be erased.
-            * 
-            */
-            void loadIndividual(unsigned int genotype, unsigned int populationLabel);
-
-
-           /** \brief Label of a population
-            * 
-            * The index corresponds to the local mapping of populations
-            * regardless of the ranking of population labels. (No out
-            * of bound checking.)
-            * 
-            */
-            unsigned int populationLabel(unsigned int populationIndex);
-
-
-           /** \brief Value of an allele
-            * 
-            * The index corresponds to the local mapping of alleles
-            * regardless of the ranking of allele values. (No out of
-            * bound checking.)
-            * 
-            */
-            unsigned int alleleValue(unsigned int alleleIndex);
-
-
-            /// Allele of a given individual (no checking)
-            unsigned int allele(unsigned int individualIndex) const;
-
-            /// Population label of a given individual (no checking)
-            unsigned int individualLabel(unsigned int individualIndex) const;
-
-
-           /** \brief Number of alleles
-            * 
-            */
-            unsigned int numberOfAlleles();
-
-
-           /** \brief Number of populations
-            * 
-            */
-            unsigned int numberOfPopulations();
-
-
-           /** \brief Number of loaded genotypes
-            * 
-            */
-            unsigned int numberOfGenotypes() const;
-
-
-           /** \brief Absolute total allele frequency
-            * 
-            */
-            unsigned int alleleFrequencyTotal(unsigned int alleleIndex);
-            
-
-           /** \brief Absolute allele frequency in a population
-            * 
-            */
-            unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex);
-
-
-           /** \brief Sample size of a population
-            * 
-            */
-            unsigned int populationFrequency(unsigned int populationIndex);
-
-
-           /** \brief Weir-Cockerham theta-statistic
-            * 
-            * Note: equivalent to Fst.
-            * 
-            */
-            double theta();
-
-
-           /** \brief Between-population component of variance
-            * 
-            */
-            double T1();
-
-
-           /** \brief Total variance
-            * 
-            */
-            double T2();
-            
-
-        protected:
-    
-            bool d_flag;
-            void d_init();
-            void d_clear();
-            unsigned int  d_reserved;
-            unsigned int  d_numberOfGenotypes;
-            unsigned int *d_genotypes;
-            unsigned int *d_populationLabels;
-
-            bool s_flag;
-            void s_init();
-            void s_clear();
-            void s_compute();
-            void processPopulations();
-            void processAlleles();
-            unsigned int getPopulationIndex(unsigned int) const;
-            unsigned int getAlleleIndex(unsigned int) const;
-            unsigned int    s_numberOfAlleles;
-            unsigned int   *s_alleleValueMapping;
-            unsigned int    s_numberOfPopulations;
-            unsigned int   *s_populationLabelMapping;
-            unsigned int   *s_populationFrequencies;
-            unsigned int   *s_alleleFrequenciesTotal;
-            unsigned int  **s_alleleFrequenciesPerPopulation;
-
-            bool w_flag;
-            void w_init();
-            void w_clear();
-            void w_compute();
-            double  w_T;
-            double *w_T1;
-            double *w_T2;
-            double  w_nbar;
-            double  w_nc;
-            double *w_pbar;
-            double *w_ssquare;
-            double  w_sum_T1;
-            double  w_sum_T2;
-
-    
-        private:
-            
-            HFStatistics(const HFStatistics& source) { }
-            
-            HFStatistics& operator=(const HFStatistics& source) {
-                return *this;
-            }
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/HaplotypeDiversity.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/HaplotypeDiversity.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,176 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_HAPLOTYPEDIVERSITY_HPP
-#define EGGLIB_HAPLOTYPEDIVERSITY_HPP
-
-#include "BaseDiversity.hpp"
-
-namespace egglib {
-
-
-   /** \brief Computes diversity based on haplotype analysis
-    *
-    * \ingroup polymorphism
-    * 
-    * This class relies on detection of polymorphic sites, as does
-    * NucleotideDiversity, with the exception that sites with missing
-    * data cannot be processed (minimumExploitableData is enforced to
-    * 1.).
-    * 
-    * Like NucleotideDiversity, the same object can be used to analyze
-    * different data sets. Only the call to load() is required before
-    * accessing the data.
-    * 
-    * Hst, Gst and Kst are between population differenciation indices.
-    * They are respectively defined in equations 2, 5-6 and 9 of Hudson
-    * et al. 1992a (Molecular Biology and Evolution 9:138-151). Also,
-    * Fst is defined in equation 3 of Hudson et al. 1992b (Genetics
-    * 132:583-589). Finally, Snn is from Hudson 2000 Genetics. It is
-    * computed as the average of Xi for all sequences. Where Xi is the
-    * ratio of nearest neighbours from the same group to the number of
-    * nearest neighbours. Nearest neigbours are all the sequences with
-    * the lowest number of differences to the focal sequence. NOTE: 
-    * Gst/Hst are quite similar, but Fst and Kst are more different. Snn
-    * is a different statistic. Gst and Hst are two ways to estimate the
-    * between-population fraction of haplotypic diversity.
-    * 
-    */
-    class HaplotypeDiversity : public BaseDiversity {
-
-        public:
-
-           /** \brief Constructor
-            * 
-            */
-            HaplotypeDiversity();
-            
-           /** \brief Destructor
-            * 
-            */ 
-            virtual ~HaplotypeDiversity();
-
-           /** \brief Identifies polymorphic sites and computes basis
-            * statistics
-            * 
-            * \param data an alignment object (subclass of CharMatrix).
-            * The presence of outgroup or of different populations will
-            * be detected based on the populationLabel members of the
-            * passed object. The populationLabel 999 will be interpreted
-            * as outgroups. If several outgroups are passed, sites were
-            * the outgroups are not consistent will be treated as "non-
-            * orientable".
-            * 
-            * \param allowMultipleMutations if true, sites with more
-            * than two alleles will not be ignored. The sum of the
-            * frequencies of all alleles not matching the outgroup will
-            * treated as the derived allele frequency (for orientable
-            * sites).
-            * 
-            * \param ignoreFrequency removes sites that are polymorph
-            * because of an allele at absolute frequency smaller than or
-            * equal to this value. If ignoreFrequency=1, no sites are
-            * removed, if ignoreFrequency=1, singleton sites are
-            * ignored. Such sites are completely removed from the
-            * analysis (not counted in lseff). Note that if more than
-            * one mutation is allowed, the site is removed only if all
-            * the alleles but one are smaller than or equal to this
-            * value. For example, an alignment column AAAAAAGAAT is
-            * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is
-            * conserved (including the third allele T which is a
-            * singleton).
-            * 
-            * \param characterMapping a string giving the list of
-            * characters that should be considered as valid data. If a
-            * space is present in the string, the characters left of the
-            * space will be treated as valid data and the characters
-            * right of the space will be treated as missing data, that
-            * is tolerated but ignored. All characters not in the string
-            * will cause an EggInvalidCharacterError to be raised.
-            * 
-            */
-            void load(CharMatrix& data,
-                bool allowMultipleMutations=false,
-                unsigned int ignoreFrequency=0,
-                std::string characterMapping=dnaMapping
-            );
-            
-            /// Number of distinct haplotypes
-            unsigned int K() const;
-            
-            /// Haplotype diversity (unbiased)
-            double He() const;
-            
-            /** \brief Returns the allele number of a given sequence
-             * 
-             * The passed index must be given ignoring any outgroup
-             * sequence.
-             * 
-             */
-            unsigned int haplotypeIndex(unsigned int) const;
-            
-            /// Population differenciation, based on nucleotides (Hudson 1992a)
-            double Kst() const;
-
-            /// Population differenciation, based on nucleotides (Hudson 1992b)
-            double Fst() const;
-
-            /// Population differenciation, based on haplotypes (Nei version)
-            double Gst() const;
-
-            /// Population differenciation, based on haplotypes (Hudson et al. version)
-            double Hst() const;
-            
-            /// Hudson's Snn (nearest neighbor statistics)
-            double Snn() const;
-
-
-        protected:
-        
-            void init();
-            void clear();
-                        
-            inline unsigned int diff(CharMatrix& data, unsigned int ind1, unsigned int ind2) const;
-
-            bool m_loaded;
-            unsigned int m_K;
-            double m_He;
-            double m_Kst;
-            double m_Fst;
-            double m_Gst;
-            double m_Hst;
-            double m_Snn;
-            unsigned int *m_haplotypeIndex;
-
-
-        private:
-        
-            HaplotypeDiversity(const HaplotypeDiversity& source) {
-                
-            }
-            
-            HaplotypeDiversity& operator=(const HaplotypeDiversity& source) {
-                return *this;
-            }
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/LinkageDisequilibrium.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/LinkageDisequilibrium.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,233 +0,0 @@
-/*
-    Copyright 2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_LINKAGEDISEQUILIBRUM_HPP
-#define EGGLIB_LINKAGEDISEQUILIBRUM_HPP
-
-
-#include "BaseDiversity.hpp"
-#include "EggException.hpp"
-
-
-namespace egglib {
-
-   /** \brief Analyzes linkage disequilibrium per pair of polymorphic sites
-    *
-    * \ingroup polymorphism
-    * 
-    * The class considers an alignment and detects polymorphic sites
-    * using the BaseDiversity functionality (shared with other classes
-    * of the module). Only sites with exactly two alleles are
-    * considered. Statistics of pairwise linkage disequilibrium can
-    * be accessed by pair index (note that out-of-range errors are not
-    * checked). Population labels are ignored (but outgroups are
-    * excluded from the analysis).
-    *
-    */
-    class LinkageDisequilibrium : public BaseDiversity {
-
-      public:
-
-        /// Default constructor
-        LinkageDisequilibrium();
-
-        /// Destructor
-        virtual ~LinkageDisequilibrium();
-
-       /** \brief Analyzes polymorphic sites of an alignment
-        * 
-        * \param data an alignment object (subclass of CharMatrix).
-        * The presence of outgroup or of different populations will
-        * be detected based on the populationLabel members of the
-        * passed object. The populationLabel 999 will be interpreted
-        * as outgroups. If several outgroups are passed, sites were
-        * the outgroups are not consistent will be treated as "non-
-        * orientable".
-        * 
-        * \param minimumExploitableData site where the non-missing
-        * data (as defined by characterMapping) are at a frequency
-        * larger than this value will be removed from the analysis.
-        * Use 1. to take only 'complete' sites into account and 0.
-        * to use all sites.
-        * 
-        * \param ignoreFrequency removes sites that are polymorphic
-        * because of an allele at absolute frequency smaller than or
-        * equal to this value. If ignoreFrequency=1, no sites are
-        * removed, if ignoreFrequency=1, singleton sites are
-        * ignored. Such sites are completely removed from the
-        * analysis (not counted in lseff). Note that if more than
-        * one mutation is allowed, the site is removed only if all
-        * the alleles but one are smaller than or equal to this
-        * value. For example, an alignment column AAAAAAGAAT is
-        * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is
-        * conserved (including the third allele T which is a
-        * singleton).
-        * 
-        * \param characterMapping a string giving the list of
-        * characters that should be considered as valid data. If a
-        * space is present in the string, the characters left of the
-        * space will be treated as valid data and the characters
-        * right of the space will be treated as missing data, that
-        * is tolerated but ignored. All characters not in the string
-        * will cause an EggInvalidCharacterError to be raised.
-        */
-        void load(CharMatrix& data,
-                double minimumExploitableData=1.,
-                unsigned int ignoreFrequency=0,
-                std::string characterMapping=dnaMapping);
-    
-    
-        /// Number of pairs contained in the instance
-        unsigned int numberOfPairs() const;
-
-        /// Alignment distance between a given pair
-        int d(unsigned int pair_index);
-
-        /// D statistic for a given pair
-        double D(unsigned int pair_index);
-
-        /// D' statistic for a given pair
-        double Dp(unsigned int pair_index);
-
-        /// r statistic for a given pair
-        double r(unsigned int pair_index);
-
-        /// r2 statistic for a given pair
-        double r2(unsigned int pair_index);
-
-        /// position of the first site for a given pair
-        unsigned int site1(unsigned int pair_index);
-
-        /// position of the second site for a given pair
-        unsigned int site2(unsigned int pair_index);
-
-        /// correlation coefficient between r2 and distance
-        double correl() const;
-        
-       /** \brief Computes the minimal number of recombination events
-        * 
-        * The computation is performed as described in Hudson, RR and
-        * NL Kaplan. 1985. Statistical properties of the number of
-        * recombination events in the history of a sample of DNA
-        * sequences. Genetics 111: 147-164. The returned parameter is
-        * the minimal number of recombination events, given by the
-        * number of non-overlapping pairs of segregating sites violating
-        * the rule of the four gamete. Only sites with two alleles are
-        * considered. Note that homoplasy (multiple mutations) mimicks
-        * recombination. The result of this function is not stored
-        * in this instance, and re-computed at each call.
-        * 
-        * \param data the same CharMatrix instance as passed to the load
-        * method. The instance must not have been modified.
-        * 
-        */
-        unsigned int Rmin(CharMatrix& data) const;
-
-
-
-      protected:
-      
-        // adds a pair of polymorphic sites
-        // assume position2>position1,
-        //  sites are polymorphic with exactly 2 alleles
-        void add(CharMatrix& data, unsigned int position1, unsigned int position2);
-
-        // Constructor help
-        void init();
-                
-        // Destructor helper
-        void clear();
-        
-        // Resizes arrays
-        void reset();
-        
-        // Small helper
-        inline double min(double a, double b) { return (a>b)?a:b;}
-
-        // Small helper
-        inline double max(double a, double b) { return (a>b)?b:a;}
-
-        // Small helper
-        inline void check(unsigned int pos) {  if (pos>=_n) throw EggRuntimeError("tried to access an invalid index"); }
-
-       /* Performs correlation
-        *
-        * This function works independently from the rest of the class.
-        *
-        * \param n length of data arrays.
-        * \param x first data vector.
-        * \param y second data vector.
-        * \param r variable to receive the correlation coefficient.
-        * \param a variable to receive the regression slope.
-        */
-        static void _correl(unsigned int n, const int* x, const double* y, double& r, double& a);
-
-        // Distance between pairs
-        int* _d;
-        
-        // D (classical) measure of LD
-        double *_D;
-        
-        // D'
-        double *_Dp;
-        
-        // r, correlation coefficient
-        double *_r;
-        
-        // square r
-        double *_r2;
-        
-        // Data array (not managed by the instance)
-        unsigned int *_site1;
-
-        // Data array (not managed by the instance)
-        unsigned int *_site2;
-        
-        // Number of pairs
-        unsigned int _n;
-
-     private:
-     
-        /// Copy constructor not available
-        LinkageDisequilibrium(const LinkageDisequilibrium&) { }
-
-        /// Assignment operator not available
-        LinkageDisequilibrium& operator=(const LinkageDisequilibrium&) {
-            return *this;
-        }
-
-
-        class Interval {
-            public:
-                Interval(unsigned int, unsigned int);
-                unsigned int a() const;
-                unsigned int b() const;
-                bool good() const;
-                void set_false();
-            private:
-                unsigned int _a;
-                unsigned int _b;
-                unsigned int _good;
-        };
-
-
-  };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/MicrosatelliteDiversity.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/MicrosatelliteDiversity.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-/*
-    Copyright 2008-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_MICROSATELLITEDIVERSITY_HPP
-#define EGGLIB_MICROSATELLITEDIVERSITY_HPP
-
-#include "DataMatrix.hpp"
-#include <cstdlib>
-
-namespace egglib {
-
-   /** \brief Analyzes microsatellite data
-    *
-    * \ingroup polymorphism
-    * 
-    * Use the load() method to analyze data. All sites will be analyzed
-    * and accessors allow to access the value of a given statistics for
-    * a given site. There is no out-of-bound checking implemented in
-    * accessors.
-    * 
-    */
-    class MicrosatelliteDiversity {
-        
-          public:
-            
-           /** \brief Creates an object
-            * 
-            */
-            MicrosatelliteDiversity();
-            
-            
-           /** \brief Destroys an object
-            * 
-            */
-            virtual ~MicrosatelliteDiversity();
-
-
-           /** \brief Performs the analysis
-            *
-            * \param dataMatrix the object to analyze.
-            * 
-            * \param missingData the integer identifying missing data.
-            * 
-            * \param noMissingData if true, no allele will be
-            * excluded (including the one identified by the argument
-            * missingData).
-            * 
-            */
-            void load(const DataMatrix& dataMatrix,
-                    int missingData=999, bool noMissingData=false);
-            
-            
-            /// Number of sites (or markers)
-            unsigned int numberOfSites() const;
-            
-            /// Heterozygosity
-            double He(unsigned int siteIndex) const;
-            
-            /// Number of alleles
-            unsigned int numberOfAlleles(unsigned int siteIndex) const;
-            
-            /// Variance of allele size
-            double sizeVariance(unsigned int siteIndex) const;
-            
-            /// IAM-based estimator of theta
-            double thetaAssumingIAM(unsigned int siteIndex) const;
-            
-            /// SMM-based estimator of theta, calculated from He
-            double thetaAssumingSMMfromHe(unsigned int siteIndex) const;
-
-            /// SMM-based estimator of theta, calculated from VarSize
-            double thetaAssumingSMMfromSizeVariance(unsigned int siteIndex) const;
-            
-            
-        protected:
-        
-            unsigned int  v_numberOfSites;
-            double       *v_He;
-            unsigned int *v_numberOfAlleles;
-            double       *v_sizeVariance;
-            double       *v_thetaAssumingIAM;
-            double       *v_thetaAssumingSMMfromHe;
-            double       *v_thetaAssumingSMMfromSizeVariance;
-            
-            void init();
-            void clear();
-        
-        
-        private:
-        
-        
-            /// No copy allowed
-            MicrosatelliteDiversity(const MicrosatelliteDiversity& source) {
-            }
-            
-            /// No copy allowed
-            MicrosatelliteDiversity& operator=(const MicrosatelliteDiversity& source) {
-                return *this;
-            }
-        
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Ms.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Ms.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,199 +0,0 @@
-/*
-    Copyright 2008,2009,2011 Stéphane De Mita and Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_GMS_HPP
-#define EGGLIB_GMS_HPP
-
-#include "DataMatrix.hpp"
-#include <string>
-#include <istream>
-
-namespace egglib {
-
-    /** \brief ms-like sequence format parser
-     * 
-     * The class provides parsing (input) and formatting (output)
-     * operations in ms format, that is the format used by Richard
-     * Hudson's program ms for outputting genotypes and by the
-     * associated program samplestat for reading them. Both types of
-     * operations are available through static methods using either
-     * a string or a stream (which can be a stream to or from a file
-     * or a string). In either case, types from the STL are used.
-     * Although ms deals only with data coded with 0 and 1, the class Ms
-     * offers the possibility of both importing and exporting data coded
-     * with by integer. All methods have an option named "separated". If
-     * this option is true, the parser or formatter introduces a slight
-     * modification of the format: genotypes individual data are
-     * separated by a white space ("1 0 1 1" instead of "1011", allowing
-     * genotype values larger than 9: "1 0 11 1").
-     *
-     * \ingroup core
-     *
-     */
-     class Ms {
-
-      public:
-         
-       /** \brief Imports a sequence alignment
-        * 
-        * Creates a istringstream from the string and calls the
-        * overloaded method.
-        * 
-        * \param str the string to parse.
-        * \param ns the expected number of sequences.
-        * \param separated true if a white space separator is placed
-        * between genotype at each site.
-        *
-        * \return A sequence alignment as a data matrix.
-        */
-        static DataMatrix get(std::string, unsigned int ns, bool separated=false);
-
-
-       /** \brief Imports a sequence alignment
-        * 
-        * Attemps to generate a DataMatrix object from the stream.
-        * Reads only one simulation and throws a SeqlibFormatError
-        * exception in case of format error.
-        * 
-        * Allows any number of white lines before the //, but no other
-        * data. Supports \r at the end of lines (before the \n).
-        * Accepted symbols are all integers (0-9).
-        *
-        * \param stream the stream to parse.
-        * \param ns the expected number of sequences.
-        * \param separated true if a white space separator is placed
-        * between genotype at each site.
-        * 
-        * \return A sequence alignment as a data matrix.
-        */
-        static DataMatrix get(std::istream& stream, unsigned int ns, bool separated=false);
-
-
-       /** \brief Exports a sequence alignment
-        * 
-        * Internally creates a stringstream, calls the overloaded method
-        * and returns the outcome.
-        *
-        * \param dataMatrix the alignment object to write.
-        * \param separated true if a white space separator must be placed
-        * between the genotype at each site.
-        * 
-        */
-        static std::string format(DataMatrix& dataMatrix, bool separated=false);
-        
-        
-       /** \brief Exports a sequence alignment
-        * 
-        * Writes the formatted string to the stream 'on the fly'. The
-        * formatted string is guaranteed to starts with a // line and
-        * ends with an empty line. The client is expected to take care
-        * of writing any header and add an additional white line between
-        * simulations if needed. The method throws a SeqlibRuntimeError
-        * if the stream is not writable. The data matrix should contain
-        * only data within range 0-9 if separated is false (default) and
-        * any positive (>=0) integer if separated is true. Note that
-        * output generated with separated=true is never compatible with
-        * the original ms format, and that output generated with
-        * separator=false is compatible with the original ms format only
-        * if all alleles are 0 or 1 (which is not checked by this
-        * formatted).
-        * 
-        * \param stream the stream (file or string stream) where to
-        * write the output.
-        * \param dataMatrix the alignment object to write.
-        * \param separated true if a white space separator must be placed
-        * between the genotype at each site.
-        * 
-        */
-        static void format(std::ostream& stream, DataMatrix& dataMatrix, bool separated=false);
-
-
-       /** \brief Returns the last tMRCA read by any Ms instance
-        * 
-        * If a tMRCA value was present in the last simulation read by
-        * any Ms instance, it will be returned by this method. A value
-        * of -1. is returned if no simulation was read, or if the last
-        * simulation didn't contain a tMRCA value or if the last
-        * simulation provoked an exception before reaching the tMRCA
-        * line.
-        * 
-        */
-        static double tMRCA();
-
-
-       /** \brief Returns the last "prob" read by any Ms instance
-        * 
-        * "prob" is returned by ms when a fixed number of segregating
-        * sites is used in conjunction with a theta value. If a "prob"
-        * value was present in the last simulation read by any Ms
-        * instance, it will be returned by this method. A value of -1
-        * is returned if no simulation was read, or if the last
-        * simulation didn't contain a "prob" value or if the last
-        * simulation provoked an exception before reaching the "prob"
-        * line.
-        * 
-        */
-        static double prob();
-    
-
-       /** \brief Returns the tree string found in the last simulation read by any Ms instance
-        * 
-        * If one or more trees were present in the last simulation read
-        * by any Ms instance, they will be returned as a unique string
-        * by this method. An empty string is returned if no simulation
-        * was read, or if the last simulation, or if the last simulation
-        * didn't contain any tree value or if the last simulation
-        * provoked an exception before reaching the tree line.
-        * 
-        * Note: the trees are returned as a single line.
-        * 
-        */
-        static std::string trees();
-
-         
-      private:
-        // Line parser (the last \n is extracted and discarded - no error upon EOF)
-        std::string next_line(std::istream& stream);
-        
-        /// tMRCA (-1 if not found in ms output)
-        static double _tMRCA;
-        
-        /// probability (-1 if not found in ms output)
-        static double _prob;
-        
-        /// tree string (maybe contain several trees) (empty string if not found in ms output)
-        static std::string _trees;
-
-        
-        /// No instantiation allowed
-        Ms() { }
-        
-        /// A fortiori no destruction allowed
-        ~Ms() { }
-
-        /// No copy allowed
-        Ms(const Ms&) { }
-
-        /// No copy allowed
-        Ms& operator=(const Ms&) { return *this; }
-                
-    };
-}
-    
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Mutation.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Mutation.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_MUTATION_HPP
-#define EGGLIB_MUTATION_HPP
-
-#include <vector>
-#include "Edge.hpp"
-
-namespace egglib {
-
-   /** \brief Very simple container of some information relative to a mutation
-    * 
-    * \ingroup coalesce
-    *
-    */
-    class Mutation {
-
-        public:
-    
-            /// Default constructor
-            Mutation();
-            
-            /// Age
-            //double age;
-            
-            /// Mutation index (for finding in Edge)
-            unsigned int actualSiteIndex;
-            
-            /// Position
-            double position;
-            
-            /// Segment index
-            unsigned int segmentIndex;
-            
-            /// Pointer to edge
-            //const Edge* edge;
-            
-        private:
-        
-            void init();
-
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Mutator.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Mutator.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,397 +0,0 @@
-/*
-    Copyright 2009, 2010, 2012 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_MUTATOR_HPP
-#define EGGLIB_MUTATOR_HPP
-
-
-#include "DataMatrix.hpp"
-#include "Random.hpp"
-#include "Arg.hpp"
-#include "Mutation.hpp"
-
-
-namespace egglib {
-    
-
-   /** \brief Implements mutation models
-    *
-    * \ingroup coalesce
-    * 
-    * Works with a previously built Ancestral Reconbination Graph. The
-    * user must sets options using the setter-based interface. After
-    * that he or she can call the method mute() that will generates
-    * a DataMatrix object.
-    * 
-    * Genotype data are represented by integer numbers. Regardless of
-    * the mutation model, the ancestral state is always 0. The user can
-    * set the rate of mutation (or, alternatively, fix the number of
-    * mutations that occurred - which is the number of segregating sites
-    * only with an infinite site model).
-    * 
-    * Other options fall into two separate groups: the positions of the
-    * mutated sites and the process of mutation (how new alleles are
-    * generated).
-    * 
-    * Concerning allele generation, several mutation models are available
-    * (coded by single letters):
-    *   - F: fixed number of alleles. Among other markers, this model is
-    *        appropriate for simulating nucleotides. The user is able
-    *        to choose the number of alleles (where 2 is the standard
-    *        for an infinite site model and 4 for a finite site model).
-    *        Mutator allows assigning independent weights between all
-    *        different transition types and can draw randomly the
-    *        ancestral states, providing a way to emulate evolution of
-    *        nucleotides with multiple mutations at the same site and
-    *        reversion.
-    *   - I: infinite number of alleles. At a given site, each mutation
-    *        raises a new allele. The value of the alleles is therefore
-    *        irrelevant (it only denotes its order of appearance). This
-    *        model does not permit homoplasy.
-    *   - S: stepwise mutation model. In this model the value of the
-    *        alleles are interpreted as a size (typically for simulating
-    *        a microsatellite marker). Each mutation either increases
-    *        or decreases the allele size by an increment of one.
-    *   - T: two-phase mutation model. This model is a generalization
-    *        of the stepwise mutation model (S). For a mutation, the
-    *        increment (either increase or decrease) is 1 with the
-    *        probability given by the parameter (1-TPMproba). With
-    *        probability TPMproba, the increment is drawn from a
-    *        geometric distribution of parameter given by the other
-    *        parameter (TPMparam).
-    * 
-    * By default, the program will assume an infinite site model (ISM).
-    * Each mutation will occur to a new position drawn from the interval
-    * [0,1]. It is possible to set any mutation model with an ISM 
-    * (including microsatellite-like models I, S and T). Alternatively,
-    * the user can specify a finite number of sites available for
-    * mutation. For a microsatellite marker, the user will want to
-    * specify a single site. It is possible to set a finite number of
-    * sites for all mutation models. In all cases, the mutations will
-    * be forced to target these sites. It is possible to apply weights
-    * independently to all sites. The higher the weight value
-    * (comparatively to the other sites), the higher the probability
-    * that this site mutes. The weights needs not to be relative. In
-    * addition, the user can set the positions of the different sites.
-    * Nothings forces him or her to place them in order. Note that this
-    * does not affect the mutation process, but on the amount of
-    * recombination that will be allowed between sites.
-    *
-    */
-    class Mutator {
-
-        public:
-        
-           /** \brief Initializes with default values
-            * 
-            * List of default values:
-            *   - theta = 0
-            *   - fixedNumberOfMutations = 0
-            *   - model = F (fixed number of alleles)
-            *   - fixed number of alleles = 2
-            *   - infinite site model
-            *   - TPM parameters are both preset to 0.5
-            * 
-            */
-            Mutator();
-
-            
-           /** \brief Destroys the object
-            * 
-            */
-            ~Mutator();
-            
-            
-           /** \brief Copy constructor
-            * 
-            */
-            Mutator(const Mutator&);
-        
-        
-           /** \brief Assignement operator
-            * 
-            */
-            Mutator& operator=(const Mutator&);
-
-
-           /** \brief Restores default values of all parameters
-            * 
-            */
-            void reset();
-            
-            
-           /** \brief Gets the fixed number of mutations
-            * 
-            */
-            unsigned int fixedNumberOfMutations() const;
-        
-
-           /** \brief Sets the fixed number of mutations
-            * 
-            * The value can be 0. It is not allowed to set both the
-            * fixed number of mutations and the mutation rate at
-            * non-zero value
-            * 
-            */
-            void fixedNumberOfMutations(unsigned int);
-
-
-           /** \brief Gets the mutation rate
-            * 
-            */
-            double mutationRate() const;
-        
-        
-           /** \brief Sets the mutation rate
-            * 
-            * The value cannot be negative. The value can be 0.  It is
-            * not allowed to set both the fixed number of mutations and
-            * the mutation rate at non-zero value
-            * 
-            */
-            void mutationRate(double);
-
-
-           /** \brief Gets the mutation model
-            * 
-            * See the class documentation for the signification of the
-            * different one-letter codes.
-            * 
-            */
-            char mutationModel() const;
-            
-            
-           /** \brief Sets the mutation model
-            * 
-            * The passed character must be one of F, I, S and T. See the
-            * class documentation for their signification.
-            * 
-            */
-            void mutationModel(char);
-            
-            
-           /** \brief Gets the fixed number of possible alleles
-            * 
-            */
-            unsigned int numberOfAlleles() const;
-           
-            
-           /** \brief Sets the fixed number of possible alleles
-            * 
-            * The value must be larger than 1. This parameter is
-            * meaningful only for the fixed number allele model of
-            * mutation, and ignored otherwise.
-            *
-            */
-            void numberOfAlleles(unsigned int);
-           
-           
-           /** \brief Sets a transition weight
-            * 
-            * \param i row (previous allele index).
-            * \param j column (next allele index).
-            * \param value weight to apply.
-            * 
-            * Indices i and j must be different. Weights can be any
-            * strictly positive value.
-            * 
-            */
-            void transitionWeight(unsigned int i, unsigned int j, double value);
-
-
-           /** \brief Gets a transition weight
-            * 
-            * \param i row (previous allele index).
-            * \param j column (next allele index).
-            * 
-            * Indices i and j must be different.
-            * 
-            */
-            double transitionWeight(unsigned int i, unsigned int j);
-            
-            
-           /** \brief Set to true to draw ancestral alleles randomly
-            * 
-            * By default, the ancestral allele is always 0. If this
-            * variable is set to true, the ancestral allele will be
-            * randomly drawn from the defined number of alleles. This
-            * option is always ignored unless in combination with the
-            * Fixed Allele Number model.
-            * 
-            */
-            void randomAncestralAllele(bool flag);
-
-            
-            /** \brief true if ancestral alleles must be drawn randomly
-             * 
-             */
-            bool randomAncestralAllele() const;
-
-           
-           /** \brief Gets the TPM probability parameter
-            * 
-            */
-            double TPMproba() const;
-            
-            
-           /** \brief Sets the TPM probability parameter
-            * 
-            * This parameter is considered only if the mutation model
-            * is T (two-phase mutation model). It gives the probability
-            * that a mutation step is not fixed to be 1. If TPMproba is
-            * 0, the mutation model is SMM.
-            * 
-            * The value must be >=0. and <=1. 
-            * 
-            */
-            void TPMproba(double value);
-           
-            
-           /** \brief Gets the TPM distribution parameter
-            * 
-            */
-            double TPMparam() const;
-            
-            
-           /** \brief Sets the TPM distribution parameter
-            * 
-            * This parameter is considered only if the mutation model
-            * is T (two-phase mutation model). It gives the parameter
-            * of the geometric distribution which is used to generate
-            * the mutation step (if it is not one).
-            * 
-            * The value must be >=0. and <=1. 
-            * 
-            */
-            void TPMparam(double value);
-
-
-           /** \brief Gets the number of mutable sites
-            * 
-            * A value a zero must be interpreted as the infinite site
-            * model. Note that after all calls all data from the tables
-            * sitePositions and siteWeights will be reset.
-            * 
-            */
-            unsigned int numberOfSites() const;
-           
-            
-           /** \brief Sets the number of mutable sites
-            * 
-            * The value of zero is accepted and imposed the infinite
-            * site model.
-            * 
-            */
-            void numberOfSites(unsigned int);
-            
-            
-           /** \brief Gets the position of a given site
-            * 
-            */
-            double sitePosition(unsigned int siteIndex) const;
-
-            
-           /** \brief Set the position of a given site
-            * 
-            * The position must be >=0 and <=1
-            * 
-            */
-            void sitePosition(unsigned int siteIndex, double position);
-
-
-           /** \brief Gets the mutation weight of a given site
-            * 
-            */
-            double siteWeight(unsigned int siteIndex) const;
-
-            
-           /** \brief Set the site weight of a given site
-            * 
-            * The weight must be strictly positive.
-            * 
-            */
-            void siteWeight(unsigned int siteIndex, double weight);
-
-
-           /** \brief Performs mutation
-            * 
-            * \param arg Ancestral recombination graph instance. If the
-            * ARG is partially built or not a all, or improperly so,
-            * the behaviour of this method is not defined.
-            * 
-            * \param random The address of a Random instance to be
-            * used for generating random numbers.
-            * 
-            * \return A DataMatrix instance containing simulated data.
-            * 
-            */
-            DataMatrix mute(Arg* arg, Random* random);
-
-
-          /** \brief Gets the last number of mutations
-            *
-            * Returns the number of mutations of the last call of mute( ).
-            * By default, this method returns 0.
-            *
-            */
-            unsigned int numberOfMutations() const; 
-
-
-        private:
-        
-            void clear();
-            void init();
-            void copy(const Mutator&);
-
-            //int nextAllele(int allele, Random* random);
-            int TPMstep(double inTPMproba, Random* random);
-            void apply_mutation(unsigned int matrixIndex,
-                                unsigned int actualSite, DataMatrix& data,
-                                const Edge* edge, int allele,
-                                unsigned int segment, Random* random);
-
-        
-            char _model;
-            double _mutationRate;
-            unsigned int _fixedNumberOfMutations;
-            unsigned int _numberOfAlleles;
-            double** _transitionWeights;
-            bool _randomAncestralAllele;
-            unsigned int _numberOfSites;
-            double* _sitePositions;
-            double* _siteWeights;
-            double _TPMproba;
-            double _TPMparam;
-            int maxAllele;
-            unsigned int _numberOfMutations;
-            std::vector<Mutation> _cache_mutations;
-            unsigned int _cache_mutations_reserved;
-
-    };
-
-
-    bool compare(Mutation mutation1, Mutation mutation2); // returns True if mutation1 is older
-
-}
-
-
-
-
-#endif
-
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/NucleotideDiversity.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/NucleotideDiversity.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,377 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_NUCLEOTIDEDIVERSITY_HPP
-#define EGGLIB_NUCLEOTIDEDIVERSITY_HPP
-
-
-#include "BaseDiversity.hpp"
-#include <string>
-#include <vector>
-
-
-
-namespace egglib {
-
-
-   /** \brief Performs analyzes of population genetics
-    *
-    * \ingroup polymorphism
-    * 
-    * This class computes several summary statistics based on
-    * nucleotide analysis. Note that it is possible to use the same
-    * object to analyze different data set. Calling the load() method
-    * erases all data preivously computed (if any). Calling the load()
-    * method is absolutely required to compute any statistics. Some
-    * statistics are not computed by default, but are if the
-    * corresponding accessor is used (only load() is required).
-    * 
-    * Note that "unsecure" accessors don't perform out-of-bound checks.
-    * 
-    * S is the number of varying sites (only in sites that were not
-    * rejected).
-    * 
-    * eta is the minimum number of mutations, that is the sum of the
-    * number of alleles minus 1 for each varying site. eta = S if all
-    * sites have no variant or 2 alleles. eta is computed independently
-    * of the option multiple and IS NOT computed over lseff sites.
-    *
-    * Pi is the average number of pairwise differences between sequences
-    * (expressed here per site) or (as computed here) the mean per site
-    * (unbiased) heterozygosity. Pi is zero if no polymorphic sites.
-    *
-    * D is the Tajima's test of neutrality
-    * Ref. Tajima F.: Statistical method for testing the neutral
-    * mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
-    * It is arbitrary set to 0 if no polymorphic sites.
-    *
-    * tW: thetaW: estimator of theta based on polymorphic sites (ref.
-    * e.g. Watterson 1975 Theor. Pop. Biol.).
-    * Both D and thetaW are computed assuming that rounded nseff samples
-    * have been sampled.
-    * The variance of D is computed using rounded nseff instead of ns.
-    *
-    * H is the Fay and Wu's test of neutrality.
-    * Z is the standardized version and E a similar test.
-    * Ref. Fay J. C., Wu C.-I.: Hitchhiking under positive Darwinian
-    * selection. Genetics 2000, 155:1405-1413. and Zeng K., Fu Y. X.,
-    * Shi S., Wu C.-I.: Statistical tests for detecting positive
-    * selection by utilizing high-frequency variants. Genetics 2006,
-    * 174:1431-9. Both are arbitrary set to 0 if no polymorphic or
-    * orientable sites.
-    *
-    * tH and tL: theta H: estimators of theta based on derived
-    * polymorphic sites (ref in Fay and Wu and Zeng al.). The variance
-    * of H/Z are computed assuming that rounded nseff samples have
-    * been sampled.
-    * 
-    */
-    class NucleotideDiversity : public BaseDiversity {
-
-        public:
-
-           /** \brief Builds an object
-            * 
-            */
-            NucleotideDiversity();
-
-
-           /** \brief Destroys an object
-            * 
-            */
-            virtual ~NucleotideDiversity();
-
-
-           /** \brief Identifies polymorphic sites and computes basis
-            * statistics
-            * 
-            * \param data an alignment object (subclass of CharMatrix).
-            * The presence of outgroup or of different populations will
-            * be detected based on the populationLabel members of the
-            * passed object. The populationLabel 999 will be interpreted
-            * as outgroups. If several outgroups are passed, sites were
-            * the outgroups are not consistent will be treated as "non-
-            * orientable".
-            * 
-            * \param allowMultipleMutations if true, sites with more
-            * than two alleles will not be ignored. The sum of the
-            * frequencies of all alleles not matching the outgroup will
-            * treated as the derived allele frequency (for orientable
-            * sites).
-            * 
-            * \param minimumExploitableData sites where the non-missing
-            * data (as defined by characterMapping) are at a frequency
-            * larger than this value will be removed from the analysis.
-            * Use 1. to take only 'complete' sites into account and 0.
-            * to use all sites. (The outgroup is not considered in this
-            * computation.)
-            * 
-            * \param ignoreFrequency removes sites that are polymorph
-            * because of an allele at absolute frequency smaller than or
-            * equal to this value. If ignoreFrequency=1, no sites are
-            * removed, if ignoreFrequency=0, singleton sites are
-            * ignored. Such sites are completely removed from the
-            * analysis (not counted in lseff). Note that if more than
-            * one mutation is allowed, the site is removed only if all
-            * the alleles but one are smaller than or equal to this
-            * value. For example, an alignment column AAAAAAGAAT is
-            * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is
-            * conserved (including the third allele T which is a
-            * singleton).
-            * 
-            * \param characterMapping a string giving the list of
-            * characters that should be considered as valid data. If a
-            * space is present in the string, the characters left of the
-            * space will be treated as valid data and the characters
-            * right of the space will be treated as missing data, that
-            * is tolerated but ignored. All characters not in the string
-            * will cause an EggInvalidCharacterError to be raised.
-            * 
-            * \param useZeroAsAncestral if true, all outgroups (if
-            * present) will be ignored and the character "0" will be
-            * considered as ancestral for all sites, whatever the
-            * character mapping.
-            * 
-            */
-            virtual void load(
-                CharMatrix& data,
-                bool allowMultipleMutations=false,
-                double minimumExploitableData=1.,
-                unsigned int ignoreFrequency=0,
-                std::string characterMapping=dnaMapping,
-                bool useZeroAsAncestral=false
-            );
-
-
-        // accessors for the "site analysis" section
-
-            /// Number of polymorphic sites
-            unsigned int S() const;
-            
-            /// Number of polymorphic orientable sites
-            unsigned int So() const;
-            
-            /// Minimum number of mutations
-            unsigned int eta() const;
-            
-            /// Average of per-site number of sequences effectively used
-            double nseff() const;
-            
-            /// Number of sites effectively used
-            unsigned int lseff() const;
-            
-            /// Average of number of sequences effectively used at orientable sites
-            double nseffo() const;
-            
-            /// Number of orientable sites
-            unsigned int lseffo() const;
-            
-            /// Number of detected populations
-            unsigned int  npop() const;
-            
-            /// Label of the population with given index (unsecure)
-            unsigned int popLabel(unsigned int popIndex) const; // no check!
-
-
-        // accessors for the "diversity" section
-
-            /// Nucleotide diversity
-            double Pi();
-            
-            /// Watterson estimator of theta
-            double thetaW();
-            
-            /// Average of Pi over populations
-            double average_Pi();
-            
-            /// Pi of a given population (unsecure)
-            double pop_Pi(unsigned int popIndex);  // no check!
-            
-            /// Tajima's D
-            double D();
-
-        // accessors for the "outgroup diversity" section
-        
-            /// Fay and Wu estimator of theta
-            double thetaH();
-            
-            /// Zeng et al. estimator of theta
-            double thetaL();
-            
-            /// Fay and Wu's H
-            double H();
-            
-            /// Standardized H
-            double Z();
-            
-            /// Zeng et al.'s E
-            double E();
-
-         // accessors for the "differentiation" section
-         
-            /// Number of sites with at least one fixed difference
-            unsigned int FixedDifferences();
-            
-            /// Number of sites with at least one allele shared among at least two populations
-            unsigned int CommonAlleles();
-            
-            /// Number of sites with at least one non-fixed allele shared among at least two populations
-            unsigned int SharedAlleles();
-            
-            /// Number of sites with at least one allele specific to one population
-            unsigned int SpecificAlleles();
-            
-            /// Number of sites with at least one derived allele specific to one population
-            unsigned int SpecificDerivedAlleles();
-            
-            /// Number of polymorphisms in a given population (unsecure)
-            unsigned int Polymorphisms(unsigned int pop);
-            
-            /// Number of specific alleles for a given population (unsecure)
-            unsigned int SpecificAlleles(unsigned int pop);
-            
-            /// Number of specific derived allele for a given population (unsecure)
-            unsigned int SpecificDerivedAlleles(unsigned int pop);
-            
-            /// Number of fixed differences between a given pair of populations (unsecure; pop2 must be larger than pop1)
-            unsigned int FixedDifferences(unsigned int pop1, unsigned int pop2);
-
-            /// Number of common alleles between a given pair of populations (unsecure; pop2 must be larger than pop1)
-            unsigned int CommonAlleles(unsigned int pop1, unsigned int pop2);
-
-            /// Number of shared non-fixed alleles between a given pair of populations (unsecure; pop2 must be larger than pop1)
-            unsigned int SharedAlleles(unsigned int pop1, unsigned int pop2);
-
-
-        // accessor for the "triConfigurations" section
-
-           /** \brief Number falling into one of the possible site configurations
-            *
-            * The statistics are limited to three populations.
-            * Assuming an unrooted A/G polymorphism (A and G can be
-            * substitued), the site configurations are:
-            *     -  0: A&G  A   A  specific 1
-            *     -  1: A&G  A   G  specific 1 + fixed 2-3
-            *     -  2:  A  A&G  A  specific 2
-            *     -  3:  A  A&G  G  specific 2 + fixed 1-3
-            *     -  4:  A   A  A&G specific 3
-            *     -  5:  A   G  A&G specific 3 + fixed 1-2
-            *     -  6: A&G A&G  A  shared 1-2
-            *     -  7: A&G  A  A&G shared 1-3
-            *     -  8:  A  A&G A&G shared 2-3
-            *     -  9: A&G A&G A&G shared 1-2-3
-            *     - 10:  A   G   G  fixed 1
-            *     - 11:  A   G   A  fixed 2
-            *     - 12:  A   A   G  fixed 3
-            *
-            * \param index must be an index from 0 to 12.
-            * 
-            */
-            unsigned int triConfiguration(unsigned int index);
-
-
-        /// Builds and returns the vector of positions of all polymorphic sites
-        std::vector<unsigned int> polymorphic_positions() const;
-
-
-        /** \brief Builds and returns the vector of positions of all singleton sites
-         * 
-         * A site singleton when it is polymorphic according to
-         * parameter of the diversity analysis, when it has exactly two
-         * alleles and one of them is at absolute frequency 1 (one
-         * copy) disregarding the outgroup.
-         * 
-         */
-        std::vector<unsigned int> singleton_positions() const;
-
-
-        protected:
-
-           /** \brief This class cannot be copied
-            * 
-            */
-            NucleotideDiversity(const NucleotideDiversity& source) { }
-
-
-           /** \brief This class cannot be copied
-            * 
-            */
-            NucleotideDiversity& operator=(const NucleotideDiversity& source) { return *this; }
-
-
-            void init();  // initializes values
-            void clear();  // free memory but doesn't initializes
-            
-            // diversity (without outgroup)
-            void diversity();
-            
-            // diversity with outgroup
-            void outgroupDiversity();
-            
-            // site patterns
-            void differentiation();
-            
-            // triconfigurations
-            void triConfigurations();
-            
-
-            // holders for statistics, with booleans flagging groups of stats
-            
-            bool b_analysisSites;
-            
-            bool b_diversity;
-            
-            double  v_Pi;             // nucleotide diversity
-            double  v_thetaW;         // theta (Watterson estimator)
-            double  v_average_Pi;     // average diversity across populations
-            double *v_pop_Pi;         // diversity per population
-            double  v_D;              // Tajima's D
-            
-            bool b_outgroupDiversity;
-            
-            double v_thetaH;        // theta (Fay and Wu estimator)
-            double v_thetaL;        // theta (Zeng estimator)
-            double v_H;             // Fay and Wu's H
-            double v_Z;             // normalized Fay and Wu's H
-            double v_E;             // Zeng et al.'s E
-            
-            bool b_differentiation;
-            
-            unsigned int  *v_pairwiseFixedDifferences;
-            unsigned int  *v_pairwiseCommonAlleles;
-            unsigned int  *v_pairwiseSharedAlleles;
-            unsigned int  *v_popPolymorphic;
-            unsigned int  *v_popSpecific;
-            unsigned int  *v_popSpecificDerived;
-            unsigned int   v_countFixedDifferences;
-            unsigned int   v_countCommonAlleles;
-            unsigned int   v_countSharedAlleles;
-            unsigned int   v_countSpecificAlleles;
-            unsigned int   v_countSpecificDerivedAlleles;
-        
-            
-            bool b_triConfigurations;
-            
-            unsigned int  *v_triConfigurations;
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/ParamSet.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/ParamSet.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,279 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_PARAMSET_HPP
-#define EGGLIB_PARAMSET_HPP
-
-
-#include "DataMatrix.hpp"
-
-
-namespace egglib {
-
-    class Change;
-    class Controller;
-
-
-   /** \brief Set of parameters
-    *
-    * \ingroup coalesce
-    *
-    */
-    class ParamSet {
-
-        public:
-    
-           /** \brief Default constructor
-            *
-            * Initializes all parameters to reasonnable values (except
-            * that the sample size is null: 1 population, 0 samples,
-            * selfing rate of 0, recombination rate of 0, growth rate of
-            * 0, population size of 1 and no changes.
-            *
-            */
-            ParamSet();
-
-           /** \brief Destructor
-            * 
-            */
-            ~ParamSet();
-            
-           /** \brief Copy constructor
-            * 
-            */
-            ParamSet(const ParamSet&);
-            
-           /** \brief Assignment operator
-            * 
-            */
-            ParamSet& operator=(const ParamSet&);
-
-           /** \brief Restores default value of all parameters
-            * 
-            */
-            void reset();
-
-           /** \brief Gets the number of populations
-            * 
-            */
-            unsigned int numberOfPopulations() const;
-            
-           /** \brief Gets a pairwise migration rate
-            * 
-            * It is allowed to access a diagonal value. Diagonal
-            * values contain the sum of values of the corresponding
-            * line (diagonal cell excepted, of course).
-            * 
-            */
-            double pairwiseMigrationRate(unsigned int source, unsigned int dest) const;
-            
-           /** \brief Sets a pairwise migration rate
-            * 
-            * It is not allowed to set a value on the diagonal (this
-            * would raise an exception). The method takes care of
-            * modifying the diagonal accordingly (still this is not
-            * relevant for the client);
-            * 
-            */
-            void pairwiseMigrationRate(unsigned int source, unsigned int dest, double value);
-            
-           /** \brief Sets the migration rate for all matrix
-            * 
-            */
-            void migrationRate(double value);
-            
-           /** \brief Gets a population size
-            * 
-            */
-            double populationSize(unsigned int populationIndex) const;
-            
-           /** \brief Sets a population size
-            * 
-            * The size must be strictly positive.
-            * 
-            */
-            void populationSize(unsigned int populationIndex, double value);
-            
-           /** \brief Gets a growth rate
-            * 
-            */
-            double growthRate(unsigned int populationIndex) const;
-            
-           /** \brief Sets a growth rate
-            * 
-            */
-            void growthRate(unsigned int populationIndex, double value);
-            
-           /** \brief Gets the recombination rate
-            * 
-            */
-            double recombinationRate() const;
-            
-           /** \brief Sets the recombination rate
-            * 
-            */
-            void recombinationRate(double value);
-
-           /** \brief Gets the number of recombining segments
-            * 
-            */
-            unsigned int numberOfSegments() const;
-            
-           /** \brief Sets the number of recombining segments
-            * 
-            */
-            void numberOfSegments(unsigned int value);
-
-           /** \brief Gets the selfing rate
-            * 
-            */
-            double selfingRate() const;
-            
-           /** \brief Sets the selfing rate
-            * 
-            */
-            void selfingRate(double value);
-            
-           /** \brief Adds a population to the model
-            * 
-            * \param migr pairwise migration rate between other
-            * population and the new one.
-            *
-            * The parameters for the new population are equivalent to
-            * the default parameters.
-            * 
-            */
-            void addPopulation(double migr);
-            
-           /** \brief Adds a change
-            * 
-            * The change can be of any type derived from Change. A
-            * const Change* must be passed, so ParamSet will neither
-            * modify or delete the object itself. All passed Change
-            * object must be kept available for use by ParamSet.
-            *
-            */
-            void addChange(const Change* change);
-
-           /** \brief Gets the date of the next change
-            * 
-            * Returns -1 if no change is planned.
-            * 
-            */
-            double nextChangeDate() const;
-            
-           /** \brief Applies the next change event
-            * 
-            * \param controller the Change event might need to have
-            * access to simulation controller (to trigger coalescent
-            * events, for example).
-            * 
-            */
-            void nextChangeDo(Controller* controller);
-            
-           /** \brief Gets the number of single sample from a population
-            * 
-            */
-            unsigned int singles(unsigned int populationIndex) const;
-
-           /** \brief Sets the number of single sample from a population
-            * 
-            */
-            void singles(unsigned int populationIndex, unsigned int value);
-
-           /** \brief Gets the number of double sample from a population
-            * 
-            */
-            unsigned int doubles(unsigned int populationIndex) const;
-
-           /** \brief Sets the number of double sample from a population
-            * 
-            */
-            void doubles(unsigned int populationIndex, unsigned int value);
-            
-           /** \brief Computes the total number of samples
-            * 
-            */
-            unsigned int numberOfSamples() const;
-            
-           /** \brief Gives the date of the last size change
-            * 
-            * \param populationIndex the index of the population.
-            * \return The date where the last change occurred, or 0. if
-            * no change occurred during the simulation.
-            *
-            */
-            double dateOfLastChange(unsigned int populationIndex) const;
-
-
-           /** \brief Sets the date of the last size change
-            * 
-            * \param populationIndex the index of the population.
-            * \param date the date where the last change occurred, or 0.
-            * if no change occurred during the simulation.
-            *
-            */
-            void dateOfLastChange(unsigned int populationIndex, double date) const;
-
-            
-           /** \brief Set groups labels
-            * 
-            * Sets the group labels of the DataMatrix, according to the
-            * current state of population structure, and assuming that
-            * the DataMatrix was generated by the class Arg.
-            * 
-            * \param dataMatrix the DataMatrix object to modify. The
-            * number of sequences must match the total number of samples
-            * defined by the ParamSet object this method is called on.
-            * 
-            * \param labelIndividuals by default, labels the different
-            * samples depending on the population they come from (0
-            * being the label of the first population). If this flag is
-            * set to true, then the samples are labelled depending on
-            * the individual they come from, regardless of populations.
-            * In that case there can be only one or two genes for a
-            * given group label.
-            * 
-            */
-            void setGroups(DataMatrix& dataMatrix, bool labelIndividuals=false);
-
-        private:
-
-            void clear();
-            void init();
-            void copy(const ParamSet&);
-        
-            double _selfingRate;
-            double _recombinationRate;
-            unsigned int _numberOfSegments;
-            unsigned int _numberOfPopulations;
-            unsigned int* _singles;
-            unsigned int* _doubles;
-            double* _growthRates;
-            double* _populationSize;
-            double* _dateOfLastChange;
-            double** migrationMatrix;
-            unsigned int _numberOfChanges;
-            unsigned int nextChangeIndex;
-            Change const** changes;
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Population.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Population.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,143 +0,0 @@
-/*
-    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_POPULATION_HPP
-#define EGGLIB_POPULATION_HPP
-
-
-#include "Edge.hpp"
-
-namespace egglib {
-
-    class Random;
-
-   /** \brief Handles a single population
-    *
-    * \ingroup coalesce
-    *
-    */
-    class Population {
-
-        public:
-    
-           /** \brief Default constructor
-            *
-            * Generates an empty population.
-            * 
-            */
-            Population();
-            
-           /** \brief Copy constructor
-            * 
-            */
-            Population(const Population& source);
-            
-           /** \brief Assignment operator
-            * 
-            */
-            Population& operator=(const Population& source);
-            
-           /** \brief Destructor
-            * 
-            * The object only cleans Edge objects currently stored in it.
-            *
-            */
-            ~Population();
-
-           /** \brief Standard constructor
-            * 
-            * The Edge instances will be handled by address and they
-            * MUST be passed using the method set().
-            * 
-            * \param numberOfSegments number of recombining segments.
-            * 
-            * \param numberOfLineages the number of lineages contained
-            * in this population.
-            * 
-            * \param firstIndex the absolute index (or ID) of the first
-            * lineage (the other will have consecutive incremented
-            * ID's).
-            *
-            */
-            Population(unsigned int numberOfSegments,
-                    unsigned int numberOfLineages, unsigned firstIndex);
-
-           /** \brief Gets the number of lineages
-            * 
-            */
-            unsigned int numberOfLineages() const;
-            
-           /** \brief Gets the efficient number of lineages
-            * 
-            * The number of lineages is multiplied by the number of
-            * covered segments of each lineages.
-            * 
-            */
-            unsigned int efficientNumberOfLineages() const;            
-            
-           /** \brief Sets the Edge of a lineage
-            * 
-            * \param index the index of the lineage within the
-            * population.
-            * \param edge the address of the Edge instance representing
-            * the lineage.
-            *
-            */
-            void set(unsigned int index, Edge* edge);
-
-           /** \brief Removes and returns a random lineage.
-            * 
-            * \param random pointer to simulator's random generator
-            * instance.
-            * 
-            */
-            Edge* extractRandomly(Random* random);
-
-           /** \brief Removes and returns a given lineage.
-            * 
-            * \param index the relative index of the lineage.
-            * 
-            */
-            Edge* extractByIndex(unsigned int index);
-
-           /** \brief Appends a lineage to the object
-            * 
-            */
-            void push(Edge* edge);
-
-           /** \brief Gets coverage
-            * 
-            */
-            unsigned int coverage(unsigned int edgeIndex) const;
-
-
-        private:
-
-            void copy(const Population& source);
-            void clear();
-            Edge* pick(unsigned int index);
-            void init();
-            unsigned int _numberOfLineages;
-            unsigned int _efficientNumberOfLineages;
-            Edge** lineages;
-    };
-
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Random.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Random.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-/*
-    Copyright 2008,2009,2012 Stéphane De Mita, Mathieu Siol
-    Adapted from MStrat, developed by Charles-Edouard Coste,
-    Thomas M. Bataillon, Mathieu Cotisson, Guy Decoux, Chistophe Rozale,
-    Daniel J. Schoen and Jacques L. David.
-    
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_RANDOM_HPP
-#define EGGLIB_RANDOM_HPP
-
-namespace egglib {
-
-    /** \brief Pseudo-random number generator
-     *
-     * \ingroup core
-     *
-     * Random is a pseudo-random number generator, adapted from a part of MStrat,
-     * developed by Charles-Edouard Coste, Thomas M. Bataillon, Mathieu Cotisson,
-     * Guy Decoux, Chistophe Rozale, Daniel J. Schoen and Jacques L. David.
-     *
-     * It uses two different seeds. By default, they are initialized to available
-     * arbitrary values. However, a given sequence can be repeated by passing the
-     * same two seeds.
-     * 
-     */
-    class Random {
-       public:
-            /** \brief Initializes using default seeds
-             *
-             * Uses the current system time and the memory address of the object as an attempt to generate unique sequences.
-             */
-            Random();
-
-            /** \brief Initializes using given seeds
-             *
-             * This constructor can be used to reproduce a given sequence.
-             */
-            Random(double seed1, double seed2);
-            
-           /** \brief Draws a number from an exponential distribution
-            * 
-            * \param expectation the distribution mean (also 1/lambda
-            * where lambda is the rate parameter).
-            *
-            */
-            double erand(double expectation);
-
-           /** \brief Draws an integer from a uniform distribution bound by 0 and max (max is not included)
-            * 
-            * max is not included.
-            * 
-            */
-            unsigned int irand(unsigned int max);
-
-            /** \brief Draws an integer from a Poisson distribution with parameter p
-             *
-             * The Poisson transformation algorithm was taken from (in French)
-             * http://www.u-picardie.fr/~cochard/IEM/demos/C107/C107_3.htm.
-             */
-            unsigned int prand(double p);
-
-           /** \brief Draws a number from a normal distribution of expectation 0 and variance 1
-            * 
-            * The algorithm used is the polar form of the Box-Muller
-            * algorithm. \todo use the Ziggurat algorithm for the
-            * nrand() method of Random.
-            * 
-            */
-            double nrand();
-            
-           /** \brief Draws a number from a geometric law
-            * 
-            * \param param the parameter of the law
-            * 
-            */
-            unsigned int grand(double);
-
-           /** \brief Draws a number from a uniform distribution between 0 and 1
-            * 
-            */
-            double uniform();
-            
-           /** \brief Gets the current value of the first seed
-            * 
-            */
-            double seed1() const;
-
-           /** \brief Gets the current value of the second seed
-            * 
-            */
-            double seed2() const;
-            
-           /** \brief Sets the current value of the first seed
-            * 
-            */
-            void seed1(double);
-
-           /** \brief Sets the current value of the second seed
-            * 
-            */
-            void seed2(double);
-
-        private:
-            // First seed
-            double _seed1;
-            
-            // Second seed
-            double _seed2;
-            
-            /* since the normal random generator draws two numbers at
-             * a time, one is cached and returned at any subsequent call
-             */
-            bool b_ncached;
-            double v_ncached;
-            
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/SitePolymorphism.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/SitePolymorphism.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,207 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of the EggLib library.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#ifndef EGGLIB_SITEPOLYMORPHISM_HPP
-#define EGGLIB_SITEPOLYMORPHISM_HPP
-
-
-
-namespace egglib {
-
-
-   /** \brief Implements diversity analysis at the site level
-    *
-    * \ingroup polymorphism
-    * 
-    * Data are loaded along with a population index. It is necessary to
-    * set the number of populations prior to use.
-    * 
-    * Outgroup sequence must be loaded separetedly. There can be any
-    * number of outgroups, but they must be all consistent otherwise the
-    * site will be considered as not orientable.
-    * 
-    */
-    class SitePolymorphism {
-
-        public:
-
-           /** \brief Builds an object
-            * 
-            */
-            SitePolymorphism();
-
-
-           /** \brief Builds an object
-            * 
-            * \param npop number of populations
-            * 
-            */
-            SitePolymorphism(unsigned int npop);
-
-
-           /** \brief Destroys an object
-            * 
-            */
-            virtual ~SitePolymorphism();
-
-
-           /** \brief Copy constructor
-            * 
-            */
-            SitePolymorphism(const SitePolymorphism& source);
-
-
-           /** \brief Assignment operator
-            * 
-            */
-            SitePolymorphism& operator=(const SitePolymorphism& source);
-
-
-           /** \brief Sets the number of populations
-            * 
-            * NOTE THAT all previous data is lost.
-            * 
-            */
-            void numberOfPopulations(unsigned int npop);
-
-
-           /** \brief Adds a character
-            * 
-            * \param populationIndex the index of the population from
-            * which is sampled this character (do not use "population
-            * label").
-            * 
-            * \param character the character value (it is assumed it
-            * represents a valid character.
-            * 
-            */
-            void load(unsigned int populationIndex, char character);
-
-
-           /** \brief Loads outgroup state
-            * 
-            * There can be any number of outgroup states. Only
-            * characters that are considered as valid (whatever the list
-            * is) should be loaded.
-            * 
-            */
-            void outgroup(char state);
-
-
-           /** \brief Number of different alleles
-            * 
-            */
-            unsigned int numberOfAlleles() const;
-            
-            
-           /** \brief Gets an allele (unsecure)
-            * 
-            * Assumes that the index provided lies in the valid range
-            * 
-            */
-            char allele(unsigned int index) const;
-
-
-           /** \brief Gets a frequency (unsecure)
-            * 
-            * The sum of of frequencies of the allele over populations
-            * is computed. Not out-of-bounds check is performed.
-            * 
-            */
-            unsigned int alleleFrequency(unsigned int alleleIndex) const;
-
-
-           /** \brief Gets the frequency of an allele in one pop (unsecure)
-            * 
-            * The frequency of the allele in the given population is
-            * returned. Not out-of-bounds check is performed.
-            * 
-            */
-            unsigned int alleleFrequency(unsigned int popIndex, unsigned int alleleIndex) const;
-
-
-           /** \brief Sums the frequency of derived allele(s)
-            * 
-            * This method assumes that the site is orientable. It will
-            * use as outgroup the first outgroup character entered,
-            * assuming at least one was entered and that all (if more
-            * than one) were identical.
-            * 
-            */
-            unsigned int derivedAlleleFrequency() const;
-
-
-           /** \brief Number of sequences that were analyzed
-            * 
-            */
-            unsigned int ns() const;
-
-
-           /** \brief Gets the number of analyzed sequences for a population
-            * 
-            * No out-of-bound check is performed
-            * 
-            */
-            unsigned int ns(unsigned int popIndex) const;
-
-
-           /** \brief Checks if the site can be oriented
-            * 
-            * Returns true if at least one outgroup datum has been
-            * loaded, if all outgroup data are identical (regardless of
-            * their value) and if the outgroup allele is one of the
-            * allele in the sample.
-            * 
-            */
-            bool isOrientable() const;
-
-            bool isPolymorphic(unsigned int popIndex) const;
-            bool hasSpecificAllele(unsigned int popIndex, bool restrictToDerived) const;
-            bool haveFixedDifference(unsigned int pop1, unsigned int pop2) const;
-            bool haveCommonAllele(unsigned int pop1, unsigned int pop2) const;
-            bool haveSharedAllele(unsigned int pop1, unsigned int pop2) const;
-
-
-
-
-        protected:
-
-            // helpers
-            void init();
-            void clear();
-            void copy(const SitePolymorphism& site);
-
-
-            // data
-            unsigned int m_numberOfPopulations;
-            unsigned int m_numberOfStates;
-            char * m_states;
-            unsigned int ** m_frequencies;
-            unsigned int m_numberOfOutgroups;
-            char * m_outgroups;
-            unsigned int m_ns;
-            unsigned int * m_pop_ns;
-            
-            bool m_cache_orientable;
-
-    };
-}
-
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/Staden.hpp
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Staden.hpp	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-/*
-    Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
-
-    This file is part of EggLib.
-
-    EggLib is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    EggLib is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#ifndef EGGLIB_STADEN_HPP
-#define EGGLIB_STADEN_HPP
-
-#include <string>
-#include <istream>
-#include "Align.hpp"
-
-namespace egglib {
-
-    /** \brief Parser of Staden output format
-     *
-     * \ingroup core
-     *
-     * The parser is available as a static method. It takes either a
-     * stream or a string containing data formatted by the program GAP4
-     * of the Staden package (command 'dump contig to file').
-     * 
-     */
-    class Staden {
-        
-        public:
-
-
-           /** \brief Parses a string
-            * 
-            * \param string a string containing an alignment formatted
-            * by the program GAP4 of the Staden package.
-            * 
-            * \param deleteConsensus if true, the sequence named
-            * "CONSENSUS" is deleted from the file (if it is present).
-            * 
-            * \return An Align instance containing the data found in
-            * the Staden while, after recoding the character following
-            * the standard codes.
-            *
-            * This method opens a stream to the string and calls the
-            * overloaded method.
-            * 
-            * The character replacement rules assume Staden default
-            * convention, as follows:
-            *    - "-" codes for an unknown base and is replaced by "N".
-            *    - "*" codes for an alignment gap and is replaced by "-".
-            *    - A white space represents missing data and is replaced
-            * by "?".
-            * 
-            */
-            static Align parse(const std::string& string, bool deleteConsensus=true);
-            
-
-           /** \brief Parses an open stream
-            * 
-            * \param stream the open containing an alignment formatted
-            * by the program GAP4 of the Staden package.
-            * 
-            * \param deleteConsensus if true, the sequence named
-            * "CONSENSUS" is deleted from the file (if it is present).
-            * 
-            * \return An Align instance containing the data found in
-            * the Staden while, after recoding the character following
-            * the standard codes.
-            *
-            * The character replacement rules assume Staden default
-            * convention, as follows:
-            *    - "-" codes for an unknown base and is replaced by "N".
-            *    - "*" codes for an alignment gap and is replaced by "-".
-            *    - A white space represents missing data and is replaced
-            * by "?".
-            * 
-            */
-            static Align parse(std::istream& stream, bool deleteConsensus=true);
-
-
-        private:
-        
-            /// Not allowed to instantiate this class
-            Staden() { }
-            
-            /// Not allowed to instantiate this class
-            Staden(const Staden& source) { }
-            
-            /// Not allowed to instantiate this class
-            ~Staden() { }
-
-
-           /* Gets the start position of sequences
-            *
-            * The functions gives total number of characters before the start of sequences
-            * and reads through until the next backspace (ignores the first line).
-            */
-            static void getShift();
- 
-            // Translates according to the Staden format
-            static char transforme(char);
-            
-            // Imports one sequence
-            static bool readOneSequence();
-            
-            // Imports and concatenates one sequence
-            static bool readAppendOneSequence();
-            
-            // Replaces dots by the matching character from CONSENSUS
-            static void undot(bool delete_consensus=true);
-
-            // The number of characters before the start of sequences
-            static int shift;
-            
-            // The dynamically filled container (will result in an aligment)
-            static Container container;
-            
-            // The current position
-            static int currpos;
-            
-            // The reading stream
-            static std::istream* stream;
-            
-            // Stores unique 8 characters discriminating readings
-            static std::vector<std::string> ID;
-    };
-}
-    
-#endif
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/include/egglib-cpp/config.h
--- a/egglib/egglib-2.1.5/include/egglib-cpp/config.h	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-/* config.h.  Generated from config.h.in by configure.  */
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#define HAVE_INTTYPES_H 1
-
-/* Define to 1 if you have the `bpp-core' library (-lbpp-core). */
-/* #undef HAVE_LIBBPP_CORE */
-
-/* Define to 1 if you have the `bpp-seq' library (-lbpp-seq). */
-/* #undef HAVE_LIBBPP_SEQ */
-
-/* Define to 1 if you have the <memory.h> header file. */
-#define HAVE_MEMORY_H 1
-
-/* Define to 1 if you have the `sqrt' function. */
-/* #undef HAVE_SQRT */
-
-/* Define to 1 if stdbool.h conforms to C99. */
-#define HAVE_STDBOOL_H 1
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#define HAVE_STDINT_H 1
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#define HAVE_STDLIB_H 1
-
-/* Define to 1 if you have the <strings.h> header file. */
-#define HAVE_STRINGS_H 1
-
-/* Define to 1 if you have the <string.h> header file. */
-#define HAVE_STRING_H 1
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#define HAVE_SYS_STAT_H 1
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#define HAVE_SYS_TYPES_H 1
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#define HAVE_UNISTD_H 1
-
-/* Define to 1 if the system has the type `_Bool'. */
-#define HAVE__BOOL 1
-
-/* Name of package */
-#define PACKAGE "egglib-cpp"
-
-/* Define to the address where bug reports for this package should be sent. */
-#define PACKAGE_BUGREPORT "demita@gmail.com"
-
-/* Define to the full name of this package. */
-#define PACKAGE_NAME "EggLib C++ library"
-
-/* Define to the full name and version of this package. */
-#define PACKAGE_STRING "EggLib C++ library 2.1.5"
-
-/* Define to the one symbol short name of this package. */
-#define PACKAGE_TARNAME "egglib-cpp"
-
-/* Define to the home page for this package. */
-#define PACKAGE_URL ""
-
-/* Define to the version of this package. */
-#define PACKAGE_VERSION "2.1.5"
-
-/* Define to 1 if you have the ANSI C header files. */
-#define STDC_HEADERS 1
-
-/* Version number of package */
-#define VERSION "2.1.5"
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-/* #undef inline */
-#endif
-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-/* #undef size_t */
diff -r 420b57c3c185 -r feb40a9a8eae egglib/egglib-2.1.5/lib/libegglib-cpp.a
Binary file egglib/egglib-2.1.5/lib/libegglib-cpp.a has changed
diff -r 420b57c3c185 -r feb40a9a8eae hapmap2mlmm/HapmapToMLMMFiles.pl
--- a/hapmap2mlmm/HapmapToMLMMFiles.pl	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use Switch;
-use Getopt::Long;
-
-my $usage = qq~Usage:$0 <args> [<opts>]
-where <args> are:
-    -h, --hapmap       <Hapmap input file>
-    -m, --map          <Map output file>
-    -g, --geno         <Genotype output file>
-    -p, --path         <Path for transpose executable>
-~;
-$usage .= "\n";
-
-my ($hapmap,$map,$geno,$path);
-
-
-GetOptions(
-        "geno=s"       => \$geno,
-        "map=s"        => \$map,
-        "hapmap=s"     => \$hapmap,
-        "path=s"       => \$path,
-);
-
-
-die $usage
-  if ( !$geno || !$map || !$hapmap || !$path);
-  
-my $TRANSPOSE_EXE = "$path/transpose.awk";
-
-my @snps;
-my %chrom_pos;
-my $num_line = 0;
-open(my $O,">geno_transposed");
-open(my $H,$hapmap);
-while(<$H>)
-{
-	$num_line++;
-	my $line = $_;
-	chomp($line);
-	$line =~s/\r//g;
-	$line =~s/\n//g;
-	my @infos = split(/\t/,$line);
-	if ($num_line == 1)
-	{
-		print $O "Ind_id";
-		for (my $i = 11; $i <= $#infos; $i++)
-		{
-			my $individual = $infos[$i];
-			print $O "	" . $individual;
-		}
-		print $O "\n";
-	}
-	elsif ($num_line > 1)
-	{
-		my $snp = $infos[0];
-		my $variation = $infos[1];
-		my %scores;
-		if ($variation =~/(\w)\/(\w)/)
-		{
-			my $allele1 = $1;
-			my $allele2 = $2;
-			$scores{$allele1} = 0;
-			$scores{$allele2} = 1;
-		}
-		my $chrom = $infos[2];
-		my $pos = $infos[3];
-		$chrom_pos{$snp}{"chrom"} = $chrom;
-		$chrom_pos{$snp}{"pos"} = $pos;
-		push(@snps,$snp);
-		print $O "$snp";
-		for (my $i = 11; $i <= $#infos; $i++)
-		{
-			my $genotype = $infos[$i];
-			my @alleles = split("",$genotype);
-			if ($genotype ne "NN")
-			{
-				my $score = $scores{$alleles[0]} + $scores{$alleles[1]};
-				print $O "	$score";
-			}
-			else
-			{
-				print $O "	NA";
-			}
-		}
-		print $O "\n";
-	}
-}
-close($H);
-close($O);
-
-open(my $M,">$map");
-print $M "SNP	Chr	Pos\n";
-foreach my $snp(@snps)
-{
-	print $M "$snp	" . $chrom_pos{$snp}{"chrom"} . "	". $chrom_pos{$snp}{"pos"} . "\n";
-}
-close($M);
-
-system("$TRANSPOSE_EXE geno_transposed >geno_transposed2");
-
-open(my $F,">$geno");
-open(my $G,"geno_transposed2");
-while(<$G>)
-{
-	my $line = $_;
-	$line =~s/ /\t/g;
-	print $F $line;
-}
-close($G);
-close($F);
-
-unlink("geno_transposed");
-unlink("geno_transposed2");
-
-
diff -r 420b57c3c185 -r feb40a9a8eae hapmap2mlmm/HapmapToMLMMFiles.sh
--- a/hapmap2mlmm/HapmapToMLMMFiles.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#!/bin/bash
-hapmap=$1
-map=$2
-geno=$3
-
-directory=`dirname $0`
- 
-perl $directory/HapmapToMLMMFiles.pl -h $hapmap -g $geno -m $map -p $directory
-
-
-
diff -r 420b57c3c185 -r feb40a9a8eae hapmap2mlmm/HapmapToMLMMFiles.xml
--- a/hapmap2mlmm/HapmapToMLMMFiles.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,158 +0,0 @@
-<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1">
-	<description>converts a hapmap file into MLMM input files</description>
-	<command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot
-    </command>
-	<inputs>
-		<param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="snp_info" label="SNP Info file"/>
-		<data format="txt" name="genot" label="Genotyping file for MLMM"/>
-	</outputs>
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-	<help>
-	
-
-
-
-.. class:: infomark
-
-**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
-
-  | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
-.. class:: infomark
-
-**Galaxy integration** South Green.
-
----------------------------------------------------
-
-
-=================
-HapmapToMLMMFiles
-=================
-
------------
-Description
------------
-
-  | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software.
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ====================== ===========
-Name            output file(s)         format 
-=============== ====================== ===========
-VCF to Hapmap   Fasta alignment        fasta
-=============== ====================== ===========
-
-
-**Downstream tool**
-
-=========== ========================== =======
-Name            input file(s)          format
-=========== ========================== =======
-MLMM                                        
-=========== ========================== =======
-
-
-
-----------
-Input file
-----------
-
-Hapmap file
-	Allelic file in Hapmap format
-
-
-
-------------
-Output files
-------------
-
-SNP Info file
-
-Genotyping file for MLMM
-
-
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-Hapmap file
------------
-
-::
-	
-	rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panel	QCcode	Ind1	Ind2
-	SNP1	A/T	1	3102	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
-	SNP2	A/T	1	4648	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
-
-
-Output files
-============
-
-SNP Info file
--------------
-
-::
-
-	SNP	Chr	Pos
-	SNP1	1	3102
-	SNP2	1	4648
-	SNP3	1	7601
-
-
-Genotyping file for MLMM
-------------------------
-
-::
-
-	Ind_id	SNP1	SNP2	SNP3	SNP4	SNP5	SNP6	SNP7	SNP8	SNP9	SNP10	SNP11	SNP12	SNP13	SNP14
-	Ind1	0	0	0	0	0	0	2	0	2	0	0	0	2	0
-	Ind2	0	0	0	0	0	2	2	0	0	0	0	0	0	0
-
-
-	</help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae hapmap2mlmm/transpose.awk
--- a/hapmap2mlmm/transpose.awk	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-#!/usr/bin/gawk -f
-
-BEGIN {
-    max_x =0;
-    max_y =0;
-}
-
-{
-    max_y++;
-    for( i=1; i<=NF; i++ )
-    {
-        if (i>max_x) max_x=i;
-        A[i,max_y] = $i;
-    }
-}
-
-END {
-    for ( x=1; x<=max_x; x++ )
-    {
-        for ( y=1; y<=max_y; y++ )
-        {
-            if ( (x,y) in A ) printf "%s",A[x,y];
-            if ( y!=max_y ) printf " ";
-        }
-        printf "\n";
-    }
-}
diff -r 420b57c3c185 -r feb40a9a8eae ped2bed/ped2bed.sh
--- a/ped2bed/ped2bed.sh	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-#!/bin/bash
-ped=$1
-map=$2
-bed=$3
-fam=$4
-bim=$5
-logs=$6
-
-directory=`dirname $0`
-mkdir tmpdir$$
-cp -rf $ped tmpdir$$/input.ped
-cp -rf $map tmpdir$$/input.map
- 
-plink --file tmpdir$$/input --out tmpdir$$/out --make-bed --noweb >>$logs 2>&1
-
-mv tmpdir$$/out.bed $bed
-mv tmpdir$$/out.fam $fam
-mv tmpdir$$/out.bim $bim
-
-
diff -r 420b57c3c185 -r feb40a9a8eae ped2bed/ped2bed.xml
--- a/ped2bed/ped2bed.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,196 +0,0 @@
-<tool id="ped2bed" name="plink: ped2bed" version="1.24">
-	<description>Convert ped to bed</description>
-	<requirements>
-		<requirement type="package" version="1.07">plink</requirement>
-	</requirements>
-	<command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
-    </command>
-	<inputs>
-		<param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
-		<param format="txt" name="map" type="data" label="Map file" help="Map file"/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="bed" label="Bed file"/>
-		<data format="txt" name="fam" label="Fam file"/>
-		<data format="txt" name="bim" label="Bim file"/>
-		<data format="txt" name="logs" label="All Logs"/>
-	</outputs>
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
-    <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
-        <!-- [HELP] Multiple tests can be defined with different parameters -->
-<!--
-        <test>
-        </test>
--->
-    </tests>
-	<help>
-	
-
-.. class:: infomark
-
-**Authors** plink_
-
-.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
-
-  | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007.
-
-.. class:: infomark
-
-**Galaxy integration** South Green.
-
-.. class:: infomark
-
-**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
-
-
----------------------------------------------------
-
-
-
-=======
-Ped2Bed
-=======
-
------------
-Description
------------
-
-  | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
-  | For further informations, please visite the plink website_.
-
-.. _website: http://pngu.mgh.harvard.edu/purcell/plink/
-
-
------------------
-Workflow position
------------------
-
-**Upstream tool**
-
-=============== ========================== ===========
-Name            output file(s)             format 
-=============== ========================== ===========
-VCFtools filter PED and map files          ped and map
-=============== ========================== ===========
-
-
-**Downstream tool**
-
-=========== ========================== =======
-Name            input file(s)          format
-=========== ========================== =======
-Admixture   Bed, fam and bim file      txt
-=========== ========================== =======
-
-
-----------
-Input file
-----------
-
-PED file
-	Allelic file in PED format 
-
-MAP file
-
-
-
-------------
-Output files
-------------
-
-Bed file
-
-Fam file
-
-Bim file
-
-All logs 
-	Log file
-
-
-------------
-Dependencies
-------------
-plink 
-	version 1.07
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
-===========
-
-PED file
---------
-
-::
-	
-	AZUCENA	AZUCENA	0	0	0	0	G	G	A	A	C	C	T	T	T	
-	BULUPANDAK	BULUPANDAK	0	0	0	0	G	G	A	A	A	A	T	
-
-MAP file
---------
-
-::
-	
-	0	Chr1:4299	0	4299
-	0	Chr1:26710	0	26710
-	0	Chr1:56184	0	56184
-	0	Chr1:93272	0	93272
-
-
-Output files
-============
-
-Bed file
---------
-
-::
-
-	binary file
-
-Fam file
---------
-
-::
-
-	AZUCENA AZUCENA 0 0 0 -9
-	BULUPANDAK BULUPANDAK 0 0 0 -9
-
-Bim file
---------
-
-::
-
-	0	Chr1:4299	0	4299	A	G
-	0	Chr8:18058	0	18058	C	T
-
-
-	</help>
-    <citations>
-        <!-- [HELP] As DOI or BibTex entry -->
-    	<citation type="bibtex">@article{Dereeper03062015,
-author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
-title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
-year = {2015}, 
-doi = {10.1093/nar/gkv351}, 
-abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
-URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
-
-    	</citation>
-
-    </citations>
-</tool>
diff -r 420b57c3c185 -r feb40a9a8eae tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jul 10 04:39:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="plink" version="1.07">
-        <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>