# HG changeset patch
# User Richard Burhans <burhans@bx.psu.edu>
# Date 1346777393 14400
# Node ID 9b92372de9f66a3e1d4bced6d0773aaa2b51dfe1
# Parent  22fe0154fa5409c76d4c1b614f4803c574055400
rename snp to gsSnp, sap to gdSap

diff -r 22fe0154fa54 -r 9b92372de9f6 add_fst_column.xml
--- a/add_fst_column.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/add_fst_column.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -10,7 +10,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="SNP table" />
+    <param name="input" type="data" format="gdSnp" label="SNP table" />
     <param name="p1_input" type="data" format="ind" label="Population 1 individuals" />
     <param name="p2_input" type="data" format="ind" label="Population 2 individuals" />
 
@@ -40,12 +40,12 @@
   </inputs>
 
   <outputs>
-    <data name="output" format="snp" metadata_source="input" />
+    <data name="output" format="gdSnp" metadata_source="input" />
   </outputs>
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="p1_input" value="test_in/a.ind" ftype="ind" />
       <param name="p2_input" value="test_in/b.ind" ftype="ind" />
       <param name="data_source" value="0" />
@@ -54,7 +54,7 @@
       <param name="retain" value="0" />
       <param name="discard_fixed" value="1" />
       <param name="biased" value="0" />
-      <output name="output" file="test_out/add_fst_column/add_fst_column.snp" />
+      <output name="output" file="test_out/add_fst_column/add_fst_column.gdSnp" />
     </test>
   </tests>
 
diff -r 22fe0154fa54 -r 9b92372de9f6 average_fst.xml
--- a/average_fst.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/average_fst.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -15,7 +15,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="SNP table" />
+    <param name="input" type="data" format="gdSnp" label="SNP table" />
     <param name="p1_input" type="data" format="ind" label="Population 1 individuals" />
     <param name="p2_input" type="data" format="ind" label="Population 2 individuals" />
 
@@ -61,7 +61,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="p1_input" value="test_in/a.ind" ftype="ind" />
       <param name="p2_input" value="test_in/b.ind" ftype="ind" />
       <param name="ds_choice" value="0" />
diff -r 22fe0154fa54 -r 9b92372de9f6 coverage_distributions.xml
--- a/coverage_distributions.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/coverage_distributions.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -21,7 +21,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="SNP table" />
+    <param name="input" type="data" format="gdSnp" label="SNP table" />
 
     <conditional name="individuals">
       <param name="choice" type="select" label="Individuals">
@@ -54,7 +54,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="choice" value="0" />
       <output name="output" file="test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2">
         <extra_files type="file" name="coverage.pdf" value="test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/>
diff -r 22fe0154fa54 -r 9b92372de9f6 datatypes_conf.xml
--- a/datatypes_conf.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/datatypes_conf.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -6,8 +6,8 @@
   <registration>
     <datatype extension="ind" type="galaxy.datatypes.wsf:Individuals" display_in_upload="true"/>
     <datatype extension="wped" type="galaxy.datatypes.wsf:Wped" display_in_upload="true"/>
-    <datatype extension="snp" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
-    <datatype extension="sap" type="galaxy.datatypes.wsf:SapFile" display_in_upload="true"/>
+    <datatype extension="gdSnp" type="galaxy.datatypes.wsf:GDSnp" display_in_upload="true"/>
+    <datatype extension="gdSap" type="galaxy.datatypes.wsf:GDSap" display_in_upload="true"/>
   </registration>
   <sniffers/>
 </datatypes>
diff -r 22fe0154fa54 -r 9b92372de9f6 dpmix.xml
--- a/dpmix.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/dpmix.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -10,7 +10,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="Dataset">
+    <param name="input" type="data" format="gdSnp" label="Dataset">
       <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
     </param>
     <param name="ap1_input" type="data" format="ind" label="Ancestral population 1 individuals" />
@@ -32,7 +32,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="ap1_input" value="test_in/a.ind" ftype="ind" />
       <param name="ap2_input" value="test_in/b.ind" ftype="ind" />
       <param name="p_input" value="test_in/c.ind" ftype="ind" />
diff -r 22fe0154fa54 -r 9b92372de9f6 extract_flanking_dna.xml
--- a/extract_flanking_dna.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/extract_flanking_dna.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -43,7 +43,7 @@
   <!-- Need snpcalls files from Webb before uncommenting
   <tests>
     <test>
-      <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" />
+      <param name="input" value="test_out/select_snps/select_snps.gdSnp" ftype="gdSnp" />
       <param name="output_format" value="primer3" />
       <param name="choice" value="0" />
       <output name="output" file="test_out/extract_flanking_dna/extract_flanking_dna.txt" />
diff -r 22fe0154fa54 -r 9b92372de9f6 extract_primers.xml
--- a/extract_primers.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/extract_primers.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -37,7 +37,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" />
+      <param name="input" value="test_out/select_snps/select_snps.gdSnp" ftype="gdSnp" />
       <param name="choice" value="0"/>
       <output name="output" file="test_out/extract_primers/extract_primers.txt" />
     </test>
diff -r 22fe0154fa54 -r 9b92372de9f6 find_intervals.xml
--- a/find_intervals.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/find_intervals.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -71,7 +71,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="score_col" value="5" />
       <param name="type" value="value" />
       <param name="cutoff_val" value="700.0" />
diff -r 22fe0154fa54 -r 9b92372de9f6 lib/galaxy/datatypes/wsf.py
--- a/lib/galaxy/datatypes/wsf.py	Tue Jul 10 11:41:22 2012 -0400
+++ b/lib/galaxy/datatypes/wsf.py	Tue Sep 04 12:49:53 2012 -0400
@@ -139,9 +139,9 @@
         if isinstance( value_from_comment_metadata, basestring ):
             dataset.metadata.dbkey = value_from_comment_metadata
 
-class SnpFile( Fake ):
+class GDSnp( Fake ):
     """ Webb's SNP file format """
-    file_ext = 'snp'
+    file_ext = 'gdSnp'
 
     MetadataElement( name="individual_names", desc="individual names", visible=False, readonly=True )
     MetadataElement( name="individual_columns", desc="individual columns", visible=False, readonly=True )
@@ -176,9 +176,9 @@
             dataset.metadata.individual_names = individual_names[:]
             dataset.metadata.individual_columns = individual_columns[:]
 
-class SapFile( Fake ):
+class GDSap( Fake ):
     """ Webb's SAP file format """
-    file_ext = 'sap'
+    file_ext = 'gdSap'
 
     MetadataElement( name="kegg_gene", desc="KEGG gene code column", param=metadata.ColumnParameter, default=0 )
     MetadataElement( name="kegg_path", desc="KEGG pathway code/name column", param=metadata.ColumnParameter, default=0 )
diff -r 22fe0154fa54 -r 9b92372de9f6 modify_snp_table.xml
--- a/modify_snp_table.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/modify_snp_table.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -15,7 +15,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="SNP table" />
+    <param name="input" type="data" format="gdSnp" label="SNP table" />
     <param name="p1_input" type="data" format="ind" label="Population individuals" />
     <conditional name="limit_coverage">
       <param name="choice" type="select" format="integer" label="Option">
@@ -33,19 +33,19 @@
   </inputs>
 
   <outputs>
-    <data name="output" format="snp" metadata_source="input" />
+    <data name="output" format="gdSnp" metadata_source="input" />
   </outputs>
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="p1_input" value="test_in/a.ind" ftype="ind" />
       <param name="choice" value="1" />
       <param name="lo_coverage" value="0" />
       <param name="hi_coverage" value="1000" />
       <param name="low_ind_cov" value="3" />
       <param name="lo_quality" value="30" />
-      <output name="output" file="test_out/modify_snp_table/modify.snp" />
+      <output name="output" file="test_out/modify_snp_table/modify.gdSnp" />
     </test>
   </tests>
 
diff -r 22fe0154fa54 -r 9b92372de9f6 pathway_image.xml
--- a/pathway_image.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/pathway_image.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -11,7 +11,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="sap" label="Table">
+    <param name="input" type="data" format="gdSap" label="Table">
       <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata.  Click the pencil icon in the history item to edit/save the metadata attributes" />
     </param>
     <param name="pathway" type="select">
@@ -29,7 +29,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.sap" ftype="sap" />
+      <param name="input" value="test_in/sample.gdSap" ftype="gdSap" />
       <param name="pathway" value="cfa05214" />
       <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" />
     </test>
diff -r 22fe0154fa54 -r 9b92372de9f6 pca.xml
--- a/pca.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/pca.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -26,7 +26,7 @@
       <output name="output" file="test_out/pca/pca.html" ftype="html" compare="diff" lines_diff="2">
         <extra_files type="file" name="admix.geno" value="test_out/pca/admix.geno" />
         <extra_files type="file" name="admix.ind" value="test_out/pca/admix.ind" />
-        <extra_files type="file" name="admix.snp" value="test_out/pca/admix.snp" />
+        <extra_files type="file" name="admix.gdSnp" value="test_out/pca/admix.gdSnp" />
         <extra_files type="file" name="coordinates.txt" value="test_out/pca/coordinates.txt" />
         <extra_files type="file" name="explained.txt" value="test_out/pca/explained.txt" />
         <extra_files type="file" name="par.admix" value="test_out/pca/par.admix" compare="diff" lines_diff="10" />
diff -r 22fe0154fa54 -r 9b92372de9f6 phylogenetic_tree.xml
--- a/phylogenetic_tree.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/phylogenetic_tree.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -28,7 +28,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="SNP table" />
+    <param name="input" type="data" format="gdSnp" label="SNP table" />
 
     <conditional name="individuals">
       <param name="choice" type="select" label="Individuals">
@@ -86,7 +86,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="choice" value="0" />
       <param name="minimum_coverage" value="3" />
       <param name="minimum_quality" value="30" />
diff -r 22fe0154fa54 -r 9b92372de9f6 prepare_population_structure.xml
--- a/prepare_population_structure.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/prepare_population_structure.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -18,7 +18,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp" label="SNP table" />
+    <param name="input" type="data" format="gdSnp" label="SNP table" />
     <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" />
     <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" />
     <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" />
@@ -46,7 +46,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="min_reads" value="3" />
       <param name="min_qual" value="30" />
       <param name="min_spacing" value="0" />
diff -r 22fe0154fa54 -r 9b92372de9f6 rank_pathways.xml
--- a/rank_pathways.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/rank_pathways.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -16,7 +16,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="sap" label="Table">
+    <param name="input" type="data" format="gdSap" label="Table">
         <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata.  Click the pencil icon in the history item to edit/save the metadata attributes" />
     </param>
     <param name="output_format" type="select" label="Output format">
@@ -31,7 +31,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.sap" ftype="sap" />
+      <param name="input" value="test_in/sample.gdSap" ftype="gdSap" />
       <param name="output_format" value="a" />
       <output name="output" file="test_out/rank_pathways/rank_pathways.tabular" />
     </test>
diff -r 22fe0154fa54 -r 9b92372de9f6 select_individuals.xml
--- a/select_individuals.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/select_individuals.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -12,7 +12,7 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="snp"/>
+    <param name="input" type="data" format="gdSnp"/>
     <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
       <options>
         <filter type="data_meta" ref="input" key="individual_names" />
@@ -27,7 +27,7 @@
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp" />
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" />
       <param name="individuals" value="PB1,PB2" />
       <output name="output" file="test_in/a.ind" />
     </test>
diff -r 22fe0154fa54 -r 9b92372de9f6 select_snps.xml
--- a/select_snps.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/select_snps.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -35,15 +35,15 @@
   </inputs>
 
   <outputs>
-    <data format="snp" name="output" metadata_source="input"/>
+    <data format="gdSnp" name="output" metadata_source="input"/>
   </outputs>
 
   <tests>
     <test>
-      <param name="input" value="test_in/sample.snp" ftype="snp"/>
+      <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp"/>
       <param name="num_snps" value="100"/>
       <param name="choice" value="0"/>
-      <output name="output" file="test_out/select_snps/select_snps.snp" />
+      <output name="output" file="test_out/select_snps/select_snps.gdSnp" />
     </test>
   </tests>
 
diff -r 22fe0154fa54 -r 9b92372de9f6 specify_restriction_enzymes.xml
--- a/specify_restriction_enzymes.xml	Tue Jul 10 11:41:22 2012 -0400
+++ b/specify_restriction_enzymes.xml	Tue Sep 04 12:49:53 2012 -0400
@@ -40,15 +40,15 @@
   </inputs>
 
   <outputs>
-    <data format="snp" name="output" metadata_source="input"/>
+    <data format="gdSnp" name="output" metadata_source="input"/>
   </outputs>
 
   <tests>
     <test>
-      <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" />
+      <param name="input" value="test_out/select_snps/select_snps.gdSnp" ftype="gdSnp" />
       <param name="choice" value="0" />
       <param name="enzymes" value="Bsp1286I,HaeII,RsaI" />
-      <output name="output" file="test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp" />
+      <output name="output" file="test_out/specify_restriction_enzymes/specify_restriction_enzymes.gdSnp" />
     </test>
   </tests>
 
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_in/sample.gdSap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_in/sample.gdSap	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,401 @@
+#{"column_names":["contig","pos","ref","rPos","trns","pep","AA1","loc","AA2","KEGG","pred","path"],"pos":2,"rPos":4,"ref":3,"dbkey":"canFam2","scaffold":1,"species":"bear","kegg_gene":10,"kegg_path":12}
+Contig39_chr1_3261104_3261850	414	chr1	3261546	ENSCAFT00000000001	ENSCAFP00000000001	S	667	F	476153	probably damaging	cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
+Contig62_chr1_19011969_19012646	265	chr1	19012240	ENSCAFT00000000144	ENSCAFP00000000125	*	161	R	483960	probably damaging	N
+Contig36_chr1_20102654_20103213	365	chr1	20103029	ENSCAFT00000000160	ENSCAFP00000000140	R	407	Q	610160	possibly damaging	N
+Contig136_chr10_3710404_3714591	3079	chr10	3713499	ENSCAFT00000000215	ENSCAFP00000000194	T	103	P	U	benign	N
+Contig36_chr1_23682012_23682647	374	chr1	23682388	ENSCAFT00000000233	ENSCAFP00000000210	N	234	S	483973	benign	N
+Contig163_chr10_4573526_4574494	487	chr10	4574010	ENSCAFT00000000365	ENSCAFP00000000332	R	186	K	474414	benign	cfa00450=Selenocompound metabolism.cfa00970=Aminoacyl-tRNA biosynthesis
+Contig55_chr1_40056604_40059808	2081	chr1	40058686	ENSCAFT00000000507	ENSCAFP00000000458	I	247	K	484023	possibly damaging	N
+Contig17_chr1_40203628_40205630	1417	chr1	40205044	ENSCAFT00000000517	ENSCAFP00000000468	N	109	S	476233	benign	N
+Contig97_chr1_44847984_44848380	285	chr1	44848272	ENSCAFT00000000674	ENSCAFP00000000618	Q	27	R	611986	benign	N
+Contig214_chr10_16106753_16106969	121	chr10	16106873	ENSCAFT00000000724	ENSCAFP00000000668	A	301	T	609478	benign	N
+Contig75_chr1_45731970_45732932	436	chr1	45732397	ENSCAFT00000000760	ENSCAFP00000000701	I	490	V	U	benign	N
+Contig33_chr1_45614845_45617413	1835	chr1	45616685	ENSCAFT00000000760	ENSCAFP00000000701	A	4390	V	U	benign	N
+Contig95_chr10_18829724_18831056	914	chr10	18830645	ENSCAFT00000000762	ENSCAFP00000000703	A	512	V	U	possibly damaging	N
+Contig197_chr13_8622062_8623071	606	chr13	8622665	ENSCAFT00000001047	ENSCAFP00000000959	T	406	I	475067	possibly damaging	cfa00240=Pyrimidine metabolism.cfa00410=beta-Alanine metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa00983=Drug metabolism - other enzymes.cfa01100=Metabolic pathways
+Contig243_chr10_19959210_19960069	701	chr10	19959858	ENSCAFT00000001052	ENSCAFP00000000964	E	1345	K	U	benign	N
+Contig137_chr13_10622950_10624043	1039	chr13	10623979	ENSCAFT00000001063	ENSCAFP00000000975	E	10	K	481999	benign	N
+Contig137_chr13_10622950_10624043	1006	chr13	10623946	ENSCAFT00000001063	ENSCAFP00000000975	R	21	C	481999	probably damaging	N
+Contig115_chr12_4411478_4412322	124	chr12	4411614	ENSCAFT00000001076	ENSCAFP00000000986	R	177	H	U	benign	N
+Contig150_chr12_4438230_4439944	385	chr12	4438614	ENSCAFT00000001104	ENSCAFP00000001014	Y	277	D	607591	benign	N
+Contig84_chr1_52076858_52077103	80	chr1	52076943	ENSCAFT00000001141	ENSCAFP00000001046	C	147	Y	484064	benign	N
+Contig29_chr13_13215547_13217183	793	chr13	13216352	ENSCAFT00000001146	ENSCAFP00000001050	P	1	R	475076	probably damaging	N
+Contig251_chr10_22876556_22877097	152	chr10	22876714	ENSCAFT00000001204	ENSCAFP00000001103	E	1162	D	481203	benign	N
+Contig21_chr10_22964856_22965302	202	chr10	22965058	ENSCAFT00000001219	ENSCAFP00000001115	P	6	Q	474465	benign	N
+Contig199_chr12_5083018_5084534	453	chr12	5083472	ENSCAFT00000001250	ENSCAFP00000001144	I	185	T	481729.481731	benign	N.cfa04145=Phagosome.cfa04514=Cell adhesion molecules (CAMs).cfa04612=Antigen processing and presentation.cfa04672=Intestinal immune network for IgA production.cfa04940=Type I diabetes mellitus.cfa05140=Leishmaniasis.cfa05145=Toxoplasmosis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05164=Influenza A.cfa05166=HTLV-I infection.cfa05168=Herpes simplex infection.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft rejection.cfa05332=Graft-versus-host disease.cfa05416=Viral myocarditis
+Contig41_chr13_21629998_21630487	161	chr13	21630157	ENSCAFT00000001352	ENSCAFP00000001239	P	729	S	482026	possibly damaging	cfa00565=Ether lipid metabolism
+Contig16_chr13_21786766_21788016	169	chr13	21786927	ENSCAFT00000001363	ENSCAFP00000001249	V	1142	A	475084	benign	cfa03022=Basal transcription factors
+Contig60_chr1_60333035_60333884	731	chr1	60333755	ENSCAFT00000001421	ENSCAFP00000001307	V	400	I	484096	benign	N
+Contig44_chr13_24555640_24556298	499	chr13	24556139	ENSCAFT00000001523	ENSCAFP00000001400	N	660	S	475088	benign	N
+Contig153_chr12_5955114_5958935	2950	chr12	5958094	ENSCAFT00000001575	ENSCAFP00000001449	E	13	D	481744	benign	cfa04141=Protein processing in endoplasmic reticulum
+Contig146_chr13_25076435_25077249	723	chr13	25077165	ENSCAFT00000001587	ENSCAFP00000001461	T	9	S	482035	benign	N
+Contig81_chr13_25579918_25582207	874	chr13	25580772	ENSCAFT00000001597	ENSCAFP00000001469	E	62	G	609411	benign	N
+Contig159_chr10_28604683_28606028	753	chr10	28605433	ENSCAFT00000002056	ENSCAFP00000001903	S	79	P	610014	benign	N
+Contig30_chr11_29945215_29949829	3973	chr11	29949181	ENSCAFT00000002100	ENSCAFP00000001944	M	282	T	U	benign	N
+Contig102_chr10_29039231_29041280	829	chr10	29040065	ENSCAFT00000002110	ENSCAFP00000001953	R	311	Q	481249	unknown	N
+Contig187_chr1_78583588_78584279	250	chr1	78583839	ENSCAFT00000002175	ENSCAFP00000002014	K	176	R	476310	benign	N
+Contig199_chr1_79234891_79237527	384	chr1	79235278	ENSCAFT00000002259	ENSCAFP00000002095	V	403	A	484151	benign	N
+Contig119_chr12_12212738_12214663	1005	chr12	12213720	ENSCAFT00000002460	ENSCAFP00000002280	R	749	Q	481785	possibly damaging	N
+Contig119_chr12_12212738_12214663	918	chr12	12213633	ENSCAFT00000002460	ENSCAFP00000002280	R	778	Q	481785	benign	N
+Contig39_chr14_10730123_10732539	335	chr14	10730462	ENSCAFT00000002537	ENSCAFP00000002356	V	1179	E	U	benign	N
+Contig41_chr1_84886710_84894794	3494	chr1	84890207	ENSCAFT00000002577	ENSCAFP00000002394	E	1089	K	484157	possibly damaging	N
+Contig182_chr12_13881114_13883427	1690	chr12	13882828	ENSCAFT00000002578	ENSCAFP00000002395	S	99	G	608906	benign	N
+Contig34_chr11_48151988_48152712	198	chr11	48152205	ENSCAFT00000002660	ENSCAFP00000002468	C	587	R	U	possibly damaging	N
+Contig37_chr10_34118256_34119269	437	chr10	34118687	ENSCAFT00000002792	ENSCAFP00000002588	A	377	T	474523	benign	N
+Contig21_chr14_16091274_16093278	716	chr14	16091997	ENSCAFT00000002849	ENSCAFP00000002642	R	126	C	475216	probably damaging	N
+Contig57_chr1_90983602_90984717	559	chr1	90984158	ENSCAFT00000002999	ENSCAFP00000002781	A	226	V	U	benign	N
+Contig45_chr12_15798569_15798849	141	chr12	15798709	ENSCAFT00000003163	ENSCAFP00000002938	N	342	S	474921	benign	cfa03040=Spliceosome
+Contig83_chr12_17852905_17859596	2392	chr12	17855305	ENSCAFT00000003223	ENSCAFP00000002995	E	770	Q	474925	benign	N
+Contig41_chr12_18725392_18725889	169	chr12	18725560	ENSCAFT00000003307	ENSCAFP00000003070	R	80	Q	609995	benign	N
+Contig9_chr14_26125779_26127414	486	chr14	26126264	ENSCAFT00000003515	ENSCAFP00000003259	P	123	T	482316	benign	N
+Contig132_chr1_101565951_101566612	255	chr1	101566210	ENSCAFT00000003560	ENSCAFP00000003298	L	588	F	U	unknown	N
+Contig142_chr1_102093954_102094392	121	chr1	102094072	ENSCAFT00000003644	ENSCAFP00000003373	K	120	E	484216	benign	cfa00290=Valine, leucine and isoleucine biosynthesis.cfa00970=Aminoacyl-tRNA biosynthesis
+Contig129_chr14_34071666_34074617	2313	chr14	34073957	ENSCAFT00000003824	ENSCAFP00000003537	T	282	I	475249	probably damaging	N
+Contig147_chr14_34262125_34262938	340	chr14	34262468	ENSCAFT00000003840	ENSCAFP00000003553	I	70	V	482333	benign	N
+Contig52_chr12_36031985_36035244	1237	chr12	36033208	ENSCAFT00000004092	ENSCAFP00000003784	Y	564	H	474960	benign	N
+Contig176_chr1_105494865_105495258	119	chr1	105494995	ENSCAFT00000004103	ENSCAFP00000003793	A	406	V	484298	benign	N
+Contig60_chr11_63130652_63131816	702	chr11	63131349	ENSCAFT00000004208	ENSCAFP00000003892	V	260	I	481637	benign	N
+Contig9_chr10_53579958_53582510	688	chr10	53580646	ENSCAFT00000004253	ENSCAFP00000003937	S	191	G	100534006.100534007.474588	benign	N
+Contig93_chr14_38451661_38452163	221	chr14	38451882	ENSCAFT00000004311	ENSCAFP00000003990	A	420	V	482346	benign	N
+Contig70_chr12_42859511_42860010	180	chr12	42859693	ENSCAFT00000004464	ENSCAFP00000004126	P	7	S	481892	possibly damaging	N
+Contig28_chr12_43447144_43449156	1136	chr12	43448279	ENSCAFT00000004511	ENSCAFP00000004169	V	582	M	481893	benign	N
+Contig18_chr13_62535238_62535697	227	chr13	62535471	ENSCAFT00000004609	ENSCAFP00000004263	E	277	D	611755	benign	N
+Contig282_chr1_108960925_108962235	205	chr1	108961141	ENSCAFT00000004673	ENSCAFP00000004325	A	149	V	611817	benign	N
+Contig110_chr1_109196028_109197290	987	chr1	109197021	ENSCAFT00000004726	ENSCAFP00000004374	E	330	D	610047	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa03430=Mismatch repair.cfa03440=Homologous recombination.cfa05166=HTLV-I infection
+Contig89_chr11_69097905_69099099	568	chr11	69098443	ENSCAFT00000004799	ENSCAFP00000004445	E	1317	G	U	benign	N
+Contig118_chr14_46155051_46155557	173	chr14	46155218	ENSCAFT00000004933	ENSCAFP00000004572	S	110	L	482382	benign	cfa04621=NOD-like receptor signaling pathway.cfa05133=Pertussis
+Contig54_chr12_51910786_51912716	682	chr12	51911460	ENSCAFT00000004993	ENSCAFP00000004630	H	2889	Y	474995	benign	cfa03008=Ribosome biogenesis in eukaryotes
+Contig95_chr10_67698730_67699605	267	chr10	67698997	ENSCAFT00000005126	ENSCAFP00000004751	P	45	L	U	benign	N
+Contig265_chr17_3177908_3178389	332	chr17	3178241	ENSCAFT00000005142	ENSCAFP00000004763	A	306	P	606804	benign	N
+Contig322_chr17_4977962_4979371	1122	chr17	4979079	ENSCAFT00000005225	ENSCAFP00000004836	T	319	I	475647	possibly damaging	N
+Contig48_chr11_71453437_71456331	1725	chr11	71455160	ENSCAFT00000005323	ENSCAFP00000004927	A	226	V	U	benign	N
+Contig51_chr16_4789440_4790118	484	chr16	4789915	ENSCAFT00000005467	ENSCAFP00000005065	Q	318	H	U	benign	N
+Contig32_chr12_57224809_57225619	146	chr12	57224960	ENSCAFT00000005496	ENSCAFP00000005093	A	273	T	481925	benign	N
+Contig6_chr14_59310933_59312532	615	chr14	59311551	ENSCAFT00000005518	ENSCAFP00000005112	Y	304	H	492302	probably damaging	cfa02010=ABC transporters.cfa04971=Gastric acid secretion.cfa04972=Pancreatic secretion.cfa04976=Bile secretion
+Contig89_chr11_74391566_74395656	2856	chr11	74394408	ENSCAFT00000005653	ENSCAFP00000031395	R	450	H	403417	benign	cfa04145=Phagosome.cfa04620=Toll-like receptor signaling pathway.cfa05132=Salmonella infection.cfa05133=Pertussis.cfa05134=Legionellosis.cfa05140=Leishmaniasis.cfa05142=Chagas disease (American trypanosomiasis).cfa05144=Malaria.cfa05145=Toxoplasmosis.cfa05146=Amoebiasis.cfa05152=Tuberculosis.cfa05162=Measles.cfa05164=Influenza A.cfa05323=Rheumatoid arthritis
+Contig15_chr1_109713951_109714808	645	chr1	109714594	ENSCAFT00000005746	ENSCAFP00000005319	R	783	K	476410	benign	cfa00071=Fatty acid metabolism.cfa03320=PPAR signaling pathway.cfa04920=Adipocytokine signaling pathway
+Contig47_chr17_11258085_11259619	360	chr17	11258455	ENSCAFT00000005749	ENSCAFP00000005322	V	778	L	610007	benign	N
+Contig1_chr19_4352123_4352541	311	chr19	4352427	ENSCAFT00000005832	ENSCAFP00000005401	H	7	Y	403584	benign	cfa04060=Cytokine-cytokine receptor interaction.cfa04630=Jak-STAT signaling pathway.cfa04672=Intestinal immune network for IgA production.cfa05166=HTLV-I infection.cfa05168=Herpes simplex infection.cfa05323=Rheumatoid arthritis
+Contig57_chr12_66915864_66916357	337	chr12	66916199	ENSCAFT00000005972	ENSCAFP00000005534	F	1242	L	475012	benign	N
+Contig36_chr17_16182220_16182772	282	chr17	16182494	ENSCAFT00000006025	ENSCAFP00000005583	V	13	I	482980	possibly damaging	N
+Contig64_chr19_15052202_15053292	240	chr19	15052443	ENSCAFT00000006114	ENSCAFP00000005658	I	175	V	483829	benign	N
+Contig169_chr12_69415779_69417261	1136	chr12	69416908	ENSCAFT00000006157	ENSCAFP00000005701	D	85	N	475021	possibly damaging	N
+Contig200_chr18_15803806_15804082	169	chr18	15803976	ENSCAFT00000006219	ENSCAFP00000005760	A	66	V	483261	benign	cfa04972=Pancreatic secretion.cfa04978=Mineral absorption
+Contig6_chr18_15814044_15814404	97	chr18	15814150	ENSCAFT00000006219	ENSCAFP00000005760	A	413	S	483261	benign	cfa04972=Pancreatic secretion.cfa04978=Mineral absorption
+Contig104_chr1_110433641_110434230	183	chr1	110433810	ENSCAFT00000006272	ENSCAFP00000005811	A	315	T	484394	benign	cfa00280=Valine, leucine and isoleucine degradation.cfa00290=Valine, leucine and isoleucine biosynthesis.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
+Contig52_chr18_17851226_17851871	284	chr18	17851509	ENSCAFT00000006453	ENSCAFP00000005976	T	311	M	475893	probably damaging	N
+Contig63_chr16_12167721_12168304	388	chr16	12168099	ENSCAFT00000006479	ENSCAFP00000006000	M	634	V	U	benign	N
+Contig101_chr20_4702659_4703738	441	chr20	4703092	ENSCAFT00000006507	ENSCAFP00000006027	G	635	D	484622	probably damaging	cfa03030=DNA replication.cfa04110=Cell cycle
+Contig53_chr19_21456428_21457881	408	chr19	21456840	ENSCAFT00000006669	ENSCAFP00000006174	R	247	L	476094	possibly damaging	N
+Contig58_chr18_19883250_19884312	250	chr18	19883498	ENSCAFT00000006689	ENSCAFP00000006194	*	503	Y	475897	benign	N
+Contig122_chr15_17034758_17035049	142	chr15	17034893	ENSCAFT00000006827	ENSCAFP00000006320	R	117	P	U	benign	N
+Contig131_chr18_20356930_20357227	113	chr18	20357041	ENSCAFT00000006891	ENSCAFP00000006378	V	55	L	610021	benign	N
+Contig117_chr22_5859195_5860740	654	chr22	5859850	ENSCAFT00000007130	ENSCAFP00000006603	S	139	N	485445	benign	cfa04020=Calcium signaling pathway.cfa04080=Neuroactive ligand-receptor interaction
+Contig91_chr17_23506302_23507213	322	chr17	23506624	ENSCAFT00000007145	ENSCAFP00000006614	V	1644	I	607961	benign	N
+Contig3_chr21_16586556_16586852	105	chr21	16586661	ENSCAFT00000007244	ENSCAFP00000006709	C	33	Y	476781	possibly damaging	N
+Contig62_chr2_22645987_22646907	357	chr2	22646352	ENSCAFT00000007375	ENSCAFP00000006833	V	657	F	403767	probably damaging	cfa04977=Vitamin digestion and absorption
+Contig52_chr15_18032498_18034281	880	chr15	18033373	ENSCAFT00000007440	ENSCAFP00000006895	P	227	A	482516	benign	N
+Contig131_chr23_6679385_6679850	198	chr23	6679592	ENSCAFT00000007467	ENSCAFP00000006915	R	136	G	485576	possibly damaging	N
+Contig157_chr22_10584088_10586765	232	chr22	10584326	ENSCAFT00000007484	ENSCAFP00000006926	M	610	T	609336	benign	N
+Contig164_chr2_24336024_24340161	2420	chr2	24338436	ENSCAFT00000007527	ENSCAFP00000006969	S	824	C	607108	probably damaging	N
+Contig109_chr2_24557417_24558710	808	chr2	24558229	ENSCAFT00000007553	ENSCAFP00000006994	L	606	V	487123	benign	cfa03450=Non-homologous end-joining.cfa05340=Primary immunodeficiency
+Contig194_chr15_18573761_18574204	142	chr15	18573904	ENSCAFT00000007697	ENSCAFP00000007130	V	381	I	475382	benign	N
+Contig133_chr23_9924894_9925887	125	chr23	9925016	ENSCAFT00000007703	ENSCAFP00000007136	P	355	S	477019	benign	cfa03430=Mismatch repair.cfa03460=Fanconi anemia pathway.cfa05200=Pathways in cancer.cfa05210=Colorectal cancer.cfa05213=Endometrial cancer
+Contig31_chr23_10199273_10203629	4073	chr23	10203350	ENSCAFT00000007747	ENSCAFP00000007179	A	1844	V	U	benign	N
+Contig21_chr23_10308212_10309269	513	chr23	10308732	ENSCAFT00000007774	ENSCAFP00000007206	K	72	R	477021	benign	cfa04510=Focal adhesion.cfa04512=ECM-receptor interaction.cfa04514=Cell adhesion molecules (CAMs).cfa04810=Regulation of actin cytoskeleton.cfa05410=Hypertrophic cardiomyopathy (HCM).cfa05412=Arrhythmogenic right ventricular cardiomyopathy (ARVC).cfa05414=Dilated cardiomyopathy
+Contig211_chr1_114924893_114925515	171	chr1	114925067	ENSCAFT00000007776	ENSCAFP00000007208	P	1988	A	U	benign	N
+Contig35_chr2_27160577_27161526	804	chr2	27161367	ENSCAFT00000007779	ENSCAFP00000007211	G	473	R	478007.478008	probably damaging	cfa03060=Protein export.cfa04141=Protein processing in endoplasmic reticulum.cfa04145=Phagosome
+Contig79_chr17_24285444_24286769	1263	chr17	24286694	ENSCAFT00000007859	ENSCAFP00000007285	S	209	T	483010	benign	N
+Contig74_chr23_10871047_10871362	70	chr23	10871116	ENSCAFT00000007951	ENSCAFP00000007365	I	474	V	U	benign	N
+Contig34_chr16_18928689_18932806	3409	chr16	18932072	ENSCAFT00000007959	ENSCAFP00000007370	A	3754	S	482810.611087	benign	cfa00310=Lysine degradation
+Contig52_chr21_24452521_24454405	725	chr21	24453245	ENSCAFT00000008012	ENSCAFP00000007418	M	289	T	485173	possibly damaging	N
+Contig261_chr1_115563599_115564561	560	chr1	115564156	ENSCAFT00000008063	ENSCAFP00000007465	A	63	T	484489	possibly damaging	N
+Contig62_chr19_41037398_41039465	159	chr19	41037564	ENSCAFT00000008142	ENSCAFP00000007541	C	744	Y	476128	possibly damaging	N
+Contig84_chr1_115960693_115962811	1467	chr1	115962120	ENSCAFT00000008198	ENSCAFP00000007593	W	61	R	612489	benign	N
+Contig135_chr23_14160194_14160717	270	chr23	14160468	ENSCAFT00000008413	ENSCAFP00000007796	V	298	I	U	benign	N
+Contig41_chr17_26203621_26205196	1407	chr17	26205028	ENSCAFT00000008540	ENSCAFP00000007913	H	172	R	483021	benign	N
+Contig260_chr1_116076701_116078120	746	chr1	116077446	ENSCAFT00000008586	ENSCAFP00000007956	T	2486	I	484499	benign	N
+Contig19_chr23_14811332_14815323	1987	chr23	14813327	ENSCAFT00000008588	ENSCAFP00000007958	S	690	L	U	unknown	N
+Contig180_chr2_35061773_35062172	166	chr2	35061941	ENSCAFT00000008673	ENSCAFP00000008039	T	920	M	478018	probably damaging	N
+Contig106_chr21_26153874_26154496	107	chr21	26153984	ENSCAFT00000008678	ENSCAFP00000008044	A	458	T	485188	benign	N
+Contig3_chr19_45625337_45630123	2563	chr19	45627887	ENSCAFT00000008728	ENSCAFP00000008094	V	1264	I	U	benign	N
+Contig51_chr22_48760401_48761638	636	chr22	48761047	ENSCAFT00000008769	ENSCAFP00000008132	R	1071	K	485523	benign	cfa02010=ABC transporters.cfa04976=Bile secretion
+Contig10_chr15_21173640_21174011	212	chr15	21173839	ENSCAFT00000008831	ENSCAFP00000008192	V	191	I	475398	benign	N
+Contig6_chr24_14680423_14681438	782	chr24	14681208	ENSCAFT00000009074	ENSCAFP00000008417	H	562	R	485769	possibly damaging	cfa04330=Notch signaling pathway
+Contig60_chr9_4528464_4529207	262	chr9	4528727	ENSCAFT00000009114	ENSCAFP00000008453	C	24	F	483354	possibly damaging	N
+Contig54_chr15_29510545_29512205	400	chr15	29510955	ENSCAFT00000009614	ENSCAFP00000008928	H	190	R	475416	benign	N
+Contig46_chr25_5067588_5068089	39	chr25	5067627	ENSCAFT00000009698	ENSCAFP00000009003	S	17	N	486001	benign	N
+Contig126_chr25_5114359_5115799	643	chr25	5114996	ENSCAFT00000009710	ENSCAFP00000009013	R	1952	C	486002	possibly damaging	N
+Contig41_chr26_3455305_3455893	329	chr26	3455620	ENSCAFT00000010094	ENSCAFP00000009363	S	909	A	486223	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa05166=HTLV-I infection
+Contig55_chr26_3463883_3465235	1074	chr26	3464998	ENSCAFT00000010094	ENSCAFP00000009363	R	1273	S	486223	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa05166=HTLV-I infection
+Contig63_chr26_3467460_3468420	195	chr26	3467661	ENSCAFT00000010094	ENSCAFP00000009363	E	1542	Q	486223	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa05166=HTLV-I infection
+Contig13_chr16_32259141_32259752	344	chr16	32259472	ENSCAFT00000010141	ENSCAFP00000009407	I	326	T	482857	benign	cfa04360=Axon guidance
+Contig59_chr21_32994329_32995926	1195	chr21	32995538	ENSCAFT00000010439	ENSCAFP00000009680	H	230	R	610992	benign	N
+Contig39_chr20_24938452_24941620	1292	chr20	24939734	ENSCAFT00000010496	ENSCAFP00000009730	S	28	P	415126	benign	cfa04380=Osteoclast differentiation.cfa04916=Melanogenesis.cfa05200=Pathways in cancer.cfa05218=Melanoma
+Contig2_chr18_28546360_28546760	277	chr18	28546640	ENSCAFT00000010516	ENSCAFP00000009748	P	471	S	U	benign	N
+Contig23_chr20_25560598_25562858	928	chr20	25561520	ENSCAFT00000010531	ENSCAFP00000009762	T	749	I	484693	benign	N
+Contig209_chr18_28672330_28672791	376	chr18	28672689	ENSCAFT00000010559	ENSCAFP00000009790	A	33	D	483405	unknown	N
+Contig261_chr18_28694652_28696968	1808	chr18	28696427	ENSCAFT00000010559	ENSCAFP00000009790	P	1443	L	483405	possibly damaging	N
+Contig30_chr25_12008255_12009009	151	chr25	12008417	ENSCAFT00000010593	ENSCAFP00000009822	Q	151	H	U	benign	N
+Contig46_chr29_3065854_3067420	1265	chr29	3067078	ENSCAFT00000010616	ENSCAFP00000009842	V	3253	A	474176	benign	cfa03450=Non-homologous end-joining.cfa04110=Cell cycle
+Contig59_chr28_3755477_3757019	935	chr28	3756419	ENSCAFT00000010630	ENSCAFP00000009853	R	923	Q	486770	possibly damaging	N
+Contig90_chr29_6393993_6395503	951	chr29	6394948	ENSCAFT00000010829	ENSCAFP00000010033	Y	257	C	486944	benign	N
+Contig42_chr16_39015800_39016389	319	chr16	39016119	ENSCAFT00000010865	ENSCAFP00000010068	D	71	N	U	possibly damaging	N
+Contig95_chr21_34533214_34535079	1133	chr21	34534321	ENSCAFT00000010931	ENSCAFP00000010131	E	118	G	485368	benign	N
+Contig82_chr21_34524815_34525170	247	chr21	34525072	ENSCAFT00000010931	ENSCAFP00000010131	Q	499	R	485368	benign	N
+Contig32_chr24_22727492_22727986	147	chr24	22727648	ENSCAFT00000010977	ENSCAFP00000010173	P	278	L	U	possibly damaging	N
+Contig45_chr16_42405571_42406148	269	chr16	42405837	ENSCAFT00000010988	ENSCAFP00000010184	H	406	R	482891	benign	cfa04145=Phagosome
+Contig66_chr15_43321121_43321872	642	chr15	43321764	ENSCAFT00000011187	ENSCAFP00000010364	F	543	L	475441	benign	N
+Contig184_chr27_5103641_5104991	275	chr27	5103979	ENSCAFT00000011380	ENSCAFP00000010541	V	864	A	U	benign	N
+Contig88_chr17_39320200_39320765	204	chr17	39320404	ENSCAFT00000011397	ENSCAFP00000010558	S	1911	N	475750	benign	cfa04110=Cell cycle.cfa04114=Oocyte meiosis.cfa04120=Ubiquitin mediated proteolysis.cfa04914=Progesterone-mediated oocyte maturation.cfa05166=HTLV-I infection
+Contig8_chr16_47195242_47195504	193	chr16	47195429	ENSCAFT00000011721	ENSCAFP00000010862	S	4369	W	475621	benign	N
+Contig84_chr27_5882441_5882771	145	chr27	5882579	ENSCAFT00000011730	ENSCAFP00000010871	C	289	S	486534	benign	N
+Contig42_chr24_25316755_25317362	320	chr24	25317091	ENSCAFT00000011771	ENSCAFP00000010910	G	22	S	477193	benign	N
+Contig45_chr24_25318544_25319490	734	chr24	25319299	ENSCAFT00000011771	ENSCAFP00000010910	V	187	A	477193	benign	N
+Contig31_chr24_25434125_25435133	853	chr24	25434975	ENSCAFT00000011789	ENSCAFP00000010928	S	91	I	609978	benign	N
+Contig20_chr3_10579133_10580085	600	chr3	10579729	ENSCAFT00000011968	ENSCAFP00000011099	K	165	E	488881	benign	cfa00760=Nicotinate and nicotinamide metabolism.cfa04146=Peroxisome
+Contig45_chr2_54585564_54588038	1047	chr2	54586611	ENSCAFT00000012081	ENSCAFP00000011198	T	969	M	478082	benign	cfa04621=NOD-like receptor signaling pathway
+Contig156_chr1_122375741_122376035	168	chr1	122375904	ENSCAFT00000012133	ENSCAFP00000011248	R	628	K	611998	benign	N
+Contig153_chr1_124036982_124040108	1588	chr1	124038585	ENSCAFT00000012159	ENSCAFP00000011272	A	887	T	484609	benign	N
+Contig32_chr24_26900375_26900913	394	chr24	26900761	ENSCAFT00000012254	ENSCAFP00000011358	H	51	Y	U	benign	N
+Contig103_chr16_48829082_48829675	123	chr16	48829205	ENSCAFT00000012381	ENSCAFP00000011471	E	369	G	475632	possibly damaging	N
+Contig25_chr18_41490135_41493501	534	chr18	41490665	ENSCAFT00000012414	ENSCAFP00000011503	R	703	C	483489	probably damaging	cfa04520=Adherens junction.cfa04670=Leukocyte transendothelial migration
+Contig69_chr16_49314879_49317228	1810	chr16	49316689	ENSCAFT00000012456	ENSCAFP00000011541	P	431	L	475636	probably damaging	cfa00565=Ether lipid metabolism
+Contig71_chr17_42734055_42736474	2240	chr17	42736298	ENSCAFT00000012478	ENSCAFP00000011561	R	307	Q	483083	benign	cfa00830=Retinol metabolism
+Contig17_chr17_43378842_43379885	305	chr17	43379148	ENSCAFT00000012676	ENSCAFP00000011740	T	196	M	U	probably damaging	N
+Contig195_chr27_7047911_7049009	555	chr27	7048468	ENSCAFT00000012942	ENSCAFP00000011978	R	881	L	477608	benign	N
+Contig112_chr30_4254316_4256576	1478	chr30	4255785	ENSCAFT00000012974	ENSCAFP00000012007	V	2939	I	U	benign	N
+Contig43_chr20_39124486_39124798	114	chr20	39124607	ENSCAFT00000013097	ENSCAFP00000012118	G	325	R	607274	possibly damaging	N
+Contig96_chr16_55849292_55849592	194	chr16	55849494	ENSCAFT00000013360	ENSCAFP00000012363	A	41	S	482932	benign	cfa04060=Cytokine-cytokine receptor interaction.cfa04150=mTOR signaling pathway.cfa04510=Focal adhesion.cfa05200=Pathways in cancer.cfa05211=Renal cell carcinoma.cfa05212=Pancreatic cancer.cfa05219=Bladder cancer
+Contig91_chr17_51684551_51689453	4154	chr17	51688687	ENSCAFT00000013395	ENSCAFP00000012395	P	306	L	475784	benign	N
+Contig192_chr26_12794366_12794712	143	chr26	12794506	ENSCAFT00000014076	ENSCAFP00000013021	V	2478	I	477486	benign	N
+Contig191_chr31_30109152_30109760	212	chr31	30109363	ENSCAFT00000014113	ENSCAFP00000013055	A	1813	T	487735	probably damaging	N
+Contig116_chr24_29683980_29684819	101	chr24	29684079	ENSCAFT00000014115	ENSCAFP00000013057	R	836	C	485868	probably damaging	N
+Contig8_chr32_9413601_9414435	74	chr32	9413675	ENSCAFT00000014257	ENSCAFP00000013183	N	236	K	478452	probably damaging	cfa00270=Cysteine and methionine metabolism
+Contig90_chr21_43253791_43254774	189	chr21	43253974	ENSCAFT00000014325	ENSCAFP00000013248	I	758	V	U	benign	N
+Contig76_chr24_30292767_30294101	552	chr24	30293321	ENSCAFT00000014346	ENSCAFP00000013267	A	349	T	U	benign	N
+Contig21_chr25_37121451_37122072	177	chr25	37121616	ENSCAFT00000014616	ENSCAFP00000013518	V	157	L	486118	benign	N
+Contig15_chr36_6357141_6362626	5226	chr36	6362346	ENSCAFT00000014702	ENSCAFP00000013598	N	138	K	607626	possibly damaging	N
+Contig64_chr17_54734453_54734993	109	chr17	54734552	ENSCAFT00000014707	ENSCAFP00000013603	S	302	L	483124	benign	N
+Contig91_chr18_46134014_46136042	330	chr18	46134347	ENSCAFT00000014736	ENSCAFP00000013630	A	214	S	483635	benign	cfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways.cfa04070=Phosphatidylinositol signaling system
+Contig111_chr31_31237314_31238628	920	chr31	31238220	ENSCAFT00000014822	ENSCAFP00000013714	S	143	C	478408	benign	N
+Contig77_chr38_3502296_3503058	349	chr38	3502639	ENSCAFT00000015260	ENSCAFP00000014122	K	666	E	478932	benign	N
+Contig59_chr38_3998294_3999004	369	chr38	3998672	ENSCAFT00000015347	ENSCAFP00000014201	V	791	I	U	benign	N
+Contig123_chr31_34367825_34368648	664	chr31	34368468	ENSCAFT00000015534	ENSCAFP00000014373	H	204	Q	U	possibly damaging	N
+Contig43_chr30_11874641_11875130	198	chr30	11874850	ENSCAFT00000015654	ENSCAFP00000014488	R	3422	C	U	benign	N
+Contig9_chr20_40741488_40743247	1027	chr20	40742525	ENSCAFT00000015816	ENSCAFP00000014638	M	183	V	484744	benign	N
+Contig137_chr5_7048977_7051042	863	chr5	7049840	ENSCAFT00000015844	ENSCAFP00000014662	A	311	V	479391	benign	N
+Contig9_chr28_17675067_17680985	1564	chr28	17676618	ENSCAFT00000015971	ENSCAFP00000014772	R	515	P	477805	unknown	N
+Contig126_chr30_12286682_12287475	407	chr30	12287101	ENSCAFT00000016062	ENSCAFP00000014854	V	450	I	487517	benign	cfa00052=Galactose metabolism.cfa00500=Starch and sucrose metabolism.cfa01100=Metabolic pathways
+Contig127_chr30_12287497_12288447	608	chr30	12288095	ENSCAFT00000016062	ENSCAFP00000014854	T	495	M	487517	benign	cfa00052=Galactose metabolism.cfa00500=Starch and sucrose metabolism.cfa01100=Metabolic pathways
+Contig13_chr38_5058391_5058630	66	chr38	5058458	ENSCAFT00000016099	ENSCAFP00000014887	F	412	L	478943	benign	N
+Contig169_chr35_19985467_19986000	455	chr35	19985921	ENSCAFT00000016165	ENSCAFP00000014950	T	175	I	478733	benign	N
+Contig2_chr35_21794536_21795092	291	chr35	21794865	ENSCAFT00000016208	ENSCAFP00000014992	V	84	A	488238	benign	cfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways
+Contig141_chr26_19278751_19279229	364	chr26	19279128	ENSCAFT00000016284	ENSCAFP00000015064	N	29	S	404011	benign	cfa00564=Glycerophospholipid metabolism.cfa00565=Ether lipid metabolism.cfa00590=Arachidonic acid metabolism.cfa00591=Linoleic acid metabolism.cfa00592=alpha-Linolenic acid metabolism.cfa01100=Metabolic pathways.cfa04010=MAPK signaling pathway.cfa04270=Vascular smooth muscle contraction.cfa04370=VEGF signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04724=Glutamatergic synapse.cfa04730=Long-term depression.cfa04912=GnRH signaling pathway.cfa04972=Pancreatic secretion.cfa04975=Fat digestion and absorption.cfa05145=Toxoplasmosis
+Contig179_chr3_40781459_40782026	285	chr3	40781763	ENSCAFT00000016410	ENSCAFP00000015182	D	1174	N	488699	benign	N
+Contig237_chr21_53631024_53632458	203	chr21	53631227	ENSCAFT00000016459	ENSCAFP00000015227	C	47	W	403799	probably damaging	cfa04664=Fc epsilon RI signaling pathway.cfa05310=Asthma
+Contig186_chr2_71203100_71204111	202	chr2	71203303	ENSCAFT00000016485	ENSCAFP00000015250	S	188	T	478144	benign	cfa00330=Arginine and proline metabolism.cfa01100=Metabolic pathways
+Contig1_chr28_18779291_18780149	325	chr28	18779619	ENSCAFT00000016578	ENSCAFP00000015340	N	245	Y	U	probably damaging	N
+Contig166_chr4_77425871_77426835	797	chr4	77426667	ENSCAFT00000016670	ENSCAFP00000015429	D	115	G	479370	benign	cfa00970=Aminoacyl-tRNA biosynthesis
+Contig35_chr24_36806524_36807086	367	chr24	36806891	ENSCAFT00000016727	ENSCAFP00000015478	F	345	L	485910	benign	N
+Contig45_chr37_8610877_8611425	194	chr37	8611078	ENSCAFT00000016761	ENSCAFP00000015511	D	2849	N	488452	possibly damaging	N
+Contig39_chr28_19446540_19447838	1068	chr28	19447566	ENSCAFT00000016791	ENSCAFP00000015537	A	1596	E	U	benign	N
+Contig161_chr18_51013230_51015381	1494	chr18	51014735	ENSCAFT00000016827	ENSCAFP00000015571	L	977	V	475999	benign	N
+Contig25_chr28_19619108_19621267	1728	chr28	19620832	ENSCAFT00000016848	ENSCAFP00000034237	I	108	V	609723	benign	N
+Contig33_chr20_42063173_42064259	623	chr20	42063789	ENSCAFT00000017070	ENSCAFP00000015794	V	179	M	U	probably damaging	N
+Contig39_chr38_14681397_14682234	384	chr38	14681781	ENSCAFT00000017072	ENSCAFP00000015796	H	282	N	488593	unknown	N
+Contig6_chr32_27303975_27304541	425	chr32	27304407	ENSCAFT00000017178	ENSCAFP00000015896	S	354	T	610098	benign	N
+Contig173_chr38_17709765_17711029	179	chr38	17709941	ENSCAFT00000017240	ENSCAFP00000015955	G	464	R	U	benign	N
+Contig52_chr32_27452924_27453332	91	chr32	27452999	ENSCAFT00000017249	ENSCAFP00000015964	A	22	S	U	benign	N
+Contig319_chr34_14684259_14684663	353	chr34	14684613	ENSCAFT00000017314	ENSCAFP00000016025	R	5	Q	478632	benign	N
+Contig32_chr2_72269353_72269814	349	chr2	72269708	ENSCAFT00000017327	ENSCAFP00000016037	P	853	L	487317	possibly damaging	N
+Contig206_chr9_18720001_18720613	155	chr9	18720160	ENSCAFT00000017373	ENSCAFP00000016082	D	1621	E	480456	benign	cfa02010=ABC transporters
+Contig35_chr37_10562149_10562621	74	chr37	10562222	ENSCAFT00000017444	ENSCAFP00000016153	I	975	V	478858	benign	cfa04727=GABAergic synapse
+Contig1_chr30_12655575_12656916	370	chr30	12655947	ENSCAFT00000017777	ENSCAFP00000016457	L	639	M	608886	probably damaging	N
+Contig63_chr27_23738716_23739879	1131	chr27	23739850	ENSCAFT00000017892	ENSCAFP00000016566	P	642	L	486627	benign	N
+Contig44_chr28_28123120_28124627	1348	chr28	28124495	ENSCAFT00000017967	ENSCAFP00000016639	V	261	A	477827	benign	N
+Contig23_chrX_6416128_6417014	455	chrX	6416585	ENSCAFT00000018017	ENSCAFP00000016684	H	111	R	491733	possibly damaging	N
+Contig31_chr7_8282189_8286932	3631	chr7	8285875	ENSCAFT00000018057	ENSCAFP00000016724	L	655	P	490260	benign	N
+Contig318_chr6_8706066_8706350	76	chr6	8706142	ENSCAFT00000018106	ENSCAFP00000016769	K	318	N	607700	possibly damaging	cfa04062=Chemokine signaling pathway.cfa04145=Phagosome.cfa04380=Osteoclast differentiation.cfa04666=Fc gamma R-mediated phagocytosis.cfa04670=Leukocyte transendothelial migration.cfa05140=Leishmaniasis
+Contig36_chr32_33046881_33048369	1118	chr32	33047990	ENSCAFT00000018307	ENSCAFP00000016954	E	555	A	403657	benign	cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04060=Cytokine-cytokine receptor interaction.cfa04144=Endocytosis.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04810=Regulation of actin cytoskeleton.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05212=Pancreatic cancer.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05218=Melanoma.cfa05219=Bladder cancer.cfa05223=Non-small cell lung cancer
+Contig32_chr5_14476595_14477214	347	chr5	14476948	ENSCAFT00000018571	ENSCAFP00000017201	V	209	A	610296	benign	N
+Contig88_chr34_19031138_19031937	343	chr34	19031477	ENSCAFT00000018684	ENSCAFP00000017309	K	670	R	478645	benign	cfa00280=Valine, leucine and isoleucine degradation.cfa01100=Metabolic pathways
+Contig188_chr25_47927372_47928085	557	chr25	47927941	ENSCAFT00000018758	ENSCAFP00000017379	K	228	R	486167	benign	cfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways.cfa04070=Phosphatidylinositol signaling system
+Contig36_chr37_12924359_12924740	86	chr37	12924449	ENSCAFT00000018786	ENSCAFP00000017406	D	187	Y	608849	probably damaging	cfa00280=Valine, leucine and isoleucine degradation.cfa00350=Tyrosine metabolism.cfa00380=Tryptophan metabolism.cfa00750=Vitamin B6 metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00982=Drug metabolism - cytochrome P450.cfa01100=Metabolic pathways
+Contig3_chr34_19471626_19472377	337	chr34	19471956	ENSCAFT00000018788	ENSCAFP00000017408	R	239	Q	488096	possibly damaging	N
+Contig80_chr4_11155760_11156827	952	chr4	11156735	ENSCAFT00000018796	ENSCAFP00000017416	S	661	N	479204	benign	cfa00564=Glycerophospholipid metabolism.cfa04146=Peroxisome
+Contig56_chr8_7093747_7095987	683	chr8	7094428	ENSCAFT00000018813	ENSCAFP00000017431	P	126	R	490620	unknown	N
+Contig82_chr8_7111986_7114065	1351	chr8	7113329	ENSCAFT00000018871	ENSCAFP00000017488	R	608	H	480255	probably damaging	cfa00010=Glycolysis / Gluconeogenesis.cfa00020=Citrate cycle (TCA cycle).cfa00620=Pyruvate metabolism.cfa01100=Metabolic pathways.cfa03320=PPAR signaling pathway.cfa04910=Insulin signaling pathway.cfa04920=Adipocytokine signaling pathway.cfa04964=Proximal tubule bicarbonate reclamation
+Contig172_chr33_28585454_28586084	228	chr33	28585687	ENSCAFT00000018884	ENSCAFP00000017500	R	36	K	478584	benign	N
+Contig113_chr5_16682954_16684491	688	chr5	16683641	ENSCAFT00000018997	ENSCAFP00000017606	F	41	L	489360	benign	N
+Contig36_chr28_31449413_31452160	2111	chr28	31451506	ENSCAFT00000019041	ENSCAFP00000017650	P	252	H	477834	benign	cfa04144=Endocytosis
+Contig80_chr3_55628026_55628800	392	chr3	55628403	ENSCAFT00000019070	ENSCAFP00000017677	R	805	K	403913	benign	cfa00480=Glutathione metabolism.cfa01100=Metabolic pathways.cfa04614=Renin-angiotensin system.cfa04640=Hematopoietic cell lineage
+Contig99_chr7_11816365_11819255	806	chr7	11817201	ENSCAFT00000019101	ENSCAFP00000017707	C	305	G	490276	benign	N
+Contig114_chr4_12744102_12745318	148	chr4	12744256	ENSCAFT00000019279	ENSCAFP00000017880	I	700	V	U	benign	N
+Contig82_chr7_13056757_13058281	974	chr7	13057742	ENSCAFT00000019316	ENSCAFP00000017915	S	283	N	609933	benign	cfa00564=Glycerophospholipid metabolism
+Contig280_chr25_51367477_51367885	70	chr25	51367542	ENSCAFT00000019610	ENSCAFP00000018191	S	97	L	U	benign	N
+Contig35_chr20_43508791_43509352	460	chr20	43509254	ENSCAFT00000019627	ENSCAFP00000018204	V	77	A	608455	benign	cfa00190=Oxidative phosphorylation.cfa01100=Metabolic pathways.cfa04260=Cardiac muscle contraction.cfa05010=Alzheimer's disease.cfa05012=Parkinson's disease.cfa05016=Huntington's disease
+Contig36_chr20_43509362_43510980	1484	chr20	43510860	ENSCAFT00000019627	ENSCAFP00000018204	D	181	N	608455	benign	cfa00190=Oxidative phosphorylation.cfa01100=Metabolic pathways.cfa04260=Cardiac muscle contraction.cfa05010=Alzheimer's disease.cfa05012=Parkinson's disease.cfa05016=Huntington's disease
+Contig59_chr25_51807653_51809044	1064	chr25	51808739	ENSCAFT00000019760	ENSCAFP00000018330	R	235	K	U	benign	N
+Contig96_chr36_17712997_17714068	556	chr36	17713559	ENSCAFT00000019807	ENSCAFP00000018374	T	423	I	478789	benign	N
+Contig163_chr28_34927368_34929275	1128	chr28	34928486	ENSCAFT00000019866	ENSCAFP00000018425	A	2659	T	477850	benign	N
+Contig74_chr33_31230250_31230874	246	chr33	31230493	ENSCAFT00000019938	ENSCAFP00000018492	G	113	S	488016	probably damaging	N
+Contig130_chr7_15553315_15558308	3186	chr7	15556497	ENSCAFT00000020009	ENSCAFP00000018561	K	1513	N	U	benign	N
+Contig160_chr2_76816412_76817166	354	chr2	76816779	ENSCAFT00000020143	ENSCAFP00000018683	I	190	V	478173	benign	N
+Contig219_chr33_31871568_31871771	81	chr33	31871646	ENSCAFT00000020195	ENSCAFP00000018733	N	346	H	U	probably damaging	N
+Contig254_chr24_50001599_50001992	151	chr24	50001767	ENSCAFT00000020266	ENSCAFP00000018803	R	239	Q	U	benign	N
+Contig40_chr37_15283702_15285945	1908	chr37	15285621	ENSCAFT00000020408	ENSCAFP00000018937	A	809	G	U	unknown	N
+Contig59_chr20_43702094_43703358	450	chr20	43702540	ENSCAFT00000020438	ENSCAFP00000018965	S	217	A	U	benign	N
+Contig75_chr3_57465650_57466327	377	chr3	57466017	ENSCAFT00000020863	ENSCAFP00000019371	L	205	F	609716	probably damaging	N
+Contig155_chr2_79195879_79199423	2014	chr2	79197892	ENSCAFT00000021154	ENSCAFP00000019645	G	549	S	U	benign	N
+Contig155_chr2_79195879_79199423	3136	chr2	79199014	ENSCAFT00000021154	ENSCAFP00000019645	R	923	C	U	probably damaging	N
+Contig59_chr5_19784971_19787384	1310	chr5	19786293	ENSCAFT00000021222	ENSCAFP00000019707	V	171	I	479428.489393	benign	cfa03320=PPAR signaling pathway
+Contig41_chr30_14304605_14305465	206	chr30	14304816	ENSCAFT00000021612	ENSCAFP00000020069	A	157	G	U	benign	N
+Contig47_chr20_45043804_45044476	317	chr20	45044117	ENSCAFT00000021659	ENSCAFP00000020114	V	281	I	609323	benign	N
+Contig46_chr4_22849549_22849829	123	chr4	22849673	ENSCAFT00000021752	ENSCAFP00000020204	V	646	M	U	probably damaging	N
+Contig141_chr7_22360980_22361690	242	chr7	22361233	ENSCAFT00000021777	ENSCAFP00000020227	K	1862	R	U	unknown	N
+Contig59_chr30_14758622_14760653	1186	chr30	14759817	ENSCAFT00000021792	ENSCAFP00000020241	S	284	R	609256	benign	N
+Contig57_chr27_39696388_39698349	1026	chr27	39697428	ENSCAFT00000021846	ENSCAFP00000020293	Q	588	R	477699	benign	cfa04610=Complement and coagulation cascades
+Contig83_chr27_40151814_40153141	738	chr27	40152551	ENSCAFT00000022064	ENSCAFP00000020490	S	191	R	477702	benign	N
+Contig105_chr6_11901733_11904968	406	chr6	11902145	ENSCAFT00000022289	ENSCAFP00000020701	Y	55	H	479732	probably damaging	cfa04621=NOD-like receptor signaling pathway
+Contig43_chr36_25298890_25299602	235	chr36	25299132	ENSCAFT00000022319	ENSCAFP00000020728	E	11731	K	610299.610339	unknown	N
+Contig3_chr36_25193150_25202641	2802	chr36	25195983	ENSCAFT00000022319	ENSCAFP00000020728	I	30137	V	610299.610339	benign	N
+Contig585_chr3_61201332_61201904	139	chr3	61201468	ENSCAFT00000022529	ENSCAFP00000020918	L	97	V	479067	benign	cfa00071=Fatty acid metabolism.cfa03320=PPAR signaling pathway.cfa04920=Adipocytokine signaling pathway
+Contig1_chr20_46714929_46715937	434	chr20	46715327	ENSCAFT00000022571	ENSCAFP00000020958	A	18	P	484804	unknown	N
+Contig7_chr8_29376780_29378260	158	chr8	29376937	ENSCAFT00000022576	ENSCAFP00000020962	T	852	A	490678	benign	N
+Contig74_chr8_29656170_29657212	595	chr8	29656776	ENSCAFT00000022697	ENSCAFP00000021080	E	974	K	490682	possibly damaging	cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04062=Chemokine signaling pathway.cfa04320=Dorso-ventral axis formation.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04630=Jak-STAT signaling pathway.cfa04650=Natural killer cell mediated cytotoxicity.cfa04660=T cell receptor signaling pathway.cfa04662=B cell receptor signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04722=Neurotrophin signaling pathway.cfa04810=Regulation of actin cytoskeleton.cfa04910=Insulin signaling pathway.cfa04912=GnRH signaling pathway.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05211=Renal cell carcinoma.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05220=Chronic myeloid leukemia.cfa05221=Acute myeloid leukemia.cfa05223=Non-small cell lung cancer
+Contig45_chr4_25273541_25274402	608	chr4	25274121	ENSCAFT00000022760	ENSCAFP00000021140	S	30	F	479239	probably damaging	cfa04360=Axon guidance
+Contig96_chr37_26111249_26111450	108	chr37	26111364	ENSCAFT00000022884	ENSCAFP00000021256	K	260	R	478902	benign	cfa03450=Non-homologous end-joining
+Contig196_chr3_62434637_62435063	203	chr3	62434823	ENSCAFT00000022915	ENSCAFP00000021284	L	174	P	488785	benign	N
+Contig15_chr6_12238116_12239737	1287	chr6	12239420	ENSCAFT00000022961	ENSCAFP00000021328	E	165	K	479735	benign	N
+Contig175_chr5_27267391_27267870	57	chr5	27267451	ENSCAFT00000023032	ENSCAFP00000021395	N	1094	S	479450	benign	cfa04110=Cell cycle.cfa04115=p53 signaling pathway.cfa04210=Apoptosis.cfa05166=HTLV-I infection
+Contig110_chr20_47192181_47193618	93	chr20	47192262	ENSCAFT00000023054	ENSCAFP00000021407	A	308	P	484814	probably damaging	N
+Contig9_chr4_26730063_26730585	245	chr4	26730316	ENSCAFT00000023087	ENSCAFP00000021437	E	153	D	489044	benign	N
+Contig1_chr34_35420831_35421658	73	chr34	35420908	ENSCAFT00000023111	ENSCAFP00000021457	V	251	I	488144	benign	N
+Contig199_chr2_79696091_79697603	751	chr2	79696840	ENSCAFT00000023253	ENSCAFP00000021593	D	54	A	U	possibly damaging	N
+Contig146_chrX_38946913_38947473	307	chrX	38947225	ENSCAFT00000023268	ENSCAFP00000021608	L	160	V	612457	possibly damaging	N
+Contig63_chr9_23532151_23533554	1297	chr9	23533421	ENSCAFT00000023438	ENSCAFP00000021767	Q	279	R	490958	benign	N
+Contig89_chr5_32060784_32061151	293	chr5	32061079	ENSCAFT00000023913	ENSCAFP00000022199	W	106	*	489430	probably damaging	N
+Contig15_chr3_65640843_65642155	1100	chr3	65641942	ENSCAFT00000023933	ENSCAFP00000022218	V	383	A	479080	benign	N
+Contig49_chr26_33571748_33572620	689	chr26	33572452	ENSCAFT00000024062	ENSCAFP00000022339	R	478	W	486440	benign	N
+Contig96_chr20_48055741_48057197	524	chr20	48056259	ENSCAFT00000024100	ENSCAFP00000022374	R	172	Q	U	benign	N
+Contig104_chr20_48062263_48062546	210	chr20	48062492	ENSCAFT00000024100	ENSCAFP00000022374	V	775	G	U	probably damaging	N
+Contig33_chr37_28794567_28796956	2144	chr37	28796718	ENSCAFT00000024137	ENSCAFP00000022408	E	279	Q	488536	benign	N
+Contig24_chr7_32005266_32005660	212	chr7	32005479	ENSCAFT00000024154	ENSCAFP00000022424	T	92	M	U	probably damaging	N
+Contig174_chr18_56896461_56897594	274	chr18	56896734	ENSCAFT00000024637	ENSCAFP00000022858	V	157	L	483779	benign	cfa04130=SNARE interactions in vesicular transport
+Contig55_chr20_48811642_48812027	299	chr20	48811941	ENSCAFT00000024761	ENSCAFP00000022970	H	993	R	476678	benign	N
+Contig220_chr18_56925351_56927006	920	chr18	56926246	ENSCAFT00000024787	ENSCAFP00000022995	P	420	Q	476051	possibly damaging	cfa03022=Basal transcription factors.cfa05168=Herpes simplex infection
+Contig12_chr8_39044824_39045409	359	chr8	39045181	ENSCAFT00000024804	ENSCAFP00000023011	I	280	T	612894	possibly damaging	N
+Contig23_chr3_72567678_72570858	1313	chr3	72568976	ENSCAFT00000024846	ENSCAFP00000023051	L	298	P	488826	benign	N
+Contig190_chr7_35896301_35896811	232	chr7	35896528	ENSCAFT00000024892	ENSCAFP00000023095	R	3	L	480092	unknown	cfa00020=Citrate cycle (TCA cycle).cfa01100=Metabolic pathways.cfa05200=Pathways in cancer.cfa05211=Renal cell carcinoma
+Contig119_chr20_49114009_49114654	266	chr20	49114270	ENSCAFT00000024934	ENSCAFP00000023135	F	339	L	484849	benign	N
+Contig47_chr8_41487304_41487682	210	chr8	41487515	ENSCAFT00000025088	ENSCAFP00000023286	S	1743	L	490729	possibly damaging	N
+Contig67_chr2_84099157_84100880	345	chr2	84099493	ENSCAFT00000025109	ENSCAFP00000023307	I	60	L	U	benign	N
+Contig33_chr20_49727730_49730958	2192	chr20	49729935	ENSCAFT00000025308	ENSCAFP00000023495	T	448	R	U	probably damaging	N
+Contig33_chr20_49727730_49730958	2907	chr20	49730606	ENSCAFT00000025308	ENSCAFP00000023495	W	493	L	U	benign	N
+Contig93_chr8_42181027_42183022	694	chr8	42181716	ENSCAFT00000025462	ENSCAFP00000023641	L	782	P	U	benign	N
+Contig131_chrX_44937490_44940040	950	chrX	44938456	ENSCAFT00000025663	ENSCAFP00000023835	V	120	M	491894	benign	N
+Contig100_chrX_44915404_44918232	1832	chrX	44917224	ENSCAFT00000025663	ENSCAFP00000023835	R	1212	Q	491894	benign	N
+Contig100_chrX_44915404_44918232	920	chrX	44916331	ENSCAFT00000025663	ENSCAFP00000023835	L	1377	V	491894	benign	N
+Contig123_chr9_26132942_26133532	310	chr9	26133253	ENSCAFT00000025948	ENSCAFP00000024090	I	232	V	491022	benign	N
+Contig34_chr6_17772839_17773548	489	chr6	17773329	ENSCAFT00000026008	ENSCAFP00000024146	E	377	Q	U	benign	N
+Contig382_chr7_43383655_43383893	190	chr7	43383854	ENSCAFT00000026053	ENSCAFP00000024188	R	123	C	U	possibly damaging	N
+Contig163_chr2_87404548_87404792	132	chr2	87404673	ENSCAFT00000026251	ENSCAFP00000024378	D	239	N	U	benign	N
+Contig15_chr3_91850893_91851323	75	chr3	91850967	ENSCAFT00000026343	ENSCAFP00000024465	S	722	N	595148	benign	cfa04360=Axon guidance
+Contig141_chr7_44385686_44386047	166	chr7	44385857	ENSCAFT00000026393	ENSCAFP00000024510	L	166	P	490412	benign	cfa04810=Regulation of actin cytoskeleton
+Contig161_chr2_87840986_87841705	540	chr2	87841516	ENSCAFT00000026485	ENSCAFP00000024598	F	678	C	478233	probably damaging	cfa03018=RNA degradation
+Contig177_chr9_27497479_27498192	354	chr9	27497831	ENSCAFT00000026613	ENSCAFP00000024719	A	175	V	491046	possibly damaging	N
+Contig162_chr6_20156115_20157725	81	chr6	20156197	ENSCAFT00000026687	ENSCAFP00000024793	T	702	M	489923.489924.607168	benign	N
+Contig8_chr9_28287278_28288276	469	chr9	28287755	ENSCAFT00000026707	ENSCAFP00000024813	A	75	P	491060	benign	N
+Contig166_chr7_45276673_45277595	235	chr7	45276916	ENSCAFT00000026881	ENSCAFP00000024984	V	525	I	490428	benign	N
+Contig16_chr8_51223078_51223662	481	chr8	51223563	ENSCAFT00000026967	ENSCAFP00000025070	R	869	Q	490790	benign	N
+Contig65_chr9_29792446_29793465	893	chr9	29793341	ENSCAFT00000027073	ENSCAFP00000025173	S	81	A	491082	benign	N
+Contig175_chr6_30926774_30927470	446	chr6	30927229	ENSCAFT00000027269	ENSCAFP00000025361	S	663	T	403453	benign	cfa02010=ABC transporters.cfa04977=Vitamin digestion and absorption
+Contig45_chr30_33024389_33025619	471	chr30	33024857	ENSCAFT00000027320	ENSCAFP00000025407	G	986	A	487608	benign	N
+Contig60_chr20_53087461_53088013	184	chr20	53087649	ENSCAFT00000027519	ENSCAFP00000025591	S	556	L	611163	benign	N
+Contig98_chr5_37073086_37073674	378	chr5	37073467	ENSCAFT00000027596	ENSCAFP00000025664	V	38	M	479499	probably damaging	cfa04130=SNARE interactions in vesicular transport
+Contig64_chr9_36235086_36235751	475	chr9	36235563	ENSCAFT00000027673	ENSCAFP00000025737	D	260	E	491111	benign	cfa04970=Salivary secretion
+Contig72_chr30_35330469_35330831	236	chr30	35330709	ENSCAFT00000027712	ENSCAFP00000025770	G	386	C	478353	probably damaging	cfa04510=Focal adhesion.cfa04512=ECM-receptor interaction.cfa04810=Regulation of actin cytoskeleton.cfa05410=Hypertrophic cardiomyopathy (HCM).cfa05412=Arrhythmogenic right ventricular cardiomyopathy (ARVC).cfa05414=Dilated cardiomyopathy
+Contig12_chr8_66066327_66066629	89	chr8	66066402	ENSCAFT00000027927	ENSCAFP00000025970	K	158	R	490836	benign	N
+Contig212_chr8_66173086_66174259	622	chr8	66173712	ENSCAFT00000027950	ENSCAFP00000025993	K	114	Q	480421	benign	N
+Contig176_chr7_48083671_48084458	311	chr7	48083983	ENSCAFT00000027972	ENSCAFP00000026015	R	128	H	480148	probably damaging	N
+Contig3_chr4_58820541_58821952	265	chr4	58820806	ENSCAFT00000027979	ENSCAFP00000026022	A	31	T	489166	benign	N
+Contig24_chr7_48238665_48239174	383	chr7	48239049	ENSCAFT00000028007	ENSCAFP00000026049	T	227	M	480151	probably damaging	N
+Contig25_chr6_26340448_26341519	657	chr6	26341104	ENSCAFT00000028115	ENSCAFP00000026155	S	128	L	479811	possibly damaging	N
+Contig212_chr5_38871122_38871621	302	chr5	38871429	ENSCAFT00000028231	ENSCAFP00000026253	P	2265	L	489507	benign	N
+Contig147_chr6_27310627_27310983	100	chr6	27310719	ENSCAFT00000028327	ENSCAFP00000026344	V	154	A	U	benign	N
+Contig160_chr6_27318582_27318861	67	chr6	27318647	ENSCAFT00000028327	ENSCAFP00000026344	K	325	R	U	benign	N
+Contig18_chr4_61023435_61026038	385	chr4	61023825	ENSCAFT00000028363	ENSCAFP00000026377	P	4110	L	479323	benign	N
+Contig162_chr30_40685605_40687049	343	chr30	40685956	ENSCAFT00000028463	ENSCAFP00000026472	A	416	P	487646	benign	N
+Contig68_chr20_54017481_54018354	221	chr20	54017705	ENSCAFT00000028500	ENSCAFP00000026509	W	539	R	U	benign	N
+Contig50_chr7_59076761_59079381	2353	chr7	59079104	ENSCAFT00000028551	ENSCAFP00000026557	V	1487	I	490492	benign	N
+Contig51_chr7_59079274_59084588	2611	chr7	59081905	ENSCAFT00000028551	ENSCAFP00000026557	A	575	V	490492	benign	N
+Contig3_chr20_54855789_54856135	37	chr20	54855833	ENSCAFT00000028813	ENSCAFP00000026796	F	6015	S	U	unknown	N
+Contig157_chr5_43472186_43472528	168	chr5	43472353	ENSCAFT00000028826	ENSCAFP00000026807	R	355	Q	489526	benign	cfa00010=Glycolysis / Gluconeogenesis.cfa00340=Histidine metabolism.cfa00350=Tyrosine metabolism.cfa00360=Phenylalanine metabolism.cfa00410=beta-Alanine metabolism.cfa00980=Metabolism of xenobiotics by cytochrome P450.cfa00982=Drug metabolism - cytochrome P450.cfa01100=Metabolic pathways
+Contig80_chr20_55281094_55281971	129	chr20	55281228	ENSCAFT00000028936	ENSCAFP00000026914	T	931	A	U	benign	N
+Contig214_chr8_74493164_74493474	188	chr8	74493346	ENSCAFT00000029054	ENSCAFP00000027017	R	94	C	U	probably damaging	N
+Contig259_chr20_55571618_55572503	186	chr20	55571803	ENSCAFT00000029100	ENSCAFP00000027059	K	526	Q	485001	benign	N
+Contig180_chr9_41668066_41668716	357	chr9	41668451	ENSCAFT00000029122	ENSCAFP00000027081	E	990	D	491145	benign	cfa03410=Base excision repair
+Contig61_chr4_63087183_63089623	491	chr4	63087672	ENSCAFT00000029130	ENSCAFP00000027089	A	20	S	U	benign	N
+Contig261_chrX_94412915_94414298	488	chrX	94413396	ENSCAFT00000029188	ENSCAFP00000027142	D	329	E	U	unknown	N
+Contig58_chr4_70221679_70223505	1749	chr4	70223432	ENSCAFT00000029501	ENSCAFP00000027423	T	324	S	403721	benign	cfa04060=Cytokine-cytokine receptor interaction.cfa04080=Neuroactive ligand-receptor interaction.cfa04630=Jak-STAT signaling pathway
+Contig21_chr7_77985141_77986170	827	chr7	77985962	ENSCAFT00000029651	ENSCAFP00000027557	A	855	S	490545	benign	N
+Contig93_chrX_104176429_104177974	811	chrX	104177246	ENSCAFT00000029709	ENSCAFP00000027610	T	719	M	492128	benign	cfa03008=Ribosome biogenesis in eukaryotes
+Contig175_chr9_46116277_46118268	1090	chr9	46117366	ENSCAFT00000029722	ENSCAFP00000027622	Q	693	H	U	benign	N
+Contig134_chr4_76495667_76496825	860	chr4	76496507	ENSCAFT00000029827	ENSCAFP00000027720	I	113	V	612589	benign	cfa00250=Alanine, aspartate and glutamate metabolism.cfa00260=Glycine, serine and threonine metabolism.cfa01100=Metabolic pathways
+Contig247_chr6_31967574_31967796	158	chr6	31967732	ENSCAFT00000029875	ENSCAFP00000027765	P	750	T	489999	benign	N
+Contig6_chr7_81650872_81657348	3786	chr7	81654636	ENSCAFT00000030050	ENSCAFP00000027927	S	501	C	480218	benign	N
+Contig122_chr5_57147596_57148457	360	chr5	57147964	ENSCAFT00000030140	ENSCAFP00000028007	T	713	I	479558	benign	N
+Contig83_chr20_58039274_58039724	380	chr20	58039649	ENSCAFT00000030192	ENSCAFP00000028056	E	142	K	611866	benign	N
+Contig42_chr5_58023274_58024296	585	chr5	58023845	ENSCAFT00000030282	ENSCAFP00000028135	V	415	A	489580	benign	N
+Contig248_chr20_58217741_58219717	751	chr20	58218495	ENSCAFT00000030285	ENSCAFP00000028138	G	278	S	485038	unknown	N
+Contig127_chr6_39501489_39501966	83	chr6	39501576	ENSCAFT00000030381	ENSCAFP00000028228	N	155	S	490020	benign	N
+Contig123_chr6_39499974_39501056	816	chr6	39500798	ENSCAFT00000030381	ENSCAFP00000028228	A	195	P	490020	benign	N
+Contig247_chr6_39576694_39577607	493	chr6	39577171	ENSCAFT00000030386	ENSCAFP00000028233	S	745	N	490021	benign	N
+Contig6_chr9_50725202_50725646	143	chr9	50725344	ENSCAFT00000030726	ENSCAFP00000028560	M	12	T	491218	benign	N
+Contig221_chr6_41879771_41881379	766	chr6	41880519	ENSCAFT00000030883	ENSCAFP00000028717	A	184	T	606755	benign	N
+Contig231_chr5_60474911_60475630	279	chr5	60475186	ENSCAFT00000030960	ENSCAFP00000028794	C	505	Y	489618	possibly damaging	N
+Contig99_chr5_63306202_63308496	2063	chr5	63308224	ENSCAFT00000031146	ENSCAFP00000028978	A	421	V	U	unknown	N
+Contig245_chr5_66149146_66149848	349	chr5	66149499	ENSCAFT00000031407	ENSCAFP00000029234	R	207	Q	479601	benign	cfa00760=Nicotinate and nicotinamide metabolism.cfa01100=Metabolic pathways
+Contig305_chr5_67253589_67254394	375	chr5	67253954	ENSCAFT00000031570	ENSCAFP00000029391	R	203	Q	U	possibly damaging	N
+Contig94_chr9_56873843_56875505	1578	chr9	56875408	ENSCAFT00000031743	ENSCAFP00000029555	P	2937	S	U	benign	N
+Contig107_chr5_71317862_71318113	71	chr5	71317944	ENSCAFT00000031781	ENSCAFP00000029590	M	281	V	U	benign	N
+Contig134_chr9_57426140_57427208	236	chr9	57426380	ENSCAFT00000031798	ENSCAFP00000029606	V	89	I	480698	benign	cfa00590=Arachidonic acid metabolism.cfa01100=Metabolic pathways
+Contig60_chr12_5631507_5632392	818	chr12	5632313	ENSCAFT00000031814	ENSCAFP00000029621	Y	1697	C	481734	unknown	cfa04510=Focal adhesion.cfa04512=ECM-receptor interaction.cfa04974=Protein digestion and absorption.cfa05146=Amoebiasis
+Contig132_chr5_73710776_73711271	149	chr5	73710927	ENSCAFT00000031848	ENSCAFP00000029653	T	1323	M	489696	probably damaging	N
+Contig39_chr9_59278364_59279024	398	chr9	59278757	ENSCAFT00000032068	ENSCAFP00000029863	A	957	T	480718	benign	N
+Contig177_chr9_61212763_61213621	700	chr9	61213430	ENSCAFT00000032171	ENSCAFP00000029958	D	79	N	U	benign	N
+Contig67_chr6_62507717_62510152	1055	chr6	62508787	ENSCAFT00000032186	ENSCAFP00000029972	I	212	M	479959	probably damaging	cfa00380=Tryptophan metabolism.cfa00450=Selenocompound metabolism.cfa01100=Metabolic pathways
+Contig66_chr6_64570039_64570630	325	chr6	64570365	ENSCAFT00000032239	ENSCAFP00000030024	A	862	G	479964	benign	cfa04740=Olfactory transduction.cfa04972=Pancreatic secretion
+Contig22_chr6_64809414_64810661	626	chr6	64810027	ENSCAFT00000032269	ENSCAFP00000030052	Q	559	K	490179	benign	N
+Contig50_chr5_85052459_85052865	55	chr5	85052515	ENSCAFT00000032431	ENSCAFP00000030201	S	32	G	479688	benign	N
+Contig25_chr5_85095840_85098495	1627	chr5	85097474	ENSCAFT00000032433	ENSCAFP00000030203	F	681	S	U	benign	N
+Contig25_chr5_85480673_85480982	186	chr5	85480860	ENSCAFT00000032493	ENSCAFP00000030260	A	180	T	610026	possibly damaging	cfa05010=Alzheimer's disease
+Contig19_chr5_24601128_24602241	685	chr5	24601813	ENSCAFT00000035141	ENSCAFP00000030364	T	695	S	U	benign	N
+Contig59_chr26_11519273_11520242	659	chr26	11519937	ENSCAFT00000035276	ENSCAFP00000030520	P	160	L	403557	probably damaging	cfa03015=mRNA surveillance pathway.cfa04114=Oocyte meiosis.cfa04270=Vascular smooth muscle contraction.cfa04510=Focal adhesion.cfa04720=Long-term potentiation.cfa04728=Dopaminergic synapse.cfa04810=Regulation of actin cytoskeleton.cfa04910=Insulin signaling pathway.cfa05168=Herpes simplex infection
+Contig27_chr12_23130802_23131771	353	chr12	23131154	ENSCAFT00000035307	ENSCAFP00000030552	V	565	M	474935	probably damaging	N
+Contig31_chr1_8052327_8053606	234	chr1	8052570	ENSCAFT00000035442	ENSCAFP00000030703	C	153	S	U	possibly damaging	N
+Contig59_chr20_40539078_40540678	1223	chr20	40540302	ENSCAFT00000035532	ENSCAFP00000030804	H	285	R	403502	benign	cfa04620=Toll-like receptor signaling pathway.cfa05142=Chagas disease (American trypanosomiasis).cfa05143=African trypanosomiasis.cfa05144=Malaria.cfa05152=Tuberculosis.cfa05162=Measles.cfa05168=Herpes simplex infection
+Contig152_chr6_25356961_25358151	701	chr6	25357665	ENSCAFT00000035750	ENSCAFP00000031044	P	479	S	608555	benign	cfa04142=Lysosome
+Contig18_chr9_58576258_58576773	215	chr9	58576474	ENSCAFT00000035914	ENSCAFP00000031224	K	118	E	480706	benign	N
+Contig8_chr15_38734005_38734403	242	chr15	38734244	ENSCAFT00000035916	ENSCAFP00000031226	A	237	V	611996	possibly damaging	N
+Contig76_chr3_30625909_30626247	159	chr3	30626069	ENSCAFT00000036198	ENSCAFP00000031549	T	135	S	479171	benign	cfa00260=Glycine, serine and threonine metabolism.cfa00270=Cysteine and methionine metabolism.cfa01100=Metabolic pathways
+Contig86_chr37_14528768_14530343	873	chr37	14529628	ENSCAFT00000036570	ENSCAFP00000031969	V	738	D	478875.609202	possibly damaging	cfa04060=Cytokine-cytokine receptor interaction.cfa04350=TGF-beta signaling pathway
+Contig9_chr5_54124181_54125739	1134	chr5	54125291	ENSCAFT00000036640	ENSCAFP00000032043	A	187	T	610286	benign	N
+Contig107_chr9_8990420_8991676	1178	chr9	8991591	ENSCAFT00000036774	ENSCAFP00000032186	T	55	M	483288	benign	N
+Contig47_chr12_20319418_20320775	1212	chr12	20320622	ENSCAFT00000036825	ENSCAFP00000032241	K	606	T	474930	benign	cfa00280=Valine, leucine and isoleucine degradation.cfa00630=Glyoxylate and dicarboxylate metabolism.cfa00640=Propanoate metabolism.cfa01100=Metabolic pathways
+Contig4_chr2_45195542_45196115	233	chr2	45195785	ENSCAFT00000037022	ENSCAFP00000032463	D	833	N	478055	possibly damaging	N
+Contig8_chr8_77227029_77227651	339	chr8	77227366	ENSCAFT00000037096	ENSCAFP00000032544	T	61	A	490895.612602	benign	cfa04020=Calcium signaling pathway.cfa04145=Phagosome.cfa04640=Hematopoietic cell lineage.cfa04650=Natural killer cell mediated cytotoxicity.cfa04662=B cell receptor signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04666=Fc gamma R-mediated phagocytosis.cfa04672=Intestinal immune network for IgA production.cfa05140=Leishmaniasis.cfa05143=African trypanosomiasis.cfa05146=Amoebiasis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05162=Measles.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft rejection.cfa05340=Primary immunodeficiency.cfa05414=Dilated cardiomyopathy.cfa05416=Viral myocarditis
+Contig2_chr7_60049092_60051693	266	chr7	60049361	ENSCAFT00000038176	ENSCAFP00000033857	T	195	M	U	probably damaging	N
+Contig31_chr30_24179816_24187402	4867	chr30	24184686	ENSCAFT00000038211	ENSCAFP00000033897	G	103	S	U	benign	N
+Contig9_chr27_48250956_48251793	192	chr27	48251161	ENSCAFT00000038256	ENSCAFP00000033944	T	166	M	477739	probably damaging	N
+Contig45_chr27_43537046_43537944	568	chr27	43537599	ENSCAFT00000038301	ENSCAFP00000033996	M	69	I	611773	benign	cfa04010=MAPK signaling pathway.cfa04810=Regulation of actin cytoskeleton.cfa05200=Pathways in cancer.cfa05218=Melanoma
+Contig133_chr18_28371600_28372547	83	chr18	28371695	ENSCAFT00000038383	ENSCAFP00000034090	L	102	Q	475933	probably damaging	N
+Contig11_chr28_8532951_8533892	511	chr28	8533462	ENSCAFT00000038937	ENSCAFP00000034728	R	19	C	477763	probably damaging	cfa03008=Ribosome biogenesis in eukaryotes.cfa03013=RNA transport
+Contig1_chr14_5733966_5735336	783	chr14	5734754	ENSCAFT00000039094	ENSCAFP00000034905	A	166	T	U	benign	N
+Contig48_chr27_6001075_6001818	392	chr27	6001478	ENSCAFT00000039109	ENSCAFP00000034919	R	103	H	U	probably damaging	N
+Contig40_chr11_43589173_43590288	973	chr11	43590138	ENSCAFT00000039148	ENSCAFP00000034962	R	1617	P	481557	benign	N
+Contig1_chr14_30424688_30425258	179	chr14	30424861	ENSCAFT00000039390	ENSCAFP00000035239	T	648	I	475245	benign	cfa04666=Fc gamma R-mediated phagocytosis.cfa04810=Regulation of actin cytoskeleton
+Contig58_chr8_7461111_7462065	323	chr8	7461423	ENSCAFT00000039451	ENSCAFP00000035309	L	112	F	U	benign	N
+Contig1_chr25_43094809_43095852	908	chr25	43095708	ENSCAFT00000039609	ENSCAFP00000035483	W	18	G	U	unknown	N
+Contig114_chr25_43076436_43076800	141	chr25	43076581	ENSCAFT00000039609	ENSCAFP00000035483	S	45	C	U	unknown	N
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_in/sample.gdSnp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_in/sample.gdSnp	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,402 @@
+#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
+#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
+Contig161_chr1_4641264_4641879	115	C	T	73.5	chr1	4641382	C	6	0	2	45	8	0	2	51	15	0	2	72	5	0	2	42	6	0	2	45	10	0	2	57	Y	54	0.323	0
+Contig48_chr1_10150253_10151311	11	A	G	94.3	chr1	10150264	A	1	0	2	30	1	0	2	30	1	0	2	30	3	0	2	36	1	0	2	30	1	0	2	30	Y	22	+99.	0
+Contig20_chr1_21313469_21313570	66	C	T	54.0	chr1	21313534	C	4	0	2	39	4	0	2	39	5	0	2	42	4	0	2	39	4	0	2	39	5	0	2	42	N	1	+99.	0
+Contig86_chr1_30984450_30985684	670	C	T	365.0	chr1	30985133	C	9	0	2	54	10	0	2	57	13	0	2	66	3	0	2	36	9	0	2	54	7	0	2	48	Y	145	0.031	0
+Contig5_chr1_32562160_32563940	1215	G	T	163.0	chr1	32563356	G	17	0	2	78	19	0	2	84	20	0	2	87	14	0	2	69	12	0	2	63	10	0	2	57	Y	17	0.251	0
+Contig110_chr1_33385093_33386888	510	C	T	270.0	chr1	33385587	A	14	0	2	69	11	0	2	60	19	0	2	84	11	0	2	60	10	0	2	57	13	0	2	66	Y	13	0.126	0
+Contig100_chr1_33562920_33564288	743	C	T	178.0	chr1	33563655	C	6	0	2	45	10	0	2	57	8	0	2	51	5	0	2	42	13	0	2	66	7	0	2	48	Y	13	0.090	3
+Contig7_chr1_37302355_37302489	97	A	G	59.2	chr1	37302452	G	3	0	2	36	8	0	2	51	5	0	2	42	8	0	2	51	7	0	2	48	6	0	2	45	N	56	2.812	0
+Contig62_chr1_41880715_41882180	1078	T	G	57.6	chr1	41881785	T	14	0	2	69	15	0	2	72	16	0	2	75	13	0	2	66	8	0	2	51	10	0	2	57	Y	21	0.477	0
+Contig47_chr1_48409178_48409384	37	C	T	134.0	chr1	48409215	T	5	0	2	42	6	0	2	45	8	0	2	51	9	0	2	54	4	0	2	39	6	0	2	45	N	66	+99.	0
+Contig119_chr1_49647683_49650077	1618	C	A	99.7	chr1	49649276	A	8	0	2	51	11	0	2	60	10	0	2	57	9	0	2	54	10	0	2	57	14	0	2	69	Y	16	0.166	0
+Contig21_chr1_60697952_60699446	307	G	A	51.9	chr1	60698265	G	12	0	2	63	9	0	2	54	4	0	2	39	6	0	2	45	9	0	2	54	4	0	2	39	Y	98	0.507	0
+Contig131_chr1_62319542_62320564	169	C	G	103.0	chr1	62319709	C	12	0	2	63	12	0	2	66	14	0	2	69	12	0	2	63	9	0	2	54	9	0	2	54	Y	73	0.307	1
+Contig14_chr1_63450425_63450680	101	T	A	102.0	chr1	63450530	T	8	0	2	51	10	0	2	57	18	0	2	81	8	0	2	51	8	0	2	34	8	0	2	51	N	99	1.085	0
+Contig83_chr1_63869778_63869942	40	T	C	23.7	chr1	63869819	C	5	0	2	42	7	0	2	48	2	0	2	33	4	0	2	39	6	0	2	48	4	0	2	39	N	654	1.364	0
+Contig30_chr1_64702572_64703138	178	A	T	117.0	chr1	64702750	T	10	0	2	57	10	0	2	57	20	0	2	87	21	0	2	90	6	0	2	45	12	0	2	63	Y	50	3.872	0
+Contig101_chr1_69868406_69868872	287	G	A	14.6	chr1	69868689	G	13	0	2	66	17	0	2	78	10	0	2	57	8	0	2	51	7	0	2	48	8	0	2	51	N	137	0.305	0
+Contig35_chr1_74482577_74482791	170	G	A	45.4	chr1	74482751	A	3	0	2	36	4	0	2	39	13	0	2	66	2	0	2	33	5	0	2	42	2	0	2	33	N	20	+99.	3
+Contig49_chr1_83865731_83865944	85	G	A	34.1	chr1	-1	N	4	0	2	39	4	0	2	39	8	0	2	51	2	0	2	33	5	0	2	42	4	0	2	39	N	-1	1.485	0
+Contig64_chr1_87343284_87345672	163	T	A	3.76	chr1	87343443	C	0	2	2	1	0	0	-1	0	5	0	2	42	2	0	2	33	0	1	2	14	0	0	-1	0	N	3	0.039	2
+Contig20_chr1_110679280_110679687	181	C	T	87.4	chr1	110679454	-	1	0	2	30	7	0	2	48	4	0	2	39	2	0	2	33	2	0	2	33	0	0	-1	0	N	31	0.660	2
+Contig129_chr1_117547123_117548666	926	G	A	126.0	chr1	117548059	G	19	0	2	84	9	0	2	54	11	0	2	60	10	0	2	57	12	0	2	63	11	0	2	60	Y	64	0.049	0
+Contig7_chr1_125154638_125154844	190	G	T	130.0	chr1	125154818	A	5	0	2	42	4	0	2	39	7	0	2	48	2	0	2	33	7	0	2	48	4	0	2	39	N	33	+99.	0
+Contig222_chr2_9817738_9818143	220	C	T	888.0	chr2	9817960	C	17	0	2	78	12	0	2	63	20	0	2	87	8	0	2	51	11	0	2	60	12	0	2	63	Y	76	0.093	1
+Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
+Contig10_chr2_40859744_40860534	637	G	A	888.0	chr2	40860397	A	3	0	2	36	3	0	2	36	2	0	2	33	7	0	2	48	6	0	2	45	8	0	2	51	Y	42	1.435	0
+Contig52_chr2_41421981_41422725	604	C	A	888.0	chr2	41422583	A	17	0	2	78	18	0	2	81	14	0	2	69	17	0	2	78	12	0	2	63	14	0	2	69	Y	44	0.882	0
+Contig94_chr2_43869105_43870358	220	G	A	888.0	chr2	43869333	G	12	0	2	63	18	0	2	81	11	0	2	60	15	0	2	72	12	0	2	63	13	0	2	66	Y	1	0.156	0
+Contig34_chr2_48444129_48444939	695	C	T	134.0	chr2	48444828	C	14	0	2	69	8	0	2	51	16	0	2	75	17	0	2	78	9	0	2	54	15	0	2	72	Y	161	0.375	0
+Contig6_chr2_56859179_56859956	671	T	C	999.9	chr2	56859851	T	15	0	2	72	18	0	2	81	20	0	2	90	19	0	2	84	19	0	2	84	24	0	2	99	N	28	5.308	1
+Contig115_chr2_61631913_61632510	310	G	T	999.3	chr2	61632216	G	7	0	2	48	9	0	2	54	7	0	2	48	11	0	2	60	10	0	2	57	10	0	2	57	N	13	0.184	0
+Contig31_chr2_67331584_67331785	39	C	T	999.0	chr2	67331623	C	11	0	2	60	10	0	2	57	7	0	2	48	9	0	2	54	2	0	2	33	4	0	2	39	N	110	0.647	1
+Contig92_chr2_75906683_75907774	773	T	C	85.4	chr2	75907438	C	12	0	2	63	12	0	2	63	17	0	2	78	8	0	2	51	8	0	2	51	13	0	2	66	Y	93	0.166	0
+Contig163_chr2_76402959_76404830	221	C	T	127.0	chr2	76403181	C	4	0	2	42	10	0	2	57	9	0	2	54	11	0	2	60	7	0	2	48	9	0	2	54	Y	54	0.178	1
+Contig177_chr2_79559305_79560033	168	C	T	5.67	chr2	79559476	A	2	0	2	33	3	0	2	36	1	0	2	30	2	0	2	33	0	0	-1	0	1	0	2	30	N	56	0.257	0
+Contig8_chr2_82945728_82945839	61	T	C	223.0	chr2	-1	N	2	0	2	33	4	0	2	39	9	0	2	54	3	0	2	36	5	0	2	42	0	0	-1	0	N	-1	+99.	1
+Contig59_chr2_85243022_85243758	506	G	A	96.3	chr2	85243509	T	9	0	2	54	11	0	2	60	12	0	2	63	14	0	2	69	10	0	2	57	7	0	2	48	Y	6	0.459	0
+Contig56_chr3_17326225_17327548	387	G	C	91.2	chr3	17326591	G	14	0	2	69	13	0	2	66	15	0	2	72	15	0	2	72	13	0	2	66	12	0	2	63	Y	20	0.225	3
+Contig108_chr3_46210055_46210874	367	A	G	21.0	chr3	46210423	A	19	0	2	84	10	0	2	57	16	0	2	75	14	0	2	69	20	0	2	87	11	0	2	60	N	236	0.028	1
+Contig16_chr3_47113407_47114449	322	G	A	105.0	chr3	47113713	G	13	0	2	66	17	0	2	78	15	0	2	72	6	0	2	45	11	0	2	60	11	0	2	60	Y	114	0.132	5
+Contig3_chr3_47564810_47565251	262	T	G	112.0	chr3	47565104	T	14	0	2	69	16	0	2	75	20	0	2	87	10	0	2	57	9	0	2	54	8	0	2	51	Y	24	0.073	1
+Contig35_chr3_49662401_49662929	270	A	T	96.1	chr3	49662652	A	14	0	2	69	11	0	2	60	23	0	2	96	13	0	2	66	12	0	2	63	11	0	2	60	Y	36	3.583	2
+Contig97_chr3_49820354_49821631	1069	G	A	44.1	chr3	49821402	G	9	0	2	54	9	0	2	54	6	0	2	45	10	0	2	57	5	0	2	42	8	0	2	51	N	6	0.201	2
+Contig1_chr3_51588422_51589409	926	A	G	51.0	chr3	51589353	G	2	0	2	33	2	0	2	33	6	0	2	45	4	0	2	39	9	0	2	54	11	0	2	60	N	21	1.147	0
+Contig25_chr3_53260697_53262560	402	G	A	211.0	chr3	53261095	G	17	0	2	78	14	0	2	69	15	0	2	75	12	0	2	63	14	0	2	69	12	0	2	63	Y	116	1.033	0
+Contig11_chr3_53992739_53995954	2392	G	A	82.4	chr3	53995143	A	12	0	2	66	11	0	2	60	14	0	2	69	6	0	2	45	11	0	2	60	17	0	2	78	Y	358	0.321	1
+Contig236_chr3_72676275_72676473	128	G	A	278.0	chr3	72676410	G	12	0	2	63	11	0	2	60	13	0	2	66	10	0	2	57	11	0	2	60	8	0	2	51	N	36	0.496	1
+Contig48_chr3_74792236_74792388	63	T	C	111.0	chr3	74792289	-	17	0	2	78	9	0	2	54	9	0	2	54	5	0	2	42	11	0	2	60	9	0	2	54	N	-1	3.528	0
+Contig65_chr3_80727952_80728283	39	T	C	71.2	chr3	80727990	T	7	0	2	48	3	0	2	36	8	0	2	51	6	0	2	45	8	0	2	51	11	0	2	60	N	22	7.078	0
+Contig53_chr3_86407941_86409349	1406	G	A	86.9	chr3	86409317	A	5	0	2	42	5	0	2	42	4	0	2	39	10	0	2	57	8	0	2	51	12	0	2	63	N	14	3.285	1
+Contig13_chr3_92409738_92412300	718	A	G	23.3	chr3	92410450	A	12	0	2	63	16	0	2	75	18	0	2	81	13	0	2	66	22	0	2	93	7	0	2	48	Y	23	0.224	2
+Contig134_chr4_12145648_12148225	1326	C	T	164.0	chr4	12146961	C	9	0	2	54	8	0	2	51	7	0	2	48	3	0	2	36	5	0	2	42	5	0	2	42	Y	4	0.080	1
+Contig88_chr4_15557471_15557833	268	A	G	145.0	chr4	15557737	A	6	0	2	45	6	0	2	45	11	0	2	60	9	0	2	54	5	0	2	42	6	0	2	45	Y	46	4.138	0
+Contig53_chr4_18823968_18824478	149	A	G	91.3	chr4	18824115	A	18	0	2	81	15	0	2	72	21	0	2	90	13	0	2	66	9	0	2	54	12	0	2	63	N	51	0.251	0
+Contig86_chr4_24953866_24956222	1985	C	T	76.4	chr4	24955841	T	8	0	2	51	1	0	2	30	3	0	2	36	7	0	2	48	2	0	2	33	6	0	2	45	Y	12	0.357	0
+Contig19_chr4_26233601_26233991	146	G	C	51.6	chr4	26233744	G	10	0	2	57	8	0	2	51	9	0	2	54	5	0	2	42	9	0	2	54	4	0	2	39	N	41	0.163	3
+Contig78_chr4_28579975_28580134	30	T	G	19.6	chr4	28579994	-	4	0	2	39	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	2	0	2	33	N	33	0.499	0
+Contig16_chr4_30177226_30179725	621	C	T	88.4	chr4	30177859	C	20	0	2	87	13	0	2	66	13	0	2	66	11	0	2	60	8	0	2	51	8	0	2	51	Y	45	0.797	1
+Contig30_chr4_46196500_46197672	1045	A	C	33.4	chr4	46197522	C	16	0	2	75	9	0	2	54	4	0	2	39	7	0	2	48	14	0	2	69	6	0	2	45	Y	43	0.306	0
+Contig2_chr4_47039007_47039323	158	G	C	35.1	chr4	47039160	-	8	0	2	51	9	0	2	54	13	0	2	66	8	0	2	51	10	0	2	60	9	0	2	54	N	0	0.131	0
+Contig17_chr4_61310346_61311158	267	C	T	49.9	chr4	61310604	T	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	14	0	2	69	7	0	2	48	Y	219	0.098	0
+Contig26_chr4_64190783_64191295	64	A	G	162.0	chr4	64190843	A	10	0	2	57	6	0	2	45	20	0	2	87	12	0	2	63	17	0	2	78	7	0	2	48	Y	306	7.428	0
+Contig11_chr4_65500960_65501654	634	T	C	107.0	chr4	65501585	T	13	0	2	66	14	0	2	69	13	0	2	66	13	0	2	66	6	0	2	45	18	0	2	81	Y	10	6.849	0
+Contig38_chr4_67768488_67768982	113	A	G	102.0	chr4	67768598	A	9	0	2	54	8	0	2	51	9	0	2	54	11	0	2	60	10	0	2	57	7	0	2	48	Y	188	3.175	0
+Contig30_chr4_70978564_70979580	596	A	G	164.0	chr4	70979151	A	15	0	2	72	12	0	2	63	20	0	2	87	14	0	2	69	15	0	2	72	15	0	2	72	Y	111	2.458	2
+Contig72_chr4_74225793_74226492	674	A	G	110.0	chr4	74226472	A	5	0	2	42	3	0	2	36	2	0	2	33	3	0	2	36	7	0	2	48	4	0	2	39	Y	115	+99.	1
+Contig32_chr4_75618955_75620254	301	T	C	333.0	chr4	75619257	C	10	0	2	57	8	0	2	51	12	0	2	63	20	0	2	87	12	0	2	63	14	0	2	69	Y	34	0.163	2
+Contig31_chr5_4734956_4736547	1166	C	T	133.0	chr5	4736132	C	14	0	2	69	8	0	2	51	17	0	2	78	4	0	2	39	9	0	2	54	12	0	2	63	Y	1	0.021	0
+Contig113_chr5_11052263_11052603	28	C	T	38.2	chr5	11052280	C	1	2	1	12	3	2	1	10	5	0	2	42	2	1	2	13	3	0	2	36	8	0	2	51	Y	161	+99.	0
+Contig30_chr5_15698241_15699076	396	G	T	76.6	chr5	15698633	T	8	0	2	51	9	0	2	54	10	0	2	57	7	0	2	48	11	0	2	60	8	0	2	54	Y	65	0.009	0
+Contig36_chr5_17709244_17710004	373	T	C	281.0	chr5	17709624	T	6	0	2	45	9	0	2	54	7	0	2	48	4	0	2	39	10	0	2	57	4	0	2	39	Y	16	0.131	0
+Contig13_chr5_21881138_21881562	227	A	G	251.0	chr5	21881356	A	11	0	2	60	20	0	2	87	22	0	2	93	10	0	2	57	10	0	2	57	21	0	2	90	Y	182	2.013	0
+Contig5_chr5_23188121_23190168	1841	C	T	141.0	chr5	23189975	C	20	0	2	87	19	0	2	84	22	0	2	93	16	0	2	75	18	0	2	81	14	0	2	69	N	45	0.355	0
+Contig6_chr5_26899813_26900498	97	A	C	88.6	chr5	26899910	A	15	0	2	72	14	0	2	69	27	0	2	108	15	0	2	72	13	0	2	69	12	0	2	63	Y	92	7.370	3
+Contig314_chr5_34019166_34019319	72	C	A	20.1	chr5	-1	N	6	0	2	45	9	0	2	54	4	0	2	39	4	0	2	39	9	0	2	54	5	0	2	42	N	-1	+99.	4
+Contig147_chr5_38980258_38980559	221	C	T	40.8	chr5	38980477	C	15	0	2	72	15	0	2	72	19	0	2	84	10	0	2	57	12	0	2	63	20	0	2	87	Y	11	4.576	0
+Contig115_chr5_48119079_48120169	151	C	T	78.3	chr5	48119234	C	17	0	2	78	10	0	2	57	14	0	2	69	16	0	2	75	8	0	2	51	12	0	2	63	Y	205	0.320	0
+Contig45_chr5_50892738_50892968	169	C	A	25.8	chr5	50892911	C	10	0	2	57	7	0	2	48	10	0	2	60	6	0	2	45	6	0	2	45	13	0	2	66	N	244	0.497	1
+Contig40_chr5_51484164_51484696	14	A	G	53.3	chr5	51484180	A	6	0	2	45	4	0	2	39	4	0	2	39	3	0	2	36	0	0	2	13	3	0	2	36	N	63	+99.	1
+Contig40_chr5_51664286_51667573	861	C	T	148.0	chr5	51665149	C	20	0	2	87	21	0	2	90	20	0	2	87	11	0	2	60	16	0	2	75	15	0	2	72	Y	207	0.080	1
+Contig15_chr5_51889708_51891244	882	A	G	149.0	chr5	51890581	G	13	0	2	66	18	0	2	81	17	0	2	78	22	0	2	93	15	0	2	72	22	0	2	93	Y	7	0.025	1
+Contig143_chr5_57231364_57232010	294	T	C	78.5	chr5	57231644	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	10	0	2	57	6	0	2	45	Y	73	0.337	2
+Contig13_chr5_57609985_57610584	496	C	T	50.5	chr5	57610476	C	17	0	2	78	9	0	2	54	6	0	2	45	8	0	2	51	10	0	2	57	12	0	2	63	N	77	2.022	1
+Contig230_chr5_58486998_58487280	227	T	C	192.0	chr5	58487232	T	3	0	2	36	4	0	2	39	9	0	2	54	6	0	2	45	4	0	2	39	7	0	2	48	N	24	0.100	2
+Contig385_chr5_60122961_60123128	15	C	G	136.0	chr5	60122976	C	0	0	-1	0	0	0	-1	0	1	0	2	30	1	0	2	30	3	0	2	36	0	0	-1	0	N	100	+99.	2
+Contig143_chr5_65121393_65122035	558	C	A	127.0	chr5	65121959	A	0	0	-1	0	5	0	2	42	3	0	2	36	4	0	2	39	0	0	-1	0	4	0	2	39	Y	285	0.391	1
+Contig32_chr5_70852360_70853289	282	G	A	114.0	chr5	70852623	G	16	0	2	75	11	0	2	60	13	0	2	66	12	0	2	63	13	0	2	66	7	0	2	48	Y	33	0.276	0
+Contig215_chr5_70946445_70947428	363	T	G	28.2	chr5	70946809	C	4	0	2	39	0	5	0	12	9	0	2	54	6	0	2	45	3	3	2	1	9	0	2	54	N	43	0.153	0
+Contig100_chr5_71189678_71190590	813	C	T	30.8	chr5	71190523	C	11	0	2	60	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	Y	8	0.362	1
+Contig45_chr5_76133561_76134403	388	A	G	103.0	chr5	76133941	G	3	0	2	36	8	0	2	51	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	57	0.038	0
+Contig61_chr5_90202541_90204393	909	C	T	101.0	chr5	90203461	T	7	0	2	48	5	0	2	42	14	0	2	69	3	0	2	36	5	0	2	42	8	0	2	51	Y	64	1.448	0
+Contig111_chr6_5821219_5822519	1060	A	G	68.1	chr6	5822321	T	7	0	2	48	6	0	2	45	11	0	2	60	9	0	2	54	3	0	2	36	12	0	2	63	Y	7	0.231	1
+Contig220_chr6_10671338_10672441	999	T	C	36.3	chr6	10672322	T	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	5	0	2	42	9	0	2	54	Y	1	1.667	0
+Contig226_chr6_17361986_17362884	418	G	C	251.0	chr6	17362406	G	6	0	2	45	8	0	2	51	7	0	2	48	9	0	2	54	7	0	2	48	7	0	2	48	Y	7	0.147	0
+Contig380_chr6_18173971_18174169	180	C	T	4.87	chr6	18174144	T	0	0	-1	0	4	0	2	39	7	0	2	48	2	0	2	33	2	0	2	33	1	0	2	30	N	56	2.589	0
+Contig51_chr6_20231207_20231785	161	A	G	70.5	chr6	20231375	G	13	0	2	66	5	0	2	42	8	0	2	51	2	0	2	36	5	0	2	42	5	0	2	42	Y	153	1.754	0
+Contig102_chr6_30271329_30271577	39	T	G	139.0	chr6	30271371	G	3	0	2	36	4	0	2	39	6	0	2	45	1	0	2	30	4	0	2	39	4	0	2	39	N	15	1.159	0
+Contig217_chr6_31393824_31394218	97	G	A	115.0	chr6	31393921	G	9	0	2	54	19	0	2	84	15	0	2	72	12	0	2	63	7	0	2	48	10	0	2	57	N	45	0.477	0
+Contig186_chr6_31928098_31928245	73	G	A	117.0	chr6	-1	N	5	0	2	42	8	0	2	51	2	0	2	33	4	0	2	39	1	0	2	30	5	0	2	42	N	-1	0.276	1
+Contig52_chr6_33188498_33188724	123	G	A	59.0	chr6	-1	N	5	0	2	42	13	0	2	66	8	0	2	51	4	0	2	39	9	0	2	54	9	0	2	54	N	-1	0.880	1
+Contig102_chr6_38743009_38743435	290	A	G	178.0	chr6	38743311	A	11	0	2	60	13	0	2	66	9	0	2	54	11	0	2	60	12	0	2	63	13	0	2	66	Y	34	0.148	4
+Contig81_chr6_49018353_49019532	179	C	A	72.5	chr6	49018530	A	15	0	2	72	13	0	2	66	19	0	2	72	8	0	2	51	12	0	2	63	16	0	2	75	Y	15	0.145	1
+Contig112_chr6_51024554_51024851	100	A	G	121.0	chr6	51024654	A	10	0	2	57	12	0	2	63	9	0	2	54	13	0	2	66	14	0	2	69	17	0	2	78	N	75	4.287	0
+Contig40_chr6_51412751_51413807	227	T	C	94.5	chr6	51412975	C	5	0	2	42	8	0	2	51	7	0	2	48	9	0	2	54	11	0	2	60	10	0	2	57	Y	4	5.661	0
+Contig47_chr6_69073222_69074767	1315	T	C	212.0	chr6	69074558	T	20	0	2	87	17	0	2	78	18	0	2	81	12	0	2	63	17	0	2	78	7	0	2	48	Y	9	0.652	0
+Contig30_chr6_74848932_74849059	57	C	G	46.3	chr6	74848993	C	7	0	2	48	7	0	2	33	6	0	2	45	7	0	2	48	5	0	2	42	6	0	2	45	N	-1	+99.	1
+Contig84_chr7_6648683_6650255	1297	G	A	110.0	chr7	6649988	G	18	0	2	81	9	0	2	54	22	0	2	77	16	0	2	75	20	0	2	87	6	0	2	45	Y	83	0.166	0
+Contig239_chr7_13007379_13007700	275	A	G	39.8	chr7	13007642	A	8	0	2	51	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	5	0	2	42	N	46	1.511	3
+Contig119_chr7_18310707_18310948	23	A	T	133.0	chr7	18310729	A	6	0	2	45	5	0	2	42	10	0	2	57	5	0	2	42	2	0	2	33	2	0	2	33	N	4553	+99.	0
+Contig93_chr7_18513377_18513741	173	T	C	130.0	chr7	18513533	C	15	0	2	72	11	0	2	60	18	0	2	81	6	0	2	45	10	0	2	57	14	0	2	69	Y	115	0.174	0
+Contig133_chr7_19603333_19603776	414	C	G	31.9	chr7	19603734	G	10	0	2	57	4	0	2	39	4	0	2	39	5	0	2	42	9	0	2	54	9	0	2	54	N	78	+99.	5
+Contig132_chr7_20426224_20428145	1815	A	G	28.3	chr7	20428041	A	11	1	2	43	12	0	2	63	19	0	2	84	23	0	2	96	14	0	2	69	10	0	2	57	N	11	0.264	0
+Contig206_chr7_26281823_26282074	103	C	A	101.0	chr7	26281925	T	11	0	2	60	16	0	2	61	19	0	2	84	6	0	2	45	19	0	2	84	16	0	2	75	N	-1	0.947	1
+Contig116_chr7_45858984_45859111	38	T	C	73.2	chr7	-1	N	2	0	2	33	1	0	2	30	3	0	2	36	2	0	2	33	2	0	2	33	1	0	2	30	N	-1	3.442	0
+Contig38_chr7_50681997_50682600	42	T	C	92.4	chr7	50682037	G	6	0	2	45	2	0	2	33	10	0	2	57	12	0	2	63	5	0	2	42	6	0	2	45	Y	94	0.146	0
+Contig55_chr7_53147505_53148974	894	A	G	68.4	chr7	53148397	G	22	0	2	93	13	0	2	66	16	0	2	75	8	0	2	51	16	0	2	75	11	0	2	60	Y	19	0.060	0
+Contig4_chr7_53685534_53688206	1709	C	G	76.2	chr7	53687225	C	18	0	2	81	17	0	2	78	18	0	2	81	15	0	2	72	14	0	2	69	14	0	2	69	Y	32	0.659	1
+Contig61_chr7_55832923_55834065	506	T	C	185.0	chr7	55833450	C	9	0	2	54	10	0	2	57	22	0	2	93	12	0	2	63	12	0	2	63	7	0	2	48	Y	1	0.019	0
+Contig91_chr8_12804505_12805470	409	C	A	111.0	chr8	12804906	C	8	0	2	51	10	0	2	57	15	0	2	72	12	0	2	63	14	0	2	69	15	0	2	72	N	145	0.175	0
+Contig30_chr8_17147743_17147923	13	G	A	105.0	chr8	17147756	A	1	3	1	19	1	0	2	30	3	0	2	36	1	0	2	30	1	0	2	30	3	0	2	36	N	6	+99.	0
+Contig8_chr8_27811135_27812620	333	C	T	37.9	chr8	27811458	C	4	0	2	39	11	0	2	60	18	0	2	81	5	0	2	42	6	0	2	45	5	0	2	42	Y	1	0.272	0
+Contig66_chr8_28273102_28273660	175	G	C	81.6	chr8	28273263	T	9	0	2	54	17	0	2	78	19	0	2	84	8	0	2	51	16	0	2	75	19	0	2	84	Y	3	2.735	0
+Contig84_chr8_31375511_31376456	443	T	C	125.0	chr8	31375954	T	10	0	2	57	15	0	2	72	27	0	2	108	18	0	2	81	16	0	2	75	9	0	2	54	Y	2	0.650	0
+Contig18_chr8_32575859_32577431	264	T	C	151.0	chr8	32576124	T	20	0	2	87	14	0	2	69	17	0	2	78	14	0	2	69	13	0	2	66	14	0	2	69	Y	17	0.915	1
+Contig54_chr8_40913908_40916451	1275	G	A	175.0	chr8	40915190	G	10	0	2	57	8	0	2	51	11	0	2	60	7	0	2	48	8	0	2	51	9	0	2	54	Y	21	0.056	3
+Contig93_chr8_44658786_44659075	180	T	G	55.3	chr8	44658964	T	4	0	2	39	3	0	2	36	6	0	2	45	5	0	2	45	5	0	2	42	4	0	2	39	N	14	0.188	0
+Contig17_chr8_57490059_57490498	69	G	T	97.4	chr8	57490127	A	2	0	2	33	11	0	2	60	15	0	2	72	16	0	2	75	8	0	2	51	10	0	2	57	N	40	0.522	5
+Contig66_chr8_58562376_58563446	345	C	G	5.74	chr8	58562721	C	14	0	2	69	12	0	2	63	9	0	2	57	10	0	2	57	9	0	2	54	10	0	2	57	Y	6	0.685	0
+Contig44_chr8_71186368_71188207	1455	G	T	147.0	chr8	71187818	G	4	10	1	74	3	0	2	36	20	0	2	87	12	0	2	63	8	0	2	51	10	0	2	57	Y	88	0.036	0
+Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
+Contig96_chr9_39008495_39009278	215	A	C	98.7	chr9	39008708	C	7	0	2	48	13	0	2	66	28	0	2	111	16	0	2	75	17	0	2	78	17	0	2	78	Y	8	0.427	1
+Contig22_chr10_15505382_15505589	172	T	C	38.5	chr10	15505548	T	2	0	2	33	6	0	2	45	8	0	2	51	8	0	2	51	9	0	2	54	12	0	2	63	N	284	2.861	0
+Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
+Contig63_chr10_42716594_42719945	1018	A	G	88.7	chr10	42717616	G	13	0	2	66	14	0	2	69	13	0	2	66	12	0	2	63	18	0	2	81	5	0	2	42	Y	25	1.740	0
+Contig22_chr10_43255307_43255570	81	C	A	37.2	chr10	43255383	C	15	0	2	72	18	0	2	81	22	0	2	93	16	0	2	75	11	0	2	60	12	0	2	63	N	62	0.450	0
+Contig9_chr10_51475063_51476054	770	C	T	57.3	chr10	51475839	C	6	0	2	45	16	0	2	75	16	0	2	75	13	0	2	66	9	0	2	54	9	2	2	21	N	80	0.394	0
+Contig42_chr10_53816543_53818392	1642	G	A	27.5	chr10	53818172	A	7	0	2	48	13	0	2	66	17	0	2	78	14	0	2	69	19	0	2	84	16	0	2	75	N	1	0.433	0
+Contig36_chr10_53992615_53993741	229	G	C	86.2	chr10	53992846	G	17	0	2	78	14	0	2	69	13	0	2	66	15	0	2	72	12	0	2	63	15	0	2	72	N	23	1.912	0
+Contig20_chr10_58141129_58141750	575	C	T	46.1	chr10	58141701	C	7	0	2	48	8	0	2	51	9	0	2	54	3	0	2	36	4	0	2	39	9	0	2	54	N	1	4.264	0
+Contig26_chr10_59510973_59511899	146	C	A	29.0	chr10	59511126	C	8	0	2	51	13	0	2	66	18	0	2	81	13	0	2	66	10	0	2	57	7	0	2	48	Y	208	1.077	0
+Contig72_chr11_7142765_7143772	146	G	A	152.0	chr11	7142911	A	8	0	2	51	8	0	2	51	24	0	2	99	10	0	2	57	17	0	2	78	11	0	2	60	Y	90	1.137	0
+Contig103_chr11_8844784_8845095	214	T	G	135.0	chr11	8844993	T	1	1	2	12	10	0	2	57	5	4	1	26	2	3	1	13	2	7	1	34	1	1	2	13	Y	75	0.731	0
+Contig9_chr11_9904571_9905983	1284	C	T	151.0	chr11	9905857	C	16	0	2	75	19	0	2	84	17	0	2	78	16	0	2	75	12	0	2	63	13	1	2	44	Y	11	0.422	1
+Contig35_chr11_22459883_22460855	714	T	G	54.9	chr11	22460577	T	3	0	2	36	1	0	2	30	3	0	2	36	2	0	2	33	2	0	2	33	0	0	-1	0	N	24	0.382	0
+Contig7_chr11_40017076_40017630	352	C	T	46.3	chr11	40017422	C	7	0	2	48	9	0	2	54	6	0	2	45	8	0	2	51	16	0	2	75	9	0	2	54	Y	44	0.336	0
+Contig108_chr11_42953408_42955156	367	A	G	89.4	chr11	42953779	A	17	0	2	78	11	0	2	60	14	0	2	69	20	0	2	87	14	0	2	69	17	0	2	78	Y	118	0.784	1
+Contig82_chr11_43490732_43490862	60	C	T	47.3	chr11	-1	N	0	0	-1	0	0	0	-1	0	1	0	2	30	3	0	2	36	1	1	2	19	1	0	2	30	N	-1	6.763	0
+Contig16_chr11_53408448_53408790	187	A	G	153.0	chr11	53408638	A	7	0	2	48	9	0	2	54	18	0	2	81	10	0	2	57	11	0	2	60	12	0	2	63	Y	116	1.367	0
+Contig21_chr12_18403415_18404381	586	G	T	34.5	chr12	18403983	-	13	0	2	66	16	0	2	75	25	0	2	102	12	0	2	63	12	0	2	63	14	0	2	69	Y	12	0.068	0
+Contig33_chr12_19804073_19804529	178	T	C	69.4	chr12	19804261	T	13	0	2	66	13	0	2	66	22	0	2	93	11	0	2	60	12	0	2	63	18	0	2	81	Y	11	1.571	0
+Contig41_chr12_25565452_25566993	475	G	T	6.29	chr12	25565926	G	15	0	2	72	14	0	2	69	10	0	2	57	15	0	2	72	18	0	2	81	19	0	2	84	N	10	2.231	1
+Contig9_chr12_27204351_27204696	239	A	G	145.0	chr12	27204587	A	7	0	2	48	8	0	2	51	12	0	2	63	8	0	2	51	11	0	2	60	11	0	2	60	Y	14	0.046	0
+Contig45_chr12_30548282_30550498	448	C	T	124.0	chr12	30548703	-	9	0	2	54	11	0	2	60	22	0	2	93	19	0	2	84	12	0	2	63	12	0	2	63	Y	66	0.305	0
+Contig46_chr12_35571846_35572563	58	G	C	83.2	chr12	35571906	G	4	0	2	39	10	0	2	57	11	0	2	60	6	0	2	45	10	0	2	57	6	0	2	45	Y	55	+99.	1
+Contig28_chr12_42075871_42076044	136	G	A	134.0	chr12	42076006	A	6	0	2	45	5	0	2	42	7	0	2	48	7	0	2	48	2	0	2	33	4	0	2	39	N	3	9.479	0
+Contig16_chr12_42386141_42387454	194	A	G	161.0	chr12	42386323	A	11	0	2	60	8	0	2	54	23	0	2	96	17	0	2	78	6	0	2	45	13	0	2	66	Y	7	0.927	1
+Contig42_chr12_44424628_44425829	255	A	G	84.4	chr12	44424879	A	12	0	2	63	19	0	2	84	23	0	2	96	15	0	2	72	18	0	2	81	14	0	2	69	Y	18	1.190	2
+Contig10_chr12_44447953_44449698	63	C	T	105.0	chr12	44448020	C	11	0	2	60	9	0	2	54	12	0	2	63	10	0	2	57	15	0	2	72	8	0	2	51	Y	31	11.791	0
+Contig5_chr12_53880670_53882675	1221	A	C	99.4	chr12	53881888	A	16	0	2	75	18	0	2	81	23	0	2	96	10	0	2	57	15	0	2	72	17	0	2	78	Y	31	0.061	0
+Contig86_chr12_56715356_56716464	818	T	C	166.0	chr12	56716164	T	20	0	2	87	16	0	2	75	16	0	2	75	14	0	2	69	13	0	2	66	7	0	2	48	Y	22	1.092	0
+Contig3_chr12_65021967_65024097	238	T	G	92.6	chr12	65022205	T	17	0	2	78	14	0	2	69	16	0	2	75	9	0	2	54	13	0	2	66	15	0	2	72	Y	258	0.117	0
+Contig43_chr12_66499742_66500010	121	G	T	41.5	chr12	66499866	G	12	0	2	63	4	0	2	39	8	0	2	51	6	0	2	45	10	0	2	57	6	0	2	45	N	42	0.421	0
+Contig14_chr12_71364692_71365311	20	A	C	103.0	chr12	71364712	A	7	0	2	48	3	0	2	36	5	0	2	42	1	0	2	30	2	0	2	33	3	0	2	36	Y	35	+99.	0
+Contig37_chr13_15910164_15910426	245	G	A	32.9	chr13	-1	N	3	4	1	41	4	0	2	39	3	0	2	36	4	0	2	39	3	0	2	36	10	0	2	57	N	-1	2.159	1
+Contig107_chr13_26045881_26046290	341	C	G	81.4	chr13	26046230	C	16	0	2	75	20	0	2	90	14	0	2	69	15	0	2	72	9	0	2	54	9	0	2	54	Y	51	4.510	0
+Contig251_chr13_28498333_28501066	864	T	G	296.0	chr13	28499180	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	5	0	2	42	6	0	2	45	Y	9	0.068	0
+Contig154_chr13_36777857_36778736	356	G	A	95.5	chr13	36778225	A	6	0	2	45	11	0	2	60	11	0	2	60	9	0	2	54	13	0	2	66	8	0	2	51	Y	59	0.192	0
+Contig37_chr13_42529793_42530857	150	G	T	192.0	chr13	42529926	G	18	0	2	81	14	0	2	69	16	0	2	75	14	0	2	69	8	0	2	51	11	0	2	60	N	22	0.795	5
+Contig47_chr13_47045833_47046626	257	A	C	28.5	chr13	47046097	A	13	0	2	66	10	0	2	57	17	0	2	78	20	0	2	87	15	0	2	72	9	0	2	57	N	129	0.468	0
+Contig42_chr13_47730018_47730856	254	A	G	75.1	chr13	47730294	A	13	0	2	66	6	0	2	45	12	0	2	63	9	0	2	54	16	0	2	75	11	0	2	63	Y	630	0.049	1
+Contig55_chr13_53467708_53468101	221	T	G	132.0	chr13	53467925	T	25	0	2	102	12	0	2	63	26	0	2	105	7	0	2	48	16	0	2	75	16	0	2	75	N	20	5.717	1
+Contig49_chr13_55103679_55105532	503	G	A	76.0	chr13	55104178	G	21	0	2	90	19	0	2	84	18	0	2	81	20	0	2	87	8	9	1	89	17	0	2	78	Y	20	0.259	1
+Contig42_chr13_64785759_64786045	14	C	G	22.8	chr13	64785772	C	2	0	2	33	2	0	2	33	4	0	2	39	7	0	2	48	8	0	2	51	2	0	2	33	N	527	+99.	1
+Contig66_chr13_66021813_66022244	319	C	T	125.0	chr13	66022136	C	11	0	2	60	16	0	2	75	15	0	2	75	12	0	2	63	17	0	2	78	8	0	2	51	N	14	0.055	3
+Contig48_chr14_11839435_11843272	3014	A	G	163.0	chr14	11842446	A	10	0	2	57	8	0	2	51	13	0	2	66	10	0	2	57	5	0	2	42	10	0	2	57	Y	31	0.908	0
+Contig9_chr14_23353717_23354432	80	G	A	61.3	chr14	23353797	G	3	0	2	36	6	0	2	45	11	0	2	60	8	0	2	51	4	0	2	39	2	4	1	35	Y	11	0.444	0
+Contig14_chr14_24131180_24133488	1633	G	A	131.0	chr14	24132818	G	21	0	2	90	16	0	2	75	12	0	2	63	10	0	2	57	11	0	2	60	20	0	2	87	Y	36	0.347	0
+Contig28_chr14_26905747_26909514	975	G	C	3.13	chr14	26906723	G	16	0	2	75	10	0	2	57	12	0	2	63	15	0	2	72	10	0	2	57	7	0	2	48	N	287	0.117	2
+Contig14_chr14_29616948_29618316	109	G	A	80.3	chr14	29617053	-	17	0	2	78	16	0	2	75	16	0	2	75	10	0	2	57	17	0	2	78	19	0	2	84	Y	32	1.051	0
+Contig24_chr14_29728478_29728839	242	T	A	107.0	chr14	29728724	T	2	0	2	33	12	0	2	63	10	0	2	57	12	0	2	63	5	0	2	42	9	0	2	54	N	70	2.712	0
+Contig76_chr14_30028102_30029179	1046	C	T	38.5	chr14	30029169	T	3	0	2	36	6	0	2	45	9	0	2	54	7	0	2	48	9	0	2	54	8	0	2	51	Y	96	+99.	0
+Contig115_chr14_31417207_31417574	259	A	G	12.1	chr14	31417454	G	13	0	2	66	15	0	2	72	21	0	2	90	12	0	2	63	13	0	2	66	9	0	2	54	N	28	5.379	2
+Contig70_chr14_46653662_46653790	111	G	A	46.7	chr14	46653768	G	7	0	2	48	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	10	0	2	57	N	21	+99.	2
+Contig43_chr14_49991855_49993511	918	A	G	112.0	chr14	49992767	G	15	0	2	72	10	0	2	57	11	0	2	63	9	0	2	54	12	0	2	63	9	0	2	54	Y	6	0.314	1
+Contig64_chr14_56768376_56768902	473	C	T	29.0	chr14	56768832	C	15	0	2	72	11	0	2	60	14	0	2	69	14	0	2	69	7	0	2	48	9	0	2	54	Y	91	8.281	0
+Contig60_chr15_18493036_18494316	150	G	A	92.6	chr15	18493188	G	9	0	2	54	13	0	2	66	9	0	2	54	6	0	2	45	5	0	2	42	12	0	2	63	Y	45	0.125	0
+Contig213_chr15_19567788_19568626	196	A	C	13.9	chr15	19567992	A	4	0	2	39	2	0	2	33	7	0	2	48	4	0	2	39	4	0	2	39	6	0	2	45	Y	111	0.043	0
+Contig59_chr15_22138344_22138535	120	G	C	142.0	chr15	22138470	C	11	0	2	60	10	0	2	57	18	0	2	81	4	0	2	39	10	0	2	57	15	0	2	72	N	8	2.553	0
+Contig112_chr15_26772864_26773267	374	C	T	21.6	chr15	26773244	C	4	0	2	39	4	0	2	39	5	0	2	42	2	0	2	33	4	0	2	39	3	0	2	36	N	18	+99.	0
+Contig24_chr15_26894765_26895003	155	G	A	87.6	chr15	-1	N	6	0	2	45	5	0	2	42	7	0	2	48	4	0	2	39	4	0	2	39	2	0	2	33	N	-1	0.178	0
+Contig2_chr15_33944796_33947182	1860	G	A	99.5	chr15	33946654	G	10	0	2	57	11	0	2	60	16	0	2	75	14	0	2	69	14	0	2	69	16	0	2	75	Y	16	0.252	0
+Contig73_chr15_34690052_34691332	714	T	C	130.0	chr15	34690769	T	7	0	2	48	7	0	2	48	17	0	2	78	9	0	2	54	9	0	2	54	4	0	2	39	Y	7	6.003	0
+Contig68_chr15_37747190_37747426	126	G	A	130.0	chr15	37747331	G	14	0	2	69	14	0	2	69	11	0	2	63	19	0	2	84	13	0	2	66	21	0	2	90	N	229	0.255	0
+Contig35_chr15_41400484_41400672	160	A	C	143.0	chr15	-1	N	1	0	2	30	2	0	2	33	0	0	-1	0	2	0	2	33	3	0	2	36	2	0	2	33	N	-1	+99.	0
+Contig104_chr15_45106954_45107158	70	A	T	64.4	chr15	45107015	A	6	0	2	45	6	0	2	45	19	0	2	84	7	0	2	48	7	0	2	48	3	0	2	36	N	202	4.319	0
+Contig119_chr16_6160274_6160477	180	G	A	54.8	chr16	6160457	G	7	0	2	48	6	0	2	45	12	0	2	63	3	0	2	36	11	0	2	60	10	0	2	57	N	42	+99.	0
+Contig126_chr16_10611887_10612152	150	G	T	145.0	chr16	10612037	G	14	0	2	69	9	0	2	54	11	0	2	63	8	0	2	51	8	0	2	51	11	0	2	60	N	15	0.104	6
+Contig114_chr16_12565220_12565676	10	G	A	134.0	chr16	12565230	G	0	0	-1	0	2	0	2	33	2	0	2	33	0	0	-1	0	1	0	2	30	1	0	2	30	N	333	+99.	0
+Contig43_chr16_20200090_20200514	70	A	G	58.6	chr16	20200154	A	11	0	2	60	15	0	2	72	15	0	2	72	6	0	2	45	9	0	2	54	12	0	2	63	Y	2	0.466	1
+Contig60_chr16_28079136_28080263	588	T	G	157.0	chr16	28079739	T	22	0	2	93	20	0	2	87	22	0	2	93	17	0	2	78	12	0	2	63	10	0	2	57	Y	105	5.999	1
+Contig70_chr16_33758668_33759655	104	A	T	58.1	chr16	33758772	A	6	0	2	45	7	0	2	48	17	0	2	78	14	0	2	69	8	0	2	51	10	0	2	57	N	54	0.162	0
+Contig66_chr16_37935682_37935831	116	T	C	99.2	chr16	37935802	C	12	0	2	63	6	0	2	45	19	0	2	84	12	0	2	63	13	0	2	66	17	0	2	78	N	266	+99.	2
+Contig16_chr16_40451506_40451643	84	A	G	59.8	chr16	40451592	A	7	0	2	48	5	0	2	42	7	0	2	48	13	0	2	66	14	0	2	69	19	0	2	84	N	45	5.061	0
+Contig53_chr16_49888293_49888587	260	G	A	108.0	chr16	49888550	A	4	0	2	39	1	0	2	30	3	0	2	36	5	0	2	42	2	0	2	33	2	0	2	33	Y	9	0.261	1
+Contig31_chr17_12128267_12129637	205	G	A	90.5	chr17	12128484	G	7	0	2	48	6	0	2	45	6	0	2	45	11	0	2	60	7	0	2	48	4	0	2	39	Y	10	0.246	0
+Contig50_chr17_12247973_12249183	889	G	T	47.6	chr17	12248878	G	0	1	2	9	8	0	2	51	9	2	2	21	7	2	2	21	15	0	2	72	0	3	0	9	Y	1	1.181	0
+Contig1_chr17_12979232_12980380	808	G	T	12.3	chr17	12980028	G	18	0	2	81	12	0	2	63	21	0	2	90	13	0	2	66	22	0	2	93	18	0	2	81	Y	9	0.336	1
+Contig63_chr17_14186372_14186928	54	C	T	70.7	chr17	14186427	C	6	0	2	45	2	0	2	33	5	0	2	42	6	0	2	45	3	0	2	36	3	0	2	36	Y	11	0.560	3
+Contig42_chr17_23434859_23438330	2100	C	T	39.5	chr17	23436985	T	4	0	2	39	7	0	2	48	7	0	2	48	3	0	2	36	6	0	2	45	2	0	2	33	Y	25	0.344	0
+Contig63_chr17_23796320_23796814	220	A	G	54.0	chr17	23796536	G	6	0	2	45	4	0	2	39	5	0	2	42	6	0	2	45	4	0	2	39	6	0	2	45	Y	139	0.067	1
+Contig76_chr17_24107434_24107834	316	T	C	141.0	chr17	24107726	T	19	0	2	84	15	0	2	72	20	0	2	87	16	0	2	75	11	0	2	60	18	0	2	81	Y	30	0.175	2
+Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
+Contig59_chr17_26790302_26795045	287	C	T	45.1	chr17	26790582	C	8	0	2	51	6	0	2	45	13	0	2	66	6	0	2	45	15	0	2	72	12	0	2	63	Y	75	0.019	1
+Contig99_chr17_27018324_27019378	446	G	A	31.1	chr17	27018776	G	14	0	2	69	12	0	2	63	14	0	2	69	10	0	2	57	9	0	2	54	11	0	2	60	Y	13	0.290	4
+Contig125_chr17_27739115_27739410	63	G	A	107.0	chr17	27739177	G	8	0	2	51	11	0	2	60	16	0	2	75	8	0	2	51	4	0	2	39	15	0	2	72	N	100	0.819	0
+Contig115_chr17_37489899_37490101	159	G	A	62.4	chr17	37490067	G	4	0	2	39	3	0	2	36	4	0	2	39	4	0	2	39	3	0	2	36	6	0	2	45	N	4	1.411	1
+Contig180_chr17_45154356_45154925	524	A	G	146.0	chr17	45154886	G	7	0	2	48	9	0	2	54	7	0	2	48	9	0	2	54	4	0	2	39	8	0	2	51	Y	11	+99.	2
+Contig61_chr17_48221795_48223545	1404	T	A	177.0	chr17	48223216	T	15	0	2	72	14	0	2	69	24	0	2	99	17	0	2	78	18	0	2	81	24	0	2	99	Y	161	0.633	2
+Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
+Contig229_chr18_3706523_3708577	1076	A	G	83.9	chr18	3707630	A	11	0	2	60	13	0	2	66	26	0	2	105	11	0	2	60	15	0	2	72	17	0	2	78	Y	63	0.445	0
+Contig24_chr18_14049894_14050480	24	A	G	123.0	chr18	14049918	A	5	0	2	42	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	5	0	2	42	Y	17	+99.	0
+Contig30_chr18_18771753_18772121	39	C	G	48.5	chr18	18771787	C	2	0	2	33	5	0	2	42	2	0	2	33	6	0	2	45	3	0	2	36	2	0	2	33	N	5	0.135	0
+Contig123_chr18_19916160_19916379	116	G	A	79.2	chr18	19916272	A	14	0	2	69	12	0	2	63	14	0	2	69	6	0	2	45	11	0	2	60	10	0	2	57	N	26	0.172	0
+Contig82_chr18_27305489_27306229	566	C	T	49.5	chr18	27306051	A	6	0	2	45	6	0	2	45	10	0	2	57	11	0	2	60	6	0	2	45	7	0	2	48	N	1	0.349	0
+Contig71_chr18_34324706_34326687	136	G	A	151.0	chr18	34324841	G	9	0	2	54	9	0	2	54	17	0	2	78	8	0	2	51	11	0	2	60	10	0	2	57	Y	2	2.129	2
+Contig16_chr18_34672093_34673044	538	T	C	58.2	chr18	34672635	T	8	0	2	51	15	0	2	72	16	0	2	75	15	0	2	72	9	0	2	57	18	0	2	81	Y	8	0.214	1
+Contig96_chr18_38492535_38493333	624	G	A	119.0	chr18	38493162	T	17	0	2	78	12	0	2	63	13	0	2	66	16	0	2	75	8	0	2	51	15	0	2	72	Y	127	0.131	0
+Contig226_chr18_47753756_47754666	427	T	C	21.1	chr18	47754215	T	10	0	2	57	4	0	2	39	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	42	0.522	0
+Contig170_chr18_49411558_49412230	94	C	A	74.3	chr18	49411655	C	14	0	2	69	10	0	2	57	9	0	2	54	10	0	2	57	3	0	2	36	3	0	2	36	N	9	1.457	0
+Contig192_chr18_49419342_49420737	1058	C	T	42.8	chr18	49420381	A	3	0	2	36	4	0	2	39	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	Y	34	2.107	2
+Contig64_chr18_55979770_55980315	49	G	A	89.1	chr18	55979824	G	3	0	2	36	9	0	2	54	7	0	2	51	4	0	2	39	3	0	2	36	3	0	2	36	Y	-1	2.124	0
+Contig20_chr18_58130301_58130735	112	A	G	74.4	chr18	58130413	A	12	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	6	0	2	45	6	0	2	45	Y	10	0.290	0
+Contig146_chr19_5221790_5223013	143	A	G	114.0	chr19	5221916	-	1	0	2	30	4	0	2	39	3	0	2	36	5	0	2	42	2	0	2	33	5	0	2	42	Y	12	0.870	0
+Contig13_chr19_7739961_7740118	26	C	G	220.0	chr19	-1	N	3	0	2	36	1	0	2	30	2	0	2	33	3	0	2	36	1	0	2	30	2	0	2	33	N	-1	+99.	0
+Contig67_chr19_12398520_12399367	499	C	T	161.0	chr19	12399017	C	10	0	2	57	11	0	2	60	20	0	2	87	14	0	2	69	24	0	2	99	8	0	2	51	Y	137	5.634	0
+Contig66_chr19_16285672_16287223	996	C	T	190.0	chr19	16286674	C	9	0	2	57	14	0	2	69	16	0	2	78	17	0	2	78	8	0	2	51	22	0	2	93	Y	40	0.110	0
+Contig129_chr19_25541958_25542221	202	T	C	68.1	chr19	25542154	C	11	0	2	60	19	0	2	84	10	0	2	60	17	0	2	78	9	0	2	54	12	0	2	63	N	-1	2.551	1
+Contig152_chr19_34274440_34275622	1072	C	T	48.0	chr19	34275509	T	1	0	2	30	2	0	2	33	1	0	2	30	1	0	2	30	4	0	2	39	5	0	2	42	N	71	0.309	0
+Contig29_chr19_37339947_37341911	1692	C	T	211.0	chr19	37341631	C	15	0	2	72	20	0	2	87	11	0	2	60	15	0	2	72	3	0	2	36	12	0	2	63	Y	7	0.096	0
+Contig39_chr19_47709708_47711327	444	C	T	36.8	chr19	47710148	T	10	0	2	57	4	0	2	39	8	0	2	51	9	0	2	54	6	0	2	45	6	0	2	45	Y	95	1.251	1
+Contig60_chr19_54013816_54014398	281	A	G	138.0	chr19	54014103	C	6	0	2	45	15	0	2	72	7	0	2	48	10	0	2	57	15	0	2	72	10	0	2	57	Y	188	1.271	0
+Contig251_chr19_56559098_56559626	452	T	C	3.36	chr19	56559549	T	12	0	2	63	13	0	2	66	21	0	2	90	15	0	2	72	14	0	2	69	11	0	2	60	N	1	0.117	0
+Contig50_chr20_12138509_12141975	3206	C	A	248.0	chr20	12141763	C	8	0	2	51	15	0	2	72	14	0	2	69	6	0	2	45	10	0	2	57	7	0	2	48	Y	2	0.384	0
+Contig36_chr20_32631363_32632049	176	G	A	24.1	chr20	32631526	G	7	0	2	48	14	0	2	69	19	0	2	84	14	0	2	69	15	0	2	72	16	0	2	75	N	50	1.150	0
+Contig39_chr20_36316398_36316498	57	C	T	30.3	chr20	36316455	C	2	0	2	33	0	1	2	8	0	0	-1	0	0	1	2	10	0	0	-1	0	0	0	-1	0	N	-483	+99.	0
+Contig32_chr20_36468058_36468869	66	C	T	40.4	chr20	36468127	C	6	0	2	45	3	0	2	36	4	0	2	39	5	0	2	42	3	0	2	36	4	0	2	39	N	59	0.281	0
+Contig24_chr20_38203888_38204900	834	C	T	132.0	chr20	38204731	C	9	0	2	54	17	0	2	78	20	0	2	87	8	0	2	51	11	0	2	60	17	0	2	78	Y	14	0.397	0
+Contig79_chr20_44263127_44264103	456	G	T	31.5	chr20	44263573	G	22	0	2	93	16	0	2	75	15	0	2	72	19	0	2	84	13	0	2	66	26	0	2	105	Y	8	3.250	0
+Contig26_chr20_45878482_45878787	197	A	G	160.0	chr20	45878672	A	17	0	2	78	15	0	2	72	11	0	2	63	17	0	2	78	12	0	2	63	10	0	2	57	N	14	0.535	0
+Contig119_chr20_46550670_46551383	609	G	A	139.0	chr20	46551277	G	7	0	2	48	17	0	2	78	19	0	2	84	20	0	2	87	9	0	2	54	15	0	2	72	Y	7	0.488	1
+Contig50_chr21_4178523_4178687	121	G	A	362.0	chr21	4178640	G	8	0	2	51	14	0	2	69	5	0	2	42	3	0	2	36	11	0	2	60	4	0	2	39	N	392	0.483	0
+Contig103_chr21_10177255_10177765	121	G	A	125.0	chr21	10177367	G	12	0	2	63	10	0	2	57	10	0	2	57	17	0	2	78	14	0	2	69	7	0	2	51	Y	37	0.213	3
+Contig1_chr21_10805534_10806399	766	A	G	146.0	chr21	10806301	G	10	0	2	57	6	0	2	45	9	0	2	54	6	0	2	45	7	0	2	48	5	0	2	42	Y	20	0.319	0
+Contig46_chr21_21029492_21030645	443	C	T	5.37	chr21	21029910	C	15	0	2	72	11	0	2	60	16	0	2	75	15	0	2	72	13	0	2	66	6	0	2	45	Y	96	3.737	0
+Contig129_chr21_31045749_31046924	381	A	G	129.0	chr21	31046141	A	19	0	2	84	8	0	2	51	23	0	2	96	12	0	2	63	15	0	2	72	18	0	2	81	Y	69	0.028	2
+Contig23_chr21_31651123_31651986	840	C	T	71.3	chr21	31651957	T	6	0	2	45	9	0	2	54	8	0	2	51	10	0	2	57	4	0	2	39	7	0	2	48	Y	105	2.977	3
+Contig64_chr21_43341847_43342031	84	T	C	114.0	chr21	43341926	T	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	6	0	2	45	7	0	2	48	N	10	3.954	2
+Contig60_chr21_43475347_43475824	175	C	T	8.05	chr21	43475551	T	6	0	2	45	7	0	2	48	13	0	2	66	6	0	2	45	14	0	2	69	14	0	2	69	N	45	0.058	0
+Contig64_chr21_45377513_45377872	19	C	T	60.7	chr21	-1	N	3	0	2	36	2	0	2	33	1	0	2	30	0	0	-1	0	3	0	2	36	1	0	2	30	N	-1	+99.	1
+Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0
+Contig46_chr22_9416920_9417467	381	G	A	145.0	chr22	9417259	G	10	0	2	57	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	7	0	2	48	Y	154	0.242	0
+Contig86_chr22_9440787_9441725	713	T	G	119.0	chr22	9441488	G	6	0	2	45	12	0	2	63	10	0	2	57	11	0	2	60	13	0	2	66	16	0	2	75	Y	132	0.218	0
+Contig16_chr22_15636960_15637372	236	A	C	9.79	chr22	15637192	T	4	0	2	39	5	0	2	42	12	0	2	63	7	0	2	48	6	0	2	45	11	0	2	60	Y	5	2.163	0
+Contig4_chr22_16114310_16114546	128	G	C	101.0	chr22	16114432	G	10	0	2	57	13	0	2	66	20	0	2	87	20	0	2	87	16	0	2	75	9	0	2	54	N	19	0.526	0
+Contig23_chr22_34612023_34612568	167	C	G	92.3	chr22	34612181	C	11	0	2	60	18	0	2	81	13	0	2	66	8	0	2	51	12	0	2	63	14	0	2	69	Y	7	0.409	0
+Contig4_chr22_38252245_38253712	799	A	C	159.0	chr22	38253064	A	18	0	2	81	15	0	2	72	15	0	2	72	20	0	2	87	27	0	2	108	15	0	2	72	Y	90	4.330	0
+Contig122_chr22_48412466_48414788	1888	C	T	125.0	chr22	48414355	T	16	0	2	75	15	0	2	72	16	0	2	75	14	0	2	72	12	0	2	63	7	0	2	48	N	42	0.122	0
+Contig77_chr22_49764414_49764875	353	C	A	148.0	chr22	49764777	C	7	4	1	65	18	0	2	81	16	0	2	75	20	0	2	87	4	3	1	52	9	4	1	67	Y	12	0.941	0
+Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
+Contig348_chr22_62406104_62406495	189	C	A	134.0	chr22	62406302	A	9	0	2	54	14	0	2	69	11	0	2	60	10	0	2	57	12	0	2	63	6	0	2	45	Y	5	0.912	0
+Contig133_chr23_3525134_3526502	1223	A	G	201.0	chr23	3526387	A	11	0	2	60	13	0	2	66	23	0	2	96	21	0	2	90	13	0	2	66	10	0	2	57	Y	61	1.359	0
+Contig111_chr23_7058063_7058181	107	G	A	108.0	chr23	7058162	A	8	0	2	51	8	0	2	51	7	0	2	48	2	0	2	33	5	0	2	42	6	0	2	45	N	3	+99.	0
+Contig79_chr23_7844129_7844837	110	C	A	141.0	chr23	7844237	T	13	0	2	66	15	0	2	72	17	0	2	78	12	0	2	63	15	0	2	72	16	0	2	75	Y	40	0.339	0
+Contig38_chr23_9201002_9201725	597	C	T	155.0	chr23	9201609	T	17	0	2	78	8	0	2	51	13	0	2	66	5	0	2	42	11	0	2	60	7	0	2	48	Y	167	0.633	1
+Contig33_chr23_20672540_20674320	347	T	A	91.4	chr23	20672885	A	11	0	2	60	14	0	2	69	15	0	2	72	7	0	2	48	12	0	2	63	18	0	2	81	Y	31	0.452	1
+Contig35_chr23_28447813_28449115	70	T	A	21.3	chr23	28447881	T	9	0	2	54	8	0	2	51	10	0	2	57	9	0	2	54	10	0	2	57	12	0	2	63	N	251	0.163	1
+Contig51_chr23_30590939_30591162	140	C	T	142.0	chr23	30591080	C	14	0	2	69	4	0	2	39	10	0	2	57	12	0	2	63	14	0	2	69	4	0	2	39	N	13	1.658	0
+Contig57_chr23_32216351_32216721	179	T	G	143.0	chr23	32216534	T	15	0	2	72	15	0	2	72	23	0	2	96	13	0	2	66	16	0	2	75	15	0	2	72	N	32	1.387	1
+Contig93_chr23_35744841_35745791	40	A	T	30.4	chr23	35744880	T	6	0	2	45	7	0	2	48	7	0	2	48	2	0	2	33	5	0	2	42	5	0	2	42	Y	50	2.173	0
+Contig99_chr23_42543966_42544147	14	G	A	357.0	chr23	42543980	G	4	0	2	39	2	0	2	33	3	0	2	36	3	0	2	36	1	0	2	30	2	0	2	33	N	69	+99.	0
+Contig32_chr23_48285289_48286638	186	T	C	176.0	chr23	48285470	T	18	0	2	81	12	0	2	63	16	0	2	75	13	0	2	66	9	0	2	54	9	0	2	54	Y	4	4.238	1
+Contig50_chr24_22515247_22516072	761	C	T	243.0	chr24	22515981	T	11	0	2	60	10	0	2	57	8	0	2	51	9	0	2	54	18	0	2	81	8	0	2	51	Y	1	0.190	0
+Contig92_chr24_28935897_28936321	13	G	A	47.1	chr24	-1	N	2	0	2	33	1	0	2	30	0	0	-1	0	0	0	-1	0	1	0	2	30	0	0	-1	0	Y	-1	+99.	2
+Contig84_chr24_29196623_29199644	466	C	T	126.0	chr24	29197091	T	7	0	2	48	11	0	2	60	8	0	2	51	7	0	2	48	11	0	2	60	15	0	2	72	Y	42	0.215	0
+Contig35_chr24_30150986_30151507	492	A	C	114.0	chr24	30151448	A	5	0	2	42	2	0	2	33	2	0	2	33	3	0	2	36	3	0	2	36	5	0	2	42	N	41	2.587	6
+Contig61_chr24_30465488_30465834	149	G	T	68.2	chr24	30465637	G	13	0	2	66	4	2	2	11	18	0	2	81	11	0	2	60	11	0	2	60	9	0	2	54	N	99	0.105	2
+Contig145_chr24_34778364_34778898	163	T	C	372.0	chr24	34778541	C	10	0	2	57	8	0	2	51	12	0	2	63	12	0	2	63	6	1	2	31	7	0	2	48	Y	40	0.037	0
+Contig34_chr24_36147443_36150244	2679	C	T	140.0	chr24	36150125	C	13	0	2	66	7	0	2	48	14	0	2	69	14	0	2	69	10	0	2	57	13	0	2	66	N	282	0.099	1
+Contig164_chr24_46598127_46599206	84	C	T	105.0	chr24	46598214	C	13	0	2	66	12	0	2	63	15	0	2	72	15	0	2	72	11	0	2	60	8	0	2	51	Y	22	1.262	1
+Contig144_chr25_4011170_4013134	541	A	G	160.0	chr25	4011690	A	12	0	2	63	17	0	2	78	13	0	2	66	13	0	2	66	13	0	2	66	13	0	2	66	Y	5	0.087	0
+Contig81_chr25_6103472_6104760	699	G	A	378.0	chr25	6104190	A	14	0	2	69	16	0	2	75	13	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	Y	33	0.789	2
+Contig152_chr25_7486442_7487609	75	A	G	11.6	chr25	7486515	A	17	0	2	78	13	0	2	66	8	0	2	51	16	0	2	75	8	0	2	51	6	0	2	45	N	2	0.158	0
+Contig24_chr25_7695778_7698612	2714	C	T	130.0	chr25	7698446	C	16	0	2	75	13	0	2	66	22	0	2	93	17	0	2	78	10	0	2	57	17	0	2	78	Y	27	0.346	0
+Contig89_chr25_8635170_8636009	586	G	C	209.0	chr25	8635744	G	13	0	2	66	13	0	2	66	21	0	2	93	14	0	2	69	15	0	2	72	15	0	2	72	Y	14	0.067	0
+Contig77_chr25_10796299_10796481	2	T	C	17.3	chr25	-1	N	1	0	2	30	0	0	-1	0	1	0	2	30	0	0	-1	0	0	0	-1	0	0	0	-1	0	N	-1	+99.	0
+Contig73_chr25_14177327_14177474	125	A	C	6.85	chr25	14177464	A	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	N	27	+99.	1
+Contig59_chr25_18196776_18197707	785	G	A	112.0	chr25	18197551	G	8	10	1	42	27	0	2	108	21	0	2	90	18	0	2	81	10	0	2	57	14	0	2	69	N	36	3.625	0
+Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
+Contig84_chr25_42407960_42408708	55	C	T	119.0	chr25	42408013	C	6	0	2	45	9	0	2	54	11	0	2	60	9	0	2	54	7	0	2	48	8	0	2	51	Y	11	0.121	0
+Contig73_chr25_43562500_43564110	955	T	C	52.1	chr25	43563469	C	9	0	2	57	4	0	2	39	6	0	2	45	5	0	2	42	7	0	2	48	10	0	2	57	Y	4	1.406	0
+Contig37_chr25_51074433_51074885	170	A	G	102.0	chr25	51074589	G	11	0	2	60	7	0	2	48	6	0	2	45	15	0	2	72	9	0	2	54	7	0	2	48	Y	68	0.207	1
+Contig204_chr26_4311195_4311778	170	C	T	16.9	chr26	4311363	T	20	0	2	87	8	0	2	51	13	0	2	66	18	0	2	81	11	0	2	60	14	0	2	69	N	35	0.085	0
+Contig122_chr26_7622321_7623491	106	C	G	139.0	chr26	7622423	C	3	0	2	36	9	0	2	54	10	0	2	57	12	0	2	63	9	0	2	54	5	0	2	42	N	19	0.458	0
+Contig11_chr26_11062142_11062902	707	C	A	108.0	chr26	11062836	T	7	0	2	48	8	0	2	51	16	0	2	75	10	0	2	57	6	0	2	45	14	0	2	69	Y	-1	4.709	0
+Contig133_chr26_17695661_17696368	39	T	G	98.7	chr26	17695700	T	10	0	2	57	3	0	2	36	11	0	2	60	9	0	2	54	2	0	2	33	1	0	2	30	N	85	3.402	0
+Contig157_chr26_23894107_23895229	25	C	T	50.2	chr26	23894140	C	0	0	-1	0	4	0	2	39	2	0	2	33	4	0	2	39	3	0	2	36	3	0	2	36	Y	51	+99.	0
+Contig146_chr26_26622638_26623906	574	G	A	186.0	chr26	26623219	A	11	0	2	60	12	0	2	63	9	0	2	54	11	0	2	60	9	0	2	54	12	0	2	63	Y	1	0.318	0
+Contig8_chr26_27834126_27834326	140	G	A	41.7	chr26	27834268	G	13	0	2	66	7	0	2	48	13	0	2	66	11	0	2	60	12	0	2	63	6	0	2	45	N	29	0.142	1
+Contig78_chr26_31128839_31129005	123	T	C	145.0	chr26	-1	N	11	0	2	60	3	0	2	36	7	0	2	48	8	0	2	51	10	0	2	46	7	0	2	48	N	-1	1.230	1
+Contig28_chr26_32935355_32935833	289	T	C	77.9	chr26	32935638	T	15	0	2	72	22	0	2	93	15	0	2	72	9	0	2	54	15	0	2	72	17	0	2	78	Y	10	2.258	1
+Contig36_chr26_36606876_36607240	115	A	T	139.0	chr26	36606979	A	1	0	2	30	7	0	2	48	14	0	2	69	13	0	2	66	9	0	2	54	3	0	2	36	Y	8	0.071	0
+Contig135_chr27_6853874_6854079	158	C	T	116.0	chr27	6854032	T	18	0	2	81	19	0	2	84	13	0	2	66	7	0	2	48	8	0	2	51	11	0	2	60	N	4	0.060	1
+Contig47_chr27_11777710_11777915	25	A	G	67.3	chr27	11777731	A	3	0	2	36	5	0	2	42	6	0	2	45	10	0	2	57	9	0	2	54	6	0	2	45	N	97	+99.	0
+Contig23_chr27_14633002_14633153	23	G	A	128.0	chr27	14633023	A	3	0	2	36	4	0	2	39	5	0	2	42	5	0	2	42	3	0	2	36	2	0	2	33	N	240	3.881	0
+Contig31_chr27_14987233_14988055	630	A	G	48.5	chr27	14987850	G	10	0	2	57	2	0	2	33	4	0	2	39	4	0	2	39	1	0	2	30	4	0	2	39	Y	9	0.089	1
+Contig29_chr27_15428166_15429413	380	T	C	140.0	chr27	15428539	T	15	0	2	72	15	0	2	72	17	0	2	78	15	0	2	72	15	0	2	72	15	0	2	72	Y	47	0.916	1
+Contig31_chr27_19519489_19520891	129	G	T	14.9	chr27	19519624	T	12	0	2	63	19	0	2	84	20	0	2	87	16	0	2	75	10	0	2	57	11	0	2	60	Y	48	2.756	0
+Contig64_chr27_34654435_34654621	132	C	A	115.0	chr27	34654567	T	2	0	2	33	2	0	2	33	5	0	2	42	3	0	2	36	3	0	2	36	8	0	2	51	N	12	0.297	1
+Contig35_chr27_40596169_40596445	20	G	C	133.0	chr27	40596189	G	8	0	2	51	3	0	2	36	4	0	2	39	2	0	2	33	4	0	2	39	4	0	2	39	Y	4	+99.	1
+Contig85_chr27_45471750_45472022	211	G	A	53.1	chr27	45471964	G	18	0	2	81	10	0	2	57	15	0	2	72	0	13	0	36	16	0	2	75	14	0	2	69	N	75	2.502	1
+Contig131_chr28_6481806_6483783	138	C	T	36.2	chr28	6481953	C	12	0	2	63	12	0	2	63	20	0	2	87	11	0	2	60	10	0	2	57	12	0	2	63	Y	10	0.387	0
+Contig141_chr28_10027332_10028242	780	T	G	74.8	chr28	10028095	T	10	0	2	57	11	0	2	60	14	0	2	69	10	0	2	57	7	0	2	48	9	0	2	54	Y	19	3.348	0
+Contig144_chr28_15468203_15470548	743	G	A	20.0	chr28	15468942	G	13	0	2	66	12	0	2	63	10	0	2	57	11	0	2	60	16	0	2	75	7	0	2	48	N	14	0.053	0
+Contig47_chr28_21311718_21312366	541	G	A	116.0	chr28	21312258	G	9	0	2	54	6	0	2	45	12	0	2	63	6	0	2	45	5	0	2	45	12	0	2	63	N	9	0.240	0
+Contig60_chr28_30197166_30197364	92	T	C	164.0	chr28	30197258	T	10	0	2	57	13	0	2	66	15	0	2	72	16	0	2	75	12	0	2	63	11	0	2	60	N	369	1.139	0
+Contig201_chr28_36339953_36341322	260	C	T	6.36	chr28	36340213	T	4	0	2	39	0	0	-1	0	2	0	2	33	2	0	2	33	3	0	2	36	4	0	2	39	N	4	0.183	0
+Contig175_chr28_36441165_36441915	68	T	C	3.83	chr28	36441234	T	4	4	1	15	6	0	2	45	12	0	2	63	15	0	2	72	6	0	2	45	9	0	2	54	N	4	1.610	2
+Contig29_chr29_4726399_4727143	559	A	T	163.0	chr29	4726955	A	15	0	2	72	18	0	2	81	18	0	2	81	16	0	2	75	11	0	2	60	14	0	2	72	Y	161	3.114	0
+Contig48_chr29_13129286_13130137	232	A	G	92.2	chr29	13129514	G	13	0	2	66	11	0	2	60	19	0	2	84	16	0	2	75	11	0	2	60	17	0	2	78	Y	337	2.581	1
+Contig64_chr29_15736891_15737257	344	T	C	40.4	chr29	15737233	C	1	0	2	30	0	0	-1	0	0	0	-1	0	2	0	2	33	0	0	-1	0	0	0	-1	0	N	58	+99.	0
+Contig33_chr29_17000374_17000921	71	C	T	48.6	chr29	17000441	-	4	0	2	39	9	0	2	54	12	0	2	66	10	0	2	57	7	0	2	48	4	0	2	39	N	26	5.491	0
+Contig34_chr29_17581796_17584016	2105	C	T	126.0	chr29	17583890	T	14	0	2	69	11	0	2	60	18	0	2	81	12	0	2	63	10	0	2	57	10	0	2	57	Y	22	2.208	0
+Contig19_chr29_20976080_20977761	1007	G	A	115.0	chr29	20977076	G	19	0	2	84	22	0	2	93	22	0	2	93	22	0	2	93	11	0	2	60	13	0	2	66	Y	4	1.915	0
+Contig51_chr29_21149853_21150467	266	C	T	146.0	chr29	21150118	C	12	0	2	63	12	0	2	63	23	0	2	96	14	0	2	69	13	0	2	66	10	0	2	57	Y	4	0.051	0
+Contig1_chr30_5992217_5993068	106	C	T	129.0	chr30	5992319	C	10	0	2	57	11	0	2	60	7	0	2	48	11	0	2	60	10	0	2	57	12	0	2	63	Y	76	1.079	0
+Contig1_chr30_8232878_8233406	402	C	T	127.0	chr30	8233264	C	8	0	2	51	19	0	2	84	16	0	2	75	18	0	2	81	10	0	2	57	14	0	2	69	Y	358	5.283	0
+Contig108_chr30_9436961_9437520	546	C	T	39.8	chr30	9437502	C	7	0	2	48	5	0	2	42	2	0	2	33	7	0	2	48	5	0	2	42	7	0	2	48	Y	64	+99.	0
+Contig165_chr30_25804389_25804926	190	T	C	126.0	chr30	25804592	C	3	0	2	36	8	0	2	51	7	0	2	48	10	0	2	57	7	0	2	48	4	0	2	39	Y	113	0.329	0
+Contig193_chr30_27495616_27496125	434	C	A	234.0	chr30	27496024	C	13	0	2	66	16	0	2	75	25	0	2	102	16	0	2	75	13	0	2	66	14	0	2	69	Y	76	2.621	0
+Contig114_chr30_33636712_33637208	34	C	T	142.0	chr30	33636744	C	7	0	2	48	4	1	2	20	6	0	2	45	6	0	2	45	3	4	1	29	5	0	2	42	Y	14	8.028	0
+Contig38_chr31_5164423_5166573	2074	C	T	134.0	chr31	5166501	T	13	0	2	66	10	0	2	57	17	0	2	78	11	0	2	60	17	0	2	78	10	0	2	57	Y	58	+99.	0
+Contig6_chr31_9649308_9650149	431	G	T	162.0	chr31	9649742	G	31	0	2	120	23	0	2	96	17	0	2	78	17	0	2	78	10	0	2	57	16	0	2	75	Y	98	2.200	0
+Contig85_chr31_12242872_12245082	38	G	C	92.4	chr31	12242910	G	1	0	2	30	6	0	2	45	9	0	2	54	8	0	2	51	5	0	2	42	9	0	2	54	N	2	2.340	0
+Contig7_chr31_12384974_12386400	305	C	T	69.6	chr31	12385267	C	6	0	2	45	10	0	2	57	11	0	2	60	11	0	2	60	9	0	2	54	12	0	2	63	Y	44	1.165	0
+Contig90_chr31_17267583_17267778	81	C	A	143.0	chr31	17267665	C	20	0	2	87	6	0	2	45	14	0	2	72	22	0	2	93	17	0	2	78	15	0	2	72	N	7	0.565	0
+Contig68_chr31_20000241_20000597	215	C	T	131.0	chr31	20000454	T	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	Y	5	3.383	1
+Contig137_chr31_23357653_23358568	885	G	A	119.0	chr31	23358545	G	5	0	2	42	3	0	2	36	3	0	2	36	2	0	2	33	3	0	2	36	4	0	2	39	Y	11	+99.	0
+Contig17_chr31_26433828_26434459	498	T	C	9.79	chr31	26434322	T	18	0	2	81	10	0	2	57	15	0	2	72	13	0	2	66	16	0	2	75	15	0	2	72	Y	137	4.814	0
+Contig9_chr32_19479532_19479735	12	A	G	20.7	chr32	19479544	A	1	0	2	30	2	0	2	33	1	0	2	30	5	0	2	42	3	0	2	36	3	0	2	36	N	17	+99.	0
+Contig30_chr32_25902721_25905783	208	C	G	162.0	chr32	25902927	G	11	0	2	60	13	0	2	66	11	0	2	60	12	0	2	63	7	0	2	48	11	0	2	60	Y	145	0.322	2
+Contig7_chr32_27789513_27789926	20	G	A	7.19	chr32	27789530	A	0	0	-1	0	4	0	2	39	4	0	2	39	4	0	2	39	2	0	2	33	6	0	2	45	Y	14	+99.	0
+Contig42_chr32_38900713_38901320	320	A	G	134.0	chr32	38901021	T	12	0	2	63	10	0	2	57	9	11	1	104	5	0	2	42	19	0	2	84	7	6	1	56	Y	71	0.165	0
+Contig18_chr33_22207246_22209159	1363	G	T	51.5	chr33	22208619	-	16	0	2	75	8	0	2	51	11	0	2	60	10	0	2	57	15	0	2	72	12	0	2	63	Y	59	2.560	0
+Contig104_chr33_22483642_22484187	424	C	T	140.0	chr33	22484054	T	13	0	2	66	16	0	2	75	9	0	2	54	15	0	2	72	13	0	2	66	10	0	2	57	Y	36	0.404	0
+Contig170_chr33_26189421_26189940	292	T	C	98.4	chr33	26189703	T	21	0	2	90	13	0	2	66	15	0	2	72	13	0	2	66	19	0	2	84	13	0	2	66	Y	23	0.307	0
+Contig113_chr34_13341080_13341643	236	C	T	90.7	chr34	13341316	C	4	0	2	39	2	0	2	33	8	0	2	51	4	0	2	39	8	0	2	51	3	0	2	36	Y	47	0.412	3
+Contig405_chr34_14415672_14415979	59	A	G	36.2	chr34	14415731	G	8	0	2	51	2	0	2	33	8	0	2	51	6	0	2	48	3	0	2	36	7	0	2	48	Y	45	0.405	1
+Contig21_chr34_16422980_16425681	2009	G	A	19.4	chr34	16424960	G	0	0	-1	0	0	0	-1	0	0	0	-1	0	5	0	2	42	0	0	-1	0	0	0	-1	0	Y	28	0.196	0
+Contig41_chr34_16544482_16545449	46	T	C	102.0	chr34	16544523	T	5	0	2	42	11	0	2	60	6	0	2	45	0	2	0	3	7	0	2	48	8	0	2	51	Y	215	1.156	0
+Contig8_chr34_18474513_18475673	1122	C	A	129.0	chr34	18475628	A	8	0	2	51	15	0	2	72	13	0	2	66	17	0	2	78	13	0	2	66	6	0	2	45	Y	61	0.123	2
+Contig152_chr34_31794848_31795540	242	G	A	93.2	chr34	31795093	G	11	0	2	60	24	0	2	99	17	0	2	78	15	0	2	72	18	0	2	81	17	0	2	78	Y	123	2.780	0
+Contig28_chr34_41708848_41712034	1381	A	G	78.2	chr34	41710232	A	11	0	2	60	17	0	2	78	15	0	2	72	16	0	2	75	15	0	2	72	14	0	2	69	Y	236	0.234	0
+Contig85_chr34_42798284_42800584	1845	C	T	171.0	chr34	42800126	T	5	0	2	42	7	0	2	48	6	0	2	45	7	0	2	48	6	0	2	45	2	0	2	33	Y	5	2.787	0
+Contig47_chr35_3666773_3667898	348	G	T	124.0	chr35	3667121	G	9	0	2	54	20	0	2	87	18	0	2	81	15	0	2	72	12	0	2	63	14	0	2	69	Y	285	0.235	0
+Contig195_chr35_15722500_15722741	205	G	A	4.08	chr35	15722718	G	3	0	2	36	5	0	2	42	1	0	2	30	6	0	2	45	1	0	2	30	1	0	2	30	N	43	+99.	0
+Contig101_chr35_19513178_19513697	62	C	T	112.0	chr35	19513238	C	12	0	2	63	7	0	2	48	13	0	2	66	7	0	2	48	5	0	2	42	8	0	2	51	N	115	3.135	0
+Contig19_chr35_23887144_23888282	90	C	A	10.1	chr35	23887242	-	3	3	1	12	4	4	1	19	8	6	1	37	4	3	1	11	8	3	2	7	9	3	2	11	Y	105	0.199	0
+Contig47_chr35_24382042_24382526	33	G	A	87.0	chr35	24382076	G	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	4	0	2	39	2	0	2	33	Y	71	+99.	0
+Contig77_chr35_24796947_24797172	65	A	G	52.1	chr35	24797009	A	7	0	2	48	5	0	2	42	8	0	2	51	6	0	2	45	12	0	2	63	10	0	2	57	N	11	1.401	3
+Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0
+Contig5_chr36_4562983_4563634	343	C	T	151.0	chr36	4563324	T	20	0	2	87	20	0	2	87	23	0	2	96	24	0	2	99	9	0	2	54	8	0	2	51	Y	40	1.169	0
+Contig75_chr36_7885319_7885588	53	G	A	25.7	chr36	7885372	G	10	0	2	57	8	0	2	51	13	0	2	66	7	0	2	48	4	0	2	39	7	0	2	48	N	7	2.653	0
+Contig184_chr36_18956191_18958552	187	A	G	11.5	chr36	18956371	G	10	0	2	57	11	0	2	60	21	0	2	90	14	0	2	69	7	0	2	48	4	0	2	39	N	278	1.434	2
+Contig12_chr36_21557176_21557828	513	T	A	159.0	chr36	21557695	A	11	0	2	60	14	0	2	69	21	0	2	90	12	0	2	63	15	0	2	72	11	0	2	60	Y	55	0.222	0
+Contig2_chr36_22436067_22436794	653	C	T	73.0	chr36	22436730	C	11	0	2	60	16	0	2	75	13	0	2	66	11	0	2	60	21	0	2	90	21	0	2	90	Y	9	0.534	0
+Contig133_chr36_32954045_32955409	136	A	G	116.0	chr36	32954182	A	16	0	2	75	15	0	2	72	20	0	2	87	11	0	2	60	18	0	2	81	13	0	2	66	Y	74	3.772	1
+Contig53_chr37_6665763_6665919	116	C	T	111.0	chr37	6665875	C	9	0	2	54	9	0	2	54	5	0	2	42	9	0	2	54	8	0	2	51	10	0	2	57	N	15	10.875	1
+Contig42_chr37_9589176_9591269	252	G	A	25.1	chr37	9589430	G	10	0	2	40	13	0	2	66	18	0	2	81	21	0	2	90	9	0	2	54	17	0	2	78	N	67	1.170	2
+Contig2_chr37_17134963_17136513	1140	A	C	158.0	chr37	17136092	A	14	0	2	69	24	0	2	99	17	0	2	78	16	0	2	75	15	0	2	75	13	0	2	66	Y	12	0.053	1
+Contig18_chr37_17147806_17149851	291	T	G	112.0	chr37	17148084	T	4	6	1	45	16	0	2	75	17	0	2	78	14	0	2	69	22	0	2	93	13	0	2	66	Y	41	4.442	0
+Contig64_chr37_17606895_17607534	565	C	T	30.2	chr37	17607439	A	9	0	2	54	16	0	2	75	20	0	2	87	14	0	2	69	16	0	2	75	10	0	2	57	N	20	1.622	0
+Contig126_chr37_21587881_21590621	373	G	T	132.0	chr37	21588256	G	11	0	2	60	11	0	2	60	23	0	2	96	12	0	2	63	8	0	2	51	18	0	2	81	Y	12	0.549	0
+Contig2_chr37_31197993_31198256	182	C	T	39.6	chr37	31198171	T	6	0	2	45	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	12	0	2	63	N	2	0.595	0
+Contig46_chr37_31852376_31853555	825	A	G	111.0	chr37	31853191	G	19	0	2	84	14	0	2	69	15	0	2	72	7	0	2	48	8	0	2	51	16	0	2	75	Y	17	0.128	1
+Contig7_chr38_12217200_12218387	1163	A	T	44.4	chr38	12218353	A	11	0	2	60	13	0	2	66	17	0	2	78	10	0	2	57	11	0	2	60	11	0	2	60	Y	67	+99.	0
+Contig15_chr38_12282020_12282253	150	C	T	156.0	chr38	12282164	A	17	0	2	78	11	0	2	60	19	0	2	84	14	0	2	69	5	0	2	42	14	0	2	69	Y	26	2.952	1
+Contig4_chr38_14807432_14807747	275	A	G	36.5	chr38	14807715	G	1	0	2	30	2	0	2	33	2	0	2	33	4	0	2	39	1	0	2	30	0	0	-1	0	Y	28	+99.	1
+Contig6_chr38_16185744_16186110	325	A	G	74.9	chr38	16186061	A	5	0	2	42	3	0	2	36	9	0	2	54	7	0	2	48	1	0	2	30	12	0	2	63	Y	40	+99.	0
+Contig265_chrX_2689247_2689484	114	C	G	103.0	chrX	2689356	C	11	0	2	60	9	0	2	54	13	0	2	66	16	0	2	75	14	0	2	69	10	0	2	57	N	2	9.232	1
+Contig122_chrX_6026976_6027327	330	C	T	79.4	chrX	6027303	C	3	0	2	36	3	0	2	36	3	0	2	36	4	0	2	39	3	0	2	36	6	0	2	45	Y	30	+99.	0
+Contig15_chrX_15659909_15660340	15	A	C	14.9	chrX	15659924	C	1	0	2	30	1	0	2	30	3	0	2	36	6	0	2	45	2	0	2	33	0	0	-1	0	Y	216	+99.	1
+Contig12_chrX_23243561_23244412	479	C	G	67.7	chrX	23244037	C	2	0	2	33	4	2	2	8	2	6	1	43	7	0	2	48	6	0	2	45	4	0	2	39	Y	208	1.620	0
+Contig113_chrX_26287829_26288398	385	C	T	59.6	chrX	26288213	C	9	0	2	54	9	0	2	54	17	0	2	78	11	0	2	60	3	8	1	44	4	0	2	39	N	13	0.077	0
+Contig186_chrX_29118735_29118939	192	G	A	7.01	chrX	29118931	G	1	0	2	30	7	0	2	48	4	0	2	39	5	0	2	42	8	0	2	51	4	0	2	39	N	50	+99.	0
+Contig237_chrX_31256648_31257654	165	T	A	246.0	chrX	31256814	T	7	0	2	48	23	0	2	96	19	0	2	84	17	0	2	78	14	0	2	69	8	0	2	51	Y	37	1.481	0
+Contig25_chrX_40729418_40730089	332	C	T	31.2	chrX	40729745	C	0	0	-1	0	2	0	2	33	4	0	2	39	5	0	2	42	3	0	2	36	3	0	2	36	Y	34	0.212	0
+Contig90_chrX_57430715_57431566	548	C	T	116.0	chrX	57431266	T	9	0	2	54	18	0	2	81	13	0	2	66	14	0	2	69	8	0	2	54	7	0	2	48	Y	261	0.154	1
+Contig133_chrX_84833782_84834125	182	G	A	69.7	chrX	84833962	G	5	0	2	42	18	0	2	81	12	0	2	63	19	0	2	84	6	3	1	27	7	0	2	48	N	619	0.278	0
+Contig129_chrX_90586053_90586467	135	A	T	120.0	chrX	90586195	A	1	0	2	30	6	0	2	45	8	0	2	51	5	0	2	42	1	0	2	30	2	0	2	33	N	637	0.245	0
+Contig125_chrX_93319363_93320877	349	A	C	145.0	chrX	93319721	A	4	0	2	39	6	0	2	45	11	0	2	60	10	0	2	57	13	0	2	66	6	0	2	45	Y	59	1.686	0
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_in/sample.sap
--- a/test-data/test_in/sample.sap	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,401 +0,0 @@
-#{"column_names":["contig","pos","ref","rPos","trns","pep","AA1","loc","AA2","KEGG","pred","path"],"pos":2,"rPos":4,"ref":3,"dbkey":"canFam2","scaffold":1,"species":"bear","kegg_gene":10,"kegg_path":12}
-Contig39_chr1_3261104_3261850	414	chr1	3261546	ENSCAFT00000000001	ENSCAFP00000000001	S	667	F	476153	probably damaging	cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
-Contig62_chr1_19011969_19012646	265	chr1	19012240	ENSCAFT00000000144	ENSCAFP00000000125	*	161	R	483960	probably damaging	N
-Contig36_chr1_20102654_20103213	365	chr1	20103029	ENSCAFT00000000160	ENSCAFP00000000140	R	407	Q	610160	possibly damaging	N
-Contig136_chr10_3710404_3714591	3079	chr10	3713499	ENSCAFT00000000215	ENSCAFP00000000194	T	103	P	U	benign	N
-Contig36_chr1_23682012_23682647	374	chr1	23682388	ENSCAFT00000000233	ENSCAFP00000000210	N	234	S	483973	benign	N
-Contig163_chr10_4573526_4574494	487	chr10	4574010	ENSCAFT00000000365	ENSCAFP00000000332	R	186	K	474414	benign	cfa00450=Selenocompound metabolism.cfa00970=Aminoacyl-tRNA biosynthesis
-Contig55_chr1_40056604_40059808	2081	chr1	40058686	ENSCAFT00000000507	ENSCAFP00000000458	I	247	K	484023	possibly damaging	N
-Contig17_chr1_40203628_40205630	1417	chr1	40205044	ENSCAFT00000000517	ENSCAFP00000000468	N	109	S	476233	benign	N
-Contig97_chr1_44847984_44848380	285	chr1	44848272	ENSCAFT00000000674	ENSCAFP00000000618	Q	27	R	611986	benign	N
-Contig214_chr10_16106753_16106969	121	chr10	16106873	ENSCAFT00000000724	ENSCAFP00000000668	A	301	T	609478	benign	N
-Contig75_chr1_45731970_45732932	436	chr1	45732397	ENSCAFT00000000760	ENSCAFP00000000701	I	490	V	U	benign	N
-Contig33_chr1_45614845_45617413	1835	chr1	45616685	ENSCAFT00000000760	ENSCAFP00000000701	A	4390	V	U	benign	N
-Contig95_chr10_18829724_18831056	914	chr10	18830645	ENSCAFT00000000762	ENSCAFP00000000703	A	512	V	U	possibly damaging	N
-Contig197_chr13_8622062_8623071	606	chr13	8622665	ENSCAFT00000001047	ENSCAFP00000000959	T	406	I	475067	possibly damaging	cfa00240=Pyrimidine metabolism.cfa00410=beta-Alanine metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa00983=Drug metabolism - other enzymes.cfa01100=Metabolic pathways
-Contig243_chr10_19959210_19960069	701	chr10	19959858	ENSCAFT00000001052	ENSCAFP00000000964	E	1345	K	U	benign	N
-Contig137_chr13_10622950_10624043	1039	chr13	10623979	ENSCAFT00000001063	ENSCAFP00000000975	E	10	K	481999	benign	N
-Contig137_chr13_10622950_10624043	1006	chr13	10623946	ENSCAFT00000001063	ENSCAFP00000000975	R	21	C	481999	probably damaging	N
-Contig115_chr12_4411478_4412322	124	chr12	4411614	ENSCAFT00000001076	ENSCAFP00000000986	R	177	H	U	benign	N
-Contig150_chr12_4438230_4439944	385	chr12	4438614	ENSCAFT00000001104	ENSCAFP00000001014	Y	277	D	607591	benign	N
-Contig84_chr1_52076858_52077103	80	chr1	52076943	ENSCAFT00000001141	ENSCAFP00000001046	C	147	Y	484064	benign	N
-Contig29_chr13_13215547_13217183	793	chr13	13216352	ENSCAFT00000001146	ENSCAFP00000001050	P	1	R	475076	probably damaging	N
-Contig251_chr10_22876556_22877097	152	chr10	22876714	ENSCAFT00000001204	ENSCAFP00000001103	E	1162	D	481203	benign	N
-Contig21_chr10_22964856_22965302	202	chr10	22965058	ENSCAFT00000001219	ENSCAFP00000001115	P	6	Q	474465	benign	N
-Contig199_chr12_5083018_5084534	453	chr12	5083472	ENSCAFT00000001250	ENSCAFP00000001144	I	185	T	481729.481731	benign	N.cfa04145=Phagosome.cfa04514=Cell adhesion molecules (CAMs).cfa04612=Antigen processing and presentation.cfa04672=Intestinal immune network for IgA production.cfa04940=Type I diabetes mellitus.cfa05140=Leishmaniasis.cfa05145=Toxoplasmosis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05164=Influenza A.cfa05166=HTLV-I infection.cfa05168=Herpes simplex infection.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft rejection.cfa05332=Graft-versus-host disease.cfa05416=Viral myocarditis
-Contig41_chr13_21629998_21630487	161	chr13	21630157	ENSCAFT00000001352	ENSCAFP00000001239	P	729	S	482026	possibly damaging	cfa00565=Ether lipid metabolism
-Contig16_chr13_21786766_21788016	169	chr13	21786927	ENSCAFT00000001363	ENSCAFP00000001249	V	1142	A	475084	benign	cfa03022=Basal transcription factors
-Contig60_chr1_60333035_60333884	731	chr1	60333755	ENSCAFT00000001421	ENSCAFP00000001307	V	400	I	484096	benign	N
-Contig44_chr13_24555640_24556298	499	chr13	24556139	ENSCAFT00000001523	ENSCAFP00000001400	N	660	S	475088	benign	N
-Contig153_chr12_5955114_5958935	2950	chr12	5958094	ENSCAFT00000001575	ENSCAFP00000001449	E	13	D	481744	benign	cfa04141=Protein processing in endoplasmic reticulum
-Contig146_chr13_25076435_25077249	723	chr13	25077165	ENSCAFT00000001587	ENSCAFP00000001461	T	9	S	482035	benign	N
-Contig81_chr13_25579918_25582207	874	chr13	25580772	ENSCAFT00000001597	ENSCAFP00000001469	E	62	G	609411	benign	N
-Contig159_chr10_28604683_28606028	753	chr10	28605433	ENSCAFT00000002056	ENSCAFP00000001903	S	79	P	610014	benign	N
-Contig30_chr11_29945215_29949829	3973	chr11	29949181	ENSCAFT00000002100	ENSCAFP00000001944	M	282	T	U	benign	N
-Contig102_chr10_29039231_29041280	829	chr10	29040065	ENSCAFT00000002110	ENSCAFP00000001953	R	311	Q	481249	unknown	N
-Contig187_chr1_78583588_78584279	250	chr1	78583839	ENSCAFT00000002175	ENSCAFP00000002014	K	176	R	476310	benign	N
-Contig199_chr1_79234891_79237527	384	chr1	79235278	ENSCAFT00000002259	ENSCAFP00000002095	V	403	A	484151	benign	N
-Contig119_chr12_12212738_12214663	1005	chr12	12213720	ENSCAFT00000002460	ENSCAFP00000002280	R	749	Q	481785	possibly damaging	N
-Contig119_chr12_12212738_12214663	918	chr12	12213633	ENSCAFT00000002460	ENSCAFP00000002280	R	778	Q	481785	benign	N
-Contig39_chr14_10730123_10732539	335	chr14	10730462	ENSCAFT00000002537	ENSCAFP00000002356	V	1179	E	U	benign	N
-Contig41_chr1_84886710_84894794	3494	chr1	84890207	ENSCAFT00000002577	ENSCAFP00000002394	E	1089	K	484157	possibly damaging	N
-Contig182_chr12_13881114_13883427	1690	chr12	13882828	ENSCAFT00000002578	ENSCAFP00000002395	S	99	G	608906	benign	N
-Contig34_chr11_48151988_48152712	198	chr11	48152205	ENSCAFT00000002660	ENSCAFP00000002468	C	587	R	U	possibly damaging	N
-Contig37_chr10_34118256_34119269	437	chr10	34118687	ENSCAFT00000002792	ENSCAFP00000002588	A	377	T	474523	benign	N
-Contig21_chr14_16091274_16093278	716	chr14	16091997	ENSCAFT00000002849	ENSCAFP00000002642	R	126	C	475216	probably damaging	N
-Contig57_chr1_90983602_90984717	559	chr1	90984158	ENSCAFT00000002999	ENSCAFP00000002781	A	226	V	U	benign	N
-Contig45_chr12_15798569_15798849	141	chr12	15798709	ENSCAFT00000003163	ENSCAFP00000002938	N	342	S	474921	benign	cfa03040=Spliceosome
-Contig83_chr12_17852905_17859596	2392	chr12	17855305	ENSCAFT00000003223	ENSCAFP00000002995	E	770	Q	474925	benign	N
-Contig41_chr12_18725392_18725889	169	chr12	18725560	ENSCAFT00000003307	ENSCAFP00000003070	R	80	Q	609995	benign	N
-Contig9_chr14_26125779_26127414	486	chr14	26126264	ENSCAFT00000003515	ENSCAFP00000003259	P	123	T	482316	benign	N
-Contig132_chr1_101565951_101566612	255	chr1	101566210	ENSCAFT00000003560	ENSCAFP00000003298	L	588	F	U	unknown	N
-Contig142_chr1_102093954_102094392	121	chr1	102094072	ENSCAFT00000003644	ENSCAFP00000003373	K	120	E	484216	benign	cfa00290=Valine, leucine and isoleucine biosynthesis.cfa00970=Aminoacyl-tRNA biosynthesis
-Contig129_chr14_34071666_34074617	2313	chr14	34073957	ENSCAFT00000003824	ENSCAFP00000003537	T	282	I	475249	probably damaging	N
-Contig147_chr14_34262125_34262938	340	chr14	34262468	ENSCAFT00000003840	ENSCAFP00000003553	I	70	V	482333	benign	N
-Contig52_chr12_36031985_36035244	1237	chr12	36033208	ENSCAFT00000004092	ENSCAFP00000003784	Y	564	H	474960	benign	N
-Contig176_chr1_105494865_105495258	119	chr1	105494995	ENSCAFT00000004103	ENSCAFP00000003793	A	406	V	484298	benign	N
-Contig60_chr11_63130652_63131816	702	chr11	63131349	ENSCAFT00000004208	ENSCAFP00000003892	V	260	I	481637	benign	N
-Contig9_chr10_53579958_53582510	688	chr10	53580646	ENSCAFT00000004253	ENSCAFP00000003937	S	191	G	100534006.100534007.474588	benign	N
-Contig93_chr14_38451661_38452163	221	chr14	38451882	ENSCAFT00000004311	ENSCAFP00000003990	A	420	V	482346	benign	N
-Contig70_chr12_42859511_42860010	180	chr12	42859693	ENSCAFT00000004464	ENSCAFP00000004126	P	7	S	481892	possibly damaging	N
-Contig28_chr12_43447144_43449156	1136	chr12	43448279	ENSCAFT00000004511	ENSCAFP00000004169	V	582	M	481893	benign	N
-Contig18_chr13_62535238_62535697	227	chr13	62535471	ENSCAFT00000004609	ENSCAFP00000004263	E	277	D	611755	benign	N
-Contig282_chr1_108960925_108962235	205	chr1	108961141	ENSCAFT00000004673	ENSCAFP00000004325	A	149	V	611817	benign	N
-Contig110_chr1_109196028_109197290	987	chr1	109197021	ENSCAFT00000004726	ENSCAFP00000004374	E	330	D	610047	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa03430=Mismatch repair.cfa03440=Homologous recombination.cfa05166=HTLV-I infection
-Contig89_chr11_69097905_69099099	568	chr11	69098443	ENSCAFT00000004799	ENSCAFP00000004445	E	1317	G	U	benign	N
-Contig118_chr14_46155051_46155557	173	chr14	46155218	ENSCAFT00000004933	ENSCAFP00000004572	S	110	L	482382	benign	cfa04621=NOD-like receptor signaling pathway.cfa05133=Pertussis
-Contig54_chr12_51910786_51912716	682	chr12	51911460	ENSCAFT00000004993	ENSCAFP00000004630	H	2889	Y	474995	benign	cfa03008=Ribosome biogenesis in eukaryotes
-Contig95_chr10_67698730_67699605	267	chr10	67698997	ENSCAFT00000005126	ENSCAFP00000004751	P	45	L	U	benign	N
-Contig265_chr17_3177908_3178389	332	chr17	3178241	ENSCAFT00000005142	ENSCAFP00000004763	A	306	P	606804	benign	N
-Contig322_chr17_4977962_4979371	1122	chr17	4979079	ENSCAFT00000005225	ENSCAFP00000004836	T	319	I	475647	possibly damaging	N
-Contig48_chr11_71453437_71456331	1725	chr11	71455160	ENSCAFT00000005323	ENSCAFP00000004927	A	226	V	U	benign	N
-Contig51_chr16_4789440_4790118	484	chr16	4789915	ENSCAFT00000005467	ENSCAFP00000005065	Q	318	H	U	benign	N
-Contig32_chr12_57224809_57225619	146	chr12	57224960	ENSCAFT00000005496	ENSCAFP00000005093	A	273	T	481925	benign	N
-Contig6_chr14_59310933_59312532	615	chr14	59311551	ENSCAFT00000005518	ENSCAFP00000005112	Y	304	H	492302	probably damaging	cfa02010=ABC transporters.cfa04971=Gastric acid secretion.cfa04972=Pancreatic secretion.cfa04976=Bile secretion
-Contig89_chr11_74391566_74395656	2856	chr11	74394408	ENSCAFT00000005653	ENSCAFP00000031395	R	450	H	403417	benign	cfa04145=Phagosome.cfa04620=Toll-like receptor signaling pathway.cfa05132=Salmonella infection.cfa05133=Pertussis.cfa05134=Legionellosis.cfa05140=Leishmaniasis.cfa05142=Chagas disease (American trypanosomiasis).cfa05144=Malaria.cfa05145=Toxoplasmosis.cfa05146=Amoebiasis.cfa05152=Tuberculosis.cfa05162=Measles.cfa05164=Influenza A.cfa05323=Rheumatoid arthritis
-Contig15_chr1_109713951_109714808	645	chr1	109714594	ENSCAFT00000005746	ENSCAFP00000005319	R	783	K	476410	benign	cfa00071=Fatty acid metabolism.cfa03320=PPAR signaling pathway.cfa04920=Adipocytokine signaling pathway
-Contig47_chr17_11258085_11259619	360	chr17	11258455	ENSCAFT00000005749	ENSCAFP00000005322	V	778	L	610007	benign	N
-Contig1_chr19_4352123_4352541	311	chr19	4352427	ENSCAFT00000005832	ENSCAFP00000005401	H	7	Y	403584	benign	cfa04060=Cytokine-cytokine receptor interaction.cfa04630=Jak-STAT signaling pathway.cfa04672=Intestinal immune network for IgA production.cfa05166=HTLV-I infection.cfa05168=Herpes simplex infection.cfa05323=Rheumatoid arthritis
-Contig57_chr12_66915864_66916357	337	chr12	66916199	ENSCAFT00000005972	ENSCAFP00000005534	F	1242	L	475012	benign	N
-Contig36_chr17_16182220_16182772	282	chr17	16182494	ENSCAFT00000006025	ENSCAFP00000005583	V	13	I	482980	possibly damaging	N
-Contig64_chr19_15052202_15053292	240	chr19	15052443	ENSCAFT00000006114	ENSCAFP00000005658	I	175	V	483829	benign	N
-Contig169_chr12_69415779_69417261	1136	chr12	69416908	ENSCAFT00000006157	ENSCAFP00000005701	D	85	N	475021	possibly damaging	N
-Contig200_chr18_15803806_15804082	169	chr18	15803976	ENSCAFT00000006219	ENSCAFP00000005760	A	66	V	483261	benign	cfa04972=Pancreatic secretion.cfa04978=Mineral absorption
-Contig6_chr18_15814044_15814404	97	chr18	15814150	ENSCAFT00000006219	ENSCAFP00000005760	A	413	S	483261	benign	cfa04972=Pancreatic secretion.cfa04978=Mineral absorption
-Contig104_chr1_110433641_110434230	183	chr1	110433810	ENSCAFT00000006272	ENSCAFP00000005811	A	315	T	484394	benign	cfa00280=Valine, leucine and isoleucine degradation.cfa00290=Valine, leucine and isoleucine biosynthesis.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
-Contig52_chr18_17851226_17851871	284	chr18	17851509	ENSCAFT00000006453	ENSCAFP00000005976	T	311	M	475893	probably damaging	N
-Contig63_chr16_12167721_12168304	388	chr16	12168099	ENSCAFT00000006479	ENSCAFP00000006000	M	634	V	U	benign	N
-Contig101_chr20_4702659_4703738	441	chr20	4703092	ENSCAFT00000006507	ENSCAFP00000006027	G	635	D	484622	probably damaging	cfa03030=DNA replication.cfa04110=Cell cycle
-Contig53_chr19_21456428_21457881	408	chr19	21456840	ENSCAFT00000006669	ENSCAFP00000006174	R	247	L	476094	possibly damaging	N
-Contig58_chr18_19883250_19884312	250	chr18	19883498	ENSCAFT00000006689	ENSCAFP00000006194	*	503	Y	475897	benign	N
-Contig122_chr15_17034758_17035049	142	chr15	17034893	ENSCAFT00000006827	ENSCAFP00000006320	R	117	P	U	benign	N
-Contig131_chr18_20356930_20357227	113	chr18	20357041	ENSCAFT00000006891	ENSCAFP00000006378	V	55	L	610021	benign	N
-Contig117_chr22_5859195_5860740	654	chr22	5859850	ENSCAFT00000007130	ENSCAFP00000006603	S	139	N	485445	benign	cfa04020=Calcium signaling pathway.cfa04080=Neuroactive ligand-receptor interaction
-Contig91_chr17_23506302_23507213	322	chr17	23506624	ENSCAFT00000007145	ENSCAFP00000006614	V	1644	I	607961	benign	N
-Contig3_chr21_16586556_16586852	105	chr21	16586661	ENSCAFT00000007244	ENSCAFP00000006709	C	33	Y	476781	possibly damaging	N
-Contig62_chr2_22645987_22646907	357	chr2	22646352	ENSCAFT00000007375	ENSCAFP00000006833	V	657	F	403767	probably damaging	cfa04977=Vitamin digestion and absorption
-Contig52_chr15_18032498_18034281	880	chr15	18033373	ENSCAFT00000007440	ENSCAFP00000006895	P	227	A	482516	benign	N
-Contig131_chr23_6679385_6679850	198	chr23	6679592	ENSCAFT00000007467	ENSCAFP00000006915	R	136	G	485576	possibly damaging	N
-Contig157_chr22_10584088_10586765	232	chr22	10584326	ENSCAFT00000007484	ENSCAFP00000006926	M	610	T	609336	benign	N
-Contig164_chr2_24336024_24340161	2420	chr2	24338436	ENSCAFT00000007527	ENSCAFP00000006969	S	824	C	607108	probably damaging	N
-Contig109_chr2_24557417_24558710	808	chr2	24558229	ENSCAFT00000007553	ENSCAFP00000006994	L	606	V	487123	benign	cfa03450=Non-homologous end-joining.cfa05340=Primary immunodeficiency
-Contig194_chr15_18573761_18574204	142	chr15	18573904	ENSCAFT00000007697	ENSCAFP00000007130	V	381	I	475382	benign	N
-Contig133_chr23_9924894_9925887	125	chr23	9925016	ENSCAFT00000007703	ENSCAFP00000007136	P	355	S	477019	benign	cfa03430=Mismatch repair.cfa03460=Fanconi anemia pathway.cfa05200=Pathways in cancer.cfa05210=Colorectal cancer.cfa05213=Endometrial cancer
-Contig31_chr23_10199273_10203629	4073	chr23	10203350	ENSCAFT00000007747	ENSCAFP00000007179	A	1844	V	U	benign	N
-Contig21_chr23_10308212_10309269	513	chr23	10308732	ENSCAFT00000007774	ENSCAFP00000007206	K	72	R	477021	benign	cfa04510=Focal adhesion.cfa04512=ECM-receptor interaction.cfa04514=Cell adhesion molecules (CAMs).cfa04810=Regulation of actin cytoskeleton.cfa05410=Hypertrophic cardiomyopathy (HCM).cfa05412=Arrhythmogenic right ventricular cardiomyopathy (ARVC).cfa05414=Dilated cardiomyopathy
-Contig211_chr1_114924893_114925515	171	chr1	114925067	ENSCAFT00000007776	ENSCAFP00000007208	P	1988	A	U	benign	N
-Contig35_chr2_27160577_27161526	804	chr2	27161367	ENSCAFT00000007779	ENSCAFP00000007211	G	473	R	478007.478008	probably damaging	cfa03060=Protein export.cfa04141=Protein processing in endoplasmic reticulum.cfa04145=Phagosome
-Contig79_chr17_24285444_24286769	1263	chr17	24286694	ENSCAFT00000007859	ENSCAFP00000007285	S	209	T	483010	benign	N
-Contig74_chr23_10871047_10871362	70	chr23	10871116	ENSCAFT00000007951	ENSCAFP00000007365	I	474	V	U	benign	N
-Contig34_chr16_18928689_18932806	3409	chr16	18932072	ENSCAFT00000007959	ENSCAFP00000007370	A	3754	S	482810.611087	benign	cfa00310=Lysine degradation
-Contig52_chr21_24452521_24454405	725	chr21	24453245	ENSCAFT00000008012	ENSCAFP00000007418	M	289	T	485173	possibly damaging	N
-Contig261_chr1_115563599_115564561	560	chr1	115564156	ENSCAFT00000008063	ENSCAFP00000007465	A	63	T	484489	possibly damaging	N
-Contig62_chr19_41037398_41039465	159	chr19	41037564	ENSCAFT00000008142	ENSCAFP00000007541	C	744	Y	476128	possibly damaging	N
-Contig84_chr1_115960693_115962811	1467	chr1	115962120	ENSCAFT00000008198	ENSCAFP00000007593	W	61	R	612489	benign	N
-Contig135_chr23_14160194_14160717	270	chr23	14160468	ENSCAFT00000008413	ENSCAFP00000007796	V	298	I	U	benign	N
-Contig41_chr17_26203621_26205196	1407	chr17	26205028	ENSCAFT00000008540	ENSCAFP00000007913	H	172	R	483021	benign	N
-Contig260_chr1_116076701_116078120	746	chr1	116077446	ENSCAFT00000008586	ENSCAFP00000007956	T	2486	I	484499	benign	N
-Contig19_chr23_14811332_14815323	1987	chr23	14813327	ENSCAFT00000008588	ENSCAFP00000007958	S	690	L	U	unknown	N
-Contig180_chr2_35061773_35062172	166	chr2	35061941	ENSCAFT00000008673	ENSCAFP00000008039	T	920	M	478018	probably damaging	N
-Contig106_chr21_26153874_26154496	107	chr21	26153984	ENSCAFT00000008678	ENSCAFP00000008044	A	458	T	485188	benign	N
-Contig3_chr19_45625337_45630123	2563	chr19	45627887	ENSCAFT00000008728	ENSCAFP00000008094	V	1264	I	U	benign	N
-Contig51_chr22_48760401_48761638	636	chr22	48761047	ENSCAFT00000008769	ENSCAFP00000008132	R	1071	K	485523	benign	cfa02010=ABC transporters.cfa04976=Bile secretion
-Contig10_chr15_21173640_21174011	212	chr15	21173839	ENSCAFT00000008831	ENSCAFP00000008192	V	191	I	475398	benign	N
-Contig6_chr24_14680423_14681438	782	chr24	14681208	ENSCAFT00000009074	ENSCAFP00000008417	H	562	R	485769	possibly damaging	cfa04330=Notch signaling pathway
-Contig60_chr9_4528464_4529207	262	chr9	4528727	ENSCAFT00000009114	ENSCAFP00000008453	C	24	F	483354	possibly damaging	N
-Contig54_chr15_29510545_29512205	400	chr15	29510955	ENSCAFT00000009614	ENSCAFP00000008928	H	190	R	475416	benign	N
-Contig46_chr25_5067588_5068089	39	chr25	5067627	ENSCAFT00000009698	ENSCAFP00000009003	S	17	N	486001	benign	N
-Contig126_chr25_5114359_5115799	643	chr25	5114996	ENSCAFT00000009710	ENSCAFP00000009013	R	1952	C	486002	possibly damaging	N
-Contig41_chr26_3455305_3455893	329	chr26	3455620	ENSCAFT00000010094	ENSCAFP00000009363	S	909	A	486223	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa05166=HTLV-I infection
-Contig55_chr26_3463883_3465235	1074	chr26	3464998	ENSCAFT00000010094	ENSCAFP00000009363	R	1273	S	486223	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa05166=HTLV-I infection
-Contig63_chr26_3467460_3468420	195	chr26	3467661	ENSCAFT00000010094	ENSCAFP00000009363	E	1542	Q	486223	benign	cfa00230=Purine metabolism.cfa00240=Pyrimidine metabolism.cfa01100=Metabolic pathways.cfa03030=DNA replication.cfa03410=Base excision repair.cfa03420=Nucleotide excision repair.cfa05166=HTLV-I infection
-Contig13_chr16_32259141_32259752	344	chr16	32259472	ENSCAFT00000010141	ENSCAFP00000009407	I	326	T	482857	benign	cfa04360=Axon guidance
-Contig59_chr21_32994329_32995926	1195	chr21	32995538	ENSCAFT00000010439	ENSCAFP00000009680	H	230	R	610992	benign	N
-Contig39_chr20_24938452_24941620	1292	chr20	24939734	ENSCAFT00000010496	ENSCAFP00000009730	S	28	P	415126	benign	cfa04380=Osteoclast differentiation.cfa04916=Melanogenesis.cfa05200=Pathways in cancer.cfa05218=Melanoma
-Contig2_chr18_28546360_28546760	277	chr18	28546640	ENSCAFT00000010516	ENSCAFP00000009748	P	471	S	U	benign	N
-Contig23_chr20_25560598_25562858	928	chr20	25561520	ENSCAFT00000010531	ENSCAFP00000009762	T	749	I	484693	benign	N
-Contig209_chr18_28672330_28672791	376	chr18	28672689	ENSCAFT00000010559	ENSCAFP00000009790	A	33	D	483405	unknown	N
-Contig261_chr18_28694652_28696968	1808	chr18	28696427	ENSCAFT00000010559	ENSCAFP00000009790	P	1443	L	483405	possibly damaging	N
-Contig30_chr25_12008255_12009009	151	chr25	12008417	ENSCAFT00000010593	ENSCAFP00000009822	Q	151	H	U	benign	N
-Contig46_chr29_3065854_3067420	1265	chr29	3067078	ENSCAFT00000010616	ENSCAFP00000009842	V	3253	A	474176	benign	cfa03450=Non-homologous end-joining.cfa04110=Cell cycle
-Contig59_chr28_3755477_3757019	935	chr28	3756419	ENSCAFT00000010630	ENSCAFP00000009853	R	923	Q	486770	possibly damaging	N
-Contig90_chr29_6393993_6395503	951	chr29	6394948	ENSCAFT00000010829	ENSCAFP00000010033	Y	257	C	486944	benign	N
-Contig42_chr16_39015800_39016389	319	chr16	39016119	ENSCAFT00000010865	ENSCAFP00000010068	D	71	N	U	possibly damaging	N
-Contig95_chr21_34533214_34535079	1133	chr21	34534321	ENSCAFT00000010931	ENSCAFP00000010131	E	118	G	485368	benign	N
-Contig82_chr21_34524815_34525170	247	chr21	34525072	ENSCAFT00000010931	ENSCAFP00000010131	Q	499	R	485368	benign	N
-Contig32_chr24_22727492_22727986	147	chr24	22727648	ENSCAFT00000010977	ENSCAFP00000010173	P	278	L	U	possibly damaging	N
-Contig45_chr16_42405571_42406148	269	chr16	42405837	ENSCAFT00000010988	ENSCAFP00000010184	H	406	R	482891	benign	cfa04145=Phagosome
-Contig66_chr15_43321121_43321872	642	chr15	43321764	ENSCAFT00000011187	ENSCAFP00000010364	F	543	L	475441	benign	N
-Contig184_chr27_5103641_5104991	275	chr27	5103979	ENSCAFT00000011380	ENSCAFP00000010541	V	864	A	U	benign	N
-Contig88_chr17_39320200_39320765	204	chr17	39320404	ENSCAFT00000011397	ENSCAFP00000010558	S	1911	N	475750	benign	cfa04110=Cell cycle.cfa04114=Oocyte meiosis.cfa04120=Ubiquitin mediated proteolysis.cfa04914=Progesterone-mediated oocyte maturation.cfa05166=HTLV-I infection
-Contig8_chr16_47195242_47195504	193	chr16	47195429	ENSCAFT00000011721	ENSCAFP00000010862	S	4369	W	475621	benign	N
-Contig84_chr27_5882441_5882771	145	chr27	5882579	ENSCAFT00000011730	ENSCAFP00000010871	C	289	S	486534	benign	N
-Contig42_chr24_25316755_25317362	320	chr24	25317091	ENSCAFT00000011771	ENSCAFP00000010910	G	22	S	477193	benign	N
-Contig45_chr24_25318544_25319490	734	chr24	25319299	ENSCAFT00000011771	ENSCAFP00000010910	V	187	A	477193	benign	N
-Contig31_chr24_25434125_25435133	853	chr24	25434975	ENSCAFT00000011789	ENSCAFP00000010928	S	91	I	609978	benign	N
-Contig20_chr3_10579133_10580085	600	chr3	10579729	ENSCAFT00000011968	ENSCAFP00000011099	K	165	E	488881	benign	cfa00760=Nicotinate and nicotinamide metabolism.cfa04146=Peroxisome
-Contig45_chr2_54585564_54588038	1047	chr2	54586611	ENSCAFT00000012081	ENSCAFP00000011198	T	969	M	478082	benign	cfa04621=NOD-like receptor signaling pathway
-Contig156_chr1_122375741_122376035	168	chr1	122375904	ENSCAFT00000012133	ENSCAFP00000011248	R	628	K	611998	benign	N
-Contig153_chr1_124036982_124040108	1588	chr1	124038585	ENSCAFT00000012159	ENSCAFP00000011272	A	887	T	484609	benign	N
-Contig32_chr24_26900375_26900913	394	chr24	26900761	ENSCAFT00000012254	ENSCAFP00000011358	H	51	Y	U	benign	N
-Contig103_chr16_48829082_48829675	123	chr16	48829205	ENSCAFT00000012381	ENSCAFP00000011471	E	369	G	475632	possibly damaging	N
-Contig25_chr18_41490135_41493501	534	chr18	41490665	ENSCAFT00000012414	ENSCAFP00000011503	R	703	C	483489	probably damaging	cfa04520=Adherens junction.cfa04670=Leukocyte transendothelial migration
-Contig69_chr16_49314879_49317228	1810	chr16	49316689	ENSCAFT00000012456	ENSCAFP00000011541	P	431	L	475636	probably damaging	cfa00565=Ether lipid metabolism
-Contig71_chr17_42734055_42736474	2240	chr17	42736298	ENSCAFT00000012478	ENSCAFP00000011561	R	307	Q	483083	benign	cfa00830=Retinol metabolism
-Contig17_chr17_43378842_43379885	305	chr17	43379148	ENSCAFT00000012676	ENSCAFP00000011740	T	196	M	U	probably damaging	N
-Contig195_chr27_7047911_7049009	555	chr27	7048468	ENSCAFT00000012942	ENSCAFP00000011978	R	881	L	477608	benign	N
-Contig112_chr30_4254316_4256576	1478	chr30	4255785	ENSCAFT00000012974	ENSCAFP00000012007	V	2939	I	U	benign	N
-Contig43_chr20_39124486_39124798	114	chr20	39124607	ENSCAFT00000013097	ENSCAFP00000012118	G	325	R	607274	possibly damaging	N
-Contig96_chr16_55849292_55849592	194	chr16	55849494	ENSCAFT00000013360	ENSCAFP00000012363	A	41	S	482932	benign	cfa04060=Cytokine-cytokine receptor interaction.cfa04150=mTOR signaling pathway.cfa04510=Focal adhesion.cfa05200=Pathways in cancer.cfa05211=Renal cell carcinoma.cfa05212=Pancreatic cancer.cfa05219=Bladder cancer
-Contig91_chr17_51684551_51689453	4154	chr17	51688687	ENSCAFT00000013395	ENSCAFP00000012395	P	306	L	475784	benign	N
-Contig192_chr26_12794366_12794712	143	chr26	12794506	ENSCAFT00000014076	ENSCAFP00000013021	V	2478	I	477486	benign	N
-Contig191_chr31_30109152_30109760	212	chr31	30109363	ENSCAFT00000014113	ENSCAFP00000013055	A	1813	T	487735	probably damaging	N
-Contig116_chr24_29683980_29684819	101	chr24	29684079	ENSCAFT00000014115	ENSCAFP00000013057	R	836	C	485868	probably damaging	N
-Contig8_chr32_9413601_9414435	74	chr32	9413675	ENSCAFT00000014257	ENSCAFP00000013183	N	236	K	478452	probably damaging	cfa00270=Cysteine and methionine metabolism
-Contig90_chr21_43253791_43254774	189	chr21	43253974	ENSCAFT00000014325	ENSCAFP00000013248	I	758	V	U	benign	N
-Contig76_chr24_30292767_30294101	552	chr24	30293321	ENSCAFT00000014346	ENSCAFP00000013267	A	349	T	U	benign	N
-Contig21_chr25_37121451_37122072	177	chr25	37121616	ENSCAFT00000014616	ENSCAFP00000013518	V	157	L	486118	benign	N
-Contig15_chr36_6357141_6362626	5226	chr36	6362346	ENSCAFT00000014702	ENSCAFP00000013598	N	138	K	607626	possibly damaging	N
-Contig64_chr17_54734453_54734993	109	chr17	54734552	ENSCAFT00000014707	ENSCAFP00000013603	S	302	L	483124	benign	N
-Contig91_chr18_46134014_46136042	330	chr18	46134347	ENSCAFT00000014736	ENSCAFP00000013630	A	214	S	483635	benign	cfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways.cfa04070=Phosphatidylinositol signaling system
-Contig111_chr31_31237314_31238628	920	chr31	31238220	ENSCAFT00000014822	ENSCAFP00000013714	S	143	C	478408	benign	N
-Contig77_chr38_3502296_3503058	349	chr38	3502639	ENSCAFT00000015260	ENSCAFP00000014122	K	666	E	478932	benign	N
-Contig59_chr38_3998294_3999004	369	chr38	3998672	ENSCAFT00000015347	ENSCAFP00000014201	V	791	I	U	benign	N
-Contig123_chr31_34367825_34368648	664	chr31	34368468	ENSCAFT00000015534	ENSCAFP00000014373	H	204	Q	U	possibly damaging	N
-Contig43_chr30_11874641_11875130	198	chr30	11874850	ENSCAFT00000015654	ENSCAFP00000014488	R	3422	C	U	benign	N
-Contig9_chr20_40741488_40743247	1027	chr20	40742525	ENSCAFT00000015816	ENSCAFP00000014638	M	183	V	484744	benign	N
-Contig137_chr5_7048977_7051042	863	chr5	7049840	ENSCAFT00000015844	ENSCAFP00000014662	A	311	V	479391	benign	N
-Contig9_chr28_17675067_17680985	1564	chr28	17676618	ENSCAFT00000015971	ENSCAFP00000014772	R	515	P	477805	unknown	N
-Contig126_chr30_12286682_12287475	407	chr30	12287101	ENSCAFT00000016062	ENSCAFP00000014854	V	450	I	487517	benign	cfa00052=Galactose metabolism.cfa00500=Starch and sucrose metabolism.cfa01100=Metabolic pathways
-Contig127_chr30_12287497_12288447	608	chr30	12288095	ENSCAFT00000016062	ENSCAFP00000014854	T	495	M	487517	benign	cfa00052=Galactose metabolism.cfa00500=Starch and sucrose metabolism.cfa01100=Metabolic pathways
-Contig13_chr38_5058391_5058630	66	chr38	5058458	ENSCAFT00000016099	ENSCAFP00000014887	F	412	L	478943	benign	N
-Contig169_chr35_19985467_19986000	455	chr35	19985921	ENSCAFT00000016165	ENSCAFP00000014950	T	175	I	478733	benign	N
-Contig2_chr35_21794536_21795092	291	chr35	21794865	ENSCAFT00000016208	ENSCAFP00000014992	V	84	A	488238	benign	cfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways
-Contig141_chr26_19278751_19279229	364	chr26	19279128	ENSCAFT00000016284	ENSCAFP00000015064	N	29	S	404011	benign	cfa00564=Glycerophospholipid metabolism.cfa00565=Ether lipid metabolism.cfa00590=Arachidonic acid metabolism.cfa00591=Linoleic acid metabolism.cfa00592=alpha-Linolenic acid metabolism.cfa01100=Metabolic pathways.cfa04010=MAPK signaling pathway.cfa04270=Vascular smooth muscle contraction.cfa04370=VEGF signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04724=Glutamatergic synapse.cfa04730=Long-term depression.cfa04912=GnRH signaling pathway.cfa04972=Pancreatic secretion.cfa04975=Fat digestion and absorption.cfa05145=Toxoplasmosis
-Contig179_chr3_40781459_40782026	285	chr3	40781763	ENSCAFT00000016410	ENSCAFP00000015182	D	1174	N	488699	benign	N
-Contig237_chr21_53631024_53632458	203	chr21	53631227	ENSCAFT00000016459	ENSCAFP00000015227	C	47	W	403799	probably damaging	cfa04664=Fc epsilon RI signaling pathway.cfa05310=Asthma
-Contig186_chr2_71203100_71204111	202	chr2	71203303	ENSCAFT00000016485	ENSCAFP00000015250	S	188	T	478144	benign	cfa00330=Arginine and proline metabolism.cfa01100=Metabolic pathways
-Contig1_chr28_18779291_18780149	325	chr28	18779619	ENSCAFT00000016578	ENSCAFP00000015340	N	245	Y	U	probably damaging	N
-Contig166_chr4_77425871_77426835	797	chr4	77426667	ENSCAFT00000016670	ENSCAFP00000015429	D	115	G	479370	benign	cfa00970=Aminoacyl-tRNA biosynthesis
-Contig35_chr24_36806524_36807086	367	chr24	36806891	ENSCAFT00000016727	ENSCAFP00000015478	F	345	L	485910	benign	N
-Contig45_chr37_8610877_8611425	194	chr37	8611078	ENSCAFT00000016761	ENSCAFP00000015511	D	2849	N	488452	possibly damaging	N
-Contig39_chr28_19446540_19447838	1068	chr28	19447566	ENSCAFT00000016791	ENSCAFP00000015537	A	1596	E	U	benign	N
-Contig161_chr18_51013230_51015381	1494	chr18	51014735	ENSCAFT00000016827	ENSCAFP00000015571	L	977	V	475999	benign	N
-Contig25_chr28_19619108_19621267	1728	chr28	19620832	ENSCAFT00000016848	ENSCAFP00000034237	I	108	V	609723	benign	N
-Contig33_chr20_42063173_42064259	623	chr20	42063789	ENSCAFT00000017070	ENSCAFP00000015794	V	179	M	U	probably damaging	N
-Contig39_chr38_14681397_14682234	384	chr38	14681781	ENSCAFT00000017072	ENSCAFP00000015796	H	282	N	488593	unknown	N
-Contig6_chr32_27303975_27304541	425	chr32	27304407	ENSCAFT00000017178	ENSCAFP00000015896	S	354	T	610098	benign	N
-Contig173_chr38_17709765_17711029	179	chr38	17709941	ENSCAFT00000017240	ENSCAFP00000015955	G	464	R	U	benign	N
-Contig52_chr32_27452924_27453332	91	chr32	27452999	ENSCAFT00000017249	ENSCAFP00000015964	A	22	S	U	benign	N
-Contig319_chr34_14684259_14684663	353	chr34	14684613	ENSCAFT00000017314	ENSCAFP00000016025	R	5	Q	478632	benign	N
-Contig32_chr2_72269353_72269814	349	chr2	72269708	ENSCAFT00000017327	ENSCAFP00000016037	P	853	L	487317	possibly damaging	N
-Contig206_chr9_18720001_18720613	155	chr9	18720160	ENSCAFT00000017373	ENSCAFP00000016082	D	1621	E	480456	benign	cfa02010=ABC transporters
-Contig35_chr37_10562149_10562621	74	chr37	10562222	ENSCAFT00000017444	ENSCAFP00000016153	I	975	V	478858	benign	cfa04727=GABAergic synapse
-Contig1_chr30_12655575_12656916	370	chr30	12655947	ENSCAFT00000017777	ENSCAFP00000016457	L	639	M	608886	probably damaging	N
-Contig63_chr27_23738716_23739879	1131	chr27	23739850	ENSCAFT00000017892	ENSCAFP00000016566	P	642	L	486627	benign	N
-Contig44_chr28_28123120_28124627	1348	chr28	28124495	ENSCAFT00000017967	ENSCAFP00000016639	V	261	A	477827	benign	N
-Contig23_chrX_6416128_6417014	455	chrX	6416585	ENSCAFT00000018017	ENSCAFP00000016684	H	111	R	491733	possibly damaging	N
-Contig31_chr7_8282189_8286932	3631	chr7	8285875	ENSCAFT00000018057	ENSCAFP00000016724	L	655	P	490260	benign	N
-Contig318_chr6_8706066_8706350	76	chr6	8706142	ENSCAFT00000018106	ENSCAFP00000016769	K	318	N	607700	possibly damaging	cfa04062=Chemokine signaling pathway.cfa04145=Phagosome.cfa04380=Osteoclast differentiation.cfa04666=Fc gamma R-mediated phagocytosis.cfa04670=Leukocyte transendothelial migration.cfa05140=Leishmaniasis
-Contig36_chr32_33046881_33048369	1118	chr32	33047990	ENSCAFT00000018307	ENSCAFP00000016954	E	555	A	403657	benign	cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04060=Cytokine-cytokine receptor interaction.cfa04144=Endocytosis.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04810=Regulation of actin cytoskeleton.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05212=Pancreatic cancer.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05218=Melanoma.cfa05219=Bladder cancer.cfa05223=Non-small cell lung cancer
-Contig32_chr5_14476595_14477214	347	chr5	14476948	ENSCAFT00000018571	ENSCAFP00000017201	V	209	A	610296	benign	N
-Contig88_chr34_19031138_19031937	343	chr34	19031477	ENSCAFT00000018684	ENSCAFP00000017309	K	670	R	478645	benign	cfa00280=Valine, leucine and isoleucine degradation.cfa01100=Metabolic pathways
-Contig188_chr25_47927372_47928085	557	chr25	47927941	ENSCAFT00000018758	ENSCAFP00000017379	K	228	R	486167	benign	cfa00561=Glycerolipid metabolism.cfa00564=Glycerophospholipid metabolism.cfa01100=Metabolic pathways.cfa04070=Phosphatidylinositol signaling system
-Contig36_chr37_12924359_12924740	86	chr37	12924449	ENSCAFT00000018786	ENSCAFP00000017406	D	187	Y	608849	probably damaging	cfa00280=Valine, leucine and isoleucine degradation.cfa00350=Tyrosine metabolism.cfa00380=Tryptophan metabolism.cfa00750=Vitamin B6 metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00982=Drug metabolism - cytochrome P450.cfa01100=Metabolic pathways
-Contig3_chr34_19471626_19472377	337	chr34	19471956	ENSCAFT00000018788	ENSCAFP00000017408	R	239	Q	488096	possibly damaging	N
-Contig80_chr4_11155760_11156827	952	chr4	11156735	ENSCAFT00000018796	ENSCAFP00000017416	S	661	N	479204	benign	cfa00564=Glycerophospholipid metabolism.cfa04146=Peroxisome
-Contig56_chr8_7093747_7095987	683	chr8	7094428	ENSCAFT00000018813	ENSCAFP00000017431	P	126	R	490620	unknown	N
-Contig82_chr8_7111986_7114065	1351	chr8	7113329	ENSCAFT00000018871	ENSCAFP00000017488	R	608	H	480255	probably damaging	cfa00010=Glycolysis / Gluconeogenesis.cfa00020=Citrate cycle (TCA cycle).cfa00620=Pyruvate metabolism.cfa01100=Metabolic pathways.cfa03320=PPAR signaling pathway.cfa04910=Insulin signaling pathway.cfa04920=Adipocytokine signaling pathway.cfa04964=Proximal tubule bicarbonate reclamation
-Contig172_chr33_28585454_28586084	228	chr33	28585687	ENSCAFT00000018884	ENSCAFP00000017500	R	36	K	478584	benign	N
-Contig113_chr5_16682954_16684491	688	chr5	16683641	ENSCAFT00000018997	ENSCAFP00000017606	F	41	L	489360	benign	N
-Contig36_chr28_31449413_31452160	2111	chr28	31451506	ENSCAFT00000019041	ENSCAFP00000017650	P	252	H	477834	benign	cfa04144=Endocytosis
-Contig80_chr3_55628026_55628800	392	chr3	55628403	ENSCAFT00000019070	ENSCAFP00000017677	R	805	K	403913	benign	cfa00480=Glutathione metabolism.cfa01100=Metabolic pathways.cfa04614=Renin-angiotensin system.cfa04640=Hematopoietic cell lineage
-Contig99_chr7_11816365_11819255	806	chr7	11817201	ENSCAFT00000019101	ENSCAFP00000017707	C	305	G	490276	benign	N
-Contig114_chr4_12744102_12745318	148	chr4	12744256	ENSCAFT00000019279	ENSCAFP00000017880	I	700	V	U	benign	N
-Contig82_chr7_13056757_13058281	974	chr7	13057742	ENSCAFT00000019316	ENSCAFP00000017915	S	283	N	609933	benign	cfa00564=Glycerophospholipid metabolism
-Contig280_chr25_51367477_51367885	70	chr25	51367542	ENSCAFT00000019610	ENSCAFP00000018191	S	97	L	U	benign	N
-Contig35_chr20_43508791_43509352	460	chr20	43509254	ENSCAFT00000019627	ENSCAFP00000018204	V	77	A	608455	benign	cfa00190=Oxidative phosphorylation.cfa01100=Metabolic pathways.cfa04260=Cardiac muscle contraction.cfa05010=Alzheimer's disease.cfa05012=Parkinson's disease.cfa05016=Huntington's disease
-Contig36_chr20_43509362_43510980	1484	chr20	43510860	ENSCAFT00000019627	ENSCAFP00000018204	D	181	N	608455	benign	cfa00190=Oxidative phosphorylation.cfa01100=Metabolic pathways.cfa04260=Cardiac muscle contraction.cfa05010=Alzheimer's disease.cfa05012=Parkinson's disease.cfa05016=Huntington's disease
-Contig59_chr25_51807653_51809044	1064	chr25	51808739	ENSCAFT00000019760	ENSCAFP00000018330	R	235	K	U	benign	N
-Contig96_chr36_17712997_17714068	556	chr36	17713559	ENSCAFT00000019807	ENSCAFP00000018374	T	423	I	478789	benign	N
-Contig163_chr28_34927368_34929275	1128	chr28	34928486	ENSCAFT00000019866	ENSCAFP00000018425	A	2659	T	477850	benign	N
-Contig74_chr33_31230250_31230874	246	chr33	31230493	ENSCAFT00000019938	ENSCAFP00000018492	G	113	S	488016	probably damaging	N
-Contig130_chr7_15553315_15558308	3186	chr7	15556497	ENSCAFT00000020009	ENSCAFP00000018561	K	1513	N	U	benign	N
-Contig160_chr2_76816412_76817166	354	chr2	76816779	ENSCAFT00000020143	ENSCAFP00000018683	I	190	V	478173	benign	N
-Contig219_chr33_31871568_31871771	81	chr33	31871646	ENSCAFT00000020195	ENSCAFP00000018733	N	346	H	U	probably damaging	N
-Contig254_chr24_50001599_50001992	151	chr24	50001767	ENSCAFT00000020266	ENSCAFP00000018803	R	239	Q	U	benign	N
-Contig40_chr37_15283702_15285945	1908	chr37	15285621	ENSCAFT00000020408	ENSCAFP00000018937	A	809	G	U	unknown	N
-Contig59_chr20_43702094_43703358	450	chr20	43702540	ENSCAFT00000020438	ENSCAFP00000018965	S	217	A	U	benign	N
-Contig75_chr3_57465650_57466327	377	chr3	57466017	ENSCAFT00000020863	ENSCAFP00000019371	L	205	F	609716	probably damaging	N
-Contig155_chr2_79195879_79199423	2014	chr2	79197892	ENSCAFT00000021154	ENSCAFP00000019645	G	549	S	U	benign	N
-Contig155_chr2_79195879_79199423	3136	chr2	79199014	ENSCAFT00000021154	ENSCAFP00000019645	R	923	C	U	probably damaging	N
-Contig59_chr5_19784971_19787384	1310	chr5	19786293	ENSCAFT00000021222	ENSCAFP00000019707	V	171	I	479428.489393	benign	cfa03320=PPAR signaling pathway
-Contig41_chr30_14304605_14305465	206	chr30	14304816	ENSCAFT00000021612	ENSCAFP00000020069	A	157	G	U	benign	N
-Contig47_chr20_45043804_45044476	317	chr20	45044117	ENSCAFT00000021659	ENSCAFP00000020114	V	281	I	609323	benign	N
-Contig46_chr4_22849549_22849829	123	chr4	22849673	ENSCAFT00000021752	ENSCAFP00000020204	V	646	M	U	probably damaging	N
-Contig141_chr7_22360980_22361690	242	chr7	22361233	ENSCAFT00000021777	ENSCAFP00000020227	K	1862	R	U	unknown	N
-Contig59_chr30_14758622_14760653	1186	chr30	14759817	ENSCAFT00000021792	ENSCAFP00000020241	S	284	R	609256	benign	N
-Contig57_chr27_39696388_39698349	1026	chr27	39697428	ENSCAFT00000021846	ENSCAFP00000020293	Q	588	R	477699	benign	cfa04610=Complement and coagulation cascades
-Contig83_chr27_40151814_40153141	738	chr27	40152551	ENSCAFT00000022064	ENSCAFP00000020490	S	191	R	477702	benign	N
-Contig105_chr6_11901733_11904968	406	chr6	11902145	ENSCAFT00000022289	ENSCAFP00000020701	Y	55	H	479732	probably damaging	cfa04621=NOD-like receptor signaling pathway
-Contig43_chr36_25298890_25299602	235	chr36	25299132	ENSCAFT00000022319	ENSCAFP00000020728	E	11731	K	610299.610339	unknown	N
-Contig3_chr36_25193150_25202641	2802	chr36	25195983	ENSCAFT00000022319	ENSCAFP00000020728	I	30137	V	610299.610339	benign	N
-Contig585_chr3_61201332_61201904	139	chr3	61201468	ENSCAFT00000022529	ENSCAFP00000020918	L	97	V	479067	benign	cfa00071=Fatty acid metabolism.cfa03320=PPAR signaling pathway.cfa04920=Adipocytokine signaling pathway
-Contig1_chr20_46714929_46715937	434	chr20	46715327	ENSCAFT00000022571	ENSCAFP00000020958	A	18	P	484804	unknown	N
-Contig7_chr8_29376780_29378260	158	chr8	29376937	ENSCAFT00000022576	ENSCAFP00000020962	T	852	A	490678	benign	N
-Contig74_chr8_29656170_29657212	595	chr8	29656776	ENSCAFT00000022697	ENSCAFP00000021080	E	974	K	490682	possibly damaging	cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04062=Chemokine signaling pathway.cfa04320=Dorso-ventral axis formation.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04630=Jak-STAT signaling pathway.cfa04650=Natural killer cell mediated cytotoxicity.cfa04660=T cell receptor signaling pathway.cfa04662=B cell receptor signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04722=Neurotrophin signaling pathway.cfa04810=Regulation of actin cytoskeleton.cfa04910=Insulin signaling pathway.cfa04912=GnRH signaling pathway.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05211=Renal cell carcinoma.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05220=Chronic myeloid leukemia.cfa05221=Acute myeloid leukemia.cfa05223=Non-small cell lung cancer
-Contig45_chr4_25273541_25274402	608	chr4	25274121	ENSCAFT00000022760	ENSCAFP00000021140	S	30	F	479239	probably damaging	cfa04360=Axon guidance
-Contig96_chr37_26111249_26111450	108	chr37	26111364	ENSCAFT00000022884	ENSCAFP00000021256	K	260	R	478902	benign	cfa03450=Non-homologous end-joining
-Contig196_chr3_62434637_62435063	203	chr3	62434823	ENSCAFT00000022915	ENSCAFP00000021284	L	174	P	488785	benign	N
-Contig15_chr6_12238116_12239737	1287	chr6	12239420	ENSCAFT00000022961	ENSCAFP00000021328	E	165	K	479735	benign	N
-Contig175_chr5_27267391_27267870	57	chr5	27267451	ENSCAFT00000023032	ENSCAFP00000021395	N	1094	S	479450	benign	cfa04110=Cell cycle.cfa04115=p53 signaling pathway.cfa04210=Apoptosis.cfa05166=HTLV-I infection
-Contig110_chr20_47192181_47193618	93	chr20	47192262	ENSCAFT00000023054	ENSCAFP00000021407	A	308	P	484814	probably damaging	N
-Contig9_chr4_26730063_26730585	245	chr4	26730316	ENSCAFT00000023087	ENSCAFP00000021437	E	153	D	489044	benign	N
-Contig1_chr34_35420831_35421658	73	chr34	35420908	ENSCAFT00000023111	ENSCAFP00000021457	V	251	I	488144	benign	N
-Contig199_chr2_79696091_79697603	751	chr2	79696840	ENSCAFT00000023253	ENSCAFP00000021593	D	54	A	U	possibly damaging	N
-Contig146_chrX_38946913_38947473	307	chrX	38947225	ENSCAFT00000023268	ENSCAFP00000021608	L	160	V	612457	possibly damaging	N
-Contig63_chr9_23532151_23533554	1297	chr9	23533421	ENSCAFT00000023438	ENSCAFP00000021767	Q	279	R	490958	benign	N
-Contig89_chr5_32060784_32061151	293	chr5	32061079	ENSCAFT00000023913	ENSCAFP00000022199	W	106	*	489430	probably damaging	N
-Contig15_chr3_65640843_65642155	1100	chr3	65641942	ENSCAFT00000023933	ENSCAFP00000022218	V	383	A	479080	benign	N
-Contig49_chr26_33571748_33572620	689	chr26	33572452	ENSCAFT00000024062	ENSCAFP00000022339	R	478	W	486440	benign	N
-Contig96_chr20_48055741_48057197	524	chr20	48056259	ENSCAFT00000024100	ENSCAFP00000022374	R	172	Q	U	benign	N
-Contig104_chr20_48062263_48062546	210	chr20	48062492	ENSCAFT00000024100	ENSCAFP00000022374	V	775	G	U	probably damaging	N
-Contig33_chr37_28794567_28796956	2144	chr37	28796718	ENSCAFT00000024137	ENSCAFP00000022408	E	279	Q	488536	benign	N
-Contig24_chr7_32005266_32005660	212	chr7	32005479	ENSCAFT00000024154	ENSCAFP00000022424	T	92	M	U	probably damaging	N
-Contig174_chr18_56896461_56897594	274	chr18	56896734	ENSCAFT00000024637	ENSCAFP00000022858	V	157	L	483779	benign	cfa04130=SNARE interactions in vesicular transport
-Contig55_chr20_48811642_48812027	299	chr20	48811941	ENSCAFT00000024761	ENSCAFP00000022970	H	993	R	476678	benign	N
-Contig220_chr18_56925351_56927006	920	chr18	56926246	ENSCAFT00000024787	ENSCAFP00000022995	P	420	Q	476051	possibly damaging	cfa03022=Basal transcription factors.cfa05168=Herpes simplex infection
-Contig12_chr8_39044824_39045409	359	chr8	39045181	ENSCAFT00000024804	ENSCAFP00000023011	I	280	T	612894	possibly damaging	N
-Contig23_chr3_72567678_72570858	1313	chr3	72568976	ENSCAFT00000024846	ENSCAFP00000023051	L	298	P	488826	benign	N
-Contig190_chr7_35896301_35896811	232	chr7	35896528	ENSCAFT00000024892	ENSCAFP00000023095	R	3	L	480092	unknown	cfa00020=Citrate cycle (TCA cycle).cfa01100=Metabolic pathways.cfa05200=Pathways in cancer.cfa05211=Renal cell carcinoma
-Contig119_chr20_49114009_49114654	266	chr20	49114270	ENSCAFT00000024934	ENSCAFP00000023135	F	339	L	484849	benign	N
-Contig47_chr8_41487304_41487682	210	chr8	41487515	ENSCAFT00000025088	ENSCAFP00000023286	S	1743	L	490729	possibly damaging	N
-Contig67_chr2_84099157_84100880	345	chr2	84099493	ENSCAFT00000025109	ENSCAFP00000023307	I	60	L	U	benign	N
-Contig33_chr20_49727730_49730958	2192	chr20	49729935	ENSCAFT00000025308	ENSCAFP00000023495	T	448	R	U	probably damaging	N
-Contig33_chr20_49727730_49730958	2907	chr20	49730606	ENSCAFT00000025308	ENSCAFP00000023495	W	493	L	U	benign	N
-Contig93_chr8_42181027_42183022	694	chr8	42181716	ENSCAFT00000025462	ENSCAFP00000023641	L	782	P	U	benign	N
-Contig131_chrX_44937490_44940040	950	chrX	44938456	ENSCAFT00000025663	ENSCAFP00000023835	V	120	M	491894	benign	N
-Contig100_chrX_44915404_44918232	1832	chrX	44917224	ENSCAFT00000025663	ENSCAFP00000023835	R	1212	Q	491894	benign	N
-Contig100_chrX_44915404_44918232	920	chrX	44916331	ENSCAFT00000025663	ENSCAFP00000023835	L	1377	V	491894	benign	N
-Contig123_chr9_26132942_26133532	310	chr9	26133253	ENSCAFT00000025948	ENSCAFP00000024090	I	232	V	491022	benign	N
-Contig34_chr6_17772839_17773548	489	chr6	17773329	ENSCAFT00000026008	ENSCAFP00000024146	E	377	Q	U	benign	N
-Contig382_chr7_43383655_43383893	190	chr7	43383854	ENSCAFT00000026053	ENSCAFP00000024188	R	123	C	U	possibly damaging	N
-Contig163_chr2_87404548_87404792	132	chr2	87404673	ENSCAFT00000026251	ENSCAFP00000024378	D	239	N	U	benign	N
-Contig15_chr3_91850893_91851323	75	chr3	91850967	ENSCAFT00000026343	ENSCAFP00000024465	S	722	N	595148	benign	cfa04360=Axon guidance
-Contig141_chr7_44385686_44386047	166	chr7	44385857	ENSCAFT00000026393	ENSCAFP00000024510	L	166	P	490412	benign	cfa04810=Regulation of actin cytoskeleton
-Contig161_chr2_87840986_87841705	540	chr2	87841516	ENSCAFT00000026485	ENSCAFP00000024598	F	678	C	478233	probably damaging	cfa03018=RNA degradation
-Contig177_chr9_27497479_27498192	354	chr9	27497831	ENSCAFT00000026613	ENSCAFP00000024719	A	175	V	491046	possibly damaging	N
-Contig162_chr6_20156115_20157725	81	chr6	20156197	ENSCAFT00000026687	ENSCAFP00000024793	T	702	M	489923.489924.607168	benign	N
-Contig8_chr9_28287278_28288276	469	chr9	28287755	ENSCAFT00000026707	ENSCAFP00000024813	A	75	P	491060	benign	N
-Contig166_chr7_45276673_45277595	235	chr7	45276916	ENSCAFT00000026881	ENSCAFP00000024984	V	525	I	490428	benign	N
-Contig16_chr8_51223078_51223662	481	chr8	51223563	ENSCAFT00000026967	ENSCAFP00000025070	R	869	Q	490790	benign	N
-Contig65_chr9_29792446_29793465	893	chr9	29793341	ENSCAFT00000027073	ENSCAFP00000025173	S	81	A	491082	benign	N
-Contig175_chr6_30926774_30927470	446	chr6	30927229	ENSCAFT00000027269	ENSCAFP00000025361	S	663	T	403453	benign	cfa02010=ABC transporters.cfa04977=Vitamin digestion and absorption
-Contig45_chr30_33024389_33025619	471	chr30	33024857	ENSCAFT00000027320	ENSCAFP00000025407	G	986	A	487608	benign	N
-Contig60_chr20_53087461_53088013	184	chr20	53087649	ENSCAFT00000027519	ENSCAFP00000025591	S	556	L	611163	benign	N
-Contig98_chr5_37073086_37073674	378	chr5	37073467	ENSCAFT00000027596	ENSCAFP00000025664	V	38	M	479499	probably damaging	cfa04130=SNARE interactions in vesicular transport
-Contig64_chr9_36235086_36235751	475	chr9	36235563	ENSCAFT00000027673	ENSCAFP00000025737	D	260	E	491111	benign	cfa04970=Salivary secretion
-Contig72_chr30_35330469_35330831	236	chr30	35330709	ENSCAFT00000027712	ENSCAFP00000025770	G	386	C	478353	probably damaging	cfa04510=Focal adhesion.cfa04512=ECM-receptor interaction.cfa04810=Regulation of actin cytoskeleton.cfa05410=Hypertrophic cardiomyopathy (HCM).cfa05412=Arrhythmogenic right ventricular cardiomyopathy (ARVC).cfa05414=Dilated cardiomyopathy
-Contig12_chr8_66066327_66066629	89	chr8	66066402	ENSCAFT00000027927	ENSCAFP00000025970	K	158	R	490836	benign	N
-Contig212_chr8_66173086_66174259	622	chr8	66173712	ENSCAFT00000027950	ENSCAFP00000025993	K	114	Q	480421	benign	N
-Contig176_chr7_48083671_48084458	311	chr7	48083983	ENSCAFT00000027972	ENSCAFP00000026015	R	128	H	480148	probably damaging	N
-Contig3_chr4_58820541_58821952	265	chr4	58820806	ENSCAFT00000027979	ENSCAFP00000026022	A	31	T	489166	benign	N
-Contig24_chr7_48238665_48239174	383	chr7	48239049	ENSCAFT00000028007	ENSCAFP00000026049	T	227	M	480151	probably damaging	N
-Contig25_chr6_26340448_26341519	657	chr6	26341104	ENSCAFT00000028115	ENSCAFP00000026155	S	128	L	479811	possibly damaging	N
-Contig212_chr5_38871122_38871621	302	chr5	38871429	ENSCAFT00000028231	ENSCAFP00000026253	P	2265	L	489507	benign	N
-Contig147_chr6_27310627_27310983	100	chr6	27310719	ENSCAFT00000028327	ENSCAFP00000026344	V	154	A	U	benign	N
-Contig160_chr6_27318582_27318861	67	chr6	27318647	ENSCAFT00000028327	ENSCAFP00000026344	K	325	R	U	benign	N
-Contig18_chr4_61023435_61026038	385	chr4	61023825	ENSCAFT00000028363	ENSCAFP00000026377	P	4110	L	479323	benign	N
-Contig162_chr30_40685605_40687049	343	chr30	40685956	ENSCAFT00000028463	ENSCAFP00000026472	A	416	P	487646	benign	N
-Contig68_chr20_54017481_54018354	221	chr20	54017705	ENSCAFT00000028500	ENSCAFP00000026509	W	539	R	U	benign	N
-Contig50_chr7_59076761_59079381	2353	chr7	59079104	ENSCAFT00000028551	ENSCAFP00000026557	V	1487	I	490492	benign	N
-Contig51_chr7_59079274_59084588	2611	chr7	59081905	ENSCAFT00000028551	ENSCAFP00000026557	A	575	V	490492	benign	N
-Contig3_chr20_54855789_54856135	37	chr20	54855833	ENSCAFT00000028813	ENSCAFP00000026796	F	6015	S	U	unknown	N
-Contig157_chr5_43472186_43472528	168	chr5	43472353	ENSCAFT00000028826	ENSCAFP00000026807	R	355	Q	489526	benign	cfa00010=Glycolysis / Gluconeogenesis.cfa00340=Histidine metabolism.cfa00350=Tyrosine metabolism.cfa00360=Phenylalanine metabolism.cfa00410=beta-Alanine metabolism.cfa00980=Metabolism of xenobiotics by cytochrome P450.cfa00982=Drug metabolism - cytochrome P450.cfa01100=Metabolic pathways
-Contig80_chr20_55281094_55281971	129	chr20	55281228	ENSCAFT00000028936	ENSCAFP00000026914	T	931	A	U	benign	N
-Contig214_chr8_74493164_74493474	188	chr8	74493346	ENSCAFT00000029054	ENSCAFP00000027017	R	94	C	U	probably damaging	N
-Contig259_chr20_55571618_55572503	186	chr20	55571803	ENSCAFT00000029100	ENSCAFP00000027059	K	526	Q	485001	benign	N
-Contig180_chr9_41668066_41668716	357	chr9	41668451	ENSCAFT00000029122	ENSCAFP00000027081	E	990	D	491145	benign	cfa03410=Base excision repair
-Contig61_chr4_63087183_63089623	491	chr4	63087672	ENSCAFT00000029130	ENSCAFP00000027089	A	20	S	U	benign	N
-Contig261_chrX_94412915_94414298	488	chrX	94413396	ENSCAFT00000029188	ENSCAFP00000027142	D	329	E	U	unknown	N
-Contig58_chr4_70221679_70223505	1749	chr4	70223432	ENSCAFT00000029501	ENSCAFP00000027423	T	324	S	403721	benign	cfa04060=Cytokine-cytokine receptor interaction.cfa04080=Neuroactive ligand-receptor interaction.cfa04630=Jak-STAT signaling pathway
-Contig21_chr7_77985141_77986170	827	chr7	77985962	ENSCAFT00000029651	ENSCAFP00000027557	A	855	S	490545	benign	N
-Contig93_chrX_104176429_104177974	811	chrX	104177246	ENSCAFT00000029709	ENSCAFP00000027610	T	719	M	492128	benign	cfa03008=Ribosome biogenesis in eukaryotes
-Contig175_chr9_46116277_46118268	1090	chr9	46117366	ENSCAFT00000029722	ENSCAFP00000027622	Q	693	H	U	benign	N
-Contig134_chr4_76495667_76496825	860	chr4	76496507	ENSCAFT00000029827	ENSCAFP00000027720	I	113	V	612589	benign	cfa00250=Alanine, aspartate and glutamate metabolism.cfa00260=Glycine, serine and threonine metabolism.cfa01100=Metabolic pathways
-Contig247_chr6_31967574_31967796	158	chr6	31967732	ENSCAFT00000029875	ENSCAFP00000027765	P	750	T	489999	benign	N
-Contig6_chr7_81650872_81657348	3786	chr7	81654636	ENSCAFT00000030050	ENSCAFP00000027927	S	501	C	480218	benign	N
-Contig122_chr5_57147596_57148457	360	chr5	57147964	ENSCAFT00000030140	ENSCAFP00000028007	T	713	I	479558	benign	N
-Contig83_chr20_58039274_58039724	380	chr20	58039649	ENSCAFT00000030192	ENSCAFP00000028056	E	142	K	611866	benign	N
-Contig42_chr5_58023274_58024296	585	chr5	58023845	ENSCAFT00000030282	ENSCAFP00000028135	V	415	A	489580	benign	N
-Contig248_chr20_58217741_58219717	751	chr20	58218495	ENSCAFT00000030285	ENSCAFP00000028138	G	278	S	485038	unknown	N
-Contig127_chr6_39501489_39501966	83	chr6	39501576	ENSCAFT00000030381	ENSCAFP00000028228	N	155	S	490020	benign	N
-Contig123_chr6_39499974_39501056	816	chr6	39500798	ENSCAFT00000030381	ENSCAFP00000028228	A	195	P	490020	benign	N
-Contig247_chr6_39576694_39577607	493	chr6	39577171	ENSCAFT00000030386	ENSCAFP00000028233	S	745	N	490021	benign	N
-Contig6_chr9_50725202_50725646	143	chr9	50725344	ENSCAFT00000030726	ENSCAFP00000028560	M	12	T	491218	benign	N
-Contig221_chr6_41879771_41881379	766	chr6	41880519	ENSCAFT00000030883	ENSCAFP00000028717	A	184	T	606755	benign	N
-Contig231_chr5_60474911_60475630	279	chr5	60475186	ENSCAFT00000030960	ENSCAFP00000028794	C	505	Y	489618	possibly damaging	N
-Contig99_chr5_63306202_63308496	2063	chr5	63308224	ENSCAFT00000031146	ENSCAFP00000028978	A	421	V	U	unknown	N
-Contig245_chr5_66149146_66149848	349	chr5	66149499	ENSCAFT00000031407	ENSCAFP00000029234	R	207	Q	479601	benign	cfa00760=Nicotinate and nicotinamide metabolism.cfa01100=Metabolic pathways
-Contig305_chr5_67253589_67254394	375	chr5	67253954	ENSCAFT00000031570	ENSCAFP00000029391	R	203	Q	U	possibly damaging	N
-Contig94_chr9_56873843_56875505	1578	chr9	56875408	ENSCAFT00000031743	ENSCAFP00000029555	P	2937	S	U	benign	N
-Contig107_chr5_71317862_71318113	71	chr5	71317944	ENSCAFT00000031781	ENSCAFP00000029590	M	281	V	U	benign	N
-Contig134_chr9_57426140_57427208	236	chr9	57426380	ENSCAFT00000031798	ENSCAFP00000029606	V	89	I	480698	benign	cfa00590=Arachidonic acid metabolism.cfa01100=Metabolic pathways
-Contig60_chr12_5631507_5632392	818	chr12	5632313	ENSCAFT00000031814	ENSCAFP00000029621	Y	1697	C	481734	unknown	cfa04510=Focal adhesion.cfa04512=ECM-receptor interaction.cfa04974=Protein digestion and absorption.cfa05146=Amoebiasis
-Contig132_chr5_73710776_73711271	149	chr5	73710927	ENSCAFT00000031848	ENSCAFP00000029653	T	1323	M	489696	probably damaging	N
-Contig39_chr9_59278364_59279024	398	chr9	59278757	ENSCAFT00000032068	ENSCAFP00000029863	A	957	T	480718	benign	N
-Contig177_chr9_61212763_61213621	700	chr9	61213430	ENSCAFT00000032171	ENSCAFP00000029958	D	79	N	U	benign	N
-Contig67_chr6_62507717_62510152	1055	chr6	62508787	ENSCAFT00000032186	ENSCAFP00000029972	I	212	M	479959	probably damaging	cfa00380=Tryptophan metabolism.cfa00450=Selenocompound metabolism.cfa01100=Metabolic pathways
-Contig66_chr6_64570039_64570630	325	chr6	64570365	ENSCAFT00000032239	ENSCAFP00000030024	A	862	G	479964	benign	cfa04740=Olfactory transduction.cfa04972=Pancreatic secretion
-Contig22_chr6_64809414_64810661	626	chr6	64810027	ENSCAFT00000032269	ENSCAFP00000030052	Q	559	K	490179	benign	N
-Contig50_chr5_85052459_85052865	55	chr5	85052515	ENSCAFT00000032431	ENSCAFP00000030201	S	32	G	479688	benign	N
-Contig25_chr5_85095840_85098495	1627	chr5	85097474	ENSCAFT00000032433	ENSCAFP00000030203	F	681	S	U	benign	N
-Contig25_chr5_85480673_85480982	186	chr5	85480860	ENSCAFT00000032493	ENSCAFP00000030260	A	180	T	610026	possibly damaging	cfa05010=Alzheimer's disease
-Contig19_chr5_24601128_24602241	685	chr5	24601813	ENSCAFT00000035141	ENSCAFP00000030364	T	695	S	U	benign	N
-Contig59_chr26_11519273_11520242	659	chr26	11519937	ENSCAFT00000035276	ENSCAFP00000030520	P	160	L	403557	probably damaging	cfa03015=mRNA surveillance pathway.cfa04114=Oocyte meiosis.cfa04270=Vascular smooth muscle contraction.cfa04510=Focal adhesion.cfa04720=Long-term potentiation.cfa04728=Dopaminergic synapse.cfa04810=Regulation of actin cytoskeleton.cfa04910=Insulin signaling pathway.cfa05168=Herpes simplex infection
-Contig27_chr12_23130802_23131771	353	chr12	23131154	ENSCAFT00000035307	ENSCAFP00000030552	V	565	M	474935	probably damaging	N
-Contig31_chr1_8052327_8053606	234	chr1	8052570	ENSCAFT00000035442	ENSCAFP00000030703	C	153	S	U	possibly damaging	N
-Contig59_chr20_40539078_40540678	1223	chr20	40540302	ENSCAFT00000035532	ENSCAFP00000030804	H	285	R	403502	benign	cfa04620=Toll-like receptor signaling pathway.cfa05142=Chagas disease (American trypanosomiasis).cfa05143=African trypanosomiasis.cfa05144=Malaria.cfa05152=Tuberculosis.cfa05162=Measles.cfa05168=Herpes simplex infection
-Contig152_chr6_25356961_25358151	701	chr6	25357665	ENSCAFT00000035750	ENSCAFP00000031044	P	479	S	608555	benign	cfa04142=Lysosome
-Contig18_chr9_58576258_58576773	215	chr9	58576474	ENSCAFT00000035914	ENSCAFP00000031224	K	118	E	480706	benign	N
-Contig8_chr15_38734005_38734403	242	chr15	38734244	ENSCAFT00000035916	ENSCAFP00000031226	A	237	V	611996	possibly damaging	N
-Contig76_chr3_30625909_30626247	159	chr3	30626069	ENSCAFT00000036198	ENSCAFP00000031549	T	135	S	479171	benign	cfa00260=Glycine, serine and threonine metabolism.cfa00270=Cysteine and methionine metabolism.cfa01100=Metabolic pathways
-Contig86_chr37_14528768_14530343	873	chr37	14529628	ENSCAFT00000036570	ENSCAFP00000031969	V	738	D	478875.609202	possibly damaging	cfa04060=Cytokine-cytokine receptor interaction.cfa04350=TGF-beta signaling pathway
-Contig9_chr5_54124181_54125739	1134	chr5	54125291	ENSCAFT00000036640	ENSCAFP00000032043	A	187	T	610286	benign	N
-Contig107_chr9_8990420_8991676	1178	chr9	8991591	ENSCAFT00000036774	ENSCAFP00000032186	T	55	M	483288	benign	N
-Contig47_chr12_20319418_20320775	1212	chr12	20320622	ENSCAFT00000036825	ENSCAFP00000032241	K	606	T	474930	benign	cfa00280=Valine, leucine and isoleucine degradation.cfa00630=Glyoxylate and dicarboxylate metabolism.cfa00640=Propanoate metabolism.cfa01100=Metabolic pathways
-Contig4_chr2_45195542_45196115	233	chr2	45195785	ENSCAFT00000037022	ENSCAFP00000032463	D	833	N	478055	possibly damaging	N
-Contig8_chr8_77227029_77227651	339	chr8	77227366	ENSCAFT00000037096	ENSCAFP00000032544	T	61	A	490895.612602	benign	cfa04020=Calcium signaling pathway.cfa04145=Phagosome.cfa04640=Hematopoietic cell lineage.cfa04650=Natural killer cell mediated cytotoxicity.cfa04662=B cell receptor signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04666=Fc gamma R-mediated phagocytosis.cfa04672=Intestinal immune network for IgA production.cfa05140=Leishmaniasis.cfa05143=African trypanosomiasis.cfa05146=Amoebiasis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05162=Measles.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft rejection.cfa05340=Primary immunodeficiency.cfa05414=Dilated cardiomyopathy.cfa05416=Viral myocarditis
-Contig2_chr7_60049092_60051693	266	chr7	60049361	ENSCAFT00000038176	ENSCAFP00000033857	T	195	M	U	probably damaging	N
-Contig31_chr30_24179816_24187402	4867	chr30	24184686	ENSCAFT00000038211	ENSCAFP00000033897	G	103	S	U	benign	N
-Contig9_chr27_48250956_48251793	192	chr27	48251161	ENSCAFT00000038256	ENSCAFP00000033944	T	166	M	477739	probably damaging	N
-Contig45_chr27_43537046_43537944	568	chr27	43537599	ENSCAFT00000038301	ENSCAFP00000033996	M	69	I	611773	benign	cfa04010=MAPK signaling pathway.cfa04810=Regulation of actin cytoskeleton.cfa05200=Pathways in cancer.cfa05218=Melanoma
-Contig133_chr18_28371600_28372547	83	chr18	28371695	ENSCAFT00000038383	ENSCAFP00000034090	L	102	Q	475933	probably damaging	N
-Contig11_chr28_8532951_8533892	511	chr28	8533462	ENSCAFT00000038937	ENSCAFP00000034728	R	19	C	477763	probably damaging	cfa03008=Ribosome biogenesis in eukaryotes.cfa03013=RNA transport
-Contig1_chr14_5733966_5735336	783	chr14	5734754	ENSCAFT00000039094	ENSCAFP00000034905	A	166	T	U	benign	N
-Contig48_chr27_6001075_6001818	392	chr27	6001478	ENSCAFT00000039109	ENSCAFP00000034919	R	103	H	U	probably damaging	N
-Contig40_chr11_43589173_43590288	973	chr11	43590138	ENSCAFT00000039148	ENSCAFP00000034962	R	1617	P	481557	benign	N
-Contig1_chr14_30424688_30425258	179	chr14	30424861	ENSCAFT00000039390	ENSCAFP00000035239	T	648	I	475245	benign	cfa04666=Fc gamma R-mediated phagocytosis.cfa04810=Regulation of actin cytoskeleton
-Contig58_chr8_7461111_7462065	323	chr8	7461423	ENSCAFT00000039451	ENSCAFP00000035309	L	112	F	U	benign	N
-Contig1_chr25_43094809_43095852	908	chr25	43095708	ENSCAFT00000039609	ENSCAFP00000035483	W	18	G	U	unknown	N
-Contig114_chr25_43076436_43076800	141	chr25	43076581	ENSCAFT00000039609	ENSCAFP00000035483	S	45	C	U	unknown	N
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_in/sample.snp
--- a/test-data/test_in/sample.snp	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,402 +0,0 @@
-#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
-#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
-Contig161_chr1_4641264_4641879	115	C	T	73.5	chr1	4641382	C	6	0	2	45	8	0	2	51	15	0	2	72	5	0	2	42	6	0	2	45	10	0	2	57	Y	54	0.323	0
-Contig48_chr1_10150253_10151311	11	A	G	94.3	chr1	10150264	A	1	0	2	30	1	0	2	30	1	0	2	30	3	0	2	36	1	0	2	30	1	0	2	30	Y	22	+99.	0
-Contig20_chr1_21313469_21313570	66	C	T	54.0	chr1	21313534	C	4	0	2	39	4	0	2	39	5	0	2	42	4	0	2	39	4	0	2	39	5	0	2	42	N	1	+99.	0
-Contig86_chr1_30984450_30985684	670	C	T	365.0	chr1	30985133	C	9	0	2	54	10	0	2	57	13	0	2	66	3	0	2	36	9	0	2	54	7	0	2	48	Y	145	0.031	0
-Contig5_chr1_32562160_32563940	1215	G	T	163.0	chr1	32563356	G	17	0	2	78	19	0	2	84	20	0	2	87	14	0	2	69	12	0	2	63	10	0	2	57	Y	17	0.251	0
-Contig110_chr1_33385093_33386888	510	C	T	270.0	chr1	33385587	A	14	0	2	69	11	0	2	60	19	0	2	84	11	0	2	60	10	0	2	57	13	0	2	66	Y	13	0.126	0
-Contig100_chr1_33562920_33564288	743	C	T	178.0	chr1	33563655	C	6	0	2	45	10	0	2	57	8	0	2	51	5	0	2	42	13	0	2	66	7	0	2	48	Y	13	0.090	3
-Contig7_chr1_37302355_37302489	97	A	G	59.2	chr1	37302452	G	3	0	2	36	8	0	2	51	5	0	2	42	8	0	2	51	7	0	2	48	6	0	2	45	N	56	2.812	0
-Contig62_chr1_41880715_41882180	1078	T	G	57.6	chr1	41881785	T	14	0	2	69	15	0	2	72	16	0	2	75	13	0	2	66	8	0	2	51	10	0	2	57	Y	21	0.477	0
-Contig47_chr1_48409178_48409384	37	C	T	134.0	chr1	48409215	T	5	0	2	42	6	0	2	45	8	0	2	51	9	0	2	54	4	0	2	39	6	0	2	45	N	66	+99.	0
-Contig119_chr1_49647683_49650077	1618	C	A	99.7	chr1	49649276	A	8	0	2	51	11	0	2	60	10	0	2	57	9	0	2	54	10	0	2	57	14	0	2	69	Y	16	0.166	0
-Contig21_chr1_60697952_60699446	307	G	A	51.9	chr1	60698265	G	12	0	2	63	9	0	2	54	4	0	2	39	6	0	2	45	9	0	2	54	4	0	2	39	Y	98	0.507	0
-Contig131_chr1_62319542_62320564	169	C	G	103.0	chr1	62319709	C	12	0	2	63	12	0	2	66	14	0	2	69	12	0	2	63	9	0	2	54	9	0	2	54	Y	73	0.307	1
-Contig14_chr1_63450425_63450680	101	T	A	102.0	chr1	63450530	T	8	0	2	51	10	0	2	57	18	0	2	81	8	0	2	51	8	0	2	34	8	0	2	51	N	99	1.085	0
-Contig83_chr1_63869778_63869942	40	T	C	23.7	chr1	63869819	C	5	0	2	42	7	0	2	48	2	0	2	33	4	0	2	39	6	0	2	48	4	0	2	39	N	654	1.364	0
-Contig30_chr1_64702572_64703138	178	A	T	117.0	chr1	64702750	T	10	0	2	57	10	0	2	57	20	0	2	87	21	0	2	90	6	0	2	45	12	0	2	63	Y	50	3.872	0
-Contig101_chr1_69868406_69868872	287	G	A	14.6	chr1	69868689	G	13	0	2	66	17	0	2	78	10	0	2	57	8	0	2	51	7	0	2	48	8	0	2	51	N	137	0.305	0
-Contig35_chr1_74482577_74482791	170	G	A	45.4	chr1	74482751	A	3	0	2	36	4	0	2	39	13	0	2	66	2	0	2	33	5	0	2	42	2	0	2	33	N	20	+99.	3
-Contig49_chr1_83865731_83865944	85	G	A	34.1	chr1	-1	N	4	0	2	39	4	0	2	39	8	0	2	51	2	0	2	33	5	0	2	42	4	0	2	39	N	-1	1.485	0
-Contig64_chr1_87343284_87345672	163	T	A	3.76	chr1	87343443	C	0	2	2	1	0	0	-1	0	5	0	2	42	2	0	2	33	0	1	2	14	0	0	-1	0	N	3	0.039	2
-Contig20_chr1_110679280_110679687	181	C	T	87.4	chr1	110679454	-	1	0	2	30	7	0	2	48	4	0	2	39	2	0	2	33	2	0	2	33	0	0	-1	0	N	31	0.660	2
-Contig129_chr1_117547123_117548666	926	G	A	126.0	chr1	117548059	G	19	0	2	84	9	0	2	54	11	0	2	60	10	0	2	57	12	0	2	63	11	0	2	60	Y	64	0.049	0
-Contig7_chr1_125154638_125154844	190	G	T	130.0	chr1	125154818	A	5	0	2	42	4	0	2	39	7	0	2	48	2	0	2	33	7	0	2	48	4	0	2	39	N	33	+99.	0
-Contig222_chr2_9817738_9818143	220	C	T	888.0	chr2	9817960	C	17	0	2	78	12	0	2	63	20	0	2	87	8	0	2	51	11	0	2	60	12	0	2	63	Y	76	0.093	1
-Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
-Contig10_chr2_40859744_40860534	637	G	A	888.0	chr2	40860397	A	3	0	2	36	3	0	2	36	2	0	2	33	7	0	2	48	6	0	2	45	8	0	2	51	Y	42	1.435	0
-Contig52_chr2_41421981_41422725	604	C	A	888.0	chr2	41422583	A	17	0	2	78	18	0	2	81	14	0	2	69	17	0	2	78	12	0	2	63	14	0	2	69	Y	44	0.882	0
-Contig94_chr2_43869105_43870358	220	G	A	888.0	chr2	43869333	G	12	0	2	63	18	0	2	81	11	0	2	60	15	0	2	72	12	0	2	63	13	0	2	66	Y	1	0.156	0
-Contig34_chr2_48444129_48444939	695	C	T	134.0	chr2	48444828	C	14	0	2	69	8	0	2	51	16	0	2	75	17	0	2	78	9	0	2	54	15	0	2	72	Y	161	0.375	0
-Contig6_chr2_56859179_56859956	671	T	C	999.9	chr2	56859851	T	15	0	2	72	18	0	2	81	20	0	2	90	19	0	2	84	19	0	2	84	24	0	2	99	N	28	5.308	1
-Contig115_chr2_61631913_61632510	310	G	T	999.3	chr2	61632216	G	7	0	2	48	9	0	2	54	7	0	2	48	11	0	2	60	10	0	2	57	10	0	2	57	N	13	0.184	0
-Contig31_chr2_67331584_67331785	39	C	T	999.0	chr2	67331623	C	11	0	2	60	10	0	2	57	7	0	2	48	9	0	2	54	2	0	2	33	4	0	2	39	N	110	0.647	1
-Contig92_chr2_75906683_75907774	773	T	C	85.4	chr2	75907438	C	12	0	2	63	12	0	2	63	17	0	2	78	8	0	2	51	8	0	2	51	13	0	2	66	Y	93	0.166	0
-Contig163_chr2_76402959_76404830	221	C	T	127.0	chr2	76403181	C	4	0	2	42	10	0	2	57	9	0	2	54	11	0	2	60	7	0	2	48	9	0	2	54	Y	54	0.178	1
-Contig177_chr2_79559305_79560033	168	C	T	5.67	chr2	79559476	A	2	0	2	33	3	0	2	36	1	0	2	30	2	0	2	33	0	0	-1	0	1	0	2	30	N	56	0.257	0
-Contig8_chr2_82945728_82945839	61	T	C	223.0	chr2	-1	N	2	0	2	33	4	0	2	39	9	0	2	54	3	0	2	36	5	0	2	42	0	0	-1	0	N	-1	+99.	1
-Contig59_chr2_85243022_85243758	506	G	A	96.3	chr2	85243509	T	9	0	2	54	11	0	2	60	12	0	2	63	14	0	2	69	10	0	2	57	7	0	2	48	Y	6	0.459	0
-Contig56_chr3_17326225_17327548	387	G	C	91.2	chr3	17326591	G	14	0	2	69	13	0	2	66	15	0	2	72	15	0	2	72	13	0	2	66	12	0	2	63	Y	20	0.225	3
-Contig108_chr3_46210055_46210874	367	A	G	21.0	chr3	46210423	A	19	0	2	84	10	0	2	57	16	0	2	75	14	0	2	69	20	0	2	87	11	0	2	60	N	236	0.028	1
-Contig16_chr3_47113407_47114449	322	G	A	105.0	chr3	47113713	G	13	0	2	66	17	0	2	78	15	0	2	72	6	0	2	45	11	0	2	60	11	0	2	60	Y	114	0.132	5
-Contig3_chr3_47564810_47565251	262	T	G	112.0	chr3	47565104	T	14	0	2	69	16	0	2	75	20	0	2	87	10	0	2	57	9	0	2	54	8	0	2	51	Y	24	0.073	1
-Contig35_chr3_49662401_49662929	270	A	T	96.1	chr3	49662652	A	14	0	2	69	11	0	2	60	23	0	2	96	13	0	2	66	12	0	2	63	11	0	2	60	Y	36	3.583	2
-Contig97_chr3_49820354_49821631	1069	G	A	44.1	chr3	49821402	G	9	0	2	54	9	0	2	54	6	0	2	45	10	0	2	57	5	0	2	42	8	0	2	51	N	6	0.201	2
-Contig1_chr3_51588422_51589409	926	A	G	51.0	chr3	51589353	G	2	0	2	33	2	0	2	33	6	0	2	45	4	0	2	39	9	0	2	54	11	0	2	60	N	21	1.147	0
-Contig25_chr3_53260697_53262560	402	G	A	211.0	chr3	53261095	G	17	0	2	78	14	0	2	69	15	0	2	75	12	0	2	63	14	0	2	69	12	0	2	63	Y	116	1.033	0
-Contig11_chr3_53992739_53995954	2392	G	A	82.4	chr3	53995143	A	12	0	2	66	11	0	2	60	14	0	2	69	6	0	2	45	11	0	2	60	17	0	2	78	Y	358	0.321	1
-Contig236_chr3_72676275_72676473	128	G	A	278.0	chr3	72676410	G	12	0	2	63	11	0	2	60	13	0	2	66	10	0	2	57	11	0	2	60	8	0	2	51	N	36	0.496	1
-Contig48_chr3_74792236_74792388	63	T	C	111.0	chr3	74792289	-	17	0	2	78	9	0	2	54	9	0	2	54	5	0	2	42	11	0	2	60	9	0	2	54	N	-1	3.528	0
-Contig65_chr3_80727952_80728283	39	T	C	71.2	chr3	80727990	T	7	0	2	48	3	0	2	36	8	0	2	51	6	0	2	45	8	0	2	51	11	0	2	60	N	22	7.078	0
-Contig53_chr3_86407941_86409349	1406	G	A	86.9	chr3	86409317	A	5	0	2	42	5	0	2	42	4	0	2	39	10	0	2	57	8	0	2	51	12	0	2	63	N	14	3.285	1
-Contig13_chr3_92409738_92412300	718	A	G	23.3	chr3	92410450	A	12	0	2	63	16	0	2	75	18	0	2	81	13	0	2	66	22	0	2	93	7	0	2	48	Y	23	0.224	2
-Contig134_chr4_12145648_12148225	1326	C	T	164.0	chr4	12146961	C	9	0	2	54	8	0	2	51	7	0	2	48	3	0	2	36	5	0	2	42	5	0	2	42	Y	4	0.080	1
-Contig88_chr4_15557471_15557833	268	A	G	145.0	chr4	15557737	A	6	0	2	45	6	0	2	45	11	0	2	60	9	0	2	54	5	0	2	42	6	0	2	45	Y	46	4.138	0
-Contig53_chr4_18823968_18824478	149	A	G	91.3	chr4	18824115	A	18	0	2	81	15	0	2	72	21	0	2	90	13	0	2	66	9	0	2	54	12	0	2	63	N	51	0.251	0
-Contig86_chr4_24953866_24956222	1985	C	T	76.4	chr4	24955841	T	8	0	2	51	1	0	2	30	3	0	2	36	7	0	2	48	2	0	2	33	6	0	2	45	Y	12	0.357	0
-Contig19_chr4_26233601_26233991	146	G	C	51.6	chr4	26233744	G	10	0	2	57	8	0	2	51	9	0	2	54	5	0	2	42	9	0	2	54	4	0	2	39	N	41	0.163	3
-Contig78_chr4_28579975_28580134	30	T	G	19.6	chr4	28579994	-	4	0	2	39	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	2	0	2	33	N	33	0.499	0
-Contig16_chr4_30177226_30179725	621	C	T	88.4	chr4	30177859	C	20	0	2	87	13	0	2	66	13	0	2	66	11	0	2	60	8	0	2	51	8	0	2	51	Y	45	0.797	1
-Contig30_chr4_46196500_46197672	1045	A	C	33.4	chr4	46197522	C	16	0	2	75	9	0	2	54	4	0	2	39	7	0	2	48	14	0	2	69	6	0	2	45	Y	43	0.306	0
-Contig2_chr4_47039007_47039323	158	G	C	35.1	chr4	47039160	-	8	0	2	51	9	0	2	54	13	0	2	66	8	0	2	51	10	0	2	60	9	0	2	54	N	0	0.131	0
-Contig17_chr4_61310346_61311158	267	C	T	49.9	chr4	61310604	T	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	14	0	2	69	7	0	2	48	Y	219	0.098	0
-Contig26_chr4_64190783_64191295	64	A	G	162.0	chr4	64190843	A	10	0	2	57	6	0	2	45	20	0	2	87	12	0	2	63	17	0	2	78	7	0	2	48	Y	306	7.428	0
-Contig11_chr4_65500960_65501654	634	T	C	107.0	chr4	65501585	T	13	0	2	66	14	0	2	69	13	0	2	66	13	0	2	66	6	0	2	45	18	0	2	81	Y	10	6.849	0
-Contig38_chr4_67768488_67768982	113	A	G	102.0	chr4	67768598	A	9	0	2	54	8	0	2	51	9	0	2	54	11	0	2	60	10	0	2	57	7	0	2	48	Y	188	3.175	0
-Contig30_chr4_70978564_70979580	596	A	G	164.0	chr4	70979151	A	15	0	2	72	12	0	2	63	20	0	2	87	14	0	2	69	15	0	2	72	15	0	2	72	Y	111	2.458	2
-Contig72_chr4_74225793_74226492	674	A	G	110.0	chr4	74226472	A	5	0	2	42	3	0	2	36	2	0	2	33	3	0	2	36	7	0	2	48	4	0	2	39	Y	115	+99.	1
-Contig32_chr4_75618955_75620254	301	T	C	333.0	chr4	75619257	C	10	0	2	57	8	0	2	51	12	0	2	63	20	0	2	87	12	0	2	63	14	0	2	69	Y	34	0.163	2
-Contig31_chr5_4734956_4736547	1166	C	T	133.0	chr5	4736132	C	14	0	2	69	8	0	2	51	17	0	2	78	4	0	2	39	9	0	2	54	12	0	2	63	Y	1	0.021	0
-Contig113_chr5_11052263_11052603	28	C	T	38.2	chr5	11052280	C	1	2	1	12	3	2	1	10	5	0	2	42	2	1	2	13	3	0	2	36	8	0	2	51	Y	161	+99.	0
-Contig30_chr5_15698241_15699076	396	G	T	76.6	chr5	15698633	T	8	0	2	51	9	0	2	54	10	0	2	57	7	0	2	48	11	0	2	60	8	0	2	54	Y	65	0.009	0
-Contig36_chr5_17709244_17710004	373	T	C	281.0	chr5	17709624	T	6	0	2	45	9	0	2	54	7	0	2	48	4	0	2	39	10	0	2	57	4	0	2	39	Y	16	0.131	0
-Contig13_chr5_21881138_21881562	227	A	G	251.0	chr5	21881356	A	11	0	2	60	20	0	2	87	22	0	2	93	10	0	2	57	10	0	2	57	21	0	2	90	Y	182	2.013	0
-Contig5_chr5_23188121_23190168	1841	C	T	141.0	chr5	23189975	C	20	0	2	87	19	0	2	84	22	0	2	93	16	0	2	75	18	0	2	81	14	0	2	69	N	45	0.355	0
-Contig6_chr5_26899813_26900498	97	A	C	88.6	chr5	26899910	A	15	0	2	72	14	0	2	69	27	0	2	108	15	0	2	72	13	0	2	69	12	0	2	63	Y	92	7.370	3
-Contig314_chr5_34019166_34019319	72	C	A	20.1	chr5	-1	N	6	0	2	45	9	0	2	54	4	0	2	39	4	0	2	39	9	0	2	54	5	0	2	42	N	-1	+99.	4
-Contig147_chr5_38980258_38980559	221	C	T	40.8	chr5	38980477	C	15	0	2	72	15	0	2	72	19	0	2	84	10	0	2	57	12	0	2	63	20	0	2	87	Y	11	4.576	0
-Contig115_chr5_48119079_48120169	151	C	T	78.3	chr5	48119234	C	17	0	2	78	10	0	2	57	14	0	2	69	16	0	2	75	8	0	2	51	12	0	2	63	Y	205	0.320	0
-Contig45_chr5_50892738_50892968	169	C	A	25.8	chr5	50892911	C	10	0	2	57	7	0	2	48	10	0	2	60	6	0	2	45	6	0	2	45	13	0	2	66	N	244	0.497	1
-Contig40_chr5_51484164_51484696	14	A	G	53.3	chr5	51484180	A	6	0	2	45	4	0	2	39	4	0	2	39	3	0	2	36	0	0	2	13	3	0	2	36	N	63	+99.	1
-Contig40_chr5_51664286_51667573	861	C	T	148.0	chr5	51665149	C	20	0	2	87	21	0	2	90	20	0	2	87	11	0	2	60	16	0	2	75	15	0	2	72	Y	207	0.080	1
-Contig15_chr5_51889708_51891244	882	A	G	149.0	chr5	51890581	G	13	0	2	66	18	0	2	81	17	0	2	78	22	0	2	93	15	0	2	72	22	0	2	93	Y	7	0.025	1
-Contig143_chr5_57231364_57232010	294	T	C	78.5	chr5	57231644	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	10	0	2	57	6	0	2	45	Y	73	0.337	2
-Contig13_chr5_57609985_57610584	496	C	T	50.5	chr5	57610476	C	17	0	2	78	9	0	2	54	6	0	2	45	8	0	2	51	10	0	2	57	12	0	2	63	N	77	2.022	1
-Contig230_chr5_58486998_58487280	227	T	C	192.0	chr5	58487232	T	3	0	2	36	4	0	2	39	9	0	2	54	6	0	2	45	4	0	2	39	7	0	2	48	N	24	0.100	2
-Contig385_chr5_60122961_60123128	15	C	G	136.0	chr5	60122976	C	0	0	-1	0	0	0	-1	0	1	0	2	30	1	0	2	30	3	0	2	36	0	0	-1	0	N	100	+99.	2
-Contig143_chr5_65121393_65122035	558	C	A	127.0	chr5	65121959	A	0	0	-1	0	5	0	2	42	3	0	2	36	4	0	2	39	0	0	-1	0	4	0	2	39	Y	285	0.391	1
-Contig32_chr5_70852360_70853289	282	G	A	114.0	chr5	70852623	G	16	0	2	75	11	0	2	60	13	0	2	66	12	0	2	63	13	0	2	66	7	0	2	48	Y	33	0.276	0
-Contig215_chr5_70946445_70947428	363	T	G	28.2	chr5	70946809	C	4	0	2	39	0	5	0	12	9	0	2	54	6	0	2	45	3	3	2	1	9	0	2	54	N	43	0.153	0
-Contig100_chr5_71189678_71190590	813	C	T	30.8	chr5	71190523	C	11	0	2	60	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	Y	8	0.362	1
-Contig45_chr5_76133561_76134403	388	A	G	103.0	chr5	76133941	G	3	0	2	36	8	0	2	51	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	57	0.038	0
-Contig61_chr5_90202541_90204393	909	C	T	101.0	chr5	90203461	T	7	0	2	48	5	0	2	42	14	0	2	69	3	0	2	36	5	0	2	42	8	0	2	51	Y	64	1.448	0
-Contig111_chr6_5821219_5822519	1060	A	G	68.1	chr6	5822321	T	7	0	2	48	6	0	2	45	11	0	2	60	9	0	2	54	3	0	2	36	12	0	2	63	Y	7	0.231	1
-Contig220_chr6_10671338_10672441	999	T	C	36.3	chr6	10672322	T	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	5	0	2	42	9	0	2	54	Y	1	1.667	0
-Contig226_chr6_17361986_17362884	418	G	C	251.0	chr6	17362406	G	6	0	2	45	8	0	2	51	7	0	2	48	9	0	2	54	7	0	2	48	7	0	2	48	Y	7	0.147	0
-Contig380_chr6_18173971_18174169	180	C	T	4.87	chr6	18174144	T	0	0	-1	0	4	0	2	39	7	0	2	48	2	0	2	33	2	0	2	33	1	0	2	30	N	56	2.589	0
-Contig51_chr6_20231207_20231785	161	A	G	70.5	chr6	20231375	G	13	0	2	66	5	0	2	42	8	0	2	51	2	0	2	36	5	0	2	42	5	0	2	42	Y	153	1.754	0
-Contig102_chr6_30271329_30271577	39	T	G	139.0	chr6	30271371	G	3	0	2	36	4	0	2	39	6	0	2	45	1	0	2	30	4	0	2	39	4	0	2	39	N	15	1.159	0
-Contig217_chr6_31393824_31394218	97	G	A	115.0	chr6	31393921	G	9	0	2	54	19	0	2	84	15	0	2	72	12	0	2	63	7	0	2	48	10	0	2	57	N	45	0.477	0
-Contig186_chr6_31928098_31928245	73	G	A	117.0	chr6	-1	N	5	0	2	42	8	0	2	51	2	0	2	33	4	0	2	39	1	0	2	30	5	0	2	42	N	-1	0.276	1
-Contig52_chr6_33188498_33188724	123	G	A	59.0	chr6	-1	N	5	0	2	42	13	0	2	66	8	0	2	51	4	0	2	39	9	0	2	54	9	0	2	54	N	-1	0.880	1
-Contig102_chr6_38743009_38743435	290	A	G	178.0	chr6	38743311	A	11	0	2	60	13	0	2	66	9	0	2	54	11	0	2	60	12	0	2	63	13	0	2	66	Y	34	0.148	4
-Contig81_chr6_49018353_49019532	179	C	A	72.5	chr6	49018530	A	15	0	2	72	13	0	2	66	19	0	2	72	8	0	2	51	12	0	2	63	16	0	2	75	Y	15	0.145	1
-Contig112_chr6_51024554_51024851	100	A	G	121.0	chr6	51024654	A	10	0	2	57	12	0	2	63	9	0	2	54	13	0	2	66	14	0	2	69	17	0	2	78	N	75	4.287	0
-Contig40_chr6_51412751_51413807	227	T	C	94.5	chr6	51412975	C	5	0	2	42	8	0	2	51	7	0	2	48	9	0	2	54	11	0	2	60	10	0	2	57	Y	4	5.661	0
-Contig47_chr6_69073222_69074767	1315	T	C	212.0	chr6	69074558	T	20	0	2	87	17	0	2	78	18	0	2	81	12	0	2	63	17	0	2	78	7	0	2	48	Y	9	0.652	0
-Contig30_chr6_74848932_74849059	57	C	G	46.3	chr6	74848993	C	7	0	2	48	7	0	2	33	6	0	2	45	7	0	2	48	5	0	2	42	6	0	2	45	N	-1	+99.	1
-Contig84_chr7_6648683_6650255	1297	G	A	110.0	chr7	6649988	G	18	0	2	81	9	0	2	54	22	0	2	77	16	0	2	75	20	0	2	87	6	0	2	45	Y	83	0.166	0
-Contig239_chr7_13007379_13007700	275	A	G	39.8	chr7	13007642	A	8	0	2	51	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	5	0	2	42	N	46	1.511	3
-Contig119_chr7_18310707_18310948	23	A	T	133.0	chr7	18310729	A	6	0	2	45	5	0	2	42	10	0	2	57	5	0	2	42	2	0	2	33	2	0	2	33	N	4553	+99.	0
-Contig93_chr7_18513377_18513741	173	T	C	130.0	chr7	18513533	C	15	0	2	72	11	0	2	60	18	0	2	81	6	0	2	45	10	0	2	57	14	0	2	69	Y	115	0.174	0
-Contig133_chr7_19603333_19603776	414	C	G	31.9	chr7	19603734	G	10	0	2	57	4	0	2	39	4	0	2	39	5	0	2	42	9	0	2	54	9	0	2	54	N	78	+99.	5
-Contig132_chr7_20426224_20428145	1815	A	G	28.3	chr7	20428041	A	11	1	2	43	12	0	2	63	19	0	2	84	23	0	2	96	14	0	2	69	10	0	2	57	N	11	0.264	0
-Contig206_chr7_26281823_26282074	103	C	A	101.0	chr7	26281925	T	11	0	2	60	16	0	2	61	19	0	2	84	6	0	2	45	19	0	2	84	16	0	2	75	N	-1	0.947	1
-Contig116_chr7_45858984_45859111	38	T	C	73.2	chr7	-1	N	2	0	2	33	1	0	2	30	3	0	2	36	2	0	2	33	2	0	2	33	1	0	2	30	N	-1	3.442	0
-Contig38_chr7_50681997_50682600	42	T	C	92.4	chr7	50682037	G	6	0	2	45	2	0	2	33	10	0	2	57	12	0	2	63	5	0	2	42	6	0	2	45	Y	94	0.146	0
-Contig55_chr7_53147505_53148974	894	A	G	68.4	chr7	53148397	G	22	0	2	93	13	0	2	66	16	0	2	75	8	0	2	51	16	0	2	75	11	0	2	60	Y	19	0.060	0
-Contig4_chr7_53685534_53688206	1709	C	G	76.2	chr7	53687225	C	18	0	2	81	17	0	2	78	18	0	2	81	15	0	2	72	14	0	2	69	14	0	2	69	Y	32	0.659	1
-Contig61_chr7_55832923_55834065	506	T	C	185.0	chr7	55833450	C	9	0	2	54	10	0	2	57	22	0	2	93	12	0	2	63	12	0	2	63	7	0	2	48	Y	1	0.019	0
-Contig91_chr8_12804505_12805470	409	C	A	111.0	chr8	12804906	C	8	0	2	51	10	0	2	57	15	0	2	72	12	0	2	63	14	0	2	69	15	0	2	72	N	145	0.175	0
-Contig30_chr8_17147743_17147923	13	G	A	105.0	chr8	17147756	A	1	3	1	19	1	0	2	30	3	0	2	36	1	0	2	30	1	0	2	30	3	0	2	36	N	6	+99.	0
-Contig8_chr8_27811135_27812620	333	C	T	37.9	chr8	27811458	C	4	0	2	39	11	0	2	60	18	0	2	81	5	0	2	42	6	0	2	45	5	0	2	42	Y	1	0.272	0
-Contig66_chr8_28273102_28273660	175	G	C	81.6	chr8	28273263	T	9	0	2	54	17	0	2	78	19	0	2	84	8	0	2	51	16	0	2	75	19	0	2	84	Y	3	2.735	0
-Contig84_chr8_31375511_31376456	443	T	C	125.0	chr8	31375954	T	10	0	2	57	15	0	2	72	27	0	2	108	18	0	2	81	16	0	2	75	9	0	2	54	Y	2	0.650	0
-Contig18_chr8_32575859_32577431	264	T	C	151.0	chr8	32576124	T	20	0	2	87	14	0	2	69	17	0	2	78	14	0	2	69	13	0	2	66	14	0	2	69	Y	17	0.915	1
-Contig54_chr8_40913908_40916451	1275	G	A	175.0	chr8	40915190	G	10	0	2	57	8	0	2	51	11	0	2	60	7	0	2	48	8	0	2	51	9	0	2	54	Y	21	0.056	3
-Contig93_chr8_44658786_44659075	180	T	G	55.3	chr8	44658964	T	4	0	2	39	3	0	2	36	6	0	2	45	5	0	2	45	5	0	2	42	4	0	2	39	N	14	0.188	0
-Contig17_chr8_57490059_57490498	69	G	T	97.4	chr8	57490127	A	2	0	2	33	11	0	2	60	15	0	2	72	16	0	2	75	8	0	2	51	10	0	2	57	N	40	0.522	5
-Contig66_chr8_58562376_58563446	345	C	G	5.74	chr8	58562721	C	14	0	2	69	12	0	2	63	9	0	2	57	10	0	2	57	9	0	2	54	10	0	2	57	Y	6	0.685	0
-Contig44_chr8_71186368_71188207	1455	G	T	147.0	chr8	71187818	G	4	10	1	74	3	0	2	36	20	0	2	87	12	0	2	63	8	0	2	51	10	0	2	57	Y	88	0.036	0
-Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
-Contig96_chr9_39008495_39009278	215	A	C	98.7	chr9	39008708	C	7	0	2	48	13	0	2	66	28	0	2	111	16	0	2	75	17	0	2	78	17	0	2	78	Y	8	0.427	1
-Contig22_chr10_15505382_15505589	172	T	C	38.5	chr10	15505548	T	2	0	2	33	6	0	2	45	8	0	2	51	8	0	2	51	9	0	2	54	12	0	2	63	N	284	2.861	0
-Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
-Contig63_chr10_42716594_42719945	1018	A	G	88.7	chr10	42717616	G	13	0	2	66	14	0	2	69	13	0	2	66	12	0	2	63	18	0	2	81	5	0	2	42	Y	25	1.740	0
-Contig22_chr10_43255307_43255570	81	C	A	37.2	chr10	43255383	C	15	0	2	72	18	0	2	81	22	0	2	93	16	0	2	75	11	0	2	60	12	0	2	63	N	62	0.450	0
-Contig9_chr10_51475063_51476054	770	C	T	57.3	chr10	51475839	C	6	0	2	45	16	0	2	75	16	0	2	75	13	0	2	66	9	0	2	54	9	2	2	21	N	80	0.394	0
-Contig42_chr10_53816543_53818392	1642	G	A	27.5	chr10	53818172	A	7	0	2	48	13	0	2	66	17	0	2	78	14	0	2	69	19	0	2	84	16	0	2	75	N	1	0.433	0
-Contig36_chr10_53992615_53993741	229	G	C	86.2	chr10	53992846	G	17	0	2	78	14	0	2	69	13	0	2	66	15	0	2	72	12	0	2	63	15	0	2	72	N	23	1.912	0
-Contig20_chr10_58141129_58141750	575	C	T	46.1	chr10	58141701	C	7	0	2	48	8	0	2	51	9	0	2	54	3	0	2	36	4	0	2	39	9	0	2	54	N	1	4.264	0
-Contig26_chr10_59510973_59511899	146	C	A	29.0	chr10	59511126	C	8	0	2	51	13	0	2	66	18	0	2	81	13	0	2	66	10	0	2	57	7	0	2	48	Y	208	1.077	0
-Contig72_chr11_7142765_7143772	146	G	A	152.0	chr11	7142911	A	8	0	2	51	8	0	2	51	24	0	2	99	10	0	2	57	17	0	2	78	11	0	2	60	Y	90	1.137	0
-Contig103_chr11_8844784_8845095	214	T	G	135.0	chr11	8844993	T	1	1	2	12	10	0	2	57	5	4	1	26	2	3	1	13	2	7	1	34	1	1	2	13	Y	75	0.731	0
-Contig9_chr11_9904571_9905983	1284	C	T	151.0	chr11	9905857	C	16	0	2	75	19	0	2	84	17	0	2	78	16	0	2	75	12	0	2	63	13	1	2	44	Y	11	0.422	1
-Contig35_chr11_22459883_22460855	714	T	G	54.9	chr11	22460577	T	3	0	2	36	1	0	2	30	3	0	2	36	2	0	2	33	2	0	2	33	0	0	-1	0	N	24	0.382	0
-Contig7_chr11_40017076_40017630	352	C	T	46.3	chr11	40017422	C	7	0	2	48	9	0	2	54	6	0	2	45	8	0	2	51	16	0	2	75	9	0	2	54	Y	44	0.336	0
-Contig108_chr11_42953408_42955156	367	A	G	89.4	chr11	42953779	A	17	0	2	78	11	0	2	60	14	0	2	69	20	0	2	87	14	0	2	69	17	0	2	78	Y	118	0.784	1
-Contig82_chr11_43490732_43490862	60	C	T	47.3	chr11	-1	N	0	0	-1	0	0	0	-1	0	1	0	2	30	3	0	2	36	1	1	2	19	1	0	2	30	N	-1	6.763	0
-Contig16_chr11_53408448_53408790	187	A	G	153.0	chr11	53408638	A	7	0	2	48	9	0	2	54	18	0	2	81	10	0	2	57	11	0	2	60	12	0	2	63	Y	116	1.367	0
-Contig21_chr12_18403415_18404381	586	G	T	34.5	chr12	18403983	-	13	0	2	66	16	0	2	75	25	0	2	102	12	0	2	63	12	0	2	63	14	0	2	69	Y	12	0.068	0
-Contig33_chr12_19804073_19804529	178	T	C	69.4	chr12	19804261	T	13	0	2	66	13	0	2	66	22	0	2	93	11	0	2	60	12	0	2	63	18	0	2	81	Y	11	1.571	0
-Contig41_chr12_25565452_25566993	475	G	T	6.29	chr12	25565926	G	15	0	2	72	14	0	2	69	10	0	2	57	15	0	2	72	18	0	2	81	19	0	2	84	N	10	2.231	1
-Contig9_chr12_27204351_27204696	239	A	G	145.0	chr12	27204587	A	7	0	2	48	8	0	2	51	12	0	2	63	8	0	2	51	11	0	2	60	11	0	2	60	Y	14	0.046	0
-Contig45_chr12_30548282_30550498	448	C	T	124.0	chr12	30548703	-	9	0	2	54	11	0	2	60	22	0	2	93	19	0	2	84	12	0	2	63	12	0	2	63	Y	66	0.305	0
-Contig46_chr12_35571846_35572563	58	G	C	83.2	chr12	35571906	G	4	0	2	39	10	0	2	57	11	0	2	60	6	0	2	45	10	0	2	57	6	0	2	45	Y	55	+99.	1
-Contig28_chr12_42075871_42076044	136	G	A	134.0	chr12	42076006	A	6	0	2	45	5	0	2	42	7	0	2	48	7	0	2	48	2	0	2	33	4	0	2	39	N	3	9.479	0
-Contig16_chr12_42386141_42387454	194	A	G	161.0	chr12	42386323	A	11	0	2	60	8	0	2	54	23	0	2	96	17	0	2	78	6	0	2	45	13	0	2	66	Y	7	0.927	1
-Contig42_chr12_44424628_44425829	255	A	G	84.4	chr12	44424879	A	12	0	2	63	19	0	2	84	23	0	2	96	15	0	2	72	18	0	2	81	14	0	2	69	Y	18	1.190	2
-Contig10_chr12_44447953_44449698	63	C	T	105.0	chr12	44448020	C	11	0	2	60	9	0	2	54	12	0	2	63	10	0	2	57	15	0	2	72	8	0	2	51	Y	31	11.791	0
-Contig5_chr12_53880670_53882675	1221	A	C	99.4	chr12	53881888	A	16	0	2	75	18	0	2	81	23	0	2	96	10	0	2	57	15	0	2	72	17	0	2	78	Y	31	0.061	0
-Contig86_chr12_56715356_56716464	818	T	C	166.0	chr12	56716164	T	20	0	2	87	16	0	2	75	16	0	2	75	14	0	2	69	13	0	2	66	7	0	2	48	Y	22	1.092	0
-Contig3_chr12_65021967_65024097	238	T	G	92.6	chr12	65022205	T	17	0	2	78	14	0	2	69	16	0	2	75	9	0	2	54	13	0	2	66	15	0	2	72	Y	258	0.117	0
-Contig43_chr12_66499742_66500010	121	G	T	41.5	chr12	66499866	G	12	0	2	63	4	0	2	39	8	0	2	51	6	0	2	45	10	0	2	57	6	0	2	45	N	42	0.421	0
-Contig14_chr12_71364692_71365311	20	A	C	103.0	chr12	71364712	A	7	0	2	48	3	0	2	36	5	0	2	42	1	0	2	30	2	0	2	33	3	0	2	36	Y	35	+99.	0
-Contig37_chr13_15910164_15910426	245	G	A	32.9	chr13	-1	N	3	4	1	41	4	0	2	39	3	0	2	36	4	0	2	39	3	0	2	36	10	0	2	57	N	-1	2.159	1
-Contig107_chr13_26045881_26046290	341	C	G	81.4	chr13	26046230	C	16	0	2	75	20	0	2	90	14	0	2	69	15	0	2	72	9	0	2	54	9	0	2	54	Y	51	4.510	0
-Contig251_chr13_28498333_28501066	864	T	G	296.0	chr13	28499180	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	5	0	2	42	6	0	2	45	Y	9	0.068	0
-Contig154_chr13_36777857_36778736	356	G	A	95.5	chr13	36778225	A	6	0	2	45	11	0	2	60	11	0	2	60	9	0	2	54	13	0	2	66	8	0	2	51	Y	59	0.192	0
-Contig37_chr13_42529793_42530857	150	G	T	192.0	chr13	42529926	G	18	0	2	81	14	0	2	69	16	0	2	75	14	0	2	69	8	0	2	51	11	0	2	60	N	22	0.795	5
-Contig47_chr13_47045833_47046626	257	A	C	28.5	chr13	47046097	A	13	0	2	66	10	0	2	57	17	0	2	78	20	0	2	87	15	0	2	72	9	0	2	57	N	129	0.468	0
-Contig42_chr13_47730018_47730856	254	A	G	75.1	chr13	47730294	A	13	0	2	66	6	0	2	45	12	0	2	63	9	0	2	54	16	0	2	75	11	0	2	63	Y	630	0.049	1
-Contig55_chr13_53467708_53468101	221	T	G	132.0	chr13	53467925	T	25	0	2	102	12	0	2	63	26	0	2	105	7	0	2	48	16	0	2	75	16	0	2	75	N	20	5.717	1
-Contig49_chr13_55103679_55105532	503	G	A	76.0	chr13	55104178	G	21	0	2	90	19	0	2	84	18	0	2	81	20	0	2	87	8	9	1	89	17	0	2	78	Y	20	0.259	1
-Contig42_chr13_64785759_64786045	14	C	G	22.8	chr13	64785772	C	2	0	2	33	2	0	2	33	4	0	2	39	7	0	2	48	8	0	2	51	2	0	2	33	N	527	+99.	1
-Contig66_chr13_66021813_66022244	319	C	T	125.0	chr13	66022136	C	11	0	2	60	16	0	2	75	15	0	2	75	12	0	2	63	17	0	2	78	8	0	2	51	N	14	0.055	3
-Contig48_chr14_11839435_11843272	3014	A	G	163.0	chr14	11842446	A	10	0	2	57	8	0	2	51	13	0	2	66	10	0	2	57	5	0	2	42	10	0	2	57	Y	31	0.908	0
-Contig9_chr14_23353717_23354432	80	G	A	61.3	chr14	23353797	G	3	0	2	36	6	0	2	45	11	0	2	60	8	0	2	51	4	0	2	39	2	4	1	35	Y	11	0.444	0
-Contig14_chr14_24131180_24133488	1633	G	A	131.0	chr14	24132818	G	21	0	2	90	16	0	2	75	12	0	2	63	10	0	2	57	11	0	2	60	20	0	2	87	Y	36	0.347	0
-Contig28_chr14_26905747_26909514	975	G	C	3.13	chr14	26906723	G	16	0	2	75	10	0	2	57	12	0	2	63	15	0	2	72	10	0	2	57	7	0	2	48	N	287	0.117	2
-Contig14_chr14_29616948_29618316	109	G	A	80.3	chr14	29617053	-	17	0	2	78	16	0	2	75	16	0	2	75	10	0	2	57	17	0	2	78	19	0	2	84	Y	32	1.051	0
-Contig24_chr14_29728478_29728839	242	T	A	107.0	chr14	29728724	T	2	0	2	33	12	0	2	63	10	0	2	57	12	0	2	63	5	0	2	42	9	0	2	54	N	70	2.712	0
-Contig76_chr14_30028102_30029179	1046	C	T	38.5	chr14	30029169	T	3	0	2	36	6	0	2	45	9	0	2	54	7	0	2	48	9	0	2	54	8	0	2	51	Y	96	+99.	0
-Contig115_chr14_31417207_31417574	259	A	G	12.1	chr14	31417454	G	13	0	2	66	15	0	2	72	21	0	2	90	12	0	2	63	13	0	2	66	9	0	2	54	N	28	5.379	2
-Contig70_chr14_46653662_46653790	111	G	A	46.7	chr14	46653768	G	7	0	2	48	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	10	0	2	57	N	21	+99.	2
-Contig43_chr14_49991855_49993511	918	A	G	112.0	chr14	49992767	G	15	0	2	72	10	0	2	57	11	0	2	63	9	0	2	54	12	0	2	63	9	0	2	54	Y	6	0.314	1
-Contig64_chr14_56768376_56768902	473	C	T	29.0	chr14	56768832	C	15	0	2	72	11	0	2	60	14	0	2	69	14	0	2	69	7	0	2	48	9	0	2	54	Y	91	8.281	0
-Contig60_chr15_18493036_18494316	150	G	A	92.6	chr15	18493188	G	9	0	2	54	13	0	2	66	9	0	2	54	6	0	2	45	5	0	2	42	12	0	2	63	Y	45	0.125	0
-Contig213_chr15_19567788_19568626	196	A	C	13.9	chr15	19567992	A	4	0	2	39	2	0	2	33	7	0	2	48	4	0	2	39	4	0	2	39	6	0	2	45	Y	111	0.043	0
-Contig59_chr15_22138344_22138535	120	G	C	142.0	chr15	22138470	C	11	0	2	60	10	0	2	57	18	0	2	81	4	0	2	39	10	0	2	57	15	0	2	72	N	8	2.553	0
-Contig112_chr15_26772864_26773267	374	C	T	21.6	chr15	26773244	C	4	0	2	39	4	0	2	39	5	0	2	42	2	0	2	33	4	0	2	39	3	0	2	36	N	18	+99.	0
-Contig24_chr15_26894765_26895003	155	G	A	87.6	chr15	-1	N	6	0	2	45	5	0	2	42	7	0	2	48	4	0	2	39	4	0	2	39	2	0	2	33	N	-1	0.178	0
-Contig2_chr15_33944796_33947182	1860	G	A	99.5	chr15	33946654	G	10	0	2	57	11	0	2	60	16	0	2	75	14	0	2	69	14	0	2	69	16	0	2	75	Y	16	0.252	0
-Contig73_chr15_34690052_34691332	714	T	C	130.0	chr15	34690769	T	7	0	2	48	7	0	2	48	17	0	2	78	9	0	2	54	9	0	2	54	4	0	2	39	Y	7	6.003	0
-Contig68_chr15_37747190_37747426	126	G	A	130.0	chr15	37747331	G	14	0	2	69	14	0	2	69	11	0	2	63	19	0	2	84	13	0	2	66	21	0	2	90	N	229	0.255	0
-Contig35_chr15_41400484_41400672	160	A	C	143.0	chr15	-1	N	1	0	2	30	2	0	2	33	0	0	-1	0	2	0	2	33	3	0	2	36	2	0	2	33	N	-1	+99.	0
-Contig104_chr15_45106954_45107158	70	A	T	64.4	chr15	45107015	A	6	0	2	45	6	0	2	45	19	0	2	84	7	0	2	48	7	0	2	48	3	0	2	36	N	202	4.319	0
-Contig119_chr16_6160274_6160477	180	G	A	54.8	chr16	6160457	G	7	0	2	48	6	0	2	45	12	0	2	63	3	0	2	36	11	0	2	60	10	0	2	57	N	42	+99.	0
-Contig126_chr16_10611887_10612152	150	G	T	145.0	chr16	10612037	G	14	0	2	69	9	0	2	54	11	0	2	63	8	0	2	51	8	0	2	51	11	0	2	60	N	15	0.104	6
-Contig114_chr16_12565220_12565676	10	G	A	134.0	chr16	12565230	G	0	0	-1	0	2	0	2	33	2	0	2	33	0	0	-1	0	1	0	2	30	1	0	2	30	N	333	+99.	0
-Contig43_chr16_20200090_20200514	70	A	G	58.6	chr16	20200154	A	11	0	2	60	15	0	2	72	15	0	2	72	6	0	2	45	9	0	2	54	12	0	2	63	Y	2	0.466	1
-Contig60_chr16_28079136_28080263	588	T	G	157.0	chr16	28079739	T	22	0	2	93	20	0	2	87	22	0	2	93	17	0	2	78	12	0	2	63	10	0	2	57	Y	105	5.999	1
-Contig70_chr16_33758668_33759655	104	A	T	58.1	chr16	33758772	A	6	0	2	45	7	0	2	48	17	0	2	78	14	0	2	69	8	0	2	51	10	0	2	57	N	54	0.162	0
-Contig66_chr16_37935682_37935831	116	T	C	99.2	chr16	37935802	C	12	0	2	63	6	0	2	45	19	0	2	84	12	0	2	63	13	0	2	66	17	0	2	78	N	266	+99.	2
-Contig16_chr16_40451506_40451643	84	A	G	59.8	chr16	40451592	A	7	0	2	48	5	0	2	42	7	0	2	48	13	0	2	66	14	0	2	69	19	0	2	84	N	45	5.061	0
-Contig53_chr16_49888293_49888587	260	G	A	108.0	chr16	49888550	A	4	0	2	39	1	0	2	30	3	0	2	36	5	0	2	42	2	0	2	33	2	0	2	33	Y	9	0.261	1
-Contig31_chr17_12128267_12129637	205	G	A	90.5	chr17	12128484	G	7	0	2	48	6	0	2	45	6	0	2	45	11	0	2	60	7	0	2	48	4	0	2	39	Y	10	0.246	0
-Contig50_chr17_12247973_12249183	889	G	T	47.6	chr17	12248878	G	0	1	2	9	8	0	2	51	9	2	2	21	7	2	2	21	15	0	2	72	0	3	0	9	Y	1	1.181	0
-Contig1_chr17_12979232_12980380	808	G	T	12.3	chr17	12980028	G	18	0	2	81	12	0	2	63	21	0	2	90	13	0	2	66	22	0	2	93	18	0	2	81	Y	9	0.336	1
-Contig63_chr17_14186372_14186928	54	C	T	70.7	chr17	14186427	C	6	0	2	45	2	0	2	33	5	0	2	42	6	0	2	45	3	0	2	36	3	0	2	36	Y	11	0.560	3
-Contig42_chr17_23434859_23438330	2100	C	T	39.5	chr17	23436985	T	4	0	2	39	7	0	2	48	7	0	2	48	3	0	2	36	6	0	2	45	2	0	2	33	Y	25	0.344	0
-Contig63_chr17_23796320_23796814	220	A	G	54.0	chr17	23796536	G	6	0	2	45	4	0	2	39	5	0	2	42	6	0	2	45	4	0	2	39	6	0	2	45	Y	139	0.067	1
-Contig76_chr17_24107434_24107834	316	T	C	141.0	chr17	24107726	T	19	0	2	84	15	0	2	72	20	0	2	87	16	0	2	75	11	0	2	60	18	0	2	81	Y	30	0.175	2
-Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
-Contig59_chr17_26790302_26795045	287	C	T	45.1	chr17	26790582	C	8	0	2	51	6	0	2	45	13	0	2	66	6	0	2	45	15	0	2	72	12	0	2	63	Y	75	0.019	1
-Contig99_chr17_27018324_27019378	446	G	A	31.1	chr17	27018776	G	14	0	2	69	12	0	2	63	14	0	2	69	10	0	2	57	9	0	2	54	11	0	2	60	Y	13	0.290	4
-Contig125_chr17_27739115_27739410	63	G	A	107.0	chr17	27739177	G	8	0	2	51	11	0	2	60	16	0	2	75	8	0	2	51	4	0	2	39	15	0	2	72	N	100	0.819	0
-Contig115_chr17_37489899_37490101	159	G	A	62.4	chr17	37490067	G	4	0	2	39	3	0	2	36	4	0	2	39	4	0	2	39	3	0	2	36	6	0	2	45	N	4	1.411	1
-Contig180_chr17_45154356_45154925	524	A	G	146.0	chr17	45154886	G	7	0	2	48	9	0	2	54	7	0	2	48	9	0	2	54	4	0	2	39	8	0	2	51	Y	11	+99.	2
-Contig61_chr17_48221795_48223545	1404	T	A	177.0	chr17	48223216	T	15	0	2	72	14	0	2	69	24	0	2	99	17	0	2	78	18	0	2	81	24	0	2	99	Y	161	0.633	2
-Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
-Contig229_chr18_3706523_3708577	1076	A	G	83.9	chr18	3707630	A	11	0	2	60	13	0	2	66	26	0	2	105	11	0	2	60	15	0	2	72	17	0	2	78	Y	63	0.445	0
-Contig24_chr18_14049894_14050480	24	A	G	123.0	chr18	14049918	A	5	0	2	42	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	5	0	2	42	Y	17	+99.	0
-Contig30_chr18_18771753_18772121	39	C	G	48.5	chr18	18771787	C	2	0	2	33	5	0	2	42	2	0	2	33	6	0	2	45	3	0	2	36	2	0	2	33	N	5	0.135	0
-Contig123_chr18_19916160_19916379	116	G	A	79.2	chr18	19916272	A	14	0	2	69	12	0	2	63	14	0	2	69	6	0	2	45	11	0	2	60	10	0	2	57	N	26	0.172	0
-Contig82_chr18_27305489_27306229	566	C	T	49.5	chr18	27306051	A	6	0	2	45	6	0	2	45	10	0	2	57	11	0	2	60	6	0	2	45	7	0	2	48	N	1	0.349	0
-Contig71_chr18_34324706_34326687	136	G	A	151.0	chr18	34324841	G	9	0	2	54	9	0	2	54	17	0	2	78	8	0	2	51	11	0	2	60	10	0	2	57	Y	2	2.129	2
-Contig16_chr18_34672093_34673044	538	T	C	58.2	chr18	34672635	T	8	0	2	51	15	0	2	72	16	0	2	75	15	0	2	72	9	0	2	57	18	0	2	81	Y	8	0.214	1
-Contig96_chr18_38492535_38493333	624	G	A	119.0	chr18	38493162	T	17	0	2	78	12	0	2	63	13	0	2	66	16	0	2	75	8	0	2	51	15	0	2	72	Y	127	0.131	0
-Contig226_chr18_47753756_47754666	427	T	C	21.1	chr18	47754215	T	10	0	2	57	4	0	2	39	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	42	0.522	0
-Contig170_chr18_49411558_49412230	94	C	A	74.3	chr18	49411655	C	14	0	2	69	10	0	2	57	9	0	2	54	10	0	2	57	3	0	2	36	3	0	2	36	N	9	1.457	0
-Contig192_chr18_49419342_49420737	1058	C	T	42.8	chr18	49420381	A	3	0	2	36	4	0	2	39	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	Y	34	2.107	2
-Contig64_chr18_55979770_55980315	49	G	A	89.1	chr18	55979824	G	3	0	2	36	9	0	2	54	7	0	2	51	4	0	2	39	3	0	2	36	3	0	2	36	Y	-1	2.124	0
-Contig20_chr18_58130301_58130735	112	A	G	74.4	chr18	58130413	A	12	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	6	0	2	45	6	0	2	45	Y	10	0.290	0
-Contig146_chr19_5221790_5223013	143	A	G	114.0	chr19	5221916	-	1	0	2	30	4	0	2	39	3	0	2	36	5	0	2	42	2	0	2	33	5	0	2	42	Y	12	0.870	0
-Contig13_chr19_7739961_7740118	26	C	G	220.0	chr19	-1	N	3	0	2	36	1	0	2	30	2	0	2	33	3	0	2	36	1	0	2	30	2	0	2	33	N	-1	+99.	0
-Contig67_chr19_12398520_12399367	499	C	T	161.0	chr19	12399017	C	10	0	2	57	11	0	2	60	20	0	2	87	14	0	2	69	24	0	2	99	8	0	2	51	Y	137	5.634	0
-Contig66_chr19_16285672_16287223	996	C	T	190.0	chr19	16286674	C	9	0	2	57	14	0	2	69	16	0	2	78	17	0	2	78	8	0	2	51	22	0	2	93	Y	40	0.110	0
-Contig129_chr19_25541958_25542221	202	T	C	68.1	chr19	25542154	C	11	0	2	60	19	0	2	84	10	0	2	60	17	0	2	78	9	0	2	54	12	0	2	63	N	-1	2.551	1
-Contig152_chr19_34274440_34275622	1072	C	T	48.0	chr19	34275509	T	1	0	2	30	2	0	2	33	1	0	2	30	1	0	2	30	4	0	2	39	5	0	2	42	N	71	0.309	0
-Contig29_chr19_37339947_37341911	1692	C	T	211.0	chr19	37341631	C	15	0	2	72	20	0	2	87	11	0	2	60	15	0	2	72	3	0	2	36	12	0	2	63	Y	7	0.096	0
-Contig39_chr19_47709708_47711327	444	C	T	36.8	chr19	47710148	T	10	0	2	57	4	0	2	39	8	0	2	51	9	0	2	54	6	0	2	45	6	0	2	45	Y	95	1.251	1
-Contig60_chr19_54013816_54014398	281	A	G	138.0	chr19	54014103	C	6	0	2	45	15	0	2	72	7	0	2	48	10	0	2	57	15	0	2	72	10	0	2	57	Y	188	1.271	0
-Contig251_chr19_56559098_56559626	452	T	C	3.36	chr19	56559549	T	12	0	2	63	13	0	2	66	21	0	2	90	15	0	2	72	14	0	2	69	11	0	2	60	N	1	0.117	0
-Contig50_chr20_12138509_12141975	3206	C	A	248.0	chr20	12141763	C	8	0	2	51	15	0	2	72	14	0	2	69	6	0	2	45	10	0	2	57	7	0	2	48	Y	2	0.384	0
-Contig36_chr20_32631363_32632049	176	G	A	24.1	chr20	32631526	G	7	0	2	48	14	0	2	69	19	0	2	84	14	0	2	69	15	0	2	72	16	0	2	75	N	50	1.150	0
-Contig39_chr20_36316398_36316498	57	C	T	30.3	chr20	36316455	C	2	0	2	33	0	1	2	8	0	0	-1	0	0	1	2	10	0	0	-1	0	0	0	-1	0	N	-483	+99.	0
-Contig32_chr20_36468058_36468869	66	C	T	40.4	chr20	36468127	C	6	0	2	45	3	0	2	36	4	0	2	39	5	0	2	42	3	0	2	36	4	0	2	39	N	59	0.281	0
-Contig24_chr20_38203888_38204900	834	C	T	132.0	chr20	38204731	C	9	0	2	54	17	0	2	78	20	0	2	87	8	0	2	51	11	0	2	60	17	0	2	78	Y	14	0.397	0
-Contig79_chr20_44263127_44264103	456	G	T	31.5	chr20	44263573	G	22	0	2	93	16	0	2	75	15	0	2	72	19	0	2	84	13	0	2	66	26	0	2	105	Y	8	3.250	0
-Contig26_chr20_45878482_45878787	197	A	G	160.0	chr20	45878672	A	17	0	2	78	15	0	2	72	11	0	2	63	17	0	2	78	12	0	2	63	10	0	2	57	N	14	0.535	0
-Contig119_chr20_46550670_46551383	609	G	A	139.0	chr20	46551277	G	7	0	2	48	17	0	2	78	19	0	2	84	20	0	2	87	9	0	2	54	15	0	2	72	Y	7	0.488	1
-Contig50_chr21_4178523_4178687	121	G	A	362.0	chr21	4178640	G	8	0	2	51	14	0	2	69	5	0	2	42	3	0	2	36	11	0	2	60	4	0	2	39	N	392	0.483	0
-Contig103_chr21_10177255_10177765	121	G	A	125.0	chr21	10177367	G	12	0	2	63	10	0	2	57	10	0	2	57	17	0	2	78	14	0	2	69	7	0	2	51	Y	37	0.213	3
-Contig1_chr21_10805534_10806399	766	A	G	146.0	chr21	10806301	G	10	0	2	57	6	0	2	45	9	0	2	54	6	0	2	45	7	0	2	48	5	0	2	42	Y	20	0.319	0
-Contig46_chr21_21029492_21030645	443	C	T	5.37	chr21	21029910	C	15	0	2	72	11	0	2	60	16	0	2	75	15	0	2	72	13	0	2	66	6	0	2	45	Y	96	3.737	0
-Contig129_chr21_31045749_31046924	381	A	G	129.0	chr21	31046141	A	19	0	2	84	8	0	2	51	23	0	2	96	12	0	2	63	15	0	2	72	18	0	2	81	Y	69	0.028	2
-Contig23_chr21_31651123_31651986	840	C	T	71.3	chr21	31651957	T	6	0	2	45	9	0	2	54	8	0	2	51	10	0	2	57	4	0	2	39	7	0	2	48	Y	105	2.977	3
-Contig64_chr21_43341847_43342031	84	T	C	114.0	chr21	43341926	T	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	6	0	2	45	7	0	2	48	N	10	3.954	2
-Contig60_chr21_43475347_43475824	175	C	T	8.05	chr21	43475551	T	6	0	2	45	7	0	2	48	13	0	2	66	6	0	2	45	14	0	2	69	14	0	2	69	N	45	0.058	0
-Contig64_chr21_45377513_45377872	19	C	T	60.7	chr21	-1	N	3	0	2	36	2	0	2	33	1	0	2	30	0	0	-1	0	3	0	2	36	1	0	2	30	N	-1	+99.	1
-Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0
-Contig46_chr22_9416920_9417467	381	G	A	145.0	chr22	9417259	G	10	0	2	57	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	7	0	2	48	Y	154	0.242	0
-Contig86_chr22_9440787_9441725	713	T	G	119.0	chr22	9441488	G	6	0	2	45	12	0	2	63	10	0	2	57	11	0	2	60	13	0	2	66	16	0	2	75	Y	132	0.218	0
-Contig16_chr22_15636960_15637372	236	A	C	9.79	chr22	15637192	T	4	0	2	39	5	0	2	42	12	0	2	63	7	0	2	48	6	0	2	45	11	0	2	60	Y	5	2.163	0
-Contig4_chr22_16114310_16114546	128	G	C	101.0	chr22	16114432	G	10	0	2	57	13	0	2	66	20	0	2	87	20	0	2	87	16	0	2	75	9	0	2	54	N	19	0.526	0
-Contig23_chr22_34612023_34612568	167	C	G	92.3	chr22	34612181	C	11	0	2	60	18	0	2	81	13	0	2	66	8	0	2	51	12	0	2	63	14	0	2	69	Y	7	0.409	0
-Contig4_chr22_38252245_38253712	799	A	C	159.0	chr22	38253064	A	18	0	2	81	15	0	2	72	15	0	2	72	20	0	2	87	27	0	2	108	15	0	2	72	Y	90	4.330	0
-Contig122_chr22_48412466_48414788	1888	C	T	125.0	chr22	48414355	T	16	0	2	75	15	0	2	72	16	0	2	75	14	0	2	72	12	0	2	63	7	0	2	48	N	42	0.122	0
-Contig77_chr22_49764414_49764875	353	C	A	148.0	chr22	49764777	C	7	4	1	65	18	0	2	81	16	0	2	75	20	0	2	87	4	3	1	52	9	4	1	67	Y	12	0.941	0
-Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
-Contig348_chr22_62406104_62406495	189	C	A	134.0	chr22	62406302	A	9	0	2	54	14	0	2	69	11	0	2	60	10	0	2	57	12	0	2	63	6	0	2	45	Y	5	0.912	0
-Contig133_chr23_3525134_3526502	1223	A	G	201.0	chr23	3526387	A	11	0	2	60	13	0	2	66	23	0	2	96	21	0	2	90	13	0	2	66	10	0	2	57	Y	61	1.359	0
-Contig111_chr23_7058063_7058181	107	G	A	108.0	chr23	7058162	A	8	0	2	51	8	0	2	51	7	0	2	48	2	0	2	33	5	0	2	42	6	0	2	45	N	3	+99.	0
-Contig79_chr23_7844129_7844837	110	C	A	141.0	chr23	7844237	T	13	0	2	66	15	0	2	72	17	0	2	78	12	0	2	63	15	0	2	72	16	0	2	75	Y	40	0.339	0
-Contig38_chr23_9201002_9201725	597	C	T	155.0	chr23	9201609	T	17	0	2	78	8	0	2	51	13	0	2	66	5	0	2	42	11	0	2	60	7	0	2	48	Y	167	0.633	1
-Contig33_chr23_20672540_20674320	347	T	A	91.4	chr23	20672885	A	11	0	2	60	14	0	2	69	15	0	2	72	7	0	2	48	12	0	2	63	18	0	2	81	Y	31	0.452	1
-Contig35_chr23_28447813_28449115	70	T	A	21.3	chr23	28447881	T	9	0	2	54	8	0	2	51	10	0	2	57	9	0	2	54	10	0	2	57	12	0	2	63	N	251	0.163	1
-Contig51_chr23_30590939_30591162	140	C	T	142.0	chr23	30591080	C	14	0	2	69	4	0	2	39	10	0	2	57	12	0	2	63	14	0	2	69	4	0	2	39	N	13	1.658	0
-Contig57_chr23_32216351_32216721	179	T	G	143.0	chr23	32216534	T	15	0	2	72	15	0	2	72	23	0	2	96	13	0	2	66	16	0	2	75	15	0	2	72	N	32	1.387	1
-Contig93_chr23_35744841_35745791	40	A	T	30.4	chr23	35744880	T	6	0	2	45	7	0	2	48	7	0	2	48	2	0	2	33	5	0	2	42	5	0	2	42	Y	50	2.173	0
-Contig99_chr23_42543966_42544147	14	G	A	357.0	chr23	42543980	G	4	0	2	39	2	0	2	33	3	0	2	36	3	0	2	36	1	0	2	30	2	0	2	33	N	69	+99.	0
-Contig32_chr23_48285289_48286638	186	T	C	176.0	chr23	48285470	T	18	0	2	81	12	0	2	63	16	0	2	75	13	0	2	66	9	0	2	54	9	0	2	54	Y	4	4.238	1
-Contig50_chr24_22515247_22516072	761	C	T	243.0	chr24	22515981	T	11	0	2	60	10	0	2	57	8	0	2	51	9	0	2	54	18	0	2	81	8	0	2	51	Y	1	0.190	0
-Contig92_chr24_28935897_28936321	13	G	A	47.1	chr24	-1	N	2	0	2	33	1	0	2	30	0	0	-1	0	0	0	-1	0	1	0	2	30	0	0	-1	0	Y	-1	+99.	2
-Contig84_chr24_29196623_29199644	466	C	T	126.0	chr24	29197091	T	7	0	2	48	11	0	2	60	8	0	2	51	7	0	2	48	11	0	2	60	15	0	2	72	Y	42	0.215	0
-Contig35_chr24_30150986_30151507	492	A	C	114.0	chr24	30151448	A	5	0	2	42	2	0	2	33	2	0	2	33	3	0	2	36	3	0	2	36	5	0	2	42	N	41	2.587	6
-Contig61_chr24_30465488_30465834	149	G	T	68.2	chr24	30465637	G	13	0	2	66	4	2	2	11	18	0	2	81	11	0	2	60	11	0	2	60	9	0	2	54	N	99	0.105	2
-Contig145_chr24_34778364_34778898	163	T	C	372.0	chr24	34778541	C	10	0	2	57	8	0	2	51	12	0	2	63	12	0	2	63	6	1	2	31	7	0	2	48	Y	40	0.037	0
-Contig34_chr24_36147443_36150244	2679	C	T	140.0	chr24	36150125	C	13	0	2	66	7	0	2	48	14	0	2	69	14	0	2	69	10	0	2	57	13	0	2	66	N	282	0.099	1
-Contig164_chr24_46598127_46599206	84	C	T	105.0	chr24	46598214	C	13	0	2	66	12	0	2	63	15	0	2	72	15	0	2	72	11	0	2	60	8	0	2	51	Y	22	1.262	1
-Contig144_chr25_4011170_4013134	541	A	G	160.0	chr25	4011690	A	12	0	2	63	17	0	2	78	13	0	2	66	13	0	2	66	13	0	2	66	13	0	2	66	Y	5	0.087	0
-Contig81_chr25_6103472_6104760	699	G	A	378.0	chr25	6104190	A	14	0	2	69	16	0	2	75	13	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	Y	33	0.789	2
-Contig152_chr25_7486442_7487609	75	A	G	11.6	chr25	7486515	A	17	0	2	78	13	0	2	66	8	0	2	51	16	0	2	75	8	0	2	51	6	0	2	45	N	2	0.158	0
-Contig24_chr25_7695778_7698612	2714	C	T	130.0	chr25	7698446	C	16	0	2	75	13	0	2	66	22	0	2	93	17	0	2	78	10	0	2	57	17	0	2	78	Y	27	0.346	0
-Contig89_chr25_8635170_8636009	586	G	C	209.0	chr25	8635744	G	13	0	2	66	13	0	2	66	21	0	2	93	14	0	2	69	15	0	2	72	15	0	2	72	Y	14	0.067	0
-Contig77_chr25_10796299_10796481	2	T	C	17.3	chr25	-1	N	1	0	2	30	0	0	-1	0	1	0	2	30	0	0	-1	0	0	0	-1	0	0	0	-1	0	N	-1	+99.	0
-Contig73_chr25_14177327_14177474	125	A	C	6.85	chr25	14177464	A	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	N	27	+99.	1
-Contig59_chr25_18196776_18197707	785	G	A	112.0	chr25	18197551	G	8	10	1	42	27	0	2	108	21	0	2	90	18	0	2	81	10	0	2	57	14	0	2	69	N	36	3.625	0
-Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
-Contig84_chr25_42407960_42408708	55	C	T	119.0	chr25	42408013	C	6	0	2	45	9	0	2	54	11	0	2	60	9	0	2	54	7	0	2	48	8	0	2	51	Y	11	0.121	0
-Contig73_chr25_43562500_43564110	955	T	C	52.1	chr25	43563469	C	9	0	2	57	4	0	2	39	6	0	2	45	5	0	2	42	7	0	2	48	10	0	2	57	Y	4	1.406	0
-Contig37_chr25_51074433_51074885	170	A	G	102.0	chr25	51074589	G	11	0	2	60	7	0	2	48	6	0	2	45	15	0	2	72	9	0	2	54	7	0	2	48	Y	68	0.207	1
-Contig204_chr26_4311195_4311778	170	C	T	16.9	chr26	4311363	T	20	0	2	87	8	0	2	51	13	0	2	66	18	0	2	81	11	0	2	60	14	0	2	69	N	35	0.085	0
-Contig122_chr26_7622321_7623491	106	C	G	139.0	chr26	7622423	C	3	0	2	36	9	0	2	54	10	0	2	57	12	0	2	63	9	0	2	54	5	0	2	42	N	19	0.458	0
-Contig11_chr26_11062142_11062902	707	C	A	108.0	chr26	11062836	T	7	0	2	48	8	0	2	51	16	0	2	75	10	0	2	57	6	0	2	45	14	0	2	69	Y	-1	4.709	0
-Contig133_chr26_17695661_17696368	39	T	G	98.7	chr26	17695700	T	10	0	2	57	3	0	2	36	11	0	2	60	9	0	2	54	2	0	2	33	1	0	2	30	N	85	3.402	0
-Contig157_chr26_23894107_23895229	25	C	T	50.2	chr26	23894140	C	0	0	-1	0	4	0	2	39	2	0	2	33	4	0	2	39	3	0	2	36	3	0	2	36	Y	51	+99.	0
-Contig146_chr26_26622638_26623906	574	G	A	186.0	chr26	26623219	A	11	0	2	60	12	0	2	63	9	0	2	54	11	0	2	60	9	0	2	54	12	0	2	63	Y	1	0.318	0
-Contig8_chr26_27834126_27834326	140	G	A	41.7	chr26	27834268	G	13	0	2	66	7	0	2	48	13	0	2	66	11	0	2	60	12	0	2	63	6	0	2	45	N	29	0.142	1
-Contig78_chr26_31128839_31129005	123	T	C	145.0	chr26	-1	N	11	0	2	60	3	0	2	36	7	0	2	48	8	0	2	51	10	0	2	46	7	0	2	48	N	-1	1.230	1
-Contig28_chr26_32935355_32935833	289	T	C	77.9	chr26	32935638	T	15	0	2	72	22	0	2	93	15	0	2	72	9	0	2	54	15	0	2	72	17	0	2	78	Y	10	2.258	1
-Contig36_chr26_36606876_36607240	115	A	T	139.0	chr26	36606979	A	1	0	2	30	7	0	2	48	14	0	2	69	13	0	2	66	9	0	2	54	3	0	2	36	Y	8	0.071	0
-Contig135_chr27_6853874_6854079	158	C	T	116.0	chr27	6854032	T	18	0	2	81	19	0	2	84	13	0	2	66	7	0	2	48	8	0	2	51	11	0	2	60	N	4	0.060	1
-Contig47_chr27_11777710_11777915	25	A	G	67.3	chr27	11777731	A	3	0	2	36	5	0	2	42	6	0	2	45	10	0	2	57	9	0	2	54	6	0	2	45	N	97	+99.	0
-Contig23_chr27_14633002_14633153	23	G	A	128.0	chr27	14633023	A	3	0	2	36	4	0	2	39	5	0	2	42	5	0	2	42	3	0	2	36	2	0	2	33	N	240	3.881	0
-Contig31_chr27_14987233_14988055	630	A	G	48.5	chr27	14987850	G	10	0	2	57	2	0	2	33	4	0	2	39	4	0	2	39	1	0	2	30	4	0	2	39	Y	9	0.089	1
-Contig29_chr27_15428166_15429413	380	T	C	140.0	chr27	15428539	T	15	0	2	72	15	0	2	72	17	0	2	78	15	0	2	72	15	0	2	72	15	0	2	72	Y	47	0.916	1
-Contig31_chr27_19519489_19520891	129	G	T	14.9	chr27	19519624	T	12	0	2	63	19	0	2	84	20	0	2	87	16	0	2	75	10	0	2	57	11	0	2	60	Y	48	2.756	0
-Contig64_chr27_34654435_34654621	132	C	A	115.0	chr27	34654567	T	2	0	2	33	2	0	2	33	5	0	2	42	3	0	2	36	3	0	2	36	8	0	2	51	N	12	0.297	1
-Contig35_chr27_40596169_40596445	20	G	C	133.0	chr27	40596189	G	8	0	2	51	3	0	2	36	4	0	2	39	2	0	2	33	4	0	2	39	4	0	2	39	Y	4	+99.	1
-Contig85_chr27_45471750_45472022	211	G	A	53.1	chr27	45471964	G	18	0	2	81	10	0	2	57	15	0	2	72	0	13	0	36	16	0	2	75	14	0	2	69	N	75	2.502	1
-Contig131_chr28_6481806_6483783	138	C	T	36.2	chr28	6481953	C	12	0	2	63	12	0	2	63	20	0	2	87	11	0	2	60	10	0	2	57	12	0	2	63	Y	10	0.387	0
-Contig141_chr28_10027332_10028242	780	T	G	74.8	chr28	10028095	T	10	0	2	57	11	0	2	60	14	0	2	69	10	0	2	57	7	0	2	48	9	0	2	54	Y	19	3.348	0
-Contig144_chr28_15468203_15470548	743	G	A	20.0	chr28	15468942	G	13	0	2	66	12	0	2	63	10	0	2	57	11	0	2	60	16	0	2	75	7	0	2	48	N	14	0.053	0
-Contig47_chr28_21311718_21312366	541	G	A	116.0	chr28	21312258	G	9	0	2	54	6	0	2	45	12	0	2	63	6	0	2	45	5	0	2	45	12	0	2	63	N	9	0.240	0
-Contig60_chr28_30197166_30197364	92	T	C	164.0	chr28	30197258	T	10	0	2	57	13	0	2	66	15	0	2	72	16	0	2	75	12	0	2	63	11	0	2	60	N	369	1.139	0
-Contig201_chr28_36339953_36341322	260	C	T	6.36	chr28	36340213	T	4	0	2	39	0	0	-1	0	2	0	2	33	2	0	2	33	3	0	2	36	4	0	2	39	N	4	0.183	0
-Contig175_chr28_36441165_36441915	68	T	C	3.83	chr28	36441234	T	4	4	1	15	6	0	2	45	12	0	2	63	15	0	2	72	6	0	2	45	9	0	2	54	N	4	1.610	2
-Contig29_chr29_4726399_4727143	559	A	T	163.0	chr29	4726955	A	15	0	2	72	18	0	2	81	18	0	2	81	16	0	2	75	11	0	2	60	14	0	2	72	Y	161	3.114	0
-Contig48_chr29_13129286_13130137	232	A	G	92.2	chr29	13129514	G	13	0	2	66	11	0	2	60	19	0	2	84	16	0	2	75	11	0	2	60	17	0	2	78	Y	337	2.581	1
-Contig64_chr29_15736891_15737257	344	T	C	40.4	chr29	15737233	C	1	0	2	30	0	0	-1	0	0	0	-1	0	2	0	2	33	0	0	-1	0	0	0	-1	0	N	58	+99.	0
-Contig33_chr29_17000374_17000921	71	C	T	48.6	chr29	17000441	-	4	0	2	39	9	0	2	54	12	0	2	66	10	0	2	57	7	0	2	48	4	0	2	39	N	26	5.491	0
-Contig34_chr29_17581796_17584016	2105	C	T	126.0	chr29	17583890	T	14	0	2	69	11	0	2	60	18	0	2	81	12	0	2	63	10	0	2	57	10	0	2	57	Y	22	2.208	0
-Contig19_chr29_20976080_20977761	1007	G	A	115.0	chr29	20977076	G	19	0	2	84	22	0	2	93	22	0	2	93	22	0	2	93	11	0	2	60	13	0	2	66	Y	4	1.915	0
-Contig51_chr29_21149853_21150467	266	C	T	146.0	chr29	21150118	C	12	0	2	63	12	0	2	63	23	0	2	96	14	0	2	69	13	0	2	66	10	0	2	57	Y	4	0.051	0
-Contig1_chr30_5992217_5993068	106	C	T	129.0	chr30	5992319	C	10	0	2	57	11	0	2	60	7	0	2	48	11	0	2	60	10	0	2	57	12	0	2	63	Y	76	1.079	0
-Contig1_chr30_8232878_8233406	402	C	T	127.0	chr30	8233264	C	8	0	2	51	19	0	2	84	16	0	2	75	18	0	2	81	10	0	2	57	14	0	2	69	Y	358	5.283	0
-Contig108_chr30_9436961_9437520	546	C	T	39.8	chr30	9437502	C	7	0	2	48	5	0	2	42	2	0	2	33	7	0	2	48	5	0	2	42	7	0	2	48	Y	64	+99.	0
-Contig165_chr30_25804389_25804926	190	T	C	126.0	chr30	25804592	C	3	0	2	36	8	0	2	51	7	0	2	48	10	0	2	57	7	0	2	48	4	0	2	39	Y	113	0.329	0
-Contig193_chr30_27495616_27496125	434	C	A	234.0	chr30	27496024	C	13	0	2	66	16	0	2	75	25	0	2	102	16	0	2	75	13	0	2	66	14	0	2	69	Y	76	2.621	0
-Contig114_chr30_33636712_33637208	34	C	T	142.0	chr30	33636744	C	7	0	2	48	4	1	2	20	6	0	2	45	6	0	2	45	3	4	1	29	5	0	2	42	Y	14	8.028	0
-Contig38_chr31_5164423_5166573	2074	C	T	134.0	chr31	5166501	T	13	0	2	66	10	0	2	57	17	0	2	78	11	0	2	60	17	0	2	78	10	0	2	57	Y	58	+99.	0
-Contig6_chr31_9649308_9650149	431	G	T	162.0	chr31	9649742	G	31	0	2	120	23	0	2	96	17	0	2	78	17	0	2	78	10	0	2	57	16	0	2	75	Y	98	2.200	0
-Contig85_chr31_12242872_12245082	38	G	C	92.4	chr31	12242910	G	1	0	2	30	6	0	2	45	9	0	2	54	8	0	2	51	5	0	2	42	9	0	2	54	N	2	2.340	0
-Contig7_chr31_12384974_12386400	305	C	T	69.6	chr31	12385267	C	6	0	2	45	10	0	2	57	11	0	2	60	11	0	2	60	9	0	2	54	12	0	2	63	Y	44	1.165	0
-Contig90_chr31_17267583_17267778	81	C	A	143.0	chr31	17267665	C	20	0	2	87	6	0	2	45	14	0	2	72	22	0	2	93	17	0	2	78	15	0	2	72	N	7	0.565	0
-Contig68_chr31_20000241_20000597	215	C	T	131.0	chr31	20000454	T	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	0	0	-1	0	Y	5	3.383	1
-Contig137_chr31_23357653_23358568	885	G	A	119.0	chr31	23358545	G	5	0	2	42	3	0	2	36	3	0	2	36	2	0	2	33	3	0	2	36	4	0	2	39	Y	11	+99.	0
-Contig17_chr31_26433828_26434459	498	T	C	9.79	chr31	26434322	T	18	0	2	81	10	0	2	57	15	0	2	72	13	0	2	66	16	0	2	75	15	0	2	72	Y	137	4.814	0
-Contig9_chr32_19479532_19479735	12	A	G	20.7	chr32	19479544	A	1	0	2	30	2	0	2	33	1	0	2	30	5	0	2	42	3	0	2	36	3	0	2	36	N	17	+99.	0
-Contig30_chr32_25902721_25905783	208	C	G	162.0	chr32	25902927	G	11	0	2	60	13	0	2	66	11	0	2	60	12	0	2	63	7	0	2	48	11	0	2	60	Y	145	0.322	2
-Contig7_chr32_27789513_27789926	20	G	A	7.19	chr32	27789530	A	0	0	-1	0	4	0	2	39	4	0	2	39	4	0	2	39	2	0	2	33	6	0	2	45	Y	14	+99.	0
-Contig42_chr32_38900713_38901320	320	A	G	134.0	chr32	38901021	T	12	0	2	63	10	0	2	57	9	11	1	104	5	0	2	42	19	0	2	84	7	6	1	56	Y	71	0.165	0
-Contig18_chr33_22207246_22209159	1363	G	T	51.5	chr33	22208619	-	16	0	2	75	8	0	2	51	11	0	2	60	10	0	2	57	15	0	2	72	12	0	2	63	Y	59	2.560	0
-Contig104_chr33_22483642_22484187	424	C	T	140.0	chr33	22484054	T	13	0	2	66	16	0	2	75	9	0	2	54	15	0	2	72	13	0	2	66	10	0	2	57	Y	36	0.404	0
-Contig170_chr33_26189421_26189940	292	T	C	98.4	chr33	26189703	T	21	0	2	90	13	0	2	66	15	0	2	72	13	0	2	66	19	0	2	84	13	0	2	66	Y	23	0.307	0
-Contig113_chr34_13341080_13341643	236	C	T	90.7	chr34	13341316	C	4	0	2	39	2	0	2	33	8	0	2	51	4	0	2	39	8	0	2	51	3	0	2	36	Y	47	0.412	3
-Contig405_chr34_14415672_14415979	59	A	G	36.2	chr34	14415731	G	8	0	2	51	2	0	2	33	8	0	2	51	6	0	2	48	3	0	2	36	7	0	2	48	Y	45	0.405	1
-Contig21_chr34_16422980_16425681	2009	G	A	19.4	chr34	16424960	G	0	0	-1	0	0	0	-1	0	0	0	-1	0	5	0	2	42	0	0	-1	0	0	0	-1	0	Y	28	0.196	0
-Contig41_chr34_16544482_16545449	46	T	C	102.0	chr34	16544523	T	5	0	2	42	11	0	2	60	6	0	2	45	0	2	0	3	7	0	2	48	8	0	2	51	Y	215	1.156	0
-Contig8_chr34_18474513_18475673	1122	C	A	129.0	chr34	18475628	A	8	0	2	51	15	0	2	72	13	0	2	66	17	0	2	78	13	0	2	66	6	0	2	45	Y	61	0.123	2
-Contig152_chr34_31794848_31795540	242	G	A	93.2	chr34	31795093	G	11	0	2	60	24	0	2	99	17	0	2	78	15	0	2	72	18	0	2	81	17	0	2	78	Y	123	2.780	0
-Contig28_chr34_41708848_41712034	1381	A	G	78.2	chr34	41710232	A	11	0	2	60	17	0	2	78	15	0	2	72	16	0	2	75	15	0	2	72	14	0	2	69	Y	236	0.234	0
-Contig85_chr34_42798284_42800584	1845	C	T	171.0	chr34	42800126	T	5	0	2	42	7	0	2	48	6	0	2	45	7	0	2	48	6	0	2	45	2	0	2	33	Y	5	2.787	0
-Contig47_chr35_3666773_3667898	348	G	T	124.0	chr35	3667121	G	9	0	2	54	20	0	2	87	18	0	2	81	15	0	2	72	12	0	2	63	14	0	2	69	Y	285	0.235	0
-Contig195_chr35_15722500_15722741	205	G	A	4.08	chr35	15722718	G	3	0	2	36	5	0	2	42	1	0	2	30	6	0	2	45	1	0	2	30	1	0	2	30	N	43	+99.	0
-Contig101_chr35_19513178_19513697	62	C	T	112.0	chr35	19513238	C	12	0	2	63	7	0	2	48	13	0	2	66	7	0	2	48	5	0	2	42	8	0	2	51	N	115	3.135	0
-Contig19_chr35_23887144_23888282	90	C	A	10.1	chr35	23887242	-	3	3	1	12	4	4	1	19	8	6	1	37	4	3	1	11	8	3	2	7	9	3	2	11	Y	105	0.199	0
-Contig47_chr35_24382042_24382526	33	G	A	87.0	chr35	24382076	G	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	4	0	2	39	2	0	2	33	Y	71	+99.	0
-Contig77_chr35_24796947_24797172	65	A	G	52.1	chr35	24797009	A	7	0	2	48	5	0	2	42	8	0	2	51	6	0	2	45	12	0	2	63	10	0	2	57	N	11	1.401	3
-Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0
-Contig5_chr36_4562983_4563634	343	C	T	151.0	chr36	4563324	T	20	0	2	87	20	0	2	87	23	0	2	96	24	0	2	99	9	0	2	54	8	0	2	51	Y	40	1.169	0
-Contig75_chr36_7885319_7885588	53	G	A	25.7	chr36	7885372	G	10	0	2	57	8	0	2	51	13	0	2	66	7	0	2	48	4	0	2	39	7	0	2	48	N	7	2.653	0
-Contig184_chr36_18956191_18958552	187	A	G	11.5	chr36	18956371	G	10	0	2	57	11	0	2	60	21	0	2	90	14	0	2	69	7	0	2	48	4	0	2	39	N	278	1.434	2
-Contig12_chr36_21557176_21557828	513	T	A	159.0	chr36	21557695	A	11	0	2	60	14	0	2	69	21	0	2	90	12	0	2	63	15	0	2	72	11	0	2	60	Y	55	0.222	0
-Contig2_chr36_22436067_22436794	653	C	T	73.0	chr36	22436730	C	11	0	2	60	16	0	2	75	13	0	2	66	11	0	2	60	21	0	2	90	21	0	2	90	Y	9	0.534	0
-Contig133_chr36_32954045_32955409	136	A	G	116.0	chr36	32954182	A	16	0	2	75	15	0	2	72	20	0	2	87	11	0	2	60	18	0	2	81	13	0	2	66	Y	74	3.772	1
-Contig53_chr37_6665763_6665919	116	C	T	111.0	chr37	6665875	C	9	0	2	54	9	0	2	54	5	0	2	42	9	0	2	54	8	0	2	51	10	0	2	57	N	15	10.875	1
-Contig42_chr37_9589176_9591269	252	G	A	25.1	chr37	9589430	G	10	0	2	40	13	0	2	66	18	0	2	81	21	0	2	90	9	0	2	54	17	0	2	78	N	67	1.170	2
-Contig2_chr37_17134963_17136513	1140	A	C	158.0	chr37	17136092	A	14	0	2	69	24	0	2	99	17	0	2	78	16	0	2	75	15	0	2	75	13	0	2	66	Y	12	0.053	1
-Contig18_chr37_17147806_17149851	291	T	G	112.0	chr37	17148084	T	4	6	1	45	16	0	2	75	17	0	2	78	14	0	2	69	22	0	2	93	13	0	2	66	Y	41	4.442	0
-Contig64_chr37_17606895_17607534	565	C	T	30.2	chr37	17607439	A	9	0	2	54	16	0	2	75	20	0	2	87	14	0	2	69	16	0	2	75	10	0	2	57	N	20	1.622	0
-Contig126_chr37_21587881_21590621	373	G	T	132.0	chr37	21588256	G	11	0	2	60	11	0	2	60	23	0	2	96	12	0	2	63	8	0	2	51	18	0	2	81	Y	12	0.549	0
-Contig2_chr37_31197993_31198256	182	C	T	39.6	chr37	31198171	T	6	0	2	45	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	12	0	2	63	N	2	0.595	0
-Contig46_chr37_31852376_31853555	825	A	G	111.0	chr37	31853191	G	19	0	2	84	14	0	2	69	15	0	2	72	7	0	2	48	8	0	2	51	16	0	2	75	Y	17	0.128	1
-Contig7_chr38_12217200_12218387	1163	A	T	44.4	chr38	12218353	A	11	0	2	60	13	0	2	66	17	0	2	78	10	0	2	57	11	0	2	60	11	0	2	60	Y	67	+99.	0
-Contig15_chr38_12282020_12282253	150	C	T	156.0	chr38	12282164	A	17	0	2	78	11	0	2	60	19	0	2	84	14	0	2	69	5	0	2	42	14	0	2	69	Y	26	2.952	1
-Contig4_chr38_14807432_14807747	275	A	G	36.5	chr38	14807715	G	1	0	2	30	2	0	2	33	2	0	2	33	4	0	2	39	1	0	2	30	0	0	-1	0	Y	28	+99.	1
-Contig6_chr38_16185744_16186110	325	A	G	74.9	chr38	16186061	A	5	0	2	42	3	0	2	36	9	0	2	54	7	0	2	48	1	0	2	30	12	0	2	63	Y	40	+99.	0
-Contig265_chrX_2689247_2689484	114	C	G	103.0	chrX	2689356	C	11	0	2	60	9	0	2	54	13	0	2	66	16	0	2	75	14	0	2	69	10	0	2	57	N	2	9.232	1
-Contig122_chrX_6026976_6027327	330	C	T	79.4	chrX	6027303	C	3	0	2	36	3	0	2	36	3	0	2	36	4	0	2	39	3	0	2	36	6	0	2	45	Y	30	+99.	0
-Contig15_chrX_15659909_15660340	15	A	C	14.9	chrX	15659924	C	1	0	2	30	1	0	2	30	3	0	2	36	6	0	2	45	2	0	2	33	0	0	-1	0	Y	216	+99.	1
-Contig12_chrX_23243561_23244412	479	C	G	67.7	chrX	23244037	C	2	0	2	33	4	2	2	8	2	6	1	43	7	0	2	48	6	0	2	45	4	0	2	39	Y	208	1.620	0
-Contig113_chrX_26287829_26288398	385	C	T	59.6	chrX	26288213	C	9	0	2	54	9	0	2	54	17	0	2	78	11	0	2	60	3	8	1	44	4	0	2	39	N	13	0.077	0
-Contig186_chrX_29118735_29118939	192	G	A	7.01	chrX	29118931	G	1	0	2	30	7	0	2	48	4	0	2	39	5	0	2	42	8	0	2	51	4	0	2	39	N	50	+99.	0
-Contig237_chrX_31256648_31257654	165	T	A	246.0	chrX	31256814	T	7	0	2	48	23	0	2	96	19	0	2	84	17	0	2	78	14	0	2	69	8	0	2	51	Y	37	1.481	0
-Contig25_chrX_40729418_40730089	332	C	T	31.2	chrX	40729745	C	0	0	-1	0	2	0	2	33	4	0	2	39	5	0	2	42	3	0	2	36	3	0	2	36	Y	34	0.212	0
-Contig90_chrX_57430715_57431566	548	C	T	116.0	chrX	57431266	T	9	0	2	54	18	0	2	81	13	0	2	66	14	0	2	69	8	0	2	54	7	0	2	48	Y	261	0.154	1
-Contig133_chrX_84833782_84834125	182	G	A	69.7	chrX	84833962	G	5	0	2	42	18	0	2	81	12	0	2	63	19	0	2	84	6	3	1	27	7	0	2	48	N	619	0.278	0
-Contig129_chrX_90586053_90586467	135	A	T	120.0	chrX	90586195	A	1	0	2	30	6	0	2	45	8	0	2	51	5	0	2	42	1	0	2	30	2	0	2	33	N	637	0.245	0
-Contig125_chrX_93319363_93320877	349	A	C	145.0	chrX	93319721	A	4	0	2	39	6	0	2	45	11	0	2	60	10	0	2	57	13	0	2	66	6	0	2	45	Y	59	1.686	0
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/add_fst_column/add_fst_column.gdSnp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out/add_fst_column/add_fst_column.gdSnp	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,21 @@
+Contig113_chr5_11052263_11052603	28	C	T	38.2	chr5	11052280	C	1	2	1	12	3	2	1	10	5	0	2	42	2	1	2	13	3	0	2	36	8	0	2	51	Y	161	+99.	0	0.1636
+Contig215_chr5_70946445_70947428	363	T	G	28.2	chr5	70946809	C	4	0	2	39	0	5	0	12	9	0	2	54	6	0	2	45	3	3	2	1	9	0	2	54	N	43	0.153	0	0.3846
+Contig132_chr7_20426224_20428145	1815	A	G	28.3	chr7	20428041	A	11	1	2	43	12	0	2	63	19	0	2	84	23	0	2	96	14	0	2	69	10	0	2	57	N	11	0.264	0	0.0213
+Contig30_chr8_17147743_17147923	13	G	A	105.0	chr8	17147756	A	1	3	1	19	1	0	2	30	3	0	2	36	1	0	2	30	1	0	2	30	3	0	2	36	N	6	+99.	0	0.4286
+Contig44_chr8_71186368_71188207	1455	G	T	147.0	chr8	71187818	G	4	10	1	74	3	0	2	36	20	0	2	87	12	0	2	63	8	0	2	51	10	0	2	57	Y	88	0.036	0	0.4167
+Contig103_chr11_8844784_8845095	214	T	G	135.0	chr11	8844993	T	1	1	2	12	10	0	2	57	5	4	1	26	2	3	1	13	2	7	1	34	1	1	2	13	Y	75	0.731	0	0.2101
+Contig37_chr13_15910164_15910426	245	G	A	32.9	chr13	-1	N	3	4	1	41	4	0	2	39	3	0	2	36	4	0	2	39	3	0	2	36	10	0	2	57	N	-1	2.159	1	0.2222
+Contig50_chr17_12247973_12249183	889	G	T	47.6	chr17	12248878	G	0	1	2	9	8	0	2	51	9	2	2	21	7	2	2	21	15	0	2	72	0	3	0	9	Y	1	1.181	0	0.0150
+Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0	0.1429
+Contig77_chr22_49764414_49764875	353	C	A	148.0	chr22	49764777	C	7	4	1	65	18	0	2	81	16	0	2	75	20	0	2	87	4	3	1	52	9	4	1	67	Y	12	0.941	0	0.0741
+Contig61_chr24_30465488_30465834	149	G	T	68.2	chr24	30465637	G	13	0	2	66	4	2	2	11	18	0	2	81	11	0	2	60	11	0	2	60	9	0	2	54	N	99	0.105	2	0.0556
+Contig59_chr25_18196776_18197707	785	G	A	112.0	chr25	18197551	G	8	10	1	42	27	0	2	108	21	0	2	90	18	0	2	81	10	0	2	57	14	0	2	69	N	36	3.625	0	0.1250
+Contig85_chr27_45471750_45472022	211	G	A	53.1	chr27	45471964	G	18	0	2	81	10	0	2	57	15	0	2	72	0	13	0	36	16	0	2	75	14	0	2	69	N	75	2.502	1	0.3023
+Contig175_chr28_36441165_36441915	68	T	C	3.83	chr28	36441234	T	4	4	1	15	6	0	2	45	12	0	2	63	15	0	2	72	6	0	2	45	9	0	2	54	N	4	1.610	2	0.1667
+Contig114_chr30_33636712_33637208	34	C	T	142.0	chr30	33636744	C	7	0	2	48	4	1	2	20	6	0	2	45	6	0	2	45	3	4	1	29	5	0	2	42	Y	14	8.028	0	0.0435
+Contig42_chr32_38900713_38901320	320	A	G	134.0	chr32	38901021	T	12	0	2	63	10	0	2	57	9	11	1	104	5	0	2	42	19	0	2	84	7	6	1	56	Y	71	0.165	0	0.2821
+Contig41_chr34_16544482_16545449	46	T	C	102.0	chr34	16544523	T	5	0	2	42	11	0	2	60	6	0	2	45	0	2	0	3	7	0	2	48	8	0	2	51	Y	215	1.156	0	0.1429
+Contig19_chr35_23887144_23888282	90	C	A	10.1	chr35	23887242	-	3	3	1	12	4	4	1	19	8	6	1	37	4	3	1	11	8	3	2	7	9	3	2	11	Y	105	0.199	0	0.0051
+Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0	0.0986
+Contig18_chr37_17147806_17149851	291	T	G	112.0	chr37	17148084	T	4	6	1	45	16	0	2	75	17	0	2	78	14	0	2	69	22	0	2	93	13	0	2	66	Y	41	4.442	0	0.1304
+Contig12_chrX_23243561_23244412	479	C	G	67.7	chrX	23244037	C	2	0	2	33	4	2	2	8	2	6	1	43	7	0	2	48	6	0	2	45	4	0	2	39	Y	208	1.620	0	0.0256
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/add_fst_column/add_fst_column.snp
--- a/test-data/test_out/add_fst_column/add_fst_column.snp	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-Contig113_chr5_11052263_11052603	28	C	T	38.2	chr5	11052280	C	1	2	1	12	3	2	1	10	5	0	2	42	2	1	2	13	3	0	2	36	8	0	2	51	Y	161	+99.	0	0.1636
-Contig215_chr5_70946445_70947428	363	T	G	28.2	chr5	70946809	C	4	0	2	39	0	5	0	12	9	0	2	54	6	0	2	45	3	3	2	1	9	0	2	54	N	43	0.153	0	0.3846
-Contig132_chr7_20426224_20428145	1815	A	G	28.3	chr7	20428041	A	11	1	2	43	12	0	2	63	19	0	2	84	23	0	2	96	14	0	2	69	10	0	2	57	N	11	0.264	0	0.0213
-Contig30_chr8_17147743_17147923	13	G	A	105.0	chr8	17147756	A	1	3	1	19	1	0	2	30	3	0	2	36	1	0	2	30	1	0	2	30	3	0	2	36	N	6	+99.	0	0.4286
-Contig44_chr8_71186368_71188207	1455	G	T	147.0	chr8	71187818	G	4	10	1	74	3	0	2	36	20	0	2	87	12	0	2	63	8	0	2	51	10	0	2	57	Y	88	0.036	0	0.4167
-Contig103_chr11_8844784_8845095	214	T	G	135.0	chr11	8844993	T	1	1	2	12	10	0	2	57	5	4	1	26	2	3	1	13	2	7	1	34	1	1	2	13	Y	75	0.731	0	0.2101
-Contig37_chr13_15910164_15910426	245	G	A	32.9	chr13	-1	N	3	4	1	41	4	0	2	39	3	0	2	36	4	0	2	39	3	0	2	36	10	0	2	57	N	-1	2.159	1	0.2222
-Contig50_chr17_12247973_12249183	889	G	T	47.6	chr17	12248878	G	0	1	2	9	8	0	2	51	9	2	2	21	7	2	2	21	15	0	2	72	0	3	0	9	Y	1	1.181	0	0.0150
-Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0	0.1429
-Contig77_chr22_49764414_49764875	353	C	A	148.0	chr22	49764777	C	7	4	1	65	18	0	2	81	16	0	2	75	20	0	2	87	4	3	1	52	9	4	1	67	Y	12	0.941	0	0.0741
-Contig61_chr24_30465488_30465834	149	G	T	68.2	chr24	30465637	G	13	0	2	66	4	2	2	11	18	0	2	81	11	0	2	60	11	0	2	60	9	0	2	54	N	99	0.105	2	0.0556
-Contig59_chr25_18196776_18197707	785	G	A	112.0	chr25	18197551	G	8	10	1	42	27	0	2	108	21	0	2	90	18	0	2	81	10	0	2	57	14	0	2	69	N	36	3.625	0	0.1250
-Contig85_chr27_45471750_45472022	211	G	A	53.1	chr27	45471964	G	18	0	2	81	10	0	2	57	15	0	2	72	0	13	0	36	16	0	2	75	14	0	2	69	N	75	2.502	1	0.3023
-Contig175_chr28_36441165_36441915	68	T	C	3.83	chr28	36441234	T	4	4	1	15	6	0	2	45	12	0	2	63	15	0	2	72	6	0	2	45	9	0	2	54	N	4	1.610	2	0.1667
-Contig114_chr30_33636712_33637208	34	C	T	142.0	chr30	33636744	C	7	0	2	48	4	1	2	20	6	0	2	45	6	0	2	45	3	4	1	29	5	0	2	42	Y	14	8.028	0	0.0435
-Contig42_chr32_38900713_38901320	320	A	G	134.0	chr32	38901021	T	12	0	2	63	10	0	2	57	9	11	1	104	5	0	2	42	19	0	2	84	7	6	1	56	Y	71	0.165	0	0.2821
-Contig41_chr34_16544482_16545449	46	T	C	102.0	chr34	16544523	T	5	0	2	42	11	0	2	60	6	0	2	45	0	2	0	3	7	0	2	48	8	0	2	51	Y	215	1.156	0	0.1429
-Contig19_chr35_23887144_23888282	90	C	A	10.1	chr35	23887242	-	3	3	1	12	4	4	1	19	8	6	1	37	4	3	1	11	8	3	2	7	9	3	2	11	Y	105	0.199	0	0.0051
-Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0	0.0986
-Contig18_chr37_17147806_17149851	291	T	G	112.0	chr37	17148084	T	4	6	1	45	16	0	2	75	17	0	2	78	14	0	2	69	22	0	2	93	13	0	2	66	Y	41	4.442	0	0.1304
-Contig12_chrX_23243561_23244412	479	C	G	67.7	chrX	23244037	C	2	0	2	33	4	2	2	8	2	6	1	43	7	0	2	48	6	0	2	45	4	0	2	39	Y	208	1.620	0	0.0256
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/modify_snp_table/modify.gdSnp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out/modify_snp_table/modify.gdSnp	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,338 @@
+Contig161_chr1_4641264_4641879	115	C	T	73.5	chr1	4641382	C	6	0	2	45	8	0	2	51	15	0	2	72	5	0	2	42	6	0	2	45	10	0	2	57	Y	54	0.323	0
+Contig20_chr1_21313469_21313570	66	C	T	54.0	chr1	21313534	C	4	0	2	39	4	0	2	39	5	0	2	42	4	0	2	39	4	0	2	39	5	0	2	42	N	1	+99.	0
+Contig86_chr1_30984450_30985684	670	C	T	365.0	chr1	30985133	C	9	0	2	54	10	0	2	57	13	0	2	66	3	0	2	36	9	0	2	54	7	0	2	48	Y	145	0.031	0
+Contig5_chr1_32562160_32563940	1215	G	T	163.0	chr1	32563356	G	17	0	2	78	19	0	2	84	20	0	2	87	14	0	2	69	12	0	2	63	10	0	2	57	Y	17	0.251	0
+Contig110_chr1_33385093_33386888	510	C	T	270.0	chr1	33385587	A	14	0	2	69	11	0	2	60	19	0	2	84	11	0	2	60	10	0	2	57	13	0	2	66	Y	13	0.126	0
+Contig100_chr1_33562920_33564288	743	C	T	178.0	chr1	33563655	C	6	0	2	45	10	0	2	57	8	0	2	51	5	0	2	42	13	0	2	66	7	0	2	48	Y	13	0.090	3
+Contig7_chr1_37302355_37302489	97	A	G	59.2	chr1	37302452	G	3	0	2	36	8	0	2	51	5	0	2	42	8	0	2	51	7	0	2	48	6	0	2	45	N	56	2.812	0
+Contig62_chr1_41880715_41882180	1078	T	G	57.6	chr1	41881785	T	14	0	2	69	15	0	2	72	16	0	2	75	13	0	2	66	8	0	2	51	10	0	2	57	Y	21	0.477	0
+Contig47_chr1_48409178_48409384	37	C	T	134.0	chr1	48409215	T	5	0	2	42	6	0	2	45	8	0	2	51	9	0	2	54	4	0	2	39	6	0	2	45	N	66	+99.	0
+Contig119_chr1_49647683_49650077	1618	C	A	99.7	chr1	49649276	A	8	0	2	51	11	0	2	60	10	0	2	57	9	0	2	54	10	0	2	57	14	0	2	69	Y	16	0.166	0
+Contig21_chr1_60697952_60699446	307	G	A	51.9	chr1	60698265	G	12	0	2	63	9	0	2	54	4	0	2	39	6	0	2	45	9	0	2	54	4	0	2	39	Y	98	0.507	0
+Contig131_chr1_62319542_62320564	169	C	G	103.0	chr1	62319709	C	12	0	2	63	12	0	2	66	14	0	2	69	12	0	2	63	9	0	2	54	9	0	2	54	Y	73	0.307	1
+Contig14_chr1_63450425_63450680	101	T	A	102.0	chr1	63450530	T	8	0	2	51	10	0	2	57	18	0	2	81	8	0	2	51	8	0	2	34	8	0	2	51	N	99	1.085	0
+Contig83_chr1_63869778_63869942	40	T	C	23.7	chr1	63869819	C	5	0	2	42	7	0	2	48	2	0	2	33	4	0	2	39	6	0	2	48	4	0	2	39	N	654	1.364	0
+Contig30_chr1_64702572_64703138	178	A	T	117.0	chr1	64702750	T	10	0	2	57	10	0	2	57	20	0	2	87	21	0	2	90	6	0	2	45	12	0	2	63	Y	50	3.872	0
+Contig101_chr1_69868406_69868872	287	G	A	14.6	chr1	69868689	G	13	0	2	66	17	0	2	78	10	0	2	57	8	0	2	51	7	0	2	48	8	0	2	51	N	137	0.305	0
+Contig35_chr1_74482577_74482791	170	G	A	45.4	chr1	74482751	A	3	0	2	36	4	0	2	39	13	0	2	66	2	0	2	33	5	0	2	42	2	0	2	33	N	20	+99.	3
+Contig49_chr1_83865731_83865944	85	G	A	34.1	chr1	-1	N	4	0	2	39	4	0	2	39	8	0	2	51	2	0	2	33	5	0	2	42	4	0	2	39	N	-1	1.485	0
+Contig129_chr1_117547123_117548666	926	G	A	126.0	chr1	117548059	G	19	0	2	84	9	0	2	54	11	0	2	60	10	0	2	57	12	0	2	63	11	0	2	60	Y	64	0.049	0
+Contig7_chr1_125154638_125154844	190	G	T	130.0	chr1	125154818	A	5	0	2	42	4	0	2	39	7	0	2	48	2	0	2	33	7	0	2	48	4	0	2	39	N	33	+99.	0
+Contig222_chr2_9817738_9818143	220	C	T	888.0	chr2	9817960	C	17	0	2	78	12	0	2	63	20	0	2	87	8	0	2	51	11	0	2	60	12	0	2	63	Y	76	0.093	1
+Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
+Contig10_chr2_40859744_40860534	637	G	A	888.0	chr2	40860397	A	3	0	2	36	3	0	2	36	2	0	2	33	7	0	2	48	6	0	2	45	8	0	2	51	Y	42	1.435	0
+Contig52_chr2_41421981_41422725	604	C	A	888.0	chr2	41422583	A	17	0	2	78	18	0	2	81	14	0	2	69	17	0	2	78	12	0	2	63	14	0	2	69	Y	44	0.882	0
+Contig94_chr2_43869105_43870358	220	G	A	888.0	chr2	43869333	G	12	0	2	63	18	0	2	81	11	0	2	60	15	0	2	72	12	0	2	63	13	0	2	66	Y	1	0.156	0
+Contig34_chr2_48444129_48444939	695	C	T	134.0	chr2	48444828	C	14	0	2	69	8	0	2	51	16	0	2	75	17	0	2	78	9	0	2	54	15	0	2	72	Y	161	0.375	0
+Contig6_chr2_56859179_56859956	671	T	C	999.9	chr2	56859851	T	15	0	2	72	18	0	2	81	20	0	2	90	19	0	2	84	19	0	2	84	24	0	2	99	N	28	5.308	1
+Contig115_chr2_61631913_61632510	310	G	T	999.3	chr2	61632216	G	7	0	2	48	9	0	2	54	7	0	2	48	11	0	2	60	10	0	2	57	10	0	2	57	N	13	0.184	0
+Contig31_chr2_67331584_67331785	39	C	T	999.0	chr2	67331623	C	11	0	2	60	10	0	2	57	7	0	2	48	9	0	2	54	2	0	2	33	4	0	2	39	N	110	0.647	1
+Contig92_chr2_75906683_75907774	773	T	C	85.4	chr2	75907438	C	12	0	2	63	12	0	2	63	17	0	2	78	8	0	2	51	8	0	2	51	13	0	2	66	Y	93	0.166	0
+Contig163_chr2_76402959_76404830	221	C	T	127.0	chr2	76403181	C	4	0	2	42	10	0	2	57	9	0	2	54	11	0	2	60	7	0	2	48	9	0	2	54	Y	54	0.178	1
+Contig59_chr2_85243022_85243758	506	G	A	96.3	chr2	85243509	T	9	0	2	54	11	0	2	60	12	0	2	63	14	0	2	69	10	0	2	57	7	0	2	48	Y	6	0.459	0
+Contig56_chr3_17326225_17327548	387	G	C	91.2	chr3	17326591	G	14	0	2	69	13	0	2	66	15	0	2	72	15	0	2	72	13	0	2	66	12	0	2	63	Y	20	0.225	3
+Contig108_chr3_46210055_46210874	367	A	G	21.0	chr3	46210423	A	19	0	2	84	10	0	2	57	16	0	2	75	14	0	2	69	20	0	2	87	11	0	2	60	N	236	0.028	1
+Contig16_chr3_47113407_47114449	322	G	A	105.0	chr3	47113713	G	13	0	2	66	17	0	2	78	15	0	2	72	6	0	2	45	11	0	2	60	11	0	2	60	Y	114	0.132	5
+Contig3_chr3_47564810_47565251	262	T	G	112.0	chr3	47565104	T	14	0	2	69	16	0	2	75	20	0	2	87	10	0	2	57	9	0	2	54	8	0	2	51	Y	24	0.073	1
+Contig35_chr3_49662401_49662929	270	A	T	96.1	chr3	49662652	A	14	0	2	69	11	0	2	60	23	0	2	96	13	0	2	66	12	0	2	63	11	0	2	60	Y	36	3.583	2
+Contig97_chr3_49820354_49821631	1069	G	A	44.1	chr3	49821402	G	9	0	2	54	9	0	2	54	6	0	2	45	10	0	2	57	5	0	2	42	8	0	2	51	N	6	0.201	2
+Contig25_chr3_53260697_53262560	402	G	A	211.0	chr3	53261095	G	17	0	2	78	14	0	2	69	15	0	2	75	12	0	2	63	14	0	2	69	12	0	2	63	Y	116	1.033	0
+Contig11_chr3_53992739_53995954	2392	G	A	82.4	chr3	53995143	A	12	0	2	66	11	0	2	60	14	0	2	69	6	0	2	45	11	0	2	60	17	0	2	78	Y	358	0.321	1
+Contig236_chr3_72676275_72676473	128	G	A	278.0	chr3	72676410	G	12	0	2	63	11	0	2	60	13	0	2	66	10	0	2	57	11	0	2	60	8	0	2	51	N	36	0.496	1
+Contig48_chr3_74792236_74792388	63	T	C	111.0	chr3	74792289	-	17	0	2	78	9	0	2	54	9	0	2	54	5	0	2	42	11	0	2	60	9	0	2	54	N	-1	3.528	0
+Contig65_chr3_80727952_80728283	39	T	C	71.2	chr3	80727990	T	7	0	2	48	3	0	2	36	8	0	2	51	6	0	2	45	8	0	2	51	11	0	2	60	N	22	7.078	0
+Contig53_chr3_86407941_86409349	1406	G	A	86.9	chr3	86409317	A	5	0	2	42	5	0	2	42	4	0	2	39	10	0	2	57	8	0	2	51	12	0	2	63	N	14	3.285	1
+Contig13_chr3_92409738_92412300	718	A	G	23.3	chr3	92410450	A	12	0	2	63	16	0	2	75	18	0	2	81	13	0	2	66	22	0	2	93	7	0	2	48	Y	23	0.224	2
+Contig134_chr4_12145648_12148225	1326	C	T	164.0	chr4	12146961	C	9	0	2	54	8	0	2	51	7	0	2	48	3	0	2	36	5	0	2	42	5	0	2	42	Y	4	0.080	1
+Contig88_chr4_15557471_15557833	268	A	G	145.0	chr4	15557737	A	6	0	2	45	6	0	2	45	11	0	2	60	9	0	2	54	5	0	2	42	6	0	2	45	Y	46	4.138	0
+Contig53_chr4_18823968_18824478	149	A	G	91.3	chr4	18824115	A	18	0	2	81	15	0	2	72	21	0	2	90	13	0	2	66	9	0	2	54	12	0	2	63	N	51	0.251	0
+Contig19_chr4_26233601_26233991	146	G	C	51.6	chr4	26233744	G	10	0	2	57	8	0	2	51	9	0	2	54	5	0	2	42	9	0	2	54	4	0	2	39	N	41	0.163	3
+Contig78_chr4_28579975_28580134	30	T	G	19.6	chr4	28579994	-	4	0	2	39	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	2	0	2	33	N	33	0.499	0
+Contig16_chr4_30177226_30179725	621	C	T	88.4	chr4	30177859	C	20	0	2	87	13	0	2	66	13	0	2	66	11	0	2	60	8	0	2	51	8	0	2	51	Y	45	0.797	1
+Contig30_chr4_46196500_46197672	1045	A	C	33.4	chr4	46197522	C	16	0	2	75	9	0	2	54	4	0	2	39	7	0	2	48	14	0	2	69	6	0	2	45	Y	43	0.306	0
+Contig2_chr4_47039007_47039323	158	G	C	35.1	chr4	47039160	-	8	0	2	51	9	0	2	54	13	0	2	66	8	0	2	51	10	0	2	60	9	0	2	54	N	0	0.131	0
+Contig17_chr4_61310346_61311158	267	C	T	49.9	chr4	61310604	T	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	14	0	2	69	7	0	2	48	Y	219	0.098	0
+Contig26_chr4_64190783_64191295	64	A	G	162.0	chr4	64190843	A	10	0	2	57	6	0	2	45	20	0	2	87	12	0	2	63	17	0	2	78	7	0	2	48	Y	306	7.428	0
+Contig11_chr4_65500960_65501654	634	T	C	107.0	chr4	65501585	T	13	0	2	66	14	0	2	69	13	0	2	66	13	0	2	66	6	0	2	45	18	0	2	81	Y	10	6.849	0
+Contig38_chr4_67768488_67768982	113	A	G	102.0	chr4	67768598	A	9	0	2	54	8	0	2	51	9	0	2	54	11	0	2	60	10	0	2	57	7	0	2	48	Y	188	3.175	0
+Contig30_chr4_70978564_70979580	596	A	G	164.0	chr4	70979151	A	15	0	2	72	12	0	2	63	20	0	2	87	14	0	2	69	15	0	2	72	15	0	2	72	Y	111	2.458	2
+Contig72_chr4_74225793_74226492	674	A	G	110.0	chr4	74226472	A	5	0	2	42	3	0	2	36	2	0	2	33	3	0	2	36	7	0	2	48	4	0	2	39	Y	115	+99.	1
+Contig32_chr4_75618955_75620254	301	T	C	333.0	chr4	75619257	C	10	0	2	57	8	0	2	51	12	0	2	63	20	0	2	87	12	0	2	63	14	0	2	69	Y	34	0.163	2
+Contig31_chr5_4734956_4736547	1166	C	T	133.0	chr5	4736132	C	14	0	2	69	8	0	2	51	17	0	2	78	4	0	2	39	9	0	2	54	12	0	2	63	Y	1	0.021	0
+Contig30_chr5_15698241_15699076	396	G	T	76.6	chr5	15698633	T	8	0	2	51	9	0	2	54	10	0	2	57	7	0	2	48	11	0	2	60	8	0	2	54	Y	65	0.009	0
+Contig36_chr5_17709244_17710004	373	T	C	281.0	chr5	17709624	T	6	0	2	45	9	0	2	54	7	0	2	48	4	0	2	39	10	0	2	57	4	0	2	39	Y	16	0.131	0
+Contig13_chr5_21881138_21881562	227	A	G	251.0	chr5	21881356	A	11	0	2	60	20	0	2	87	22	0	2	93	10	0	2	57	10	0	2	57	21	0	2	90	Y	182	2.013	0
+Contig5_chr5_23188121_23190168	1841	C	T	141.0	chr5	23189975	C	20	0	2	87	19	0	2	84	22	0	2	93	16	0	2	75	18	0	2	81	14	0	2	69	N	45	0.355	0
+Contig6_chr5_26899813_26900498	97	A	C	88.6	chr5	26899910	A	15	0	2	72	14	0	2	69	27	0	2	108	15	0	2	72	13	0	2	69	12	0	2	63	Y	92	7.370	3
+Contig314_chr5_34019166_34019319	72	C	A	20.1	chr5	-1	N	6	0	2	45	9	0	2	54	4	0	2	39	4	0	2	39	9	0	2	54	5	0	2	42	N	-1	+99.	4
+Contig147_chr5_38980258_38980559	221	C	T	40.8	chr5	38980477	C	15	0	2	72	15	0	2	72	19	0	2	84	10	0	2	57	12	0	2	63	20	0	2	87	Y	11	4.576	0
+Contig115_chr5_48119079_48120169	151	C	T	78.3	chr5	48119234	C	17	0	2	78	10	0	2	57	14	0	2	69	16	0	2	75	8	0	2	51	12	0	2	63	Y	205	0.320	0
+Contig45_chr5_50892738_50892968	169	C	A	25.8	chr5	50892911	C	10	0	2	57	7	0	2	48	10	0	2	60	6	0	2	45	6	0	2	45	13	0	2	66	N	244	0.497	1
+Contig40_chr5_51484164_51484696	14	A	G	53.3	chr5	51484180	A	6	0	2	45	4	0	2	39	4	0	2	39	3	0	2	36	0	0	2	13	3	0	2	36	N	63	+99.	1
+Contig40_chr5_51664286_51667573	861	C	T	148.0	chr5	51665149	C	20	0	2	87	21	0	2	90	20	0	2	87	11	0	2	60	16	0	2	75	15	0	2	72	Y	207	0.080	1
+Contig15_chr5_51889708_51891244	882	A	G	149.0	chr5	51890581	G	13	0	2	66	18	0	2	81	17	0	2	78	22	0	2	93	15	0	2	72	22	0	2	93	Y	7	0.025	1
+Contig143_chr5_57231364_57232010	294	T	C	78.5	chr5	57231644	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	10	0	2	57	6	0	2	45	Y	73	0.337	2
+Contig13_chr5_57609985_57610584	496	C	T	50.5	chr5	57610476	C	17	0	2	78	9	0	2	54	6	0	2	45	8	0	2	51	10	0	2	57	12	0	2	63	N	77	2.022	1
+Contig230_chr5_58486998_58487280	227	T	C	192.0	chr5	58487232	T	3	0	2	36	4	0	2	39	9	0	2	54	6	0	2	45	4	0	2	39	7	0	2	48	N	24	0.100	2
+Contig32_chr5_70852360_70853289	282	G	A	114.0	chr5	70852623	G	16	0	2	75	11	0	2	60	13	0	2	66	12	0	2	63	13	0	2	66	7	0	2	48	Y	33	0.276	0
+Contig100_chr5_71189678_71190590	813	C	T	30.8	chr5	71190523	C	11	0	2	60	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	Y	8	0.362	1
+Contig45_chr5_76133561_76134403	388	A	G	103.0	chr5	76133941	G	3	0	2	36	8	0	2	51	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	57	0.038	0
+Contig61_chr5_90202541_90204393	909	C	T	101.0	chr5	90203461	T	7	0	2	48	5	0	2	42	14	0	2	69	3	0	2	36	5	0	2	42	8	0	2	51	Y	64	1.448	0
+Contig111_chr6_5821219_5822519	1060	A	G	68.1	chr6	5822321	T	7	0	2	48	6	0	2	45	11	0	2	60	9	0	2	54	3	0	2	36	12	0	2	63	Y	7	0.231	1
+Contig220_chr6_10671338_10672441	999	T	C	36.3	chr6	10672322	T	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	5	0	2	42	9	0	2	54	Y	1	1.667	0
+Contig226_chr6_17361986_17362884	418	G	C	251.0	chr6	17362406	G	6	0	2	45	8	0	2	51	7	0	2	48	9	0	2	54	7	0	2	48	7	0	2	48	Y	7	0.147	0
+Contig51_chr6_20231207_20231785	161	A	G	70.5	chr6	20231375	G	13	0	2	66	5	0	2	42	8	0	2	51	2	0	2	36	5	0	2	42	5	0	2	42	Y	153	1.754	0
+Contig102_chr6_30271329_30271577	39	T	G	139.0	chr6	30271371	G	3	0	2	36	4	0	2	39	6	0	2	45	1	0	2	30	4	0	2	39	4	0	2	39	N	15	1.159	0
+Contig217_chr6_31393824_31394218	97	G	A	115.0	chr6	31393921	G	9	0	2	54	19	0	2	84	15	0	2	72	12	0	2	63	7	0	2	48	10	0	2	57	N	45	0.477	0
+Contig186_chr6_31928098_31928245	73	G	A	117.0	chr6	-1	N	5	0	2	42	8	0	2	51	2	0	2	33	4	0	2	39	1	0	2	30	5	0	2	42	N	-1	0.276	1
+Contig52_chr6_33188498_33188724	123	G	A	59.0	chr6	-1	N	5	0	2	42	13	0	2	66	8	0	2	51	4	0	2	39	9	0	2	54	9	0	2	54	N	-1	0.880	1
+Contig102_chr6_38743009_38743435	290	A	G	178.0	chr6	38743311	A	11	0	2	60	13	0	2	66	9	0	2	54	11	0	2	60	12	0	2	63	13	0	2	66	Y	34	0.148	4
+Contig81_chr6_49018353_49019532	179	C	A	72.5	chr6	49018530	A	15	0	2	72	13	0	2	66	19	0	2	72	8	0	2	51	12	0	2	63	16	0	2	75	Y	15	0.145	1
+Contig112_chr6_51024554_51024851	100	A	G	121.0	chr6	51024654	A	10	0	2	57	12	0	2	63	9	0	2	54	13	0	2	66	14	0	2	69	17	0	2	78	N	75	4.287	0
+Contig40_chr6_51412751_51413807	227	T	C	94.5	chr6	51412975	C	5	0	2	42	8	0	2	51	7	0	2	48	9	0	2	54	11	0	2	60	10	0	2	57	Y	4	5.661	0
+Contig47_chr6_69073222_69074767	1315	T	C	212.0	chr6	69074558	T	20	0	2	87	17	0	2	78	18	0	2	81	12	0	2	63	17	0	2	78	7	0	2	48	Y	9	0.652	0
+Contig30_chr6_74848932_74849059	57	C	G	46.3	chr6	74848993	C	7	0	2	48	7	0	2	33	6	0	2	45	7	0	2	48	5	0	2	42	6	0	2	45	N	-1	+99.	1
+Contig84_chr7_6648683_6650255	1297	G	A	110.0	chr7	6649988	G	18	0	2	81	9	0	2	54	22	0	2	77	16	0	2	75	20	0	2	87	6	0	2	45	Y	83	0.166	0
+Contig239_chr7_13007379_13007700	275	A	G	39.8	chr7	13007642	A	8	0	2	51	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	5	0	2	42	N	46	1.511	3
+Contig119_chr7_18310707_18310948	23	A	T	133.0	chr7	18310729	A	6	0	2	45	5	0	2	42	10	0	2	57	5	0	2	42	2	0	2	33	2	0	2	33	N	4553	+99.	0
+Contig93_chr7_18513377_18513741	173	T	C	130.0	chr7	18513533	C	15	0	2	72	11	0	2	60	18	0	2	81	6	0	2	45	10	0	2	57	14	0	2	69	Y	115	0.174	0
+Contig133_chr7_19603333_19603776	414	C	G	31.9	chr7	19603734	G	10	0	2	57	4	0	2	39	4	0	2	39	5	0	2	42	9	0	2	54	9	0	2	54	N	78	+99.	5
+Contig132_chr7_20426224_20428145	1815	A	G	28.3	chr7	20428041	A	11	1	2	43	12	0	2	63	19	0	2	84	23	0	2	96	14	0	2	69	10	0	2	57	N	11	0.264	0
+Contig206_chr7_26281823_26282074	103	C	A	101.0	chr7	26281925	T	11	0	2	60	16	0	2	61	19	0	2	84	6	0	2	45	19	0	2	84	16	0	2	75	N	-1	0.947	1
+Contig55_chr7_53147505_53148974	894	A	G	68.4	chr7	53148397	G	22	0	2	93	13	0	2	66	16	0	2	75	8	0	2	51	16	0	2	75	11	0	2	60	Y	19	0.060	0
+Contig4_chr7_53685534_53688206	1709	C	G	76.2	chr7	53687225	C	18	0	2	81	17	0	2	78	18	0	2	81	15	0	2	72	14	0	2	69	14	0	2	69	Y	32	0.659	1
+Contig61_chr7_55832923_55834065	506	T	C	185.0	chr7	55833450	C	9	0	2	54	10	0	2	57	22	0	2	93	12	0	2	63	12	0	2	63	7	0	2	48	Y	1	0.019	0
+Contig91_chr8_12804505_12805470	409	C	A	111.0	chr8	12804906	C	8	0	2	51	10	0	2	57	15	0	2	72	12	0	2	63	14	0	2	69	15	0	2	72	N	145	0.175	0
+Contig8_chr8_27811135_27812620	333	C	T	37.9	chr8	27811458	C	4	0	2	39	11	0	2	60	18	0	2	81	5	0	2	42	6	0	2	45	5	0	2	42	Y	1	0.272	0
+Contig66_chr8_28273102_28273660	175	G	C	81.6	chr8	28273263	T	9	0	2	54	17	0	2	78	19	0	2	84	8	0	2	51	16	0	2	75	19	0	2	84	Y	3	2.735	0
+Contig84_chr8_31375511_31376456	443	T	C	125.0	chr8	31375954	T	10	0	2	57	15	0	2	72	27	0	2	108	18	0	2	81	16	0	2	75	9	0	2	54	Y	2	0.650	0
+Contig18_chr8_32575859_32577431	264	T	C	151.0	chr8	32576124	T	20	0	2	87	14	0	2	69	17	0	2	78	14	0	2	69	13	0	2	66	14	0	2	69	Y	17	0.915	1
+Contig54_chr8_40913908_40916451	1275	G	A	175.0	chr8	40915190	G	10	0	2	57	8	0	2	51	11	0	2	60	7	0	2	48	8	0	2	51	9	0	2	54	Y	21	0.056	3
+Contig93_chr8_44658786_44659075	180	T	G	55.3	chr8	44658964	T	4	0	2	39	3	0	2	36	6	0	2	45	5	0	2	45	5	0	2	42	4	0	2	39	N	14	0.188	0
+Contig66_chr8_58562376_58563446	345	C	G	5.74	chr8	58562721	C	14	0	2	69	12	0	2	63	9	0	2	57	10	0	2	57	9	0	2	54	10	0	2	57	Y	6	0.685	0
+Contig44_chr8_71186368_71188207	1455	G	T	147.0	chr8	71187818	G	4	10	1	74	3	0	2	36	20	0	2	87	12	0	2	63	8	0	2	51	10	0	2	57	Y	88	0.036	0
+Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
+Contig96_chr9_39008495_39009278	215	A	C	98.7	chr9	39008708	C	7	0	2	48	13	0	2	66	28	0	2	111	16	0	2	75	17	0	2	78	17	0	2	78	Y	8	0.427	1
+Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
+Contig63_chr10_42716594_42719945	1018	A	G	88.7	chr10	42717616	G	13	0	2	66	14	0	2	69	13	0	2	66	12	0	2	63	18	0	2	81	5	0	2	42	Y	25	1.740	0
+Contig22_chr10_43255307_43255570	81	C	A	37.2	chr10	43255383	C	15	0	2	72	18	0	2	81	22	0	2	93	16	0	2	75	11	0	2	60	12	0	2	63	N	62	0.450	0
+Contig9_chr10_51475063_51476054	770	C	T	57.3	chr10	51475839	C	6	0	2	45	16	0	2	75	16	0	2	75	13	0	2	66	9	0	2	54	9	2	2	21	N	80	0.394	0
+Contig42_chr10_53816543_53818392	1642	G	A	27.5	chr10	53818172	A	7	0	2	48	13	0	2	66	17	0	2	78	14	0	2	69	19	0	2	84	16	0	2	75	N	1	0.433	0
+Contig36_chr10_53992615_53993741	229	G	C	86.2	chr10	53992846	G	17	0	2	78	14	0	2	69	13	0	2	66	15	0	2	72	12	0	2	63	15	0	2	72	N	23	1.912	0
+Contig20_chr10_58141129_58141750	575	C	T	46.1	chr10	58141701	C	7	0	2	48	8	0	2	51	9	0	2	54	3	0	2	36	4	0	2	39	9	0	2	54	N	1	4.264	0
+Contig26_chr10_59510973_59511899	146	C	A	29.0	chr10	59511126	C	8	0	2	51	13	0	2	66	18	0	2	81	13	0	2	66	10	0	2	57	7	0	2	48	Y	208	1.077	0
+Contig72_chr11_7142765_7143772	146	G	A	152.0	chr11	7142911	A	8	0	2	51	8	0	2	51	24	0	2	99	10	0	2	57	17	0	2	78	11	0	2	60	Y	90	1.137	0
+Contig9_chr11_9904571_9905983	1284	C	T	151.0	chr11	9905857	C	16	0	2	75	19	0	2	84	17	0	2	78	16	0	2	75	12	0	2	63	13	1	2	44	Y	11	0.422	1
+Contig7_chr11_40017076_40017630	352	C	T	46.3	chr11	40017422	C	7	0	2	48	9	0	2	54	6	0	2	45	8	0	2	51	16	0	2	75	9	0	2	54	Y	44	0.336	0
+Contig108_chr11_42953408_42955156	367	A	G	89.4	chr11	42953779	A	17	0	2	78	11	0	2	60	14	0	2	69	20	0	2	87	14	0	2	69	17	0	2	78	Y	118	0.784	1
+Contig16_chr11_53408448_53408790	187	A	G	153.0	chr11	53408638	A	7	0	2	48	9	0	2	54	18	0	2	81	10	0	2	57	11	0	2	60	12	0	2	63	Y	116	1.367	0
+Contig21_chr12_18403415_18404381	586	G	T	34.5	chr12	18403983	-	13	0	2	66	16	0	2	75	25	0	2	102	12	0	2	63	12	0	2	63	14	0	2	69	Y	12	0.068	0
+Contig33_chr12_19804073_19804529	178	T	C	69.4	chr12	19804261	T	13	0	2	66	13	0	2	66	22	0	2	93	11	0	2	60	12	0	2	63	18	0	2	81	Y	11	1.571	0
+Contig41_chr12_25565452_25566993	475	G	T	6.29	chr12	25565926	G	15	0	2	72	14	0	2	69	10	0	2	57	15	0	2	72	18	0	2	81	19	0	2	84	N	10	2.231	1
+Contig9_chr12_27204351_27204696	239	A	G	145.0	chr12	27204587	A	7	0	2	48	8	0	2	51	12	0	2	63	8	0	2	51	11	0	2	60	11	0	2	60	Y	14	0.046	0
+Contig45_chr12_30548282_30550498	448	C	T	124.0	chr12	30548703	-	9	0	2	54	11	0	2	60	22	0	2	93	19	0	2	84	12	0	2	63	12	0	2	63	Y	66	0.305	0
+Contig46_chr12_35571846_35572563	58	G	C	83.2	chr12	35571906	G	4	0	2	39	10	0	2	57	11	0	2	60	6	0	2	45	10	0	2	57	6	0	2	45	Y	55	+99.	1
+Contig28_chr12_42075871_42076044	136	G	A	134.0	chr12	42076006	A	6	0	2	45	5	0	2	42	7	0	2	48	7	0	2	48	2	0	2	33	4	0	2	39	N	3	9.479	0
+Contig16_chr12_42386141_42387454	194	A	G	161.0	chr12	42386323	A	11	0	2	60	8	0	2	54	23	0	2	96	17	0	2	78	6	0	2	45	13	0	2	66	Y	7	0.927	1
+Contig42_chr12_44424628_44425829	255	A	G	84.4	chr12	44424879	A	12	0	2	63	19	0	2	84	23	0	2	96	15	0	2	72	18	0	2	81	14	0	2	69	Y	18	1.190	2
+Contig10_chr12_44447953_44449698	63	C	T	105.0	chr12	44448020	C	11	0	2	60	9	0	2	54	12	0	2	63	10	0	2	57	15	0	2	72	8	0	2	51	Y	31	11.791	0
+Contig5_chr12_53880670_53882675	1221	A	C	99.4	chr12	53881888	A	16	0	2	75	18	0	2	81	23	0	2	96	10	0	2	57	15	0	2	72	17	0	2	78	Y	31	0.061	0
+Contig86_chr12_56715356_56716464	818	T	C	166.0	chr12	56716164	T	20	0	2	87	16	0	2	75	16	0	2	75	14	0	2	69	13	0	2	66	7	0	2	48	Y	22	1.092	0
+Contig3_chr12_65021967_65024097	238	T	G	92.6	chr12	65022205	T	17	0	2	78	14	0	2	69	16	0	2	75	9	0	2	54	13	0	2	66	15	0	2	72	Y	258	0.117	0
+Contig43_chr12_66499742_66500010	121	G	T	41.5	chr12	66499866	G	12	0	2	63	4	0	2	39	8	0	2	51	6	0	2	45	10	0	2	57	6	0	2	45	N	42	0.421	0
+Contig14_chr12_71364692_71365311	20	A	C	103.0	chr12	71364712	A	7	0	2	48	3	0	2	36	5	0	2	42	1	0	2	30	2	0	2	33	3	0	2	36	Y	35	+99.	0
+Contig37_chr13_15910164_15910426	245	G	A	32.9	chr13	-1	N	3	4	1	41	4	0	2	39	3	0	2	36	4	0	2	39	3	0	2	36	10	0	2	57	N	-1	2.159	1
+Contig107_chr13_26045881_26046290	341	C	G	81.4	chr13	26046230	C	16	0	2	75	20	0	2	90	14	0	2	69	15	0	2	72	9	0	2	54	9	0	2	54	Y	51	4.510	0
+Contig251_chr13_28498333_28501066	864	T	G	296.0	chr13	28499180	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	5	0	2	42	6	0	2	45	Y	9	0.068	0
+Contig154_chr13_36777857_36778736	356	G	A	95.5	chr13	36778225	A	6	0	2	45	11	0	2	60	11	0	2	60	9	0	2	54	13	0	2	66	8	0	2	51	Y	59	0.192	0
+Contig37_chr13_42529793_42530857	150	G	T	192.0	chr13	42529926	G	18	0	2	81	14	0	2	69	16	0	2	75	14	0	2	69	8	0	2	51	11	0	2	60	N	22	0.795	5
+Contig47_chr13_47045833_47046626	257	A	C	28.5	chr13	47046097	A	13	0	2	66	10	0	2	57	17	0	2	78	20	0	2	87	15	0	2	72	9	0	2	57	N	129	0.468	0
+Contig42_chr13_47730018_47730856	254	A	G	75.1	chr13	47730294	A	13	0	2	66	6	0	2	45	12	0	2	63	9	0	2	54	16	0	2	75	11	0	2	63	Y	630	0.049	1
+Contig55_chr13_53467708_53468101	221	T	G	132.0	chr13	53467925	T	25	0	2	102	12	0	2	63	26	0	2	105	7	0	2	48	16	0	2	75	16	0	2	75	N	20	5.717	1
+Contig49_chr13_55103679_55105532	503	G	A	76.0	chr13	55104178	G	21	0	2	90	19	0	2	84	18	0	2	81	20	0	2	87	8	9	1	89	17	0	2	78	Y	20	0.259	1
+Contig66_chr13_66021813_66022244	319	C	T	125.0	chr13	66022136	C	11	0	2	60	16	0	2	75	15	0	2	75	12	0	2	63	17	0	2	78	8	0	2	51	N	14	0.055	3
+Contig48_chr14_11839435_11843272	3014	A	G	163.0	chr14	11842446	A	10	0	2	57	8	0	2	51	13	0	2	66	10	0	2	57	5	0	2	42	10	0	2	57	Y	31	0.908	0
+Contig9_chr14_23353717_23354432	80	G	A	61.3	chr14	23353797	G	3	0	2	36	6	0	2	45	11	0	2	60	8	0	2	51	4	0	2	39	2	4	1	35	Y	11	0.444	0
+Contig14_chr14_24131180_24133488	1633	G	A	131.0	chr14	24132818	G	21	0	2	90	16	0	2	75	12	0	2	63	10	0	2	57	11	0	2	60	20	0	2	87	Y	36	0.347	0
+Contig28_chr14_26905747_26909514	975	G	C	3.13	chr14	26906723	G	16	0	2	75	10	0	2	57	12	0	2	63	15	0	2	72	10	0	2	57	7	0	2	48	N	287	0.117	2
+Contig14_chr14_29616948_29618316	109	G	A	80.3	chr14	29617053	-	17	0	2	78	16	0	2	75	16	0	2	75	10	0	2	57	17	0	2	78	19	0	2	84	Y	32	1.051	0
+Contig76_chr14_30028102_30029179	1046	C	T	38.5	chr14	30029169	T	3	0	2	36	6	0	2	45	9	0	2	54	7	0	2	48	9	0	2	54	8	0	2	51	Y	96	+99.	0
+Contig115_chr14_31417207_31417574	259	A	G	12.1	chr14	31417454	G	13	0	2	66	15	0	2	72	21	0	2	90	12	0	2	63	13	0	2	66	9	0	2	54	N	28	5.379	2
+Contig70_chr14_46653662_46653790	111	G	A	46.7	chr14	46653768	G	7	0	2	48	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	10	0	2	57	N	21	+99.	2
+Contig43_chr14_49991855_49993511	918	A	G	112.0	chr14	49992767	G	15	0	2	72	10	0	2	57	11	0	2	63	9	0	2	54	12	0	2	63	9	0	2	54	Y	6	0.314	1
+Contig64_chr14_56768376_56768902	473	C	T	29.0	chr14	56768832	C	15	0	2	72	11	0	2	60	14	0	2	69	14	0	2	69	7	0	2	48	9	0	2	54	Y	91	8.281	0
+Contig60_chr15_18493036_18494316	150	G	A	92.6	chr15	18493188	G	9	0	2	54	13	0	2	66	9	0	2	54	6	0	2	45	5	0	2	42	12	0	2	63	Y	45	0.125	0
+Contig59_chr15_22138344_22138535	120	G	C	142.0	chr15	22138470	C	11	0	2	60	10	0	2	57	18	0	2	81	4	0	2	39	10	0	2	57	15	0	2	72	N	8	2.553	0
+Contig112_chr15_26772864_26773267	374	C	T	21.6	chr15	26773244	C	4	0	2	39	4	0	2	39	5	0	2	42	2	0	2	33	4	0	2	39	3	0	2	36	N	18	+99.	0
+Contig24_chr15_26894765_26895003	155	G	A	87.6	chr15	-1	N	6	0	2	45	5	0	2	42	7	0	2	48	4	0	2	39	4	0	2	39	2	0	2	33	N	-1	0.178	0
+Contig2_chr15_33944796_33947182	1860	G	A	99.5	chr15	33946654	G	10	0	2	57	11	0	2	60	16	0	2	75	14	0	2	69	14	0	2	69	16	0	2	75	Y	16	0.252	0
+Contig73_chr15_34690052_34691332	714	T	C	130.0	chr15	34690769	T	7	0	2	48	7	0	2	48	17	0	2	78	9	0	2	54	9	0	2	54	4	0	2	39	Y	7	6.003	0
+Contig68_chr15_37747190_37747426	126	G	A	130.0	chr15	37747331	G	14	0	2	69	14	0	2	69	11	0	2	63	19	0	2	84	13	0	2	66	21	0	2	90	N	229	0.255	0
+Contig104_chr15_45106954_45107158	70	A	T	64.4	chr15	45107015	A	6	0	2	45	6	0	2	45	19	0	2	84	7	0	2	48	7	0	2	48	3	0	2	36	N	202	4.319	0
+Contig119_chr16_6160274_6160477	180	G	A	54.8	chr16	6160457	G	7	0	2	48	6	0	2	45	12	0	2	63	3	0	2	36	11	0	2	60	10	0	2	57	N	42	+99.	0
+Contig126_chr16_10611887_10612152	150	G	T	145.0	chr16	10612037	G	14	0	2	69	9	0	2	54	11	0	2	63	8	0	2	51	8	0	2	51	11	0	2	60	N	15	0.104	6
+Contig43_chr16_20200090_20200514	70	A	G	58.6	chr16	20200154	A	11	0	2	60	15	0	2	72	15	0	2	72	6	0	2	45	9	0	2	54	12	0	2	63	Y	2	0.466	1
+Contig60_chr16_28079136_28080263	588	T	G	157.0	chr16	28079739	T	22	0	2	93	20	0	2	87	22	0	2	93	17	0	2	78	12	0	2	63	10	0	2	57	Y	105	5.999	1
+Contig70_chr16_33758668_33759655	104	A	T	58.1	chr16	33758772	A	6	0	2	45	7	0	2	48	17	0	2	78	14	0	2	69	8	0	2	51	10	0	2	57	N	54	0.162	0
+Contig66_chr16_37935682_37935831	116	T	C	99.2	chr16	37935802	C	12	0	2	63	6	0	2	45	19	0	2	84	12	0	2	63	13	0	2	66	17	0	2	78	N	266	+99.	2
+Contig16_chr16_40451506_40451643	84	A	G	59.8	chr16	40451592	A	7	0	2	48	5	0	2	42	7	0	2	48	13	0	2	66	14	0	2	69	19	0	2	84	N	45	5.061	0
+Contig31_chr17_12128267_12129637	205	G	A	90.5	chr17	12128484	G	7	0	2	48	6	0	2	45	6	0	2	45	11	0	2	60	7	0	2	48	4	0	2	39	Y	10	0.246	0
+Contig1_chr17_12979232_12980380	808	G	T	12.3	chr17	12980028	G	18	0	2	81	12	0	2	63	21	0	2	90	13	0	2	66	22	0	2	93	18	0	2	81	Y	9	0.336	1
+Contig42_chr17_23434859_23438330	2100	C	T	39.5	chr17	23436985	T	4	0	2	39	7	0	2	48	7	0	2	48	3	0	2	36	6	0	2	45	2	0	2	33	Y	25	0.344	0
+Contig63_chr17_23796320_23796814	220	A	G	54.0	chr17	23796536	G	6	0	2	45	4	0	2	39	5	0	2	42	6	0	2	45	4	0	2	39	6	0	2	45	Y	139	0.067	1
+Contig76_chr17_24107434_24107834	316	T	C	141.0	chr17	24107726	T	19	0	2	84	15	0	2	72	20	0	2	87	16	0	2	75	11	0	2	60	18	0	2	81	Y	30	0.175	2
+Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
+Contig59_chr17_26790302_26795045	287	C	T	45.1	chr17	26790582	C	8	0	2	51	6	0	2	45	13	0	2	66	6	0	2	45	15	0	2	72	12	0	2	63	Y	75	0.019	1
+Contig99_chr17_27018324_27019378	446	G	A	31.1	chr17	27018776	G	14	0	2	69	12	0	2	63	14	0	2	69	10	0	2	57	9	0	2	54	11	0	2	60	Y	13	0.290	4
+Contig125_chr17_27739115_27739410	63	G	A	107.0	chr17	27739177	G	8	0	2	51	11	0	2	60	16	0	2	75	8	0	2	51	4	0	2	39	15	0	2	72	N	100	0.819	0
+Contig115_chr17_37489899_37490101	159	G	A	62.4	chr17	37490067	G	4	0	2	39	3	0	2	36	4	0	2	39	4	0	2	39	3	0	2	36	6	0	2	45	N	4	1.411	1
+Contig180_chr17_45154356_45154925	524	A	G	146.0	chr17	45154886	G	7	0	2	48	9	0	2	54	7	0	2	48	9	0	2	54	4	0	2	39	8	0	2	51	Y	11	+99.	2
+Contig61_chr17_48221795_48223545	1404	T	A	177.0	chr17	48223216	T	15	0	2	72	14	0	2	69	24	0	2	99	17	0	2	78	18	0	2	81	24	0	2	99	Y	161	0.633	2
+Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
+Contig229_chr18_3706523_3708577	1076	A	G	83.9	chr18	3707630	A	11	0	2	60	13	0	2	66	26	0	2	105	11	0	2	60	15	0	2	72	17	0	2	78	Y	63	0.445	0
+Contig24_chr18_14049894_14050480	24	A	G	123.0	chr18	14049918	A	5	0	2	42	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	5	0	2	42	Y	17	+99.	0
+Contig123_chr18_19916160_19916379	116	G	A	79.2	chr18	19916272	A	14	0	2	69	12	0	2	63	14	0	2	69	6	0	2	45	11	0	2	60	10	0	2	57	N	26	0.172	0
+Contig82_chr18_27305489_27306229	566	C	T	49.5	chr18	27306051	A	6	0	2	45	6	0	2	45	10	0	2	57	11	0	2	60	6	0	2	45	7	0	2	48	N	1	0.349	0
+Contig71_chr18_34324706_34326687	136	G	A	151.0	chr18	34324841	G	9	0	2	54	9	0	2	54	17	0	2	78	8	0	2	51	11	0	2	60	10	0	2	57	Y	2	2.129	2
+Contig16_chr18_34672093_34673044	538	T	C	58.2	chr18	34672635	T	8	0	2	51	15	0	2	72	16	0	2	75	15	0	2	72	9	0	2	57	18	0	2	81	Y	8	0.214	1
+Contig96_chr18_38492535_38493333	624	G	A	119.0	chr18	38493162	T	17	0	2	78	12	0	2	63	13	0	2	66	16	0	2	75	8	0	2	51	15	0	2	72	Y	127	0.131	0
+Contig226_chr18_47753756_47754666	427	T	C	21.1	chr18	47754215	T	10	0	2	57	4	0	2	39	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	42	0.522	0
+Contig170_chr18_49411558_49412230	94	C	A	74.3	chr18	49411655	C	14	0	2	69	10	0	2	57	9	0	2	54	10	0	2	57	3	0	2	36	3	0	2	36	N	9	1.457	0
+Contig192_chr18_49419342_49420737	1058	C	T	42.8	chr18	49420381	A	3	0	2	36	4	0	2	39	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	Y	34	2.107	2
+Contig64_chr18_55979770_55980315	49	G	A	89.1	chr18	55979824	G	3	0	2	36	9	0	2	54	7	0	2	51	4	0	2	39	3	0	2	36	3	0	2	36	Y	-1	2.124	0
+Contig20_chr18_58130301_58130735	112	A	G	74.4	chr18	58130413	A	12	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	6	0	2	45	6	0	2	45	Y	10	0.290	0
+Contig67_chr19_12398520_12399367	499	C	T	161.0	chr19	12399017	C	10	0	2	57	11	0	2	60	20	0	2	87	14	0	2	69	24	0	2	99	8	0	2	51	Y	137	5.634	0
+Contig66_chr19_16285672_16287223	996	C	T	190.0	chr19	16286674	C	9	0	2	57	14	0	2	69	16	0	2	78	17	0	2	78	8	0	2	51	22	0	2	93	Y	40	0.110	0
+Contig129_chr19_25541958_25542221	202	T	C	68.1	chr19	25542154	C	11	0	2	60	19	0	2	84	10	0	2	60	17	0	2	78	9	0	2	54	12	0	2	63	N	-1	2.551	1
+Contig29_chr19_37339947_37341911	1692	C	T	211.0	chr19	37341631	C	15	0	2	72	20	0	2	87	11	0	2	60	15	0	2	72	3	0	2	36	12	0	2	63	Y	7	0.096	0
+Contig39_chr19_47709708_47711327	444	C	T	36.8	chr19	47710148	T	10	0	2	57	4	0	2	39	8	0	2	51	9	0	2	54	6	0	2	45	6	0	2	45	Y	95	1.251	1
+Contig60_chr19_54013816_54014398	281	A	G	138.0	chr19	54014103	C	6	0	2	45	15	0	2	72	7	0	2	48	10	0	2	57	15	0	2	72	10	0	2	57	Y	188	1.271	0
+Contig251_chr19_56559098_56559626	452	T	C	3.36	chr19	56559549	T	12	0	2	63	13	0	2	66	21	0	2	90	15	0	2	72	14	0	2	69	11	0	2	60	N	1	0.117	0
+Contig50_chr20_12138509_12141975	3206	C	A	248.0	chr20	12141763	C	8	0	2	51	15	0	2	72	14	0	2	69	6	0	2	45	10	0	2	57	7	0	2	48	Y	2	0.384	0
+Contig36_chr20_32631363_32632049	176	G	A	24.1	chr20	32631526	G	7	0	2	48	14	0	2	69	19	0	2	84	14	0	2	69	15	0	2	72	16	0	2	75	N	50	1.150	0
+Contig32_chr20_36468058_36468869	66	C	T	40.4	chr20	36468127	C	6	0	2	45	3	0	2	36	4	0	2	39	5	0	2	42	3	0	2	36	4	0	2	39	N	59	0.281	0
+Contig24_chr20_38203888_38204900	834	C	T	132.0	chr20	38204731	C	9	0	2	54	17	0	2	78	20	0	2	87	8	0	2	51	11	0	2	60	17	0	2	78	Y	14	0.397	0
+Contig79_chr20_44263127_44264103	456	G	T	31.5	chr20	44263573	G	22	0	2	93	16	0	2	75	15	0	2	72	19	0	2	84	13	0	2	66	26	0	2	105	Y	8	3.250	0
+Contig26_chr20_45878482_45878787	197	A	G	160.0	chr20	45878672	A	17	0	2	78	15	0	2	72	11	0	2	63	17	0	2	78	12	0	2	63	10	0	2	57	N	14	0.535	0
+Contig119_chr20_46550670_46551383	609	G	A	139.0	chr20	46551277	G	7	0	2	48	17	0	2	78	19	0	2	84	20	0	2	87	9	0	2	54	15	0	2	72	Y	7	0.488	1
+Contig50_chr21_4178523_4178687	121	G	A	362.0	chr21	4178640	G	8	0	2	51	14	0	2	69	5	0	2	42	3	0	2	36	11	0	2	60	4	0	2	39	N	392	0.483	0
+Contig103_chr21_10177255_10177765	121	G	A	125.0	chr21	10177367	G	12	0	2	63	10	0	2	57	10	0	2	57	17	0	2	78	14	0	2	69	7	0	2	51	Y	37	0.213	3
+Contig1_chr21_10805534_10806399	766	A	G	146.0	chr21	10806301	G	10	0	2	57	6	0	2	45	9	0	2	54	6	0	2	45	7	0	2	48	5	0	2	42	Y	20	0.319	0
+Contig46_chr21_21029492_21030645	443	C	T	5.37	chr21	21029910	C	15	0	2	72	11	0	2	60	16	0	2	75	15	0	2	72	13	0	2	66	6	0	2	45	Y	96	3.737	0
+Contig129_chr21_31045749_31046924	381	A	G	129.0	chr21	31046141	A	19	0	2	84	8	0	2	51	23	0	2	96	12	0	2	63	15	0	2	72	18	0	2	81	Y	69	0.028	2
+Contig23_chr21_31651123_31651986	840	C	T	71.3	chr21	31651957	T	6	0	2	45	9	0	2	54	8	0	2	51	10	0	2	57	4	0	2	39	7	0	2	48	Y	105	2.977	3
+Contig64_chr21_43341847_43342031	84	T	C	114.0	chr21	43341926	T	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	6	0	2	45	7	0	2	48	N	10	3.954	2
+Contig60_chr21_43475347_43475824	175	C	T	8.05	chr21	43475551	T	6	0	2	45	7	0	2	48	13	0	2	66	6	0	2	45	14	0	2	69	14	0	2	69	N	45	0.058	0
+Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0
+Contig46_chr22_9416920_9417467	381	G	A	145.0	chr22	9417259	G	10	0	2	57	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	7	0	2	48	Y	154	0.242	0
+Contig86_chr22_9440787_9441725	713	T	G	119.0	chr22	9441488	G	6	0	2	45	12	0	2	63	10	0	2	57	11	0	2	60	13	0	2	66	16	0	2	75	Y	132	0.218	0
+Contig16_chr22_15636960_15637372	236	A	C	9.79	chr22	15637192	T	4	0	2	39	5	0	2	42	12	0	2	63	7	0	2	48	6	0	2	45	11	0	2	60	Y	5	2.163	0
+Contig4_chr22_16114310_16114546	128	G	C	101.0	chr22	16114432	G	10	0	2	57	13	0	2	66	20	0	2	87	20	0	2	87	16	0	2	75	9	0	2	54	N	19	0.526	0
+Contig23_chr22_34612023_34612568	167	C	G	92.3	chr22	34612181	C	11	0	2	60	18	0	2	81	13	0	2	66	8	0	2	51	12	0	2	63	14	0	2	69	Y	7	0.409	0
+Contig4_chr22_38252245_38253712	799	A	C	159.0	chr22	38253064	A	18	0	2	81	15	0	2	72	15	0	2	72	20	0	2	87	27	0	2	108	15	0	2	72	Y	90	4.330	0
+Contig122_chr22_48412466_48414788	1888	C	T	125.0	chr22	48414355	T	16	0	2	75	15	0	2	72	16	0	2	75	14	0	2	72	12	0	2	63	7	0	2	48	N	42	0.122	0
+Contig77_chr22_49764414_49764875	353	C	A	148.0	chr22	49764777	C	7	4	1	65	18	0	2	81	16	0	2	75	20	0	2	87	4	3	1	52	9	4	1	67	Y	12	0.941	0
+Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
+Contig348_chr22_62406104_62406495	189	C	A	134.0	chr22	62406302	A	9	0	2	54	14	0	2	69	11	0	2	60	10	0	2	57	12	0	2	63	6	0	2	45	Y	5	0.912	0
+Contig133_chr23_3525134_3526502	1223	A	G	201.0	chr23	3526387	A	11	0	2	60	13	0	2	66	23	0	2	96	21	0	2	90	13	0	2	66	10	0	2	57	Y	61	1.359	0
+Contig111_chr23_7058063_7058181	107	G	A	108.0	chr23	7058162	A	8	0	2	51	8	0	2	51	7	0	2	48	2	0	2	33	5	0	2	42	6	0	2	45	N	3	+99.	0
+Contig79_chr23_7844129_7844837	110	C	A	141.0	chr23	7844237	T	13	0	2	66	15	0	2	72	17	0	2	78	12	0	2	63	15	0	2	72	16	0	2	75	Y	40	0.339	0
+Contig38_chr23_9201002_9201725	597	C	T	155.0	chr23	9201609	T	17	0	2	78	8	0	2	51	13	0	2	66	5	0	2	42	11	0	2	60	7	0	2	48	Y	167	0.633	1
+Contig33_chr23_20672540_20674320	347	T	A	91.4	chr23	20672885	A	11	0	2	60	14	0	2	69	15	0	2	72	7	0	2	48	12	0	2	63	18	0	2	81	Y	31	0.452	1
+Contig35_chr23_28447813_28449115	70	T	A	21.3	chr23	28447881	T	9	0	2	54	8	0	2	51	10	0	2	57	9	0	2	54	10	0	2	57	12	0	2	63	N	251	0.163	1
+Contig51_chr23_30590939_30591162	140	C	T	142.0	chr23	30591080	C	14	0	2	69	4	0	2	39	10	0	2	57	12	0	2	63	14	0	2	69	4	0	2	39	N	13	1.658	0
+Contig57_chr23_32216351_32216721	179	T	G	143.0	chr23	32216534	T	15	0	2	72	15	0	2	72	23	0	2	96	13	0	2	66	16	0	2	75	15	0	2	72	N	32	1.387	1
+Contig93_chr23_35744841_35745791	40	A	T	30.4	chr23	35744880	T	6	0	2	45	7	0	2	48	7	0	2	48	2	0	2	33	5	0	2	42	5	0	2	42	Y	50	2.173	0
+Contig32_chr23_48285289_48286638	186	T	C	176.0	chr23	48285470	T	18	0	2	81	12	0	2	63	16	0	2	75	13	0	2	66	9	0	2	54	9	0	2	54	Y	4	4.238	1
+Contig50_chr24_22515247_22516072	761	C	T	243.0	chr24	22515981	T	11	0	2	60	10	0	2	57	8	0	2	51	9	0	2	54	18	0	2	81	8	0	2	51	Y	1	0.190	0
+Contig84_chr24_29196623_29199644	466	C	T	126.0	chr24	29197091	T	7	0	2	48	11	0	2	60	8	0	2	51	7	0	2	48	11	0	2	60	15	0	2	72	Y	42	0.215	0
+Contig145_chr24_34778364_34778898	163	T	C	372.0	chr24	34778541	C	10	0	2	57	8	0	2	51	12	0	2	63	12	0	2	63	6	1	2	31	7	0	2	48	Y	40	0.037	0
+Contig34_chr24_36147443_36150244	2679	C	T	140.0	chr24	36150125	C	13	0	2	66	7	0	2	48	14	0	2	69	14	0	2	69	10	0	2	57	13	0	2	66	N	282	0.099	1
+Contig164_chr24_46598127_46599206	84	C	T	105.0	chr24	46598214	C	13	0	2	66	12	0	2	63	15	0	2	72	15	0	2	72	11	0	2	60	8	0	2	51	Y	22	1.262	1
+Contig144_chr25_4011170_4013134	541	A	G	160.0	chr25	4011690	A	12	0	2	63	17	0	2	78	13	0	2	66	13	0	2	66	13	0	2	66	13	0	2	66	Y	5	0.087	0
+Contig81_chr25_6103472_6104760	699	G	A	378.0	chr25	6104190	A	14	0	2	69	16	0	2	75	13	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	Y	33	0.789	2
+Contig152_chr25_7486442_7487609	75	A	G	11.6	chr25	7486515	A	17	0	2	78	13	0	2	66	8	0	2	51	16	0	2	75	8	0	2	51	6	0	2	45	N	2	0.158	0
+Contig24_chr25_7695778_7698612	2714	C	T	130.0	chr25	7698446	C	16	0	2	75	13	0	2	66	22	0	2	93	17	0	2	78	10	0	2	57	17	0	2	78	Y	27	0.346	0
+Contig89_chr25_8635170_8636009	586	G	C	209.0	chr25	8635744	G	13	0	2	66	13	0	2	66	21	0	2	93	14	0	2	69	15	0	2	72	15	0	2	72	Y	14	0.067	0
+Contig59_chr25_18196776_18197707	785	G	A	112.0	chr25	18197551	G	8	10	1	42	27	0	2	108	21	0	2	90	18	0	2	81	10	0	2	57	14	0	2	69	N	36	3.625	0
+Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
+Contig84_chr25_42407960_42408708	55	C	T	119.0	chr25	42408013	C	6	0	2	45	9	0	2	54	11	0	2	60	9	0	2	54	7	0	2	48	8	0	2	51	Y	11	0.121	0
+Contig73_chr25_43562500_43564110	955	T	C	52.1	chr25	43563469	C	9	0	2	57	4	0	2	39	6	0	2	45	5	0	2	42	7	0	2	48	10	0	2	57	Y	4	1.406	0
+Contig37_chr25_51074433_51074885	170	A	G	102.0	chr25	51074589	G	11	0	2	60	7	0	2	48	6	0	2	45	15	0	2	72	9	0	2	54	7	0	2	48	Y	68	0.207	1
+Contig204_chr26_4311195_4311778	170	C	T	16.9	chr26	4311363	T	20	0	2	87	8	0	2	51	13	0	2	66	18	0	2	81	11	0	2	60	14	0	2	69	N	35	0.085	0
+Contig122_chr26_7622321_7623491	106	C	G	139.0	chr26	7622423	C	3	0	2	36	9	0	2	54	10	0	2	57	12	0	2	63	9	0	2	54	5	0	2	42	N	19	0.458	0
+Contig11_chr26_11062142_11062902	707	C	A	108.0	chr26	11062836	T	7	0	2	48	8	0	2	51	16	0	2	75	10	0	2	57	6	0	2	45	14	0	2	69	Y	-1	4.709	0
+Contig133_chr26_17695661_17696368	39	T	G	98.7	chr26	17695700	T	10	0	2	57	3	0	2	36	11	0	2	60	9	0	2	54	2	0	2	33	1	0	2	30	N	85	3.402	0
+Contig146_chr26_26622638_26623906	574	G	A	186.0	chr26	26623219	A	11	0	2	60	12	0	2	63	9	0	2	54	11	0	2	60	9	0	2	54	12	0	2	63	Y	1	0.318	0
+Contig8_chr26_27834126_27834326	140	G	A	41.7	chr26	27834268	G	13	0	2	66	7	0	2	48	13	0	2	66	11	0	2	60	12	0	2	63	6	0	2	45	N	29	0.142	1
+Contig78_chr26_31128839_31129005	123	T	C	145.0	chr26	-1	N	11	0	2	60	3	0	2	36	7	0	2	48	8	0	2	51	10	0	2	46	7	0	2	48	N	-1	1.230	1
+Contig28_chr26_32935355_32935833	289	T	C	77.9	chr26	32935638	T	15	0	2	72	22	0	2	93	15	0	2	72	9	0	2	54	15	0	2	72	17	0	2	78	Y	10	2.258	1
+Contig135_chr27_6853874_6854079	158	C	T	116.0	chr27	6854032	T	18	0	2	81	19	0	2	84	13	0	2	66	7	0	2	48	8	0	2	51	11	0	2	60	N	4	0.060	1
+Contig47_chr27_11777710_11777915	25	A	G	67.3	chr27	11777731	A	3	0	2	36	5	0	2	42	6	0	2	45	10	0	2	57	9	0	2	54	6	0	2	45	N	97	+99.	0
+Contig23_chr27_14633002_14633153	23	G	A	128.0	chr27	14633023	A	3	0	2	36	4	0	2	39	5	0	2	42	5	0	2	42	3	0	2	36	2	0	2	33	N	240	3.881	0
+Contig29_chr27_15428166_15429413	380	T	C	140.0	chr27	15428539	T	15	0	2	72	15	0	2	72	17	0	2	78	15	0	2	72	15	0	2	72	15	0	2	72	Y	47	0.916	1
+Contig31_chr27_19519489_19520891	129	G	T	14.9	chr27	19519624	T	12	0	2	63	19	0	2	84	20	0	2	87	16	0	2	75	10	0	2	57	11	0	2	60	Y	48	2.756	0
+Contig35_chr27_40596169_40596445	20	G	C	133.0	chr27	40596189	G	8	0	2	51	3	0	2	36	4	0	2	39	2	0	2	33	4	0	2	39	4	0	2	39	Y	4	+99.	1
+Contig85_chr27_45471750_45472022	211	G	A	53.1	chr27	45471964	G	18	0	2	81	10	0	2	57	15	0	2	72	0	13	0	36	16	0	2	75	14	0	2	69	N	75	2.502	1
+Contig131_chr28_6481806_6483783	138	C	T	36.2	chr28	6481953	C	12	0	2	63	12	0	2	63	20	0	2	87	11	0	2	60	10	0	2	57	12	0	2	63	Y	10	0.387	0
+Contig141_chr28_10027332_10028242	780	T	G	74.8	chr28	10028095	T	10	0	2	57	11	0	2	60	14	0	2	69	10	0	2	57	7	0	2	48	9	0	2	54	Y	19	3.348	0
+Contig144_chr28_15468203_15470548	743	G	A	20.0	chr28	15468942	G	13	0	2	66	12	0	2	63	10	0	2	57	11	0	2	60	16	0	2	75	7	0	2	48	N	14	0.053	0
+Contig47_chr28_21311718_21312366	541	G	A	116.0	chr28	21312258	G	9	0	2	54	6	0	2	45	12	0	2	63	6	0	2	45	5	0	2	45	12	0	2	63	N	9	0.240	0
+Contig60_chr28_30197166_30197364	92	T	C	164.0	chr28	30197258	T	10	0	2	57	13	0	2	66	15	0	2	72	16	0	2	75	12	0	2	63	11	0	2	60	N	369	1.139	0
+Contig29_chr29_4726399_4727143	559	A	T	163.0	chr29	4726955	A	15	0	2	72	18	0	2	81	18	0	2	81	16	0	2	75	11	0	2	60	14	0	2	72	Y	161	3.114	0
+Contig48_chr29_13129286_13130137	232	A	G	92.2	chr29	13129514	G	13	0	2	66	11	0	2	60	19	0	2	84	16	0	2	75	11	0	2	60	17	0	2	78	Y	337	2.581	1
+Contig33_chr29_17000374_17000921	71	C	T	48.6	chr29	17000441	-	4	0	2	39	9	0	2	54	12	0	2	66	10	0	2	57	7	0	2	48	4	0	2	39	N	26	5.491	0
+Contig34_chr29_17581796_17584016	2105	C	T	126.0	chr29	17583890	T	14	0	2	69	11	0	2	60	18	0	2	81	12	0	2	63	10	0	2	57	10	0	2	57	Y	22	2.208	0
+Contig19_chr29_20976080_20977761	1007	G	A	115.0	chr29	20977076	G	19	0	2	84	22	0	2	93	22	0	2	93	22	0	2	93	11	0	2	60	13	0	2	66	Y	4	1.915	0
+Contig51_chr29_21149853_21150467	266	C	T	146.0	chr29	21150118	C	12	0	2	63	12	0	2	63	23	0	2	96	14	0	2	69	13	0	2	66	10	0	2	57	Y	4	0.051	0
+Contig1_chr30_5992217_5993068	106	C	T	129.0	chr30	5992319	C	10	0	2	57	11	0	2	60	7	0	2	48	11	0	2	60	10	0	2	57	12	0	2	63	Y	76	1.079	0
+Contig1_chr30_8232878_8233406	402	C	T	127.0	chr30	8233264	C	8	0	2	51	19	0	2	84	16	0	2	75	18	0	2	81	10	0	2	57	14	0	2	69	Y	358	5.283	0
+Contig108_chr30_9436961_9437520	546	C	T	39.8	chr30	9437502	C	7	0	2	48	5	0	2	42	2	0	2	33	7	0	2	48	5	0	2	42	7	0	2	48	Y	64	+99.	0
+Contig165_chr30_25804389_25804926	190	T	C	126.0	chr30	25804592	C	3	0	2	36	8	0	2	51	7	0	2	48	10	0	2	57	7	0	2	48	4	0	2	39	Y	113	0.329	0
+Contig193_chr30_27495616_27496125	434	C	A	234.0	chr30	27496024	C	13	0	2	66	16	0	2	75	25	0	2	102	16	0	2	75	13	0	2	66	14	0	2	69	Y	76	2.621	0
+Contig38_chr31_5164423_5166573	2074	C	T	134.0	chr31	5166501	T	13	0	2	66	10	0	2	57	17	0	2	78	11	0	2	60	17	0	2	78	10	0	2	57	Y	58	+99.	0
+Contig6_chr31_9649308_9650149	431	G	T	162.0	chr31	9649742	G	31	0	2	120	23	0	2	96	17	0	2	78	17	0	2	78	10	0	2	57	16	0	2	75	Y	98	2.200	0
+Contig7_chr31_12384974_12386400	305	C	T	69.6	chr31	12385267	C	6	0	2	45	10	0	2	57	11	0	2	60	11	0	2	60	9	0	2	54	12	0	2	63	Y	44	1.165	0
+Contig90_chr31_17267583_17267778	81	C	A	143.0	chr31	17267665	C	20	0	2	87	6	0	2	45	14	0	2	72	22	0	2	93	17	0	2	78	15	0	2	72	N	7	0.565	0
+Contig137_chr31_23357653_23358568	885	G	A	119.0	chr31	23358545	G	5	0	2	42	3	0	2	36	3	0	2	36	2	0	2	33	3	0	2	36	4	0	2	39	Y	11	+99.	0
+Contig17_chr31_26433828_26434459	498	T	C	9.79	chr31	26434322	T	18	0	2	81	10	0	2	57	15	0	2	72	13	0	2	66	16	0	2	75	15	0	2	72	Y	137	4.814	0
+Contig30_chr32_25902721_25905783	208	C	G	162.0	chr32	25902927	G	11	0	2	60	13	0	2	66	11	0	2	60	12	0	2	63	7	0	2	48	11	0	2	60	Y	145	0.322	2
+Contig42_chr32_38900713_38901320	320	A	G	134.0	chr32	38901021	T	12	0	2	63	10	0	2	57	9	11	1	104	5	0	2	42	19	0	2	84	7	6	1	56	Y	71	0.165	0
+Contig18_chr33_22207246_22209159	1363	G	T	51.5	chr33	22208619	-	16	0	2	75	8	0	2	51	11	0	2	60	10	0	2	57	15	0	2	72	12	0	2	63	Y	59	2.560	0
+Contig104_chr33_22483642_22484187	424	C	T	140.0	chr33	22484054	T	13	0	2	66	16	0	2	75	9	0	2	54	15	0	2	72	13	0	2	66	10	0	2	57	Y	36	0.404	0
+Contig170_chr33_26189421_26189940	292	T	C	98.4	chr33	26189703	T	21	0	2	90	13	0	2	66	15	0	2	72	13	0	2	66	19	0	2	84	13	0	2	66	Y	23	0.307	0
+Contig41_chr34_16544482_16545449	46	T	C	102.0	chr34	16544523	T	5	0	2	42	11	0	2	60	6	0	2	45	0	2	0	3	7	0	2	48	8	0	2	51	Y	215	1.156	0
+Contig8_chr34_18474513_18475673	1122	C	A	129.0	chr34	18475628	A	8	0	2	51	15	0	2	72	13	0	2	66	17	0	2	78	13	0	2	66	6	0	2	45	Y	61	0.123	2
+Contig152_chr34_31794848_31795540	242	G	A	93.2	chr34	31795093	G	11	0	2	60	24	0	2	99	17	0	2	78	15	0	2	72	18	0	2	81	17	0	2	78	Y	123	2.780	0
+Contig28_chr34_41708848_41712034	1381	A	G	78.2	chr34	41710232	A	11	0	2	60	17	0	2	78	15	0	2	72	16	0	2	75	15	0	2	72	14	0	2	69	Y	236	0.234	0
+Contig85_chr34_42798284_42800584	1845	C	T	171.0	chr34	42800126	T	5	0	2	42	7	0	2	48	6	0	2	45	7	0	2	48	6	0	2	45	2	0	2	33	Y	5	2.787	0
+Contig47_chr35_3666773_3667898	348	G	T	124.0	chr35	3667121	G	9	0	2	54	20	0	2	87	18	0	2	81	15	0	2	72	12	0	2	63	14	0	2	69	Y	285	0.235	0
+Contig195_chr35_15722500_15722741	205	G	A	4.08	chr35	15722718	G	3	0	2	36	5	0	2	42	1	0	2	30	6	0	2	45	1	0	2	30	1	0	2	30	N	43	+99.	0
+Contig101_chr35_19513178_19513697	62	C	T	112.0	chr35	19513238	C	12	0	2	63	7	0	2	48	13	0	2	66	7	0	2	48	5	0	2	42	8	0	2	51	N	115	3.135	0
+Contig47_chr35_24382042_24382526	33	G	A	87.0	chr35	24382076	G	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	4	0	2	39	2	0	2	33	Y	71	+99.	0
+Contig77_chr35_24796947_24797172	65	A	G	52.1	chr35	24797009	A	7	0	2	48	5	0	2	42	8	0	2	51	6	0	2	45	12	0	2	63	10	0	2	57	N	11	1.401	3
+Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0
+Contig5_chr36_4562983_4563634	343	C	T	151.0	chr36	4563324	T	20	0	2	87	20	0	2	87	23	0	2	96	24	0	2	99	9	0	2	54	8	0	2	51	Y	40	1.169	0
+Contig75_chr36_7885319_7885588	53	G	A	25.7	chr36	7885372	G	10	0	2	57	8	0	2	51	13	0	2	66	7	0	2	48	4	0	2	39	7	0	2	48	N	7	2.653	0
+Contig184_chr36_18956191_18958552	187	A	G	11.5	chr36	18956371	G	10	0	2	57	11	0	2	60	21	0	2	90	14	0	2	69	7	0	2	48	4	0	2	39	N	278	1.434	2
+Contig12_chr36_21557176_21557828	513	T	A	159.0	chr36	21557695	A	11	0	2	60	14	0	2	69	21	0	2	90	12	0	2	63	15	0	2	72	11	0	2	60	Y	55	0.222	0
+Contig2_chr36_22436067_22436794	653	C	T	73.0	chr36	22436730	C	11	0	2	60	16	0	2	75	13	0	2	66	11	0	2	60	21	0	2	90	21	0	2	90	Y	9	0.534	0
+Contig133_chr36_32954045_32955409	136	A	G	116.0	chr36	32954182	A	16	0	2	75	15	0	2	72	20	0	2	87	11	0	2	60	18	0	2	81	13	0	2	66	Y	74	3.772	1
+Contig53_chr37_6665763_6665919	116	C	T	111.0	chr37	6665875	C	9	0	2	54	9	0	2	54	5	0	2	42	9	0	2	54	8	0	2	51	10	0	2	57	N	15	10.875	1
+Contig42_chr37_9589176_9591269	252	G	A	25.1	chr37	9589430	G	10	0	2	40	13	0	2	66	18	0	2	81	21	0	2	90	9	0	2	54	17	0	2	78	N	67	1.170	2
+Contig2_chr37_17134963_17136513	1140	A	C	158.0	chr37	17136092	A	14	0	2	69	24	0	2	99	17	0	2	78	16	0	2	75	15	0	2	75	13	0	2	66	Y	12	0.053	1
+Contig18_chr37_17147806_17149851	291	T	G	112.0	chr37	17148084	T	4	6	1	45	16	0	2	75	17	0	2	78	14	0	2	69	22	0	2	93	13	0	2	66	Y	41	4.442	0
+Contig64_chr37_17606895_17607534	565	C	T	30.2	chr37	17607439	A	9	0	2	54	16	0	2	75	20	0	2	87	14	0	2	69	16	0	2	75	10	0	2	57	N	20	1.622	0
+Contig126_chr37_21587881_21590621	373	G	T	132.0	chr37	21588256	G	11	0	2	60	11	0	2	60	23	0	2	96	12	0	2	63	8	0	2	51	18	0	2	81	Y	12	0.549	0
+Contig2_chr37_31197993_31198256	182	C	T	39.6	chr37	31198171	T	6	0	2	45	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	12	0	2	63	N	2	0.595	0
+Contig46_chr37_31852376_31853555	825	A	G	111.0	chr37	31853191	G	19	0	2	84	14	0	2	69	15	0	2	72	7	0	2	48	8	0	2	51	16	0	2	75	Y	17	0.128	1
+Contig7_chr38_12217200_12218387	1163	A	T	44.4	chr38	12218353	A	11	0	2	60	13	0	2	66	17	0	2	78	10	0	2	57	11	0	2	60	11	0	2	60	Y	67	+99.	0
+Contig15_chr38_12282020_12282253	150	C	T	156.0	chr38	12282164	A	17	0	2	78	11	0	2	60	19	0	2	84	14	0	2	69	5	0	2	42	14	0	2	69	Y	26	2.952	1
+Contig6_chr38_16185744_16186110	325	A	G	74.9	chr38	16186061	A	5	0	2	42	3	0	2	36	9	0	2	54	7	0	2	48	1	0	2	30	12	0	2	63	Y	40	+99.	0
+Contig265_chrX_2689247_2689484	114	C	G	103.0	chrX	2689356	C	11	0	2	60	9	0	2	54	13	0	2	66	16	0	2	75	14	0	2	69	10	0	2	57	N	2	9.232	1
+Contig122_chrX_6026976_6027327	330	C	T	79.4	chrX	6027303	C	3	0	2	36	3	0	2	36	3	0	2	36	4	0	2	39	3	0	2	36	6	0	2	45	Y	30	+99.	0
+Contig113_chrX_26287829_26288398	385	C	T	59.6	chrX	26288213	C	9	0	2	54	9	0	2	54	17	0	2	78	11	0	2	60	3	8	1	44	4	0	2	39	N	13	0.077	0
+Contig237_chrX_31256648_31257654	165	T	A	246.0	chrX	31256814	T	7	0	2	48	23	0	2	96	19	0	2	84	17	0	2	78	14	0	2	69	8	0	2	51	Y	37	1.481	0
+Contig90_chrX_57430715_57431566	548	C	T	116.0	chrX	57431266	T	9	0	2	54	18	0	2	81	13	0	2	66	14	0	2	69	8	0	2	54	7	0	2	48	Y	261	0.154	1
+Contig133_chrX_84833782_84834125	182	G	A	69.7	chrX	84833962	G	5	0	2	42	18	0	2	81	12	0	2	63	19	0	2	84	6	3	1	27	7	0	2	48	N	619	0.278	0
+Contig125_chrX_93319363_93320877	349	A	C	145.0	chrX	93319721	A	4	0	2	39	6	0	2	45	11	0	2	60	10	0	2	57	13	0	2	66	6	0	2	45	Y	59	1.686	0
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/modify_snp_table/modify.snp
--- a/test-data/test_out/modify_snp_table/modify.snp	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,338 +0,0 @@
-Contig161_chr1_4641264_4641879	115	C	T	73.5	chr1	4641382	C	6	0	2	45	8	0	2	51	15	0	2	72	5	0	2	42	6	0	2	45	10	0	2	57	Y	54	0.323	0
-Contig20_chr1_21313469_21313570	66	C	T	54.0	chr1	21313534	C	4	0	2	39	4	0	2	39	5	0	2	42	4	0	2	39	4	0	2	39	5	0	2	42	N	1	+99.	0
-Contig86_chr1_30984450_30985684	670	C	T	365.0	chr1	30985133	C	9	0	2	54	10	0	2	57	13	0	2	66	3	0	2	36	9	0	2	54	7	0	2	48	Y	145	0.031	0
-Contig5_chr1_32562160_32563940	1215	G	T	163.0	chr1	32563356	G	17	0	2	78	19	0	2	84	20	0	2	87	14	0	2	69	12	0	2	63	10	0	2	57	Y	17	0.251	0
-Contig110_chr1_33385093_33386888	510	C	T	270.0	chr1	33385587	A	14	0	2	69	11	0	2	60	19	0	2	84	11	0	2	60	10	0	2	57	13	0	2	66	Y	13	0.126	0
-Contig100_chr1_33562920_33564288	743	C	T	178.0	chr1	33563655	C	6	0	2	45	10	0	2	57	8	0	2	51	5	0	2	42	13	0	2	66	7	0	2	48	Y	13	0.090	3
-Contig7_chr1_37302355_37302489	97	A	G	59.2	chr1	37302452	G	3	0	2	36	8	0	2	51	5	0	2	42	8	0	2	51	7	0	2	48	6	0	2	45	N	56	2.812	0
-Contig62_chr1_41880715_41882180	1078	T	G	57.6	chr1	41881785	T	14	0	2	69	15	0	2	72	16	0	2	75	13	0	2	66	8	0	2	51	10	0	2	57	Y	21	0.477	0
-Contig47_chr1_48409178_48409384	37	C	T	134.0	chr1	48409215	T	5	0	2	42	6	0	2	45	8	0	2	51	9	0	2	54	4	0	2	39	6	0	2	45	N	66	+99.	0
-Contig119_chr1_49647683_49650077	1618	C	A	99.7	chr1	49649276	A	8	0	2	51	11	0	2	60	10	0	2	57	9	0	2	54	10	0	2	57	14	0	2	69	Y	16	0.166	0
-Contig21_chr1_60697952_60699446	307	G	A	51.9	chr1	60698265	G	12	0	2	63	9	0	2	54	4	0	2	39	6	0	2	45	9	0	2	54	4	0	2	39	Y	98	0.507	0
-Contig131_chr1_62319542_62320564	169	C	G	103.0	chr1	62319709	C	12	0	2	63	12	0	2	66	14	0	2	69	12	0	2	63	9	0	2	54	9	0	2	54	Y	73	0.307	1
-Contig14_chr1_63450425_63450680	101	T	A	102.0	chr1	63450530	T	8	0	2	51	10	0	2	57	18	0	2	81	8	0	2	51	8	0	2	34	8	0	2	51	N	99	1.085	0
-Contig83_chr1_63869778_63869942	40	T	C	23.7	chr1	63869819	C	5	0	2	42	7	0	2	48	2	0	2	33	4	0	2	39	6	0	2	48	4	0	2	39	N	654	1.364	0
-Contig30_chr1_64702572_64703138	178	A	T	117.0	chr1	64702750	T	10	0	2	57	10	0	2	57	20	0	2	87	21	0	2	90	6	0	2	45	12	0	2	63	Y	50	3.872	0
-Contig101_chr1_69868406_69868872	287	G	A	14.6	chr1	69868689	G	13	0	2	66	17	0	2	78	10	0	2	57	8	0	2	51	7	0	2	48	8	0	2	51	N	137	0.305	0
-Contig35_chr1_74482577_74482791	170	G	A	45.4	chr1	74482751	A	3	0	2	36	4	0	2	39	13	0	2	66	2	0	2	33	5	0	2	42	2	0	2	33	N	20	+99.	3
-Contig49_chr1_83865731_83865944	85	G	A	34.1	chr1	-1	N	4	0	2	39	4	0	2	39	8	0	2	51	2	0	2	33	5	0	2	42	4	0	2	39	N	-1	1.485	0
-Contig129_chr1_117547123_117548666	926	G	A	126.0	chr1	117548059	G	19	0	2	84	9	0	2	54	11	0	2	60	10	0	2	57	12	0	2	63	11	0	2	60	Y	64	0.049	0
-Contig7_chr1_125154638_125154844	190	G	T	130.0	chr1	125154818	A	5	0	2	42	4	0	2	39	7	0	2	48	2	0	2	33	7	0	2	48	4	0	2	39	N	33	+99.	0
-Contig222_chr2_9817738_9818143	220	C	T	888.0	chr2	9817960	C	17	0	2	78	12	0	2	63	20	0	2	87	8	0	2	51	11	0	2	60	12	0	2	63	Y	76	0.093	1
-Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
-Contig10_chr2_40859744_40860534	637	G	A	888.0	chr2	40860397	A	3	0	2	36	3	0	2	36	2	0	2	33	7	0	2	48	6	0	2	45	8	0	2	51	Y	42	1.435	0
-Contig52_chr2_41421981_41422725	604	C	A	888.0	chr2	41422583	A	17	0	2	78	18	0	2	81	14	0	2	69	17	0	2	78	12	0	2	63	14	0	2	69	Y	44	0.882	0
-Contig94_chr2_43869105_43870358	220	G	A	888.0	chr2	43869333	G	12	0	2	63	18	0	2	81	11	0	2	60	15	0	2	72	12	0	2	63	13	0	2	66	Y	1	0.156	0
-Contig34_chr2_48444129_48444939	695	C	T	134.0	chr2	48444828	C	14	0	2	69	8	0	2	51	16	0	2	75	17	0	2	78	9	0	2	54	15	0	2	72	Y	161	0.375	0
-Contig6_chr2_56859179_56859956	671	T	C	999.9	chr2	56859851	T	15	0	2	72	18	0	2	81	20	0	2	90	19	0	2	84	19	0	2	84	24	0	2	99	N	28	5.308	1
-Contig115_chr2_61631913_61632510	310	G	T	999.3	chr2	61632216	G	7	0	2	48	9	0	2	54	7	0	2	48	11	0	2	60	10	0	2	57	10	0	2	57	N	13	0.184	0
-Contig31_chr2_67331584_67331785	39	C	T	999.0	chr2	67331623	C	11	0	2	60	10	0	2	57	7	0	2	48	9	0	2	54	2	0	2	33	4	0	2	39	N	110	0.647	1
-Contig92_chr2_75906683_75907774	773	T	C	85.4	chr2	75907438	C	12	0	2	63	12	0	2	63	17	0	2	78	8	0	2	51	8	0	2	51	13	0	2	66	Y	93	0.166	0
-Contig163_chr2_76402959_76404830	221	C	T	127.0	chr2	76403181	C	4	0	2	42	10	0	2	57	9	0	2	54	11	0	2	60	7	0	2	48	9	0	2	54	Y	54	0.178	1
-Contig59_chr2_85243022_85243758	506	G	A	96.3	chr2	85243509	T	9	0	2	54	11	0	2	60	12	0	2	63	14	0	2	69	10	0	2	57	7	0	2	48	Y	6	0.459	0
-Contig56_chr3_17326225_17327548	387	G	C	91.2	chr3	17326591	G	14	0	2	69	13	0	2	66	15	0	2	72	15	0	2	72	13	0	2	66	12	0	2	63	Y	20	0.225	3
-Contig108_chr3_46210055_46210874	367	A	G	21.0	chr3	46210423	A	19	0	2	84	10	0	2	57	16	0	2	75	14	0	2	69	20	0	2	87	11	0	2	60	N	236	0.028	1
-Contig16_chr3_47113407_47114449	322	G	A	105.0	chr3	47113713	G	13	0	2	66	17	0	2	78	15	0	2	72	6	0	2	45	11	0	2	60	11	0	2	60	Y	114	0.132	5
-Contig3_chr3_47564810_47565251	262	T	G	112.0	chr3	47565104	T	14	0	2	69	16	0	2	75	20	0	2	87	10	0	2	57	9	0	2	54	8	0	2	51	Y	24	0.073	1
-Contig35_chr3_49662401_49662929	270	A	T	96.1	chr3	49662652	A	14	0	2	69	11	0	2	60	23	0	2	96	13	0	2	66	12	0	2	63	11	0	2	60	Y	36	3.583	2
-Contig97_chr3_49820354_49821631	1069	G	A	44.1	chr3	49821402	G	9	0	2	54	9	0	2	54	6	0	2	45	10	0	2	57	5	0	2	42	8	0	2	51	N	6	0.201	2
-Contig25_chr3_53260697_53262560	402	G	A	211.0	chr3	53261095	G	17	0	2	78	14	0	2	69	15	0	2	75	12	0	2	63	14	0	2	69	12	0	2	63	Y	116	1.033	0
-Contig11_chr3_53992739_53995954	2392	G	A	82.4	chr3	53995143	A	12	0	2	66	11	0	2	60	14	0	2	69	6	0	2	45	11	0	2	60	17	0	2	78	Y	358	0.321	1
-Contig236_chr3_72676275_72676473	128	G	A	278.0	chr3	72676410	G	12	0	2	63	11	0	2	60	13	0	2	66	10	0	2	57	11	0	2	60	8	0	2	51	N	36	0.496	1
-Contig48_chr3_74792236_74792388	63	T	C	111.0	chr3	74792289	-	17	0	2	78	9	0	2	54	9	0	2	54	5	0	2	42	11	0	2	60	9	0	2	54	N	-1	3.528	0
-Contig65_chr3_80727952_80728283	39	T	C	71.2	chr3	80727990	T	7	0	2	48	3	0	2	36	8	0	2	51	6	0	2	45	8	0	2	51	11	0	2	60	N	22	7.078	0
-Contig53_chr3_86407941_86409349	1406	G	A	86.9	chr3	86409317	A	5	0	2	42	5	0	2	42	4	0	2	39	10	0	2	57	8	0	2	51	12	0	2	63	N	14	3.285	1
-Contig13_chr3_92409738_92412300	718	A	G	23.3	chr3	92410450	A	12	0	2	63	16	0	2	75	18	0	2	81	13	0	2	66	22	0	2	93	7	0	2	48	Y	23	0.224	2
-Contig134_chr4_12145648_12148225	1326	C	T	164.0	chr4	12146961	C	9	0	2	54	8	0	2	51	7	0	2	48	3	0	2	36	5	0	2	42	5	0	2	42	Y	4	0.080	1
-Contig88_chr4_15557471_15557833	268	A	G	145.0	chr4	15557737	A	6	0	2	45	6	0	2	45	11	0	2	60	9	0	2	54	5	0	2	42	6	0	2	45	Y	46	4.138	0
-Contig53_chr4_18823968_18824478	149	A	G	91.3	chr4	18824115	A	18	0	2	81	15	0	2	72	21	0	2	90	13	0	2	66	9	0	2	54	12	0	2	63	N	51	0.251	0
-Contig19_chr4_26233601_26233991	146	G	C	51.6	chr4	26233744	G	10	0	2	57	8	0	2	51	9	0	2	54	5	0	2	42	9	0	2	54	4	0	2	39	N	41	0.163	3
-Contig78_chr4_28579975_28580134	30	T	G	19.6	chr4	28579994	-	4	0	2	39	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	2	0	2	33	N	33	0.499	0
-Contig16_chr4_30177226_30179725	621	C	T	88.4	chr4	30177859	C	20	0	2	87	13	0	2	66	13	0	2	66	11	0	2	60	8	0	2	51	8	0	2	51	Y	45	0.797	1
-Contig30_chr4_46196500_46197672	1045	A	C	33.4	chr4	46197522	C	16	0	2	75	9	0	2	54	4	0	2	39	7	0	2	48	14	0	2	69	6	0	2	45	Y	43	0.306	0
-Contig2_chr4_47039007_47039323	158	G	C	35.1	chr4	47039160	-	8	0	2	51	9	0	2	54	13	0	2	66	8	0	2	51	10	0	2	60	9	0	2	54	N	0	0.131	0
-Contig17_chr4_61310346_61311158	267	C	T	49.9	chr4	61310604	T	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	14	0	2	69	7	0	2	48	Y	219	0.098	0
-Contig26_chr4_64190783_64191295	64	A	G	162.0	chr4	64190843	A	10	0	2	57	6	0	2	45	20	0	2	87	12	0	2	63	17	0	2	78	7	0	2	48	Y	306	7.428	0
-Contig11_chr4_65500960_65501654	634	T	C	107.0	chr4	65501585	T	13	0	2	66	14	0	2	69	13	0	2	66	13	0	2	66	6	0	2	45	18	0	2	81	Y	10	6.849	0
-Contig38_chr4_67768488_67768982	113	A	G	102.0	chr4	67768598	A	9	0	2	54	8	0	2	51	9	0	2	54	11	0	2	60	10	0	2	57	7	0	2	48	Y	188	3.175	0
-Contig30_chr4_70978564_70979580	596	A	G	164.0	chr4	70979151	A	15	0	2	72	12	0	2	63	20	0	2	87	14	0	2	69	15	0	2	72	15	0	2	72	Y	111	2.458	2
-Contig72_chr4_74225793_74226492	674	A	G	110.0	chr4	74226472	A	5	0	2	42	3	0	2	36	2	0	2	33	3	0	2	36	7	0	2	48	4	0	2	39	Y	115	+99.	1
-Contig32_chr4_75618955_75620254	301	T	C	333.0	chr4	75619257	C	10	0	2	57	8	0	2	51	12	0	2	63	20	0	2	87	12	0	2	63	14	0	2	69	Y	34	0.163	2
-Contig31_chr5_4734956_4736547	1166	C	T	133.0	chr5	4736132	C	14	0	2	69	8	0	2	51	17	0	2	78	4	0	2	39	9	0	2	54	12	0	2	63	Y	1	0.021	0
-Contig30_chr5_15698241_15699076	396	G	T	76.6	chr5	15698633	T	8	0	2	51	9	0	2	54	10	0	2	57	7	0	2	48	11	0	2	60	8	0	2	54	Y	65	0.009	0
-Contig36_chr5_17709244_17710004	373	T	C	281.0	chr5	17709624	T	6	0	2	45	9	0	2	54	7	0	2	48	4	0	2	39	10	0	2	57	4	0	2	39	Y	16	0.131	0
-Contig13_chr5_21881138_21881562	227	A	G	251.0	chr5	21881356	A	11	0	2	60	20	0	2	87	22	0	2	93	10	0	2	57	10	0	2	57	21	0	2	90	Y	182	2.013	0
-Contig5_chr5_23188121_23190168	1841	C	T	141.0	chr5	23189975	C	20	0	2	87	19	0	2	84	22	0	2	93	16	0	2	75	18	0	2	81	14	0	2	69	N	45	0.355	0
-Contig6_chr5_26899813_26900498	97	A	C	88.6	chr5	26899910	A	15	0	2	72	14	0	2	69	27	0	2	108	15	0	2	72	13	0	2	69	12	0	2	63	Y	92	7.370	3
-Contig314_chr5_34019166_34019319	72	C	A	20.1	chr5	-1	N	6	0	2	45	9	0	2	54	4	0	2	39	4	0	2	39	9	0	2	54	5	0	2	42	N	-1	+99.	4
-Contig147_chr5_38980258_38980559	221	C	T	40.8	chr5	38980477	C	15	0	2	72	15	0	2	72	19	0	2	84	10	0	2	57	12	0	2	63	20	0	2	87	Y	11	4.576	0
-Contig115_chr5_48119079_48120169	151	C	T	78.3	chr5	48119234	C	17	0	2	78	10	0	2	57	14	0	2	69	16	0	2	75	8	0	2	51	12	0	2	63	Y	205	0.320	0
-Contig45_chr5_50892738_50892968	169	C	A	25.8	chr5	50892911	C	10	0	2	57	7	0	2	48	10	0	2	60	6	0	2	45	6	0	2	45	13	0	2	66	N	244	0.497	1
-Contig40_chr5_51484164_51484696	14	A	G	53.3	chr5	51484180	A	6	0	2	45	4	0	2	39	4	0	2	39	3	0	2	36	0	0	2	13	3	0	2	36	N	63	+99.	1
-Contig40_chr5_51664286_51667573	861	C	T	148.0	chr5	51665149	C	20	0	2	87	21	0	2	90	20	0	2	87	11	0	2	60	16	0	2	75	15	0	2	72	Y	207	0.080	1
-Contig15_chr5_51889708_51891244	882	A	G	149.0	chr5	51890581	G	13	0	2	66	18	0	2	81	17	0	2	78	22	0	2	93	15	0	2	72	22	0	2	93	Y	7	0.025	1
-Contig143_chr5_57231364_57232010	294	T	C	78.5	chr5	57231644	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	10	0	2	57	6	0	2	45	Y	73	0.337	2
-Contig13_chr5_57609985_57610584	496	C	T	50.5	chr5	57610476	C	17	0	2	78	9	0	2	54	6	0	2	45	8	0	2	51	10	0	2	57	12	0	2	63	N	77	2.022	1
-Contig230_chr5_58486998_58487280	227	T	C	192.0	chr5	58487232	T	3	0	2	36	4	0	2	39	9	0	2	54	6	0	2	45	4	0	2	39	7	0	2	48	N	24	0.100	2
-Contig32_chr5_70852360_70853289	282	G	A	114.0	chr5	70852623	G	16	0	2	75	11	0	2	60	13	0	2	66	12	0	2	63	13	0	2	66	7	0	2	48	Y	33	0.276	0
-Contig100_chr5_71189678_71190590	813	C	T	30.8	chr5	71190523	C	11	0	2	60	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	Y	8	0.362	1
-Contig45_chr5_76133561_76134403	388	A	G	103.0	chr5	76133941	G	3	0	2	36	8	0	2	51	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	57	0.038	0
-Contig61_chr5_90202541_90204393	909	C	T	101.0	chr5	90203461	T	7	0	2	48	5	0	2	42	14	0	2	69	3	0	2	36	5	0	2	42	8	0	2	51	Y	64	1.448	0
-Contig111_chr6_5821219_5822519	1060	A	G	68.1	chr6	5822321	T	7	0	2	48	6	0	2	45	11	0	2	60	9	0	2	54	3	0	2	36	12	0	2	63	Y	7	0.231	1
-Contig220_chr6_10671338_10672441	999	T	C	36.3	chr6	10672322	T	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	5	0	2	42	9	0	2	54	Y	1	1.667	0
-Contig226_chr6_17361986_17362884	418	G	C	251.0	chr6	17362406	G	6	0	2	45	8	0	2	51	7	0	2	48	9	0	2	54	7	0	2	48	7	0	2	48	Y	7	0.147	0
-Contig51_chr6_20231207_20231785	161	A	G	70.5	chr6	20231375	G	13	0	2	66	5	0	2	42	8	0	2	51	2	0	2	36	5	0	2	42	5	0	2	42	Y	153	1.754	0
-Contig102_chr6_30271329_30271577	39	T	G	139.0	chr6	30271371	G	3	0	2	36	4	0	2	39	6	0	2	45	1	0	2	30	4	0	2	39	4	0	2	39	N	15	1.159	0
-Contig217_chr6_31393824_31394218	97	G	A	115.0	chr6	31393921	G	9	0	2	54	19	0	2	84	15	0	2	72	12	0	2	63	7	0	2	48	10	0	2	57	N	45	0.477	0
-Contig186_chr6_31928098_31928245	73	G	A	117.0	chr6	-1	N	5	0	2	42	8	0	2	51	2	0	2	33	4	0	2	39	1	0	2	30	5	0	2	42	N	-1	0.276	1
-Contig52_chr6_33188498_33188724	123	G	A	59.0	chr6	-1	N	5	0	2	42	13	0	2	66	8	0	2	51	4	0	2	39	9	0	2	54	9	0	2	54	N	-1	0.880	1
-Contig102_chr6_38743009_38743435	290	A	G	178.0	chr6	38743311	A	11	0	2	60	13	0	2	66	9	0	2	54	11	0	2	60	12	0	2	63	13	0	2	66	Y	34	0.148	4
-Contig81_chr6_49018353_49019532	179	C	A	72.5	chr6	49018530	A	15	0	2	72	13	0	2	66	19	0	2	72	8	0	2	51	12	0	2	63	16	0	2	75	Y	15	0.145	1
-Contig112_chr6_51024554_51024851	100	A	G	121.0	chr6	51024654	A	10	0	2	57	12	0	2	63	9	0	2	54	13	0	2	66	14	0	2	69	17	0	2	78	N	75	4.287	0
-Contig40_chr6_51412751_51413807	227	T	C	94.5	chr6	51412975	C	5	0	2	42	8	0	2	51	7	0	2	48	9	0	2	54	11	0	2	60	10	0	2	57	Y	4	5.661	0
-Contig47_chr6_69073222_69074767	1315	T	C	212.0	chr6	69074558	T	20	0	2	87	17	0	2	78	18	0	2	81	12	0	2	63	17	0	2	78	7	0	2	48	Y	9	0.652	0
-Contig30_chr6_74848932_74849059	57	C	G	46.3	chr6	74848993	C	7	0	2	48	7	0	2	33	6	0	2	45	7	0	2	48	5	0	2	42	6	0	2	45	N	-1	+99.	1
-Contig84_chr7_6648683_6650255	1297	G	A	110.0	chr7	6649988	G	18	0	2	81	9	0	2	54	22	0	2	77	16	0	2	75	20	0	2	87	6	0	2	45	Y	83	0.166	0
-Contig239_chr7_13007379_13007700	275	A	G	39.8	chr7	13007642	A	8	0	2	51	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	5	0	2	42	N	46	1.511	3
-Contig119_chr7_18310707_18310948	23	A	T	133.0	chr7	18310729	A	6	0	2	45	5	0	2	42	10	0	2	57	5	0	2	42	2	0	2	33	2	0	2	33	N	4553	+99.	0
-Contig93_chr7_18513377_18513741	173	T	C	130.0	chr7	18513533	C	15	0	2	72	11	0	2	60	18	0	2	81	6	0	2	45	10	0	2	57	14	0	2	69	Y	115	0.174	0
-Contig133_chr7_19603333_19603776	414	C	G	31.9	chr7	19603734	G	10	0	2	57	4	0	2	39	4	0	2	39	5	0	2	42	9	0	2	54	9	0	2	54	N	78	+99.	5
-Contig132_chr7_20426224_20428145	1815	A	G	28.3	chr7	20428041	A	11	1	2	43	12	0	2	63	19	0	2	84	23	0	2	96	14	0	2	69	10	0	2	57	N	11	0.264	0
-Contig206_chr7_26281823_26282074	103	C	A	101.0	chr7	26281925	T	11	0	2	60	16	0	2	61	19	0	2	84	6	0	2	45	19	0	2	84	16	0	2	75	N	-1	0.947	1
-Contig55_chr7_53147505_53148974	894	A	G	68.4	chr7	53148397	G	22	0	2	93	13	0	2	66	16	0	2	75	8	0	2	51	16	0	2	75	11	0	2	60	Y	19	0.060	0
-Contig4_chr7_53685534_53688206	1709	C	G	76.2	chr7	53687225	C	18	0	2	81	17	0	2	78	18	0	2	81	15	0	2	72	14	0	2	69	14	0	2	69	Y	32	0.659	1
-Contig61_chr7_55832923_55834065	506	T	C	185.0	chr7	55833450	C	9	0	2	54	10	0	2	57	22	0	2	93	12	0	2	63	12	0	2	63	7	0	2	48	Y	1	0.019	0
-Contig91_chr8_12804505_12805470	409	C	A	111.0	chr8	12804906	C	8	0	2	51	10	0	2	57	15	0	2	72	12	0	2	63	14	0	2	69	15	0	2	72	N	145	0.175	0
-Contig8_chr8_27811135_27812620	333	C	T	37.9	chr8	27811458	C	4	0	2	39	11	0	2	60	18	0	2	81	5	0	2	42	6	0	2	45	5	0	2	42	Y	1	0.272	0
-Contig66_chr8_28273102_28273660	175	G	C	81.6	chr8	28273263	T	9	0	2	54	17	0	2	78	19	0	2	84	8	0	2	51	16	0	2	75	19	0	2	84	Y	3	2.735	0
-Contig84_chr8_31375511_31376456	443	T	C	125.0	chr8	31375954	T	10	0	2	57	15	0	2	72	27	0	2	108	18	0	2	81	16	0	2	75	9	0	2	54	Y	2	0.650	0
-Contig18_chr8_32575859_32577431	264	T	C	151.0	chr8	32576124	T	20	0	2	87	14	0	2	69	17	0	2	78	14	0	2	69	13	0	2	66	14	0	2	69	Y	17	0.915	1
-Contig54_chr8_40913908_40916451	1275	G	A	175.0	chr8	40915190	G	10	0	2	57	8	0	2	51	11	0	2	60	7	0	2	48	8	0	2	51	9	0	2	54	Y	21	0.056	3
-Contig93_chr8_44658786_44659075	180	T	G	55.3	chr8	44658964	T	4	0	2	39	3	0	2	36	6	0	2	45	5	0	2	45	5	0	2	42	4	0	2	39	N	14	0.188	0
-Contig66_chr8_58562376_58563446	345	C	G	5.74	chr8	58562721	C	14	0	2	69	12	0	2	63	9	0	2	57	10	0	2	57	9	0	2	54	10	0	2	57	Y	6	0.685	0
-Contig44_chr8_71186368_71188207	1455	G	T	147.0	chr8	71187818	G	4	10	1	74	3	0	2	36	20	0	2	87	12	0	2	63	8	0	2	51	10	0	2	57	Y	88	0.036	0
-Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
-Contig96_chr9_39008495_39009278	215	A	C	98.7	chr9	39008708	C	7	0	2	48	13	0	2	66	28	0	2	111	16	0	2	75	17	0	2	78	17	0	2	78	Y	8	0.427	1
-Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
-Contig63_chr10_42716594_42719945	1018	A	G	88.7	chr10	42717616	G	13	0	2	66	14	0	2	69	13	0	2	66	12	0	2	63	18	0	2	81	5	0	2	42	Y	25	1.740	0
-Contig22_chr10_43255307_43255570	81	C	A	37.2	chr10	43255383	C	15	0	2	72	18	0	2	81	22	0	2	93	16	0	2	75	11	0	2	60	12	0	2	63	N	62	0.450	0
-Contig9_chr10_51475063_51476054	770	C	T	57.3	chr10	51475839	C	6	0	2	45	16	0	2	75	16	0	2	75	13	0	2	66	9	0	2	54	9	2	2	21	N	80	0.394	0
-Contig42_chr10_53816543_53818392	1642	G	A	27.5	chr10	53818172	A	7	0	2	48	13	0	2	66	17	0	2	78	14	0	2	69	19	0	2	84	16	0	2	75	N	1	0.433	0
-Contig36_chr10_53992615_53993741	229	G	C	86.2	chr10	53992846	G	17	0	2	78	14	0	2	69	13	0	2	66	15	0	2	72	12	0	2	63	15	0	2	72	N	23	1.912	0
-Contig20_chr10_58141129_58141750	575	C	T	46.1	chr10	58141701	C	7	0	2	48	8	0	2	51	9	0	2	54	3	0	2	36	4	0	2	39	9	0	2	54	N	1	4.264	0
-Contig26_chr10_59510973_59511899	146	C	A	29.0	chr10	59511126	C	8	0	2	51	13	0	2	66	18	0	2	81	13	0	2	66	10	0	2	57	7	0	2	48	Y	208	1.077	0
-Contig72_chr11_7142765_7143772	146	G	A	152.0	chr11	7142911	A	8	0	2	51	8	0	2	51	24	0	2	99	10	0	2	57	17	0	2	78	11	0	2	60	Y	90	1.137	0
-Contig9_chr11_9904571_9905983	1284	C	T	151.0	chr11	9905857	C	16	0	2	75	19	0	2	84	17	0	2	78	16	0	2	75	12	0	2	63	13	1	2	44	Y	11	0.422	1
-Contig7_chr11_40017076_40017630	352	C	T	46.3	chr11	40017422	C	7	0	2	48	9	0	2	54	6	0	2	45	8	0	2	51	16	0	2	75	9	0	2	54	Y	44	0.336	0
-Contig108_chr11_42953408_42955156	367	A	G	89.4	chr11	42953779	A	17	0	2	78	11	0	2	60	14	0	2	69	20	0	2	87	14	0	2	69	17	0	2	78	Y	118	0.784	1
-Contig16_chr11_53408448_53408790	187	A	G	153.0	chr11	53408638	A	7	0	2	48	9	0	2	54	18	0	2	81	10	0	2	57	11	0	2	60	12	0	2	63	Y	116	1.367	0
-Contig21_chr12_18403415_18404381	586	G	T	34.5	chr12	18403983	-	13	0	2	66	16	0	2	75	25	0	2	102	12	0	2	63	12	0	2	63	14	0	2	69	Y	12	0.068	0
-Contig33_chr12_19804073_19804529	178	T	C	69.4	chr12	19804261	T	13	0	2	66	13	0	2	66	22	0	2	93	11	0	2	60	12	0	2	63	18	0	2	81	Y	11	1.571	0
-Contig41_chr12_25565452_25566993	475	G	T	6.29	chr12	25565926	G	15	0	2	72	14	0	2	69	10	0	2	57	15	0	2	72	18	0	2	81	19	0	2	84	N	10	2.231	1
-Contig9_chr12_27204351_27204696	239	A	G	145.0	chr12	27204587	A	7	0	2	48	8	0	2	51	12	0	2	63	8	0	2	51	11	0	2	60	11	0	2	60	Y	14	0.046	0
-Contig45_chr12_30548282_30550498	448	C	T	124.0	chr12	30548703	-	9	0	2	54	11	0	2	60	22	0	2	93	19	0	2	84	12	0	2	63	12	0	2	63	Y	66	0.305	0
-Contig46_chr12_35571846_35572563	58	G	C	83.2	chr12	35571906	G	4	0	2	39	10	0	2	57	11	0	2	60	6	0	2	45	10	0	2	57	6	0	2	45	Y	55	+99.	1
-Contig28_chr12_42075871_42076044	136	G	A	134.0	chr12	42076006	A	6	0	2	45	5	0	2	42	7	0	2	48	7	0	2	48	2	0	2	33	4	0	2	39	N	3	9.479	0
-Contig16_chr12_42386141_42387454	194	A	G	161.0	chr12	42386323	A	11	0	2	60	8	0	2	54	23	0	2	96	17	0	2	78	6	0	2	45	13	0	2	66	Y	7	0.927	1
-Contig42_chr12_44424628_44425829	255	A	G	84.4	chr12	44424879	A	12	0	2	63	19	0	2	84	23	0	2	96	15	0	2	72	18	0	2	81	14	0	2	69	Y	18	1.190	2
-Contig10_chr12_44447953_44449698	63	C	T	105.0	chr12	44448020	C	11	0	2	60	9	0	2	54	12	0	2	63	10	0	2	57	15	0	2	72	8	0	2	51	Y	31	11.791	0
-Contig5_chr12_53880670_53882675	1221	A	C	99.4	chr12	53881888	A	16	0	2	75	18	0	2	81	23	0	2	96	10	0	2	57	15	0	2	72	17	0	2	78	Y	31	0.061	0
-Contig86_chr12_56715356_56716464	818	T	C	166.0	chr12	56716164	T	20	0	2	87	16	0	2	75	16	0	2	75	14	0	2	69	13	0	2	66	7	0	2	48	Y	22	1.092	0
-Contig3_chr12_65021967_65024097	238	T	G	92.6	chr12	65022205	T	17	0	2	78	14	0	2	69	16	0	2	75	9	0	2	54	13	0	2	66	15	0	2	72	Y	258	0.117	0
-Contig43_chr12_66499742_66500010	121	G	T	41.5	chr12	66499866	G	12	0	2	63	4	0	2	39	8	0	2	51	6	0	2	45	10	0	2	57	6	0	2	45	N	42	0.421	0
-Contig14_chr12_71364692_71365311	20	A	C	103.0	chr12	71364712	A	7	0	2	48	3	0	2	36	5	0	2	42	1	0	2	30	2	0	2	33	3	0	2	36	Y	35	+99.	0
-Contig37_chr13_15910164_15910426	245	G	A	32.9	chr13	-1	N	3	4	1	41	4	0	2	39	3	0	2	36	4	0	2	39	3	0	2	36	10	0	2	57	N	-1	2.159	1
-Contig107_chr13_26045881_26046290	341	C	G	81.4	chr13	26046230	C	16	0	2	75	20	0	2	90	14	0	2	69	15	0	2	72	9	0	2	54	9	0	2	54	Y	51	4.510	0
-Contig251_chr13_28498333_28501066	864	T	G	296.0	chr13	28499180	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	5	0	2	42	6	0	2	45	Y	9	0.068	0
-Contig154_chr13_36777857_36778736	356	G	A	95.5	chr13	36778225	A	6	0	2	45	11	0	2	60	11	0	2	60	9	0	2	54	13	0	2	66	8	0	2	51	Y	59	0.192	0
-Contig37_chr13_42529793_42530857	150	G	T	192.0	chr13	42529926	G	18	0	2	81	14	0	2	69	16	0	2	75	14	0	2	69	8	0	2	51	11	0	2	60	N	22	0.795	5
-Contig47_chr13_47045833_47046626	257	A	C	28.5	chr13	47046097	A	13	0	2	66	10	0	2	57	17	0	2	78	20	0	2	87	15	0	2	72	9	0	2	57	N	129	0.468	0
-Contig42_chr13_47730018_47730856	254	A	G	75.1	chr13	47730294	A	13	0	2	66	6	0	2	45	12	0	2	63	9	0	2	54	16	0	2	75	11	0	2	63	Y	630	0.049	1
-Contig55_chr13_53467708_53468101	221	T	G	132.0	chr13	53467925	T	25	0	2	102	12	0	2	63	26	0	2	105	7	0	2	48	16	0	2	75	16	0	2	75	N	20	5.717	1
-Contig49_chr13_55103679_55105532	503	G	A	76.0	chr13	55104178	G	21	0	2	90	19	0	2	84	18	0	2	81	20	0	2	87	8	9	1	89	17	0	2	78	Y	20	0.259	1
-Contig66_chr13_66021813_66022244	319	C	T	125.0	chr13	66022136	C	11	0	2	60	16	0	2	75	15	0	2	75	12	0	2	63	17	0	2	78	8	0	2	51	N	14	0.055	3
-Contig48_chr14_11839435_11843272	3014	A	G	163.0	chr14	11842446	A	10	0	2	57	8	0	2	51	13	0	2	66	10	0	2	57	5	0	2	42	10	0	2	57	Y	31	0.908	0
-Contig9_chr14_23353717_23354432	80	G	A	61.3	chr14	23353797	G	3	0	2	36	6	0	2	45	11	0	2	60	8	0	2	51	4	0	2	39	2	4	1	35	Y	11	0.444	0
-Contig14_chr14_24131180_24133488	1633	G	A	131.0	chr14	24132818	G	21	0	2	90	16	0	2	75	12	0	2	63	10	0	2	57	11	0	2	60	20	0	2	87	Y	36	0.347	0
-Contig28_chr14_26905747_26909514	975	G	C	3.13	chr14	26906723	G	16	0	2	75	10	0	2	57	12	0	2	63	15	0	2	72	10	0	2	57	7	0	2	48	N	287	0.117	2
-Contig14_chr14_29616948_29618316	109	G	A	80.3	chr14	29617053	-	17	0	2	78	16	0	2	75	16	0	2	75	10	0	2	57	17	0	2	78	19	0	2	84	Y	32	1.051	0
-Contig76_chr14_30028102_30029179	1046	C	T	38.5	chr14	30029169	T	3	0	2	36	6	0	2	45	9	0	2	54	7	0	2	48	9	0	2	54	8	0	2	51	Y	96	+99.	0
-Contig115_chr14_31417207_31417574	259	A	G	12.1	chr14	31417454	G	13	0	2	66	15	0	2	72	21	0	2	90	12	0	2	63	13	0	2	66	9	0	2	54	N	28	5.379	2
-Contig70_chr14_46653662_46653790	111	G	A	46.7	chr14	46653768	G	7	0	2	48	5	0	2	42	11	0	2	60	11	0	2	60	8	0	2	51	10	0	2	57	N	21	+99.	2
-Contig43_chr14_49991855_49993511	918	A	G	112.0	chr14	49992767	G	15	0	2	72	10	0	2	57	11	0	2	63	9	0	2	54	12	0	2	63	9	0	2	54	Y	6	0.314	1
-Contig64_chr14_56768376_56768902	473	C	T	29.0	chr14	56768832	C	15	0	2	72	11	0	2	60	14	0	2	69	14	0	2	69	7	0	2	48	9	0	2	54	Y	91	8.281	0
-Contig60_chr15_18493036_18494316	150	G	A	92.6	chr15	18493188	G	9	0	2	54	13	0	2	66	9	0	2	54	6	0	2	45	5	0	2	42	12	0	2	63	Y	45	0.125	0
-Contig59_chr15_22138344_22138535	120	G	C	142.0	chr15	22138470	C	11	0	2	60	10	0	2	57	18	0	2	81	4	0	2	39	10	0	2	57	15	0	2	72	N	8	2.553	0
-Contig112_chr15_26772864_26773267	374	C	T	21.6	chr15	26773244	C	4	0	2	39	4	0	2	39	5	0	2	42	2	0	2	33	4	0	2	39	3	0	2	36	N	18	+99.	0
-Contig24_chr15_26894765_26895003	155	G	A	87.6	chr15	-1	N	6	0	2	45	5	0	2	42	7	0	2	48	4	0	2	39	4	0	2	39	2	0	2	33	N	-1	0.178	0
-Contig2_chr15_33944796_33947182	1860	G	A	99.5	chr15	33946654	G	10	0	2	57	11	0	2	60	16	0	2	75	14	0	2	69	14	0	2	69	16	0	2	75	Y	16	0.252	0
-Contig73_chr15_34690052_34691332	714	T	C	130.0	chr15	34690769	T	7	0	2	48	7	0	2	48	17	0	2	78	9	0	2	54	9	0	2	54	4	0	2	39	Y	7	6.003	0
-Contig68_chr15_37747190_37747426	126	G	A	130.0	chr15	37747331	G	14	0	2	69	14	0	2	69	11	0	2	63	19	0	2	84	13	0	2	66	21	0	2	90	N	229	0.255	0
-Contig104_chr15_45106954_45107158	70	A	T	64.4	chr15	45107015	A	6	0	2	45	6	0	2	45	19	0	2	84	7	0	2	48	7	0	2	48	3	0	2	36	N	202	4.319	0
-Contig119_chr16_6160274_6160477	180	G	A	54.8	chr16	6160457	G	7	0	2	48	6	0	2	45	12	0	2	63	3	0	2	36	11	0	2	60	10	0	2	57	N	42	+99.	0
-Contig126_chr16_10611887_10612152	150	G	T	145.0	chr16	10612037	G	14	0	2	69	9	0	2	54	11	0	2	63	8	0	2	51	8	0	2	51	11	0	2	60	N	15	0.104	6
-Contig43_chr16_20200090_20200514	70	A	G	58.6	chr16	20200154	A	11	0	2	60	15	0	2	72	15	0	2	72	6	0	2	45	9	0	2	54	12	0	2	63	Y	2	0.466	1
-Contig60_chr16_28079136_28080263	588	T	G	157.0	chr16	28079739	T	22	0	2	93	20	0	2	87	22	0	2	93	17	0	2	78	12	0	2	63	10	0	2	57	Y	105	5.999	1
-Contig70_chr16_33758668_33759655	104	A	T	58.1	chr16	33758772	A	6	0	2	45	7	0	2	48	17	0	2	78	14	0	2	69	8	0	2	51	10	0	2	57	N	54	0.162	0
-Contig66_chr16_37935682_37935831	116	T	C	99.2	chr16	37935802	C	12	0	2	63	6	0	2	45	19	0	2	84	12	0	2	63	13	0	2	66	17	0	2	78	N	266	+99.	2
-Contig16_chr16_40451506_40451643	84	A	G	59.8	chr16	40451592	A	7	0	2	48	5	0	2	42	7	0	2	48	13	0	2	66	14	0	2	69	19	0	2	84	N	45	5.061	0
-Contig31_chr17_12128267_12129637	205	G	A	90.5	chr17	12128484	G	7	0	2	48	6	0	2	45	6	0	2	45	11	0	2	60	7	0	2	48	4	0	2	39	Y	10	0.246	0
-Contig1_chr17_12979232_12980380	808	G	T	12.3	chr17	12980028	G	18	0	2	81	12	0	2	63	21	0	2	90	13	0	2	66	22	0	2	93	18	0	2	81	Y	9	0.336	1
-Contig42_chr17_23434859_23438330	2100	C	T	39.5	chr17	23436985	T	4	0	2	39	7	0	2	48	7	0	2	48	3	0	2	36	6	0	2	45	2	0	2	33	Y	25	0.344	0
-Contig63_chr17_23796320_23796814	220	A	G	54.0	chr17	23796536	G	6	0	2	45	4	0	2	39	5	0	2	42	6	0	2	45	4	0	2	39	6	0	2	45	Y	139	0.067	1
-Contig76_chr17_24107434_24107834	316	T	C	141.0	chr17	24107726	T	19	0	2	84	15	0	2	72	20	0	2	87	16	0	2	75	11	0	2	60	18	0	2	81	Y	30	0.175	2
-Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
-Contig59_chr17_26790302_26795045	287	C	T	45.1	chr17	26790582	C	8	0	2	51	6	0	2	45	13	0	2	66	6	0	2	45	15	0	2	72	12	0	2	63	Y	75	0.019	1
-Contig99_chr17_27018324_27019378	446	G	A	31.1	chr17	27018776	G	14	0	2	69	12	0	2	63	14	0	2	69	10	0	2	57	9	0	2	54	11	0	2	60	Y	13	0.290	4
-Contig125_chr17_27739115_27739410	63	G	A	107.0	chr17	27739177	G	8	0	2	51	11	0	2	60	16	0	2	75	8	0	2	51	4	0	2	39	15	0	2	72	N	100	0.819	0
-Contig115_chr17_37489899_37490101	159	G	A	62.4	chr17	37490067	G	4	0	2	39	3	0	2	36	4	0	2	39	4	0	2	39	3	0	2	36	6	0	2	45	N	4	1.411	1
-Contig180_chr17_45154356_45154925	524	A	G	146.0	chr17	45154886	G	7	0	2	48	9	0	2	54	7	0	2	48	9	0	2	54	4	0	2	39	8	0	2	51	Y	11	+99.	2
-Contig61_chr17_48221795_48223545	1404	T	A	177.0	chr17	48223216	T	15	0	2	72	14	0	2	69	24	0	2	99	17	0	2	78	18	0	2	81	24	0	2	99	Y	161	0.633	2
-Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
-Contig229_chr18_3706523_3708577	1076	A	G	83.9	chr18	3707630	A	11	0	2	60	13	0	2	66	26	0	2	105	11	0	2	60	15	0	2	72	17	0	2	78	Y	63	0.445	0
-Contig24_chr18_14049894_14050480	24	A	G	123.0	chr18	14049918	A	5	0	2	42	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	5	0	2	42	Y	17	+99.	0
-Contig123_chr18_19916160_19916379	116	G	A	79.2	chr18	19916272	A	14	0	2	69	12	0	2	63	14	0	2	69	6	0	2	45	11	0	2	60	10	0	2	57	N	26	0.172	0
-Contig82_chr18_27305489_27306229	566	C	T	49.5	chr18	27306051	A	6	0	2	45	6	0	2	45	10	0	2	57	11	0	2	60	6	0	2	45	7	0	2	48	N	1	0.349	0
-Contig71_chr18_34324706_34326687	136	G	A	151.0	chr18	34324841	G	9	0	2	54	9	0	2	54	17	0	2	78	8	0	2	51	11	0	2	60	10	0	2	57	Y	2	2.129	2
-Contig16_chr18_34672093_34673044	538	T	C	58.2	chr18	34672635	T	8	0	2	51	15	0	2	72	16	0	2	75	15	0	2	72	9	0	2	57	18	0	2	81	Y	8	0.214	1
-Contig96_chr18_38492535_38493333	624	G	A	119.0	chr18	38493162	T	17	0	2	78	12	0	2	63	13	0	2	66	16	0	2	75	8	0	2	51	15	0	2	72	Y	127	0.131	0
-Contig226_chr18_47753756_47754666	427	T	C	21.1	chr18	47754215	T	10	0	2	57	4	0	2	39	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	42	0.522	0
-Contig170_chr18_49411558_49412230	94	C	A	74.3	chr18	49411655	C	14	0	2	69	10	0	2	57	9	0	2	54	10	0	2	57	3	0	2	36	3	0	2	36	N	9	1.457	0
-Contig192_chr18_49419342_49420737	1058	C	T	42.8	chr18	49420381	A	3	0	2	36	4	0	2	39	5	0	2	42	8	0	2	51	3	0	2	36	3	0	2	36	Y	34	2.107	2
-Contig64_chr18_55979770_55980315	49	G	A	89.1	chr18	55979824	G	3	0	2	36	9	0	2	54	7	0	2	51	4	0	2	39	3	0	2	36	3	0	2	36	Y	-1	2.124	0
-Contig20_chr18_58130301_58130735	112	A	G	74.4	chr18	58130413	A	12	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	6	0	2	45	6	0	2	45	Y	10	0.290	0
-Contig67_chr19_12398520_12399367	499	C	T	161.0	chr19	12399017	C	10	0	2	57	11	0	2	60	20	0	2	87	14	0	2	69	24	0	2	99	8	0	2	51	Y	137	5.634	0
-Contig66_chr19_16285672_16287223	996	C	T	190.0	chr19	16286674	C	9	0	2	57	14	0	2	69	16	0	2	78	17	0	2	78	8	0	2	51	22	0	2	93	Y	40	0.110	0
-Contig129_chr19_25541958_25542221	202	T	C	68.1	chr19	25542154	C	11	0	2	60	19	0	2	84	10	0	2	60	17	0	2	78	9	0	2	54	12	0	2	63	N	-1	2.551	1
-Contig29_chr19_37339947_37341911	1692	C	T	211.0	chr19	37341631	C	15	0	2	72	20	0	2	87	11	0	2	60	15	0	2	72	3	0	2	36	12	0	2	63	Y	7	0.096	0
-Contig39_chr19_47709708_47711327	444	C	T	36.8	chr19	47710148	T	10	0	2	57	4	0	2	39	8	0	2	51	9	0	2	54	6	0	2	45	6	0	2	45	Y	95	1.251	1
-Contig60_chr19_54013816_54014398	281	A	G	138.0	chr19	54014103	C	6	0	2	45	15	0	2	72	7	0	2	48	10	0	2	57	15	0	2	72	10	0	2	57	Y	188	1.271	0
-Contig251_chr19_56559098_56559626	452	T	C	3.36	chr19	56559549	T	12	0	2	63	13	0	2	66	21	0	2	90	15	0	2	72	14	0	2	69	11	0	2	60	N	1	0.117	0
-Contig50_chr20_12138509_12141975	3206	C	A	248.0	chr20	12141763	C	8	0	2	51	15	0	2	72	14	0	2	69	6	0	2	45	10	0	2	57	7	0	2	48	Y	2	0.384	0
-Contig36_chr20_32631363_32632049	176	G	A	24.1	chr20	32631526	G	7	0	2	48	14	0	2	69	19	0	2	84	14	0	2	69	15	0	2	72	16	0	2	75	N	50	1.150	0
-Contig32_chr20_36468058_36468869	66	C	T	40.4	chr20	36468127	C	6	0	2	45	3	0	2	36	4	0	2	39	5	0	2	42	3	0	2	36	4	0	2	39	N	59	0.281	0
-Contig24_chr20_38203888_38204900	834	C	T	132.0	chr20	38204731	C	9	0	2	54	17	0	2	78	20	0	2	87	8	0	2	51	11	0	2	60	17	0	2	78	Y	14	0.397	0
-Contig79_chr20_44263127_44264103	456	G	T	31.5	chr20	44263573	G	22	0	2	93	16	0	2	75	15	0	2	72	19	0	2	84	13	0	2	66	26	0	2	105	Y	8	3.250	0
-Contig26_chr20_45878482_45878787	197	A	G	160.0	chr20	45878672	A	17	0	2	78	15	0	2	72	11	0	2	63	17	0	2	78	12	0	2	63	10	0	2	57	N	14	0.535	0
-Contig119_chr20_46550670_46551383	609	G	A	139.0	chr20	46551277	G	7	0	2	48	17	0	2	78	19	0	2	84	20	0	2	87	9	0	2	54	15	0	2	72	Y	7	0.488	1
-Contig50_chr21_4178523_4178687	121	G	A	362.0	chr21	4178640	G	8	0	2	51	14	0	2	69	5	0	2	42	3	0	2	36	11	0	2	60	4	0	2	39	N	392	0.483	0
-Contig103_chr21_10177255_10177765	121	G	A	125.0	chr21	10177367	G	12	0	2	63	10	0	2	57	10	0	2	57	17	0	2	78	14	0	2	69	7	0	2	51	Y	37	0.213	3
-Contig1_chr21_10805534_10806399	766	A	G	146.0	chr21	10806301	G	10	0	2	57	6	0	2	45	9	0	2	54	6	0	2	45	7	0	2	48	5	0	2	42	Y	20	0.319	0
-Contig46_chr21_21029492_21030645	443	C	T	5.37	chr21	21029910	C	15	0	2	72	11	0	2	60	16	0	2	75	15	0	2	72	13	0	2	66	6	0	2	45	Y	96	3.737	0
-Contig129_chr21_31045749_31046924	381	A	G	129.0	chr21	31046141	A	19	0	2	84	8	0	2	51	23	0	2	96	12	0	2	63	15	0	2	72	18	0	2	81	Y	69	0.028	2
-Contig23_chr21_31651123_31651986	840	C	T	71.3	chr21	31651957	T	6	0	2	45	9	0	2	54	8	0	2	51	10	0	2	57	4	0	2	39	7	0	2	48	Y	105	2.977	3
-Contig64_chr21_43341847_43342031	84	T	C	114.0	chr21	43341926	T	11	0	2	60	9	0	2	54	10	0	2	57	6	0	2	45	6	0	2	45	7	0	2	48	N	10	3.954	2
-Contig60_chr21_43475347_43475824	175	C	T	8.05	chr21	43475551	T	6	0	2	45	7	0	2	48	13	0	2	66	6	0	2	45	14	0	2	69	14	0	2	69	N	45	0.058	0
-Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0
-Contig46_chr22_9416920_9417467	381	G	A	145.0	chr22	9417259	G	10	0	2	57	9	0	2	54	10	0	2	57	6	0	2	45	13	0	2	66	7	0	2	48	Y	154	0.242	0
-Contig86_chr22_9440787_9441725	713	T	G	119.0	chr22	9441488	G	6	0	2	45	12	0	2	63	10	0	2	57	11	0	2	60	13	0	2	66	16	0	2	75	Y	132	0.218	0
-Contig16_chr22_15636960_15637372	236	A	C	9.79	chr22	15637192	T	4	0	2	39	5	0	2	42	12	0	2	63	7	0	2	48	6	0	2	45	11	0	2	60	Y	5	2.163	0
-Contig4_chr22_16114310_16114546	128	G	C	101.0	chr22	16114432	G	10	0	2	57	13	0	2	66	20	0	2	87	20	0	2	87	16	0	2	75	9	0	2	54	N	19	0.526	0
-Contig23_chr22_34612023_34612568	167	C	G	92.3	chr22	34612181	C	11	0	2	60	18	0	2	81	13	0	2	66	8	0	2	51	12	0	2	63	14	0	2	69	Y	7	0.409	0
-Contig4_chr22_38252245_38253712	799	A	C	159.0	chr22	38253064	A	18	0	2	81	15	0	2	72	15	0	2	72	20	0	2	87	27	0	2	108	15	0	2	72	Y	90	4.330	0
-Contig122_chr22_48412466_48414788	1888	C	T	125.0	chr22	48414355	T	16	0	2	75	15	0	2	72	16	0	2	75	14	0	2	72	12	0	2	63	7	0	2	48	N	42	0.122	0
-Contig77_chr22_49764414_49764875	353	C	A	148.0	chr22	49764777	C	7	4	1	65	18	0	2	81	16	0	2	75	20	0	2	87	4	3	1	52	9	4	1	67	Y	12	0.941	0
-Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
-Contig348_chr22_62406104_62406495	189	C	A	134.0	chr22	62406302	A	9	0	2	54	14	0	2	69	11	0	2	60	10	0	2	57	12	0	2	63	6	0	2	45	Y	5	0.912	0
-Contig133_chr23_3525134_3526502	1223	A	G	201.0	chr23	3526387	A	11	0	2	60	13	0	2	66	23	0	2	96	21	0	2	90	13	0	2	66	10	0	2	57	Y	61	1.359	0
-Contig111_chr23_7058063_7058181	107	G	A	108.0	chr23	7058162	A	8	0	2	51	8	0	2	51	7	0	2	48	2	0	2	33	5	0	2	42	6	0	2	45	N	3	+99.	0
-Contig79_chr23_7844129_7844837	110	C	A	141.0	chr23	7844237	T	13	0	2	66	15	0	2	72	17	0	2	78	12	0	2	63	15	0	2	72	16	0	2	75	Y	40	0.339	0
-Contig38_chr23_9201002_9201725	597	C	T	155.0	chr23	9201609	T	17	0	2	78	8	0	2	51	13	0	2	66	5	0	2	42	11	0	2	60	7	0	2	48	Y	167	0.633	1
-Contig33_chr23_20672540_20674320	347	T	A	91.4	chr23	20672885	A	11	0	2	60	14	0	2	69	15	0	2	72	7	0	2	48	12	0	2	63	18	0	2	81	Y	31	0.452	1
-Contig35_chr23_28447813_28449115	70	T	A	21.3	chr23	28447881	T	9	0	2	54	8	0	2	51	10	0	2	57	9	0	2	54	10	0	2	57	12	0	2	63	N	251	0.163	1
-Contig51_chr23_30590939_30591162	140	C	T	142.0	chr23	30591080	C	14	0	2	69	4	0	2	39	10	0	2	57	12	0	2	63	14	0	2	69	4	0	2	39	N	13	1.658	0
-Contig57_chr23_32216351_32216721	179	T	G	143.0	chr23	32216534	T	15	0	2	72	15	0	2	72	23	0	2	96	13	0	2	66	16	0	2	75	15	0	2	72	N	32	1.387	1
-Contig93_chr23_35744841_35745791	40	A	T	30.4	chr23	35744880	T	6	0	2	45	7	0	2	48	7	0	2	48	2	0	2	33	5	0	2	42	5	0	2	42	Y	50	2.173	0
-Contig32_chr23_48285289_48286638	186	T	C	176.0	chr23	48285470	T	18	0	2	81	12	0	2	63	16	0	2	75	13	0	2	66	9	0	2	54	9	0	2	54	Y	4	4.238	1
-Contig50_chr24_22515247_22516072	761	C	T	243.0	chr24	22515981	T	11	0	2	60	10	0	2	57	8	0	2	51	9	0	2	54	18	0	2	81	8	0	2	51	Y	1	0.190	0
-Contig84_chr24_29196623_29199644	466	C	T	126.0	chr24	29197091	T	7	0	2	48	11	0	2	60	8	0	2	51	7	0	2	48	11	0	2	60	15	0	2	72	Y	42	0.215	0
-Contig145_chr24_34778364_34778898	163	T	C	372.0	chr24	34778541	C	10	0	2	57	8	0	2	51	12	0	2	63	12	0	2	63	6	1	2	31	7	0	2	48	Y	40	0.037	0
-Contig34_chr24_36147443_36150244	2679	C	T	140.0	chr24	36150125	C	13	0	2	66	7	0	2	48	14	0	2	69	14	0	2	69	10	0	2	57	13	0	2	66	N	282	0.099	1
-Contig164_chr24_46598127_46599206	84	C	T	105.0	chr24	46598214	C	13	0	2	66	12	0	2	63	15	0	2	72	15	0	2	72	11	0	2	60	8	0	2	51	Y	22	1.262	1
-Contig144_chr25_4011170_4013134	541	A	G	160.0	chr25	4011690	A	12	0	2	63	17	0	2	78	13	0	2	66	13	0	2	66	13	0	2	66	13	0	2	66	Y	5	0.087	0
-Contig81_chr25_6103472_6104760	699	G	A	378.0	chr25	6104190	A	14	0	2	69	16	0	2	75	13	0	2	66	11	0	2	60	11	0	2	60	12	0	2	63	Y	33	0.789	2
-Contig152_chr25_7486442_7487609	75	A	G	11.6	chr25	7486515	A	17	0	2	78	13	0	2	66	8	0	2	51	16	0	2	75	8	0	2	51	6	0	2	45	N	2	0.158	0
-Contig24_chr25_7695778_7698612	2714	C	T	130.0	chr25	7698446	C	16	0	2	75	13	0	2	66	22	0	2	93	17	0	2	78	10	0	2	57	17	0	2	78	Y	27	0.346	0
-Contig89_chr25_8635170_8636009	586	G	C	209.0	chr25	8635744	G	13	0	2	66	13	0	2	66	21	0	2	93	14	0	2	69	15	0	2	72	15	0	2	72	Y	14	0.067	0
-Contig59_chr25_18196776_18197707	785	G	A	112.0	chr25	18197551	G	8	10	1	42	27	0	2	108	21	0	2	90	18	0	2	81	10	0	2	57	14	0	2	69	N	36	3.625	0
-Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
-Contig84_chr25_42407960_42408708	55	C	T	119.0	chr25	42408013	C	6	0	2	45	9	0	2	54	11	0	2	60	9	0	2	54	7	0	2	48	8	0	2	51	Y	11	0.121	0
-Contig73_chr25_43562500_43564110	955	T	C	52.1	chr25	43563469	C	9	0	2	57	4	0	2	39	6	0	2	45	5	0	2	42	7	0	2	48	10	0	2	57	Y	4	1.406	0
-Contig37_chr25_51074433_51074885	170	A	G	102.0	chr25	51074589	G	11	0	2	60	7	0	2	48	6	0	2	45	15	0	2	72	9	0	2	54	7	0	2	48	Y	68	0.207	1
-Contig204_chr26_4311195_4311778	170	C	T	16.9	chr26	4311363	T	20	0	2	87	8	0	2	51	13	0	2	66	18	0	2	81	11	0	2	60	14	0	2	69	N	35	0.085	0
-Contig122_chr26_7622321_7623491	106	C	G	139.0	chr26	7622423	C	3	0	2	36	9	0	2	54	10	0	2	57	12	0	2	63	9	0	2	54	5	0	2	42	N	19	0.458	0
-Contig11_chr26_11062142_11062902	707	C	A	108.0	chr26	11062836	T	7	0	2	48	8	0	2	51	16	0	2	75	10	0	2	57	6	0	2	45	14	0	2	69	Y	-1	4.709	0
-Contig133_chr26_17695661_17696368	39	T	G	98.7	chr26	17695700	T	10	0	2	57	3	0	2	36	11	0	2	60	9	0	2	54	2	0	2	33	1	0	2	30	N	85	3.402	0
-Contig146_chr26_26622638_26623906	574	G	A	186.0	chr26	26623219	A	11	0	2	60	12	0	2	63	9	0	2	54	11	0	2	60	9	0	2	54	12	0	2	63	Y	1	0.318	0
-Contig8_chr26_27834126_27834326	140	G	A	41.7	chr26	27834268	G	13	0	2	66	7	0	2	48	13	0	2	66	11	0	2	60	12	0	2	63	6	0	2	45	N	29	0.142	1
-Contig78_chr26_31128839_31129005	123	T	C	145.0	chr26	-1	N	11	0	2	60	3	0	2	36	7	0	2	48	8	0	2	51	10	0	2	46	7	0	2	48	N	-1	1.230	1
-Contig28_chr26_32935355_32935833	289	T	C	77.9	chr26	32935638	T	15	0	2	72	22	0	2	93	15	0	2	72	9	0	2	54	15	0	2	72	17	0	2	78	Y	10	2.258	1
-Contig135_chr27_6853874_6854079	158	C	T	116.0	chr27	6854032	T	18	0	2	81	19	0	2	84	13	0	2	66	7	0	2	48	8	0	2	51	11	0	2	60	N	4	0.060	1
-Contig47_chr27_11777710_11777915	25	A	G	67.3	chr27	11777731	A	3	0	2	36	5	0	2	42	6	0	2	45	10	0	2	57	9	0	2	54	6	0	2	45	N	97	+99.	0
-Contig23_chr27_14633002_14633153	23	G	A	128.0	chr27	14633023	A	3	0	2	36	4	0	2	39	5	0	2	42	5	0	2	42	3	0	2	36	2	0	2	33	N	240	3.881	0
-Contig29_chr27_15428166_15429413	380	T	C	140.0	chr27	15428539	T	15	0	2	72	15	0	2	72	17	0	2	78	15	0	2	72	15	0	2	72	15	0	2	72	Y	47	0.916	1
-Contig31_chr27_19519489_19520891	129	G	T	14.9	chr27	19519624	T	12	0	2	63	19	0	2	84	20	0	2	87	16	0	2	75	10	0	2	57	11	0	2	60	Y	48	2.756	0
-Contig35_chr27_40596169_40596445	20	G	C	133.0	chr27	40596189	G	8	0	2	51	3	0	2	36	4	0	2	39	2	0	2	33	4	0	2	39	4	0	2	39	Y	4	+99.	1
-Contig85_chr27_45471750_45472022	211	G	A	53.1	chr27	45471964	G	18	0	2	81	10	0	2	57	15	0	2	72	0	13	0	36	16	0	2	75	14	0	2	69	N	75	2.502	1
-Contig131_chr28_6481806_6483783	138	C	T	36.2	chr28	6481953	C	12	0	2	63	12	0	2	63	20	0	2	87	11	0	2	60	10	0	2	57	12	0	2	63	Y	10	0.387	0
-Contig141_chr28_10027332_10028242	780	T	G	74.8	chr28	10028095	T	10	0	2	57	11	0	2	60	14	0	2	69	10	0	2	57	7	0	2	48	9	0	2	54	Y	19	3.348	0
-Contig144_chr28_15468203_15470548	743	G	A	20.0	chr28	15468942	G	13	0	2	66	12	0	2	63	10	0	2	57	11	0	2	60	16	0	2	75	7	0	2	48	N	14	0.053	0
-Contig47_chr28_21311718_21312366	541	G	A	116.0	chr28	21312258	G	9	0	2	54	6	0	2	45	12	0	2	63	6	0	2	45	5	0	2	45	12	0	2	63	N	9	0.240	0
-Contig60_chr28_30197166_30197364	92	T	C	164.0	chr28	30197258	T	10	0	2	57	13	0	2	66	15	0	2	72	16	0	2	75	12	0	2	63	11	0	2	60	N	369	1.139	0
-Contig29_chr29_4726399_4727143	559	A	T	163.0	chr29	4726955	A	15	0	2	72	18	0	2	81	18	0	2	81	16	0	2	75	11	0	2	60	14	0	2	72	Y	161	3.114	0
-Contig48_chr29_13129286_13130137	232	A	G	92.2	chr29	13129514	G	13	0	2	66	11	0	2	60	19	0	2	84	16	0	2	75	11	0	2	60	17	0	2	78	Y	337	2.581	1
-Contig33_chr29_17000374_17000921	71	C	T	48.6	chr29	17000441	-	4	0	2	39	9	0	2	54	12	0	2	66	10	0	2	57	7	0	2	48	4	0	2	39	N	26	5.491	0
-Contig34_chr29_17581796_17584016	2105	C	T	126.0	chr29	17583890	T	14	0	2	69	11	0	2	60	18	0	2	81	12	0	2	63	10	0	2	57	10	0	2	57	Y	22	2.208	0
-Contig19_chr29_20976080_20977761	1007	G	A	115.0	chr29	20977076	G	19	0	2	84	22	0	2	93	22	0	2	93	22	0	2	93	11	0	2	60	13	0	2	66	Y	4	1.915	0
-Contig51_chr29_21149853_21150467	266	C	T	146.0	chr29	21150118	C	12	0	2	63	12	0	2	63	23	0	2	96	14	0	2	69	13	0	2	66	10	0	2	57	Y	4	0.051	0
-Contig1_chr30_5992217_5993068	106	C	T	129.0	chr30	5992319	C	10	0	2	57	11	0	2	60	7	0	2	48	11	0	2	60	10	0	2	57	12	0	2	63	Y	76	1.079	0
-Contig1_chr30_8232878_8233406	402	C	T	127.0	chr30	8233264	C	8	0	2	51	19	0	2	84	16	0	2	75	18	0	2	81	10	0	2	57	14	0	2	69	Y	358	5.283	0
-Contig108_chr30_9436961_9437520	546	C	T	39.8	chr30	9437502	C	7	0	2	48	5	0	2	42	2	0	2	33	7	0	2	48	5	0	2	42	7	0	2	48	Y	64	+99.	0
-Contig165_chr30_25804389_25804926	190	T	C	126.0	chr30	25804592	C	3	0	2	36	8	0	2	51	7	0	2	48	10	0	2	57	7	0	2	48	4	0	2	39	Y	113	0.329	0
-Contig193_chr30_27495616_27496125	434	C	A	234.0	chr30	27496024	C	13	0	2	66	16	0	2	75	25	0	2	102	16	0	2	75	13	0	2	66	14	0	2	69	Y	76	2.621	0
-Contig38_chr31_5164423_5166573	2074	C	T	134.0	chr31	5166501	T	13	0	2	66	10	0	2	57	17	0	2	78	11	0	2	60	17	0	2	78	10	0	2	57	Y	58	+99.	0
-Contig6_chr31_9649308_9650149	431	G	T	162.0	chr31	9649742	G	31	0	2	120	23	0	2	96	17	0	2	78	17	0	2	78	10	0	2	57	16	0	2	75	Y	98	2.200	0
-Contig7_chr31_12384974_12386400	305	C	T	69.6	chr31	12385267	C	6	0	2	45	10	0	2	57	11	0	2	60	11	0	2	60	9	0	2	54	12	0	2	63	Y	44	1.165	0
-Contig90_chr31_17267583_17267778	81	C	A	143.0	chr31	17267665	C	20	0	2	87	6	0	2	45	14	0	2	72	22	0	2	93	17	0	2	78	15	0	2	72	N	7	0.565	0
-Contig137_chr31_23357653_23358568	885	G	A	119.0	chr31	23358545	G	5	0	2	42	3	0	2	36	3	0	2	36	2	0	2	33	3	0	2	36	4	0	2	39	Y	11	+99.	0
-Contig17_chr31_26433828_26434459	498	T	C	9.79	chr31	26434322	T	18	0	2	81	10	0	2	57	15	0	2	72	13	0	2	66	16	0	2	75	15	0	2	72	Y	137	4.814	0
-Contig30_chr32_25902721_25905783	208	C	G	162.0	chr32	25902927	G	11	0	2	60	13	0	2	66	11	0	2	60	12	0	2	63	7	0	2	48	11	0	2	60	Y	145	0.322	2
-Contig42_chr32_38900713_38901320	320	A	G	134.0	chr32	38901021	T	12	0	2	63	10	0	2	57	9	11	1	104	5	0	2	42	19	0	2	84	7	6	1	56	Y	71	0.165	0
-Contig18_chr33_22207246_22209159	1363	G	T	51.5	chr33	22208619	-	16	0	2	75	8	0	2	51	11	0	2	60	10	0	2	57	15	0	2	72	12	0	2	63	Y	59	2.560	0
-Contig104_chr33_22483642_22484187	424	C	T	140.0	chr33	22484054	T	13	0	2	66	16	0	2	75	9	0	2	54	15	0	2	72	13	0	2	66	10	0	2	57	Y	36	0.404	0
-Contig170_chr33_26189421_26189940	292	T	C	98.4	chr33	26189703	T	21	0	2	90	13	0	2	66	15	0	2	72	13	0	2	66	19	0	2	84	13	0	2	66	Y	23	0.307	0
-Contig41_chr34_16544482_16545449	46	T	C	102.0	chr34	16544523	T	5	0	2	42	11	0	2	60	6	0	2	45	0	2	0	3	7	0	2	48	8	0	2	51	Y	215	1.156	0
-Contig8_chr34_18474513_18475673	1122	C	A	129.0	chr34	18475628	A	8	0	2	51	15	0	2	72	13	0	2	66	17	0	2	78	13	0	2	66	6	0	2	45	Y	61	0.123	2
-Contig152_chr34_31794848_31795540	242	G	A	93.2	chr34	31795093	G	11	0	2	60	24	0	2	99	17	0	2	78	15	0	2	72	18	0	2	81	17	0	2	78	Y	123	2.780	0
-Contig28_chr34_41708848_41712034	1381	A	G	78.2	chr34	41710232	A	11	0	2	60	17	0	2	78	15	0	2	72	16	0	2	75	15	0	2	72	14	0	2	69	Y	236	0.234	0
-Contig85_chr34_42798284_42800584	1845	C	T	171.0	chr34	42800126	T	5	0	2	42	7	0	2	48	6	0	2	45	7	0	2	48	6	0	2	45	2	0	2	33	Y	5	2.787	0
-Contig47_chr35_3666773_3667898	348	G	T	124.0	chr35	3667121	G	9	0	2	54	20	0	2	87	18	0	2	81	15	0	2	72	12	0	2	63	14	0	2	69	Y	285	0.235	0
-Contig195_chr35_15722500_15722741	205	G	A	4.08	chr35	15722718	G	3	0	2	36	5	0	2	42	1	0	2	30	6	0	2	45	1	0	2	30	1	0	2	30	N	43	+99.	0
-Contig101_chr35_19513178_19513697	62	C	T	112.0	chr35	19513238	C	12	0	2	63	7	0	2	48	13	0	2	66	7	0	2	48	5	0	2	42	8	0	2	51	N	115	3.135	0
-Contig47_chr35_24382042_24382526	33	G	A	87.0	chr35	24382076	G	5	0	2	42	4	0	2	39	6	0	2	45	7	0	2	48	4	0	2	39	2	0	2	33	Y	71	+99.	0
-Contig77_chr35_24796947_24797172	65	A	G	52.1	chr35	24797009	A	7	0	2	48	5	0	2	42	8	0	2	51	6	0	2	45	12	0	2	63	10	0	2	57	N	11	1.401	3
-Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0
-Contig5_chr36_4562983_4563634	343	C	T	151.0	chr36	4563324	T	20	0	2	87	20	0	2	87	23	0	2	96	24	0	2	99	9	0	2	54	8	0	2	51	Y	40	1.169	0
-Contig75_chr36_7885319_7885588	53	G	A	25.7	chr36	7885372	G	10	0	2	57	8	0	2	51	13	0	2	66	7	0	2	48	4	0	2	39	7	0	2	48	N	7	2.653	0
-Contig184_chr36_18956191_18958552	187	A	G	11.5	chr36	18956371	G	10	0	2	57	11	0	2	60	21	0	2	90	14	0	2	69	7	0	2	48	4	0	2	39	N	278	1.434	2
-Contig12_chr36_21557176_21557828	513	T	A	159.0	chr36	21557695	A	11	0	2	60	14	0	2	69	21	0	2	90	12	0	2	63	15	0	2	72	11	0	2	60	Y	55	0.222	0
-Contig2_chr36_22436067_22436794	653	C	T	73.0	chr36	22436730	C	11	0	2	60	16	0	2	75	13	0	2	66	11	0	2	60	21	0	2	90	21	0	2	90	Y	9	0.534	0
-Contig133_chr36_32954045_32955409	136	A	G	116.0	chr36	32954182	A	16	0	2	75	15	0	2	72	20	0	2	87	11	0	2	60	18	0	2	81	13	0	2	66	Y	74	3.772	1
-Contig53_chr37_6665763_6665919	116	C	T	111.0	chr37	6665875	C	9	0	2	54	9	0	2	54	5	0	2	42	9	0	2	54	8	0	2	51	10	0	2	57	N	15	10.875	1
-Contig42_chr37_9589176_9591269	252	G	A	25.1	chr37	9589430	G	10	0	2	40	13	0	2	66	18	0	2	81	21	0	2	90	9	0	2	54	17	0	2	78	N	67	1.170	2
-Contig2_chr37_17134963_17136513	1140	A	C	158.0	chr37	17136092	A	14	0	2	69	24	0	2	99	17	0	2	78	16	0	2	75	15	0	2	75	13	0	2	66	Y	12	0.053	1
-Contig18_chr37_17147806_17149851	291	T	G	112.0	chr37	17148084	T	4	6	1	45	16	0	2	75	17	0	2	78	14	0	2	69	22	0	2	93	13	0	2	66	Y	41	4.442	0
-Contig64_chr37_17606895_17607534	565	C	T	30.2	chr37	17607439	A	9	0	2	54	16	0	2	75	20	0	2	87	14	0	2	69	16	0	2	75	10	0	2	57	N	20	1.622	0
-Contig126_chr37_21587881_21590621	373	G	T	132.0	chr37	21588256	G	11	0	2	60	11	0	2	60	23	0	2	96	12	0	2	63	8	0	2	51	18	0	2	81	Y	12	0.549	0
-Contig2_chr37_31197993_31198256	182	C	T	39.6	chr37	31198171	T	6	0	2	45	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	12	0	2	63	N	2	0.595	0
-Contig46_chr37_31852376_31853555	825	A	G	111.0	chr37	31853191	G	19	0	2	84	14	0	2	69	15	0	2	72	7	0	2	48	8	0	2	51	16	0	2	75	Y	17	0.128	1
-Contig7_chr38_12217200_12218387	1163	A	T	44.4	chr38	12218353	A	11	0	2	60	13	0	2	66	17	0	2	78	10	0	2	57	11	0	2	60	11	0	2	60	Y	67	+99.	0
-Contig15_chr38_12282020_12282253	150	C	T	156.0	chr38	12282164	A	17	0	2	78	11	0	2	60	19	0	2	84	14	0	2	69	5	0	2	42	14	0	2	69	Y	26	2.952	1
-Contig6_chr38_16185744_16186110	325	A	G	74.9	chr38	16186061	A	5	0	2	42	3	0	2	36	9	0	2	54	7	0	2	48	1	0	2	30	12	0	2	63	Y	40	+99.	0
-Contig265_chrX_2689247_2689484	114	C	G	103.0	chrX	2689356	C	11	0	2	60	9	0	2	54	13	0	2	66	16	0	2	75	14	0	2	69	10	0	2	57	N	2	9.232	1
-Contig122_chrX_6026976_6027327	330	C	T	79.4	chrX	6027303	C	3	0	2	36	3	0	2	36	3	0	2	36	4	0	2	39	3	0	2	36	6	0	2	45	Y	30	+99.	0
-Contig113_chrX_26287829_26288398	385	C	T	59.6	chrX	26288213	C	9	0	2	54	9	0	2	54	17	0	2	78	11	0	2	60	3	8	1	44	4	0	2	39	N	13	0.077	0
-Contig237_chrX_31256648_31257654	165	T	A	246.0	chrX	31256814	T	7	0	2	48	23	0	2	96	19	0	2	84	17	0	2	78	14	0	2	69	8	0	2	51	Y	37	1.481	0
-Contig90_chrX_57430715_57431566	548	C	T	116.0	chrX	57431266	T	9	0	2	54	18	0	2	81	13	0	2	66	14	0	2	69	8	0	2	54	7	0	2	48	Y	261	0.154	1
-Contig133_chrX_84833782_84834125	182	G	A	69.7	chrX	84833962	G	5	0	2	42	18	0	2	81	12	0	2	63	19	0	2	84	6	3	1	27	7	0	2	48	N	619	0.278	0
-Contig125_chrX_93319363_93320877	349	A	C	145.0	chrX	93319721	A	4	0	2	39	6	0	2	45	11	0	2	60	10	0	2	57	13	0	2	66	6	0	2	45	Y	59	1.686	0
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/pca/admix.gdSnp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out/pca/admix.gdSnp	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,303 @@
+  snp1 11 0.002 2000 A T
+  snp3 11 0.002 2000 A T
+  snp4 11 0.002 2000 A T
+  snp5 11 0.002 2000 A T
+  snp6 11 0.002 2000 A T
+  snp7 11 0.002 2000 A T
+  snp8 11 0.002 2000 A T
+  snp9 11 0.002 2000 A T
+  snp10 11 0.002 2000 A T
+  snp11 11 0.002 2000 A T
+  snp12 11 0.002 2000 A T
+  snp13 11 0.002 2000 A T
+  snp14 11 0.002 2000 A T
+  snp16 11 0.002 2000 A T
+  snp17 11 0.002 2000 A T
+  snp22 11 0.002 2000 A T
+  snp24 11 0.002 2000 A T
+  snp25 11 0.002 2000 A T
+  snp27 11 0.002 2000 A T
+  snp28 11 0.002 2000 A T
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diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/pca/admix.snp
--- a/test-data/test_out/pca/admix.snp	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,303 +0,0 @@
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-  snp380 11 0.002 2000 A T
-  snp381 11 0.002 2000 A T
-  snp382 11 0.002 2000 A T
-  snp383 11 0.002 2000 A T
-  snp384 11 0.002 2000 A T
-  snp385 11 0.002 2000 A T
-  snp386 11 0.002 2000 A T
-  snp389 11 0.002 2000 A T
-  snp390 11 0.002 2000 A T
-  snp393 11 0.002 2000 A T
-  snp395 11 0.002 2000 A T
-  snp397 11 0.002 2000 A T
-  snp400 11 0.002 2000 A T
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/select_snps/select_snps.gdSnp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out/select_snps/select_snps.gdSnp	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,102 @@
+#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
+#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
+Contig161_chr1_4641264_4641879	115	C	T	73.5	chr1	4641382	C	6	0	2	45	8	0	2	51	15	0	2	72	5	0	2	42	6	0	2	45	10	0	2	57	Y	54	0.323	0
+Contig86_chr1_30984450_30985684	670	C	T	365.0	chr1	30985133	C	9	0	2	54	10	0	2	57	13	0	2	66	3	0	2	36	9	0	2	54	7	0	2	48	Y	145	0.031	0
+Contig21_chr1_60697952_60699446	307	G	A	51.9	chr1	60698265	G	12	0	2	63	9	0	2	54	4	0	2	39	6	0	2	45	9	0	2	54	4	0	2	39	Y	98	0.507	0
+Contig64_chr1_87343284_87345672	163	T	A	3.76	chr1	87343443	C	0	2	2	1	0	0	-1	0	5	0	2	42	2	0	2	33	0	1	2	14	0	0	-1	0	N	3	0.039	2
+Contig20_chr1_110679280_110679687	181	C	T	87.4	chr1	110679454	-	1	0	2	30	7	0	2	48	4	0	2	39	2	0	2	33	2	0	2	33	0	0	-1	0	N	31	0.660	2
+Contig222_chr2_9817738_9818143	220	C	T	888.0	chr2	9817960	C	17	0	2	78	12	0	2	63	20	0	2	87	8	0	2	51	11	0	2	60	12	0	2	63	Y	76	0.093	1
+Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
+Contig6_chr2_56859179_56859956	671	T	C	999.9	chr2	56859851	T	15	0	2	72	18	0	2	81	20	0	2	90	19	0	2	84	19	0	2	84	24	0	2	99	N	28	5.308	1
+Contig163_chr2_76402959_76404830	221	C	T	127.0	chr2	76403181	C	4	0	2	42	10	0	2	57	9	0	2	54	11	0	2	60	7	0	2	48	9	0	2	54	Y	54	0.178	1
+Contig56_chr3_17326225_17327548	387	G	C	91.2	chr3	17326591	G	14	0	2	69	13	0	2	66	15	0	2	72	15	0	2	72	13	0	2	66	12	0	2	63	Y	20	0.225	3
+Contig108_chr3_46210055_46210874	367	A	G	21.0	chr3	46210423	A	19	0	2	84	10	0	2	57	16	0	2	75	14	0	2	69	20	0	2	87	11	0	2	60	N	236	0.028	1
+Contig1_chr3_51588422_51589409	926	A	G	51.0	chr3	51589353	G	2	0	2	33	2	0	2	33	6	0	2	45	4	0	2	39	9	0	2	54	11	0	2	60	N	21	1.147	0
+Contig65_chr3_80727952_80728283	39	T	C	71.2	chr3	80727990	T	7	0	2	48	3	0	2	36	8	0	2	51	6	0	2	45	8	0	2	51	11	0	2	60	N	22	7.078	0
+Contig134_chr4_12145648_12148225	1326	C	T	164.0	chr4	12146961	C	9	0	2	54	8	0	2	51	7	0	2	48	3	0	2	36	5	0	2	42	5	0	2	42	Y	4	0.080	1
+Contig19_chr4_26233601_26233991	146	G	C	51.6	chr4	26233744	G	10	0	2	57	8	0	2	51	9	0	2	54	5	0	2	42	9	0	2	54	4	0	2	39	N	41	0.163	3
+Contig17_chr4_61310346_61311158	267	C	T	49.9	chr4	61310604	T	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	14	0	2	69	7	0	2	48	Y	219	0.098	0
+Contig31_chr5_4734956_4736547	1166	C	T	133.0	chr5	4736132	C	14	0	2	69	8	0	2	51	17	0	2	78	4	0	2	39	9	0	2	54	12	0	2	63	Y	1	0.021	0
+Contig6_chr5_26899813_26900498	97	A	C	88.6	chr5	26899910	A	15	0	2	72	14	0	2	69	27	0	2	108	15	0	2	72	13	0	2	69	12	0	2	63	Y	92	7.370	3
+Contig45_chr5_50892738_50892968	169	C	A	25.8	chr5	50892911	C	10	0	2	57	7	0	2	48	10	0	2	60	6	0	2	45	6	0	2	45	13	0	2	66	N	244	0.497	1
+Contig45_chr5_76133561_76134403	388	A	G	103.0	chr5	76133941	G	3	0	2	36	8	0	2	51	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	57	0.038	0
+Contig111_chr6_5821219_5822519	1060	A	G	68.1	chr6	5822321	T	7	0	2	48	6	0	2	45	11	0	2	60	9	0	2	54	3	0	2	36	12	0	2	63	Y	7	0.231	1
+Contig102_chr6_30271329_30271577	39	T	G	139.0	chr6	30271371	G	3	0	2	36	4	0	2	39	6	0	2	45	1	0	2	30	4	0	2	39	4	0	2	39	N	15	1.159	0
+Contig112_chr6_51024554_51024851	100	A	G	121.0	chr6	51024654	A	10	0	2	57	12	0	2	63	9	0	2	54	13	0	2	66	14	0	2	69	17	0	2	78	N	75	4.287	0
+Contig84_chr7_6648683_6650255	1297	G	A	110.0	chr7	6649988	G	18	0	2	81	9	0	2	54	22	0	2	77	16	0	2	75	20	0	2	87	6	0	2	45	Y	83	0.166	0
+Contig206_chr7_26281823_26282074	103	C	A	101.0	chr7	26281925	T	11	0	2	60	16	0	2	61	19	0	2	84	6	0	2	45	19	0	2	84	16	0	2	75	N	-1	0.947	1
+Contig38_chr7_50681997_50682600	42	T	C	92.4	chr7	50682037	G	6	0	2	45	2	0	2	33	10	0	2	57	12	0	2	63	5	0	2	42	6	0	2	45	Y	94	0.146	0
+Contig91_chr8_12804505_12805470	409	C	A	111.0	chr8	12804906	C	8	0	2	51	10	0	2	57	15	0	2	72	12	0	2	63	14	0	2	69	15	0	2	72	N	145	0.175	0
+Contig8_chr8_27811135_27812620	333	C	T	37.9	chr8	27811458	C	4	0	2	39	11	0	2	60	18	0	2	81	5	0	2	42	6	0	2	45	5	0	2	42	Y	1	0.272	0
+Contig17_chr8_57490059_57490498	69	G	T	97.4	chr8	57490127	A	2	0	2	33	11	0	2	60	15	0	2	72	16	0	2	75	8	0	2	51	10	0	2	57	N	40	0.522	5
+Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
+Contig96_chr9_39008495_39009278	215	A	C	98.7	chr9	39008708	C	7	0	2	48	13	0	2	66	28	0	2	111	16	0	2	75	17	0	2	78	17	0	2	78	Y	8	0.427	1
+Contig22_chr10_15505382_15505589	172	T	C	38.5	chr10	15505548	T	2	0	2	33	6	0	2	45	8	0	2	51	8	0	2	51	9	0	2	54	12	0	2	63	N	284	2.861	0
+Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
+Contig9_chr10_51475063_51476054	770	C	T	57.3	chr10	51475839	C	6	0	2	45	16	0	2	75	16	0	2	75	13	0	2	66	9	0	2	54	9	2	2	21	N	80	0.394	0
+Contig72_chr11_7142765_7143772	146	G	A	152.0	chr11	7142911	A	8	0	2	51	8	0	2	51	24	0	2	99	10	0	2	57	17	0	2	78	11	0	2	60	Y	90	1.137	0
+Contig7_chr11_40017076_40017630	352	C	T	46.3	chr11	40017422	C	7	0	2	48	9	0	2	54	6	0	2	45	8	0	2	51	16	0	2	75	9	0	2	54	Y	44	0.336	0
+Contig16_chr11_53408448_53408790	187	A	G	153.0	chr11	53408638	A	7	0	2	48	9	0	2	54	18	0	2	81	10	0	2	57	11	0	2	60	12	0	2	63	Y	116	1.367	0
+Contig21_chr12_18403415_18404381	586	G	T	34.5	chr12	18403983	-	13	0	2	66	16	0	2	75	25	0	2	102	12	0	2	63	12	0	2	63	14	0	2	69	Y	12	0.068	0
+Contig41_chr12_25565452_25566993	475	G	T	6.29	chr12	25565926	G	15	0	2	72	14	0	2	69	10	0	2	57	15	0	2	72	18	0	2	81	19	0	2	84	N	10	2.231	1
+Contig5_chr12_53880670_53882675	1221	A	C	99.4	chr12	53881888	A	16	0	2	75	18	0	2	81	23	0	2	96	10	0	2	57	15	0	2	72	17	0	2	78	Y	31	0.061	0
+Contig107_chr13_26045881_26046290	341	C	G	81.4	chr13	26046230	C	16	0	2	75	20	0	2	90	14	0	2	69	15	0	2	72	9	0	2	54	9	0	2	54	Y	51	4.510	0
+Contig251_chr13_28498333_28501066	864	T	G	296.0	chr13	28499180	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	5	0	2	42	6	0	2	45	Y	9	0.068	0
+Contig55_chr13_53467708_53468101	221	T	G	132.0	chr13	53467925	T	25	0	2	102	12	0	2	63	26	0	2	105	7	0	2	48	16	0	2	75	16	0	2	75	N	20	5.717	1
+Contig48_chr14_11839435_11843272	3014	A	G	163.0	chr14	11842446	A	10	0	2	57	8	0	2	51	13	0	2	66	10	0	2	57	5	0	2	42	10	0	2	57	Y	31	0.908	0
+Contig28_chr14_26905747_26909514	975	G	C	3.13	chr14	26906723	G	16	0	2	75	10	0	2	57	12	0	2	63	15	0	2	72	10	0	2	57	7	0	2	48	N	287	0.117	2
+Contig64_chr14_56768376_56768902	473	C	T	29.0	chr14	56768832	C	15	0	2	72	11	0	2	60	14	0	2	69	14	0	2	69	7	0	2	48	9	0	2	54	Y	91	8.281	0
+Contig60_chr15_18493036_18494316	150	G	A	92.6	chr15	18493188	G	9	0	2	54	13	0	2	66	9	0	2	54	6	0	2	45	5	0	2	42	12	0	2	63	Y	45	0.125	0
+Contig112_chr15_26772864_26773267	374	C	T	21.6	chr15	26773244	C	4	0	2	39	4	0	2	39	5	0	2	42	2	0	2	33	4	0	2	39	3	0	2	36	N	18	+99.	0
+Contig119_chr16_6160274_6160477	180	G	A	54.8	chr16	6160457	G	7	0	2	48	6	0	2	45	12	0	2	63	3	0	2	36	11	0	2	60	10	0	2	57	N	42	+99.	0
+Contig60_chr16_28079136_28080263	588	T	G	157.0	chr16	28079739	T	22	0	2	93	20	0	2	87	22	0	2	93	17	0	2	78	12	0	2	63	10	0	2	57	Y	105	5.999	1
+Contig31_chr17_12128267_12129637	205	G	A	90.5	chr17	12128484	G	7	0	2	48	6	0	2	45	6	0	2	45	11	0	2	60	7	0	2	48	4	0	2	39	Y	10	0.246	0
+Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
+Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
+Contig229_chr18_3706523_3708577	1076	A	G	83.9	chr18	3707630	A	11	0	2	60	13	0	2	66	26	0	2	105	11	0	2	60	15	0	2	72	17	0	2	78	Y	63	0.445	0
+Contig82_chr18_27305489_27306229	566	C	T	49.5	chr18	27306051	A	6	0	2	45	6	0	2	45	10	0	2	57	11	0	2	60	6	0	2	45	7	0	2	48	N	1	0.349	0
+Contig64_chr18_55979770_55980315	49	G	A	89.1	chr18	55979824	G	3	0	2	36	9	0	2	54	7	0	2	51	4	0	2	39	3	0	2	36	3	0	2	36	Y	-1	2.124	0
+Contig146_chr19_5221790_5223013	143	A	G	114.0	chr19	5221916	-	1	0	2	30	4	0	2	39	3	0	2	36	5	0	2	42	2	0	2	33	5	0	2	42	Y	12	0.870	0
+Contig129_chr19_25541958_25542221	202	T	C	68.1	chr19	25542154	C	11	0	2	60	19	0	2	84	10	0	2	60	17	0	2	78	9	0	2	54	12	0	2	63	N	-1	2.551	1
+Contig60_chr19_54013816_54014398	281	A	G	138.0	chr19	54014103	C	6	0	2	45	15	0	2	72	7	0	2	48	10	0	2	57	15	0	2	72	10	0	2	57	Y	188	1.271	0
+Contig50_chr20_12138509_12141975	3206	C	A	248.0	chr20	12141763	C	8	0	2	51	15	0	2	72	14	0	2	69	6	0	2	45	10	0	2	57	7	0	2	48	Y	2	0.384	0
+Contig36_chr20_32631363_32632049	176	G	A	24.1	chr20	32631526	G	7	0	2	48	14	0	2	69	19	0	2	84	14	0	2	69	15	0	2	72	16	0	2	75	N	50	1.150	0
+Contig50_chr21_4178523_4178687	121	G	A	362.0	chr21	4178640	G	8	0	2	51	14	0	2	69	5	0	2	42	3	0	2	36	11	0	2	60	4	0	2	39	N	392	0.483	0
+Contig129_chr21_31045749_31046924	381	A	G	129.0	chr21	31046141	A	19	0	2	84	8	0	2	51	23	0	2	96	12	0	2	63	15	0	2	72	18	0	2	81	Y	69	0.028	2
+Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0
+Contig23_chr22_34612023_34612568	167	C	G	92.3	chr22	34612181	C	11	0	2	60	18	0	2	81	13	0	2	66	8	0	2	51	12	0	2	63	14	0	2	69	Y	7	0.409	0
+Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
+Contig133_chr23_3525134_3526502	1223	A	G	201.0	chr23	3526387	A	11	0	2	60	13	0	2	66	23	0	2	96	21	0	2	90	13	0	2	66	10	0	2	57	Y	61	1.359	0
+Contig35_chr23_28447813_28449115	70	T	A	21.3	chr23	28447881	T	9	0	2	54	8	0	2	51	10	0	2	57	9	0	2	54	10	0	2	57	12	0	2	63	N	251	0.163	1
+Contig50_chr24_22515247_22516072	761	C	T	243.0	chr24	22515981	T	11	0	2	60	10	0	2	57	8	0	2	51	9	0	2	54	18	0	2	81	8	0	2	51	Y	1	0.190	0
+Contig84_chr24_29196623_29199644	466	C	T	126.0	chr24	29197091	T	7	0	2	48	11	0	2	60	8	0	2	51	7	0	2	48	11	0	2	60	15	0	2	72	Y	42	0.215	0
+Contig144_chr25_4011170_4013134	541	A	G	160.0	chr25	4011690	A	12	0	2	63	17	0	2	78	13	0	2	66	13	0	2	66	13	0	2	66	13	0	2	66	Y	5	0.087	0
+Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
+Contig204_chr26_4311195_4311778	170	C	T	16.9	chr26	4311363	T	20	0	2	87	8	0	2	51	13	0	2	66	18	0	2	81	11	0	2	60	14	0	2	69	N	35	0.085	0
+Contig146_chr26_26622638_26623906	574	G	A	186.0	chr26	26623219	A	11	0	2	60	12	0	2	63	9	0	2	54	11	0	2	60	9	0	2	54	12	0	2	63	Y	1	0.318	0
+Contig135_chr27_6853874_6854079	158	C	T	116.0	chr27	6854032	T	18	0	2	81	19	0	2	84	13	0	2	66	7	0	2	48	8	0	2	51	11	0	2	60	N	4	0.060	1
+Contig64_chr27_34654435_34654621	132	C	A	115.0	chr27	34654567	T	2	0	2	33	2	0	2	33	5	0	2	42	3	0	2	36	3	0	2	36	8	0	2	51	N	12	0.297	1
+Contig131_chr28_6481806_6483783	138	C	T	36.2	chr28	6481953	C	12	0	2	63	12	0	2	63	20	0	2	87	11	0	2	60	10	0	2	57	12	0	2	63	Y	10	0.387	0
+Contig60_chr28_30197166_30197364	92	T	C	164.0	chr28	30197258	T	10	0	2	57	13	0	2	66	15	0	2	72	16	0	2	75	12	0	2	63	11	0	2	60	N	369	1.139	0
+Contig29_chr29_4726399_4727143	559	A	T	163.0	chr29	4726955	A	15	0	2	72	18	0	2	81	18	0	2	81	16	0	2	75	11	0	2	60	14	0	2	72	Y	161	3.114	0
+Contig1_chr30_5992217_5993068	106	C	T	129.0	chr30	5992319	C	10	0	2	57	11	0	2	60	7	0	2	48	11	0	2	60	10	0	2	57	12	0	2	63	Y	76	1.079	0
+Contig165_chr30_25804389_25804926	190	T	C	126.0	chr30	25804592	C	3	0	2	36	8	0	2	51	7	0	2	48	10	0	2	57	7	0	2	48	4	0	2	39	Y	113	0.329	0
+Contig38_chr31_5164423_5166573	2074	C	T	134.0	chr31	5166501	T	13	0	2	66	10	0	2	57	17	0	2	78	11	0	2	60	17	0	2	78	10	0	2	57	Y	58	+99.	0
+Contig17_chr31_26433828_26434459	498	T	C	9.79	chr31	26434322	T	18	0	2	81	10	0	2	57	15	0	2	72	13	0	2	66	16	0	2	75	15	0	2	72	Y	137	4.814	0
+Contig9_chr32_19479532_19479735	12	A	G	20.7	chr32	19479544	A	1	0	2	30	2	0	2	33	1	0	2	30	5	0	2	42	3	0	2	36	3	0	2	36	N	17	+99.	0
+Contig30_chr32_25902721_25905783	208	C	G	162.0	chr32	25902927	G	11	0	2	60	13	0	2	66	11	0	2	60	12	0	2	63	7	0	2	48	11	0	2	60	Y	145	0.322	2
+Contig18_chr33_22207246_22209159	1363	G	T	51.5	chr33	22208619	-	16	0	2	75	8	0	2	51	11	0	2	60	10	0	2	57	15	0	2	72	12	0	2	63	Y	59	2.560	0
+Contig170_chr33_26189421_26189940	292	T	C	98.4	chr33	26189703	T	21	0	2	90	13	0	2	66	15	0	2	72	13	0	2	66	19	0	2	84	13	0	2	66	Y	23	0.307	0
+Contig113_chr34_13341080_13341643	236	C	T	90.7	chr34	13341316	C	4	0	2	39	2	0	2	33	8	0	2	51	4	0	2	39	8	0	2	51	3	0	2	36	Y	47	0.412	3
+Contig152_chr34_31794848_31795540	242	G	A	93.2	chr34	31795093	G	11	0	2	60	24	0	2	99	17	0	2	78	15	0	2	72	18	0	2	81	17	0	2	78	Y	123	2.780	0
+Contig47_chr35_3666773_3667898	348	G	T	124.0	chr35	3667121	G	9	0	2	54	20	0	2	87	18	0	2	81	15	0	2	72	12	0	2	63	14	0	2	69	Y	285	0.235	0
+Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0
+Contig5_chr36_4562983_4563634	343	C	T	151.0	chr36	4563324	T	20	0	2	87	20	0	2	87	23	0	2	96	24	0	2	99	9	0	2	54	8	0	2	51	Y	40	1.169	0
+Contig133_chr36_32954045_32955409	136	A	G	116.0	chr36	32954182	A	16	0	2	75	15	0	2	72	20	0	2	87	11	0	2	60	18	0	2	81	13	0	2	66	Y	74	3.772	1
+Contig53_chr37_6665763_6665919	116	C	T	111.0	chr37	6665875	C	9	0	2	54	9	0	2	54	5	0	2	42	9	0	2	54	8	0	2	51	10	0	2	57	N	15	10.875	1
+Contig2_chr37_31197993_31198256	182	C	T	39.6	chr37	31198171	T	6	0	2	45	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	12	0	2	63	N	2	0.595	0
+Contig7_chr38_12217200_12218387	1163	A	T	44.4	chr38	12218353	A	11	0	2	60	13	0	2	66	17	0	2	78	10	0	2	57	11	0	2	60	11	0	2	60	Y	67	+99.	0
+Contig265_chrX_2689247_2689484	114	C	G	103.0	chrX	2689356	C	11	0	2	60	9	0	2	54	13	0	2	66	16	0	2	75	14	0	2	69	10	0	2	57	N	2	9.232	1
+Contig113_chrX_26287829_26288398	385	C	T	59.6	chrX	26288213	C	9	0	2	54	9	0	2	54	17	0	2	78	11	0	2	60	3	8	1	44	4	0	2	39	N	13	0.077	0
+Contig90_chrX_57430715_57431566	548	C	T	116.0	chrX	57431266	T	9	0	2	54	18	0	2	81	13	0	2	66	14	0	2	69	8	0	2	54	7	0	2	48	Y	261	0.154	1
+Contig133_chrX_84833782_84834125	182	G	A	69.7	chrX	84833962	G	5	0	2	42	18	0	2	81	12	0	2	63	19	0	2	84	6	3	1	27	7	0	2	48	N	619	0.278	0
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/select_snps/select_snps.snp
--- a/test-data/test_out/select_snps/select_snps.snp	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
-#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
-Contig161_chr1_4641264_4641879	115	C	T	73.5	chr1	4641382	C	6	0	2	45	8	0	2	51	15	0	2	72	5	0	2	42	6	0	2	45	10	0	2	57	Y	54	0.323	0
-Contig86_chr1_30984450_30985684	670	C	T	365.0	chr1	30985133	C	9	0	2	54	10	0	2	57	13	0	2	66	3	0	2	36	9	0	2	54	7	0	2	48	Y	145	0.031	0
-Contig21_chr1_60697952_60699446	307	G	A	51.9	chr1	60698265	G	12	0	2	63	9	0	2	54	4	0	2	39	6	0	2	45	9	0	2	54	4	0	2	39	Y	98	0.507	0
-Contig64_chr1_87343284_87345672	163	T	A	3.76	chr1	87343443	C	0	2	2	1	0	0	-1	0	5	0	2	42	2	0	2	33	0	1	2	14	0	0	-1	0	N	3	0.039	2
-Contig20_chr1_110679280_110679687	181	C	T	87.4	chr1	110679454	-	1	0	2	30	7	0	2	48	4	0	2	39	2	0	2	33	2	0	2	33	0	0	-1	0	N	31	0.660	2
-Contig222_chr2_9817738_9818143	220	C	T	888.0	chr2	9817960	C	17	0	2	78	12	0	2	63	20	0	2	87	8	0	2	51	11	0	2	60	12	0	2	63	Y	76	0.093	1
-Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
-Contig6_chr2_56859179_56859956	671	T	C	999.9	chr2	56859851	T	15	0	2	72	18	0	2	81	20	0	2	90	19	0	2	84	19	0	2	84	24	0	2	99	N	28	5.308	1
-Contig163_chr2_76402959_76404830	221	C	T	127.0	chr2	76403181	C	4	0	2	42	10	0	2	57	9	0	2	54	11	0	2	60	7	0	2	48	9	0	2	54	Y	54	0.178	1
-Contig56_chr3_17326225_17327548	387	G	C	91.2	chr3	17326591	G	14	0	2	69	13	0	2	66	15	0	2	72	15	0	2	72	13	0	2	66	12	0	2	63	Y	20	0.225	3
-Contig108_chr3_46210055_46210874	367	A	G	21.0	chr3	46210423	A	19	0	2	84	10	0	2	57	16	0	2	75	14	0	2	69	20	0	2	87	11	0	2	60	N	236	0.028	1
-Contig1_chr3_51588422_51589409	926	A	G	51.0	chr3	51589353	G	2	0	2	33	2	0	2	33	6	0	2	45	4	0	2	39	9	0	2	54	11	0	2	60	N	21	1.147	0
-Contig65_chr3_80727952_80728283	39	T	C	71.2	chr3	80727990	T	7	0	2	48	3	0	2	36	8	0	2	51	6	0	2	45	8	0	2	51	11	0	2	60	N	22	7.078	0
-Contig134_chr4_12145648_12148225	1326	C	T	164.0	chr4	12146961	C	9	0	2	54	8	0	2	51	7	0	2	48	3	0	2	36	5	0	2	42	5	0	2	42	Y	4	0.080	1
-Contig19_chr4_26233601_26233991	146	G	C	51.6	chr4	26233744	G	10	0	2	57	8	0	2	51	9	0	2	54	5	0	2	42	9	0	2	54	4	0	2	39	N	41	0.163	3
-Contig17_chr4_61310346_61311158	267	C	T	49.9	chr4	61310604	T	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	14	0	2	69	7	0	2	48	Y	219	0.098	0
-Contig31_chr5_4734956_4736547	1166	C	T	133.0	chr5	4736132	C	14	0	2	69	8	0	2	51	17	0	2	78	4	0	2	39	9	0	2	54	12	0	2	63	Y	1	0.021	0
-Contig6_chr5_26899813_26900498	97	A	C	88.6	chr5	26899910	A	15	0	2	72	14	0	2	69	27	0	2	108	15	0	2	72	13	0	2	69	12	0	2	63	Y	92	7.370	3
-Contig45_chr5_50892738_50892968	169	C	A	25.8	chr5	50892911	C	10	0	2	57	7	0	2	48	10	0	2	60	6	0	2	45	6	0	2	45	13	0	2	66	N	244	0.497	1
-Contig45_chr5_76133561_76134403	388	A	G	103.0	chr5	76133941	G	3	0	2	36	8	0	2	51	8	0	2	51	5	0	2	42	6	0	2	45	7	0	2	48	Y	57	0.038	0
-Contig111_chr6_5821219_5822519	1060	A	G	68.1	chr6	5822321	T	7	0	2	48	6	0	2	45	11	0	2	60	9	0	2	54	3	0	2	36	12	0	2	63	Y	7	0.231	1
-Contig102_chr6_30271329_30271577	39	T	G	139.0	chr6	30271371	G	3	0	2	36	4	0	2	39	6	0	2	45	1	0	2	30	4	0	2	39	4	0	2	39	N	15	1.159	0
-Contig112_chr6_51024554_51024851	100	A	G	121.0	chr6	51024654	A	10	0	2	57	12	0	2	63	9	0	2	54	13	0	2	66	14	0	2	69	17	0	2	78	N	75	4.287	0
-Contig84_chr7_6648683_6650255	1297	G	A	110.0	chr7	6649988	G	18	0	2	81	9	0	2	54	22	0	2	77	16	0	2	75	20	0	2	87	6	0	2	45	Y	83	0.166	0
-Contig206_chr7_26281823_26282074	103	C	A	101.0	chr7	26281925	T	11	0	2	60	16	0	2	61	19	0	2	84	6	0	2	45	19	0	2	84	16	0	2	75	N	-1	0.947	1
-Contig38_chr7_50681997_50682600	42	T	C	92.4	chr7	50682037	G	6	0	2	45	2	0	2	33	10	0	2	57	12	0	2	63	5	0	2	42	6	0	2	45	Y	94	0.146	0
-Contig91_chr8_12804505_12805470	409	C	A	111.0	chr8	12804906	C	8	0	2	51	10	0	2	57	15	0	2	72	12	0	2	63	14	0	2	69	15	0	2	72	N	145	0.175	0
-Contig8_chr8_27811135_27812620	333	C	T	37.9	chr8	27811458	C	4	0	2	39	11	0	2	60	18	0	2	81	5	0	2	42	6	0	2	45	5	0	2	42	Y	1	0.272	0
-Contig17_chr8_57490059_57490498	69	G	T	97.4	chr8	57490127	A	2	0	2	33	11	0	2	60	15	0	2	72	16	0	2	75	8	0	2	51	10	0	2	57	N	40	0.522	5
-Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
-Contig96_chr9_39008495_39009278	215	A	C	98.7	chr9	39008708	C	7	0	2	48	13	0	2	66	28	0	2	111	16	0	2	75	17	0	2	78	17	0	2	78	Y	8	0.427	1
-Contig22_chr10_15505382_15505589	172	T	C	38.5	chr10	15505548	T	2	0	2	33	6	0	2	45	8	0	2	51	8	0	2	51	9	0	2	54	12	0	2	63	N	284	2.861	0
-Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
-Contig9_chr10_51475063_51476054	770	C	T	57.3	chr10	51475839	C	6	0	2	45	16	0	2	75	16	0	2	75	13	0	2	66	9	0	2	54	9	2	2	21	N	80	0.394	0
-Contig72_chr11_7142765_7143772	146	G	A	152.0	chr11	7142911	A	8	0	2	51	8	0	2	51	24	0	2	99	10	0	2	57	17	0	2	78	11	0	2	60	Y	90	1.137	0
-Contig7_chr11_40017076_40017630	352	C	T	46.3	chr11	40017422	C	7	0	2	48	9	0	2	54	6	0	2	45	8	0	2	51	16	0	2	75	9	0	2	54	Y	44	0.336	0
-Contig16_chr11_53408448_53408790	187	A	G	153.0	chr11	53408638	A	7	0	2	48	9	0	2	54	18	0	2	81	10	0	2	57	11	0	2	60	12	0	2	63	Y	116	1.367	0
-Contig21_chr12_18403415_18404381	586	G	T	34.5	chr12	18403983	-	13	0	2	66	16	0	2	75	25	0	2	102	12	0	2	63	12	0	2	63	14	0	2	69	Y	12	0.068	0
-Contig41_chr12_25565452_25566993	475	G	T	6.29	chr12	25565926	G	15	0	2	72	14	0	2	69	10	0	2	57	15	0	2	72	18	0	2	81	19	0	2	84	N	10	2.231	1
-Contig5_chr12_53880670_53882675	1221	A	C	99.4	chr12	53881888	A	16	0	2	75	18	0	2	81	23	0	2	96	10	0	2	57	15	0	2	72	17	0	2	78	Y	31	0.061	0
-Contig107_chr13_26045881_26046290	341	C	G	81.4	chr13	26046230	C	16	0	2	75	20	0	2	90	14	0	2	69	15	0	2	72	9	0	2	54	9	0	2	54	Y	51	4.510	0
-Contig251_chr13_28498333_28501066	864	T	G	296.0	chr13	28499180	T	3	0	2	36	5	0	2	42	4	0	2	39	2	0	2	33	5	0	2	42	6	0	2	45	Y	9	0.068	0
-Contig55_chr13_53467708_53468101	221	T	G	132.0	chr13	53467925	T	25	0	2	102	12	0	2	63	26	0	2	105	7	0	2	48	16	0	2	75	16	0	2	75	N	20	5.717	1
-Contig48_chr14_11839435_11843272	3014	A	G	163.0	chr14	11842446	A	10	0	2	57	8	0	2	51	13	0	2	66	10	0	2	57	5	0	2	42	10	0	2	57	Y	31	0.908	0
-Contig28_chr14_26905747_26909514	975	G	C	3.13	chr14	26906723	G	16	0	2	75	10	0	2	57	12	0	2	63	15	0	2	72	10	0	2	57	7	0	2	48	N	287	0.117	2
-Contig64_chr14_56768376_56768902	473	C	T	29.0	chr14	56768832	C	15	0	2	72	11	0	2	60	14	0	2	69	14	0	2	69	7	0	2	48	9	0	2	54	Y	91	8.281	0
-Contig60_chr15_18493036_18494316	150	G	A	92.6	chr15	18493188	G	9	0	2	54	13	0	2	66	9	0	2	54	6	0	2	45	5	0	2	42	12	0	2	63	Y	45	0.125	0
-Contig112_chr15_26772864_26773267	374	C	T	21.6	chr15	26773244	C	4	0	2	39	4	0	2	39	5	0	2	42	2	0	2	33	4	0	2	39	3	0	2	36	N	18	+99.	0
-Contig119_chr16_6160274_6160477	180	G	A	54.8	chr16	6160457	G	7	0	2	48	6	0	2	45	12	0	2	63	3	0	2	36	11	0	2	60	10	0	2	57	N	42	+99.	0
-Contig60_chr16_28079136_28080263	588	T	G	157.0	chr16	28079739	T	22	0	2	93	20	0	2	87	22	0	2	93	17	0	2	78	12	0	2	63	10	0	2	57	Y	105	5.999	1
-Contig31_chr17_12128267_12129637	205	G	A	90.5	chr17	12128484	G	7	0	2	48	6	0	2	45	6	0	2	45	11	0	2	60	7	0	2	48	4	0	2	39	Y	10	0.246	0
-Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
-Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
-Contig229_chr18_3706523_3708577	1076	A	G	83.9	chr18	3707630	A	11	0	2	60	13	0	2	66	26	0	2	105	11	0	2	60	15	0	2	72	17	0	2	78	Y	63	0.445	0
-Contig82_chr18_27305489_27306229	566	C	T	49.5	chr18	27306051	A	6	0	2	45	6	0	2	45	10	0	2	57	11	0	2	60	6	0	2	45	7	0	2	48	N	1	0.349	0
-Contig64_chr18_55979770_55980315	49	G	A	89.1	chr18	55979824	G	3	0	2	36	9	0	2	54	7	0	2	51	4	0	2	39	3	0	2	36	3	0	2	36	Y	-1	2.124	0
-Contig146_chr19_5221790_5223013	143	A	G	114.0	chr19	5221916	-	1	0	2	30	4	0	2	39	3	0	2	36	5	0	2	42	2	0	2	33	5	0	2	42	Y	12	0.870	0
-Contig129_chr19_25541958_25542221	202	T	C	68.1	chr19	25542154	C	11	0	2	60	19	0	2	84	10	0	2	60	17	0	2	78	9	0	2	54	12	0	2	63	N	-1	2.551	1
-Contig60_chr19_54013816_54014398	281	A	G	138.0	chr19	54014103	C	6	0	2	45	15	0	2	72	7	0	2	48	10	0	2	57	15	0	2	72	10	0	2	57	Y	188	1.271	0
-Contig50_chr20_12138509_12141975	3206	C	A	248.0	chr20	12141763	C	8	0	2	51	15	0	2	72	14	0	2	69	6	0	2	45	10	0	2	57	7	0	2	48	Y	2	0.384	0
-Contig36_chr20_32631363_32632049	176	G	A	24.1	chr20	32631526	G	7	0	2	48	14	0	2	69	19	0	2	84	14	0	2	69	15	0	2	72	16	0	2	75	N	50	1.150	0
-Contig50_chr21_4178523_4178687	121	G	A	362.0	chr21	4178640	G	8	0	2	51	14	0	2	69	5	0	2	42	3	0	2	36	11	0	2	60	4	0	2	39	N	392	0.483	0
-Contig129_chr21_31045749_31046924	381	A	G	129.0	chr21	31046141	A	19	0	2	84	8	0	2	51	23	0	2	96	12	0	2	63	15	0	2	72	18	0	2	81	Y	69	0.028	2
-Contig159_chr22_7896450_7896974	109	G	C	151.0	chr22	7896570	G	16	0	2	75	5	7	1	62	14	0	2	69	16	0	2	75	13	0	2	66	13	0	2	66	Y	16	0.465	0
-Contig23_chr22_34612023_34612568	167	C	G	92.3	chr22	34612181	C	11	0	2	60	18	0	2	81	13	0	2	66	8	0	2	51	12	0	2	63	14	0	2	69	Y	7	0.409	0
-Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
-Contig133_chr23_3525134_3526502	1223	A	G	201.0	chr23	3526387	A	11	0	2	60	13	0	2	66	23	0	2	96	21	0	2	90	13	0	2	66	10	0	2	57	Y	61	1.359	0
-Contig35_chr23_28447813_28449115	70	T	A	21.3	chr23	28447881	T	9	0	2	54	8	0	2	51	10	0	2	57	9	0	2	54	10	0	2	57	12	0	2	63	N	251	0.163	1
-Contig50_chr24_22515247_22516072	761	C	T	243.0	chr24	22515981	T	11	0	2	60	10	0	2	57	8	0	2	51	9	0	2	54	18	0	2	81	8	0	2	51	Y	1	0.190	0
-Contig84_chr24_29196623_29199644	466	C	T	126.0	chr24	29197091	T	7	0	2	48	11	0	2	60	8	0	2	51	7	0	2	48	11	0	2	60	15	0	2	72	Y	42	0.215	0
-Contig144_chr25_4011170_4013134	541	A	G	160.0	chr25	4011690	A	12	0	2	63	17	0	2	78	13	0	2	66	13	0	2	66	13	0	2	66	13	0	2	66	Y	5	0.087	0
-Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
-Contig204_chr26_4311195_4311778	170	C	T	16.9	chr26	4311363	T	20	0	2	87	8	0	2	51	13	0	2	66	18	0	2	81	11	0	2	60	14	0	2	69	N	35	0.085	0
-Contig146_chr26_26622638_26623906	574	G	A	186.0	chr26	26623219	A	11	0	2	60	12	0	2	63	9	0	2	54	11	0	2	60	9	0	2	54	12	0	2	63	Y	1	0.318	0
-Contig135_chr27_6853874_6854079	158	C	T	116.0	chr27	6854032	T	18	0	2	81	19	0	2	84	13	0	2	66	7	0	2	48	8	0	2	51	11	0	2	60	N	4	0.060	1
-Contig64_chr27_34654435_34654621	132	C	A	115.0	chr27	34654567	T	2	0	2	33	2	0	2	33	5	0	2	42	3	0	2	36	3	0	2	36	8	0	2	51	N	12	0.297	1
-Contig131_chr28_6481806_6483783	138	C	T	36.2	chr28	6481953	C	12	0	2	63	12	0	2	63	20	0	2	87	11	0	2	60	10	0	2	57	12	0	2	63	Y	10	0.387	0
-Contig60_chr28_30197166_30197364	92	T	C	164.0	chr28	30197258	T	10	0	2	57	13	0	2	66	15	0	2	72	16	0	2	75	12	0	2	63	11	0	2	60	N	369	1.139	0
-Contig29_chr29_4726399_4727143	559	A	T	163.0	chr29	4726955	A	15	0	2	72	18	0	2	81	18	0	2	81	16	0	2	75	11	0	2	60	14	0	2	72	Y	161	3.114	0
-Contig1_chr30_5992217_5993068	106	C	T	129.0	chr30	5992319	C	10	0	2	57	11	0	2	60	7	0	2	48	11	0	2	60	10	0	2	57	12	0	2	63	Y	76	1.079	0
-Contig165_chr30_25804389_25804926	190	T	C	126.0	chr30	25804592	C	3	0	2	36	8	0	2	51	7	0	2	48	10	0	2	57	7	0	2	48	4	0	2	39	Y	113	0.329	0
-Contig38_chr31_5164423_5166573	2074	C	T	134.0	chr31	5166501	T	13	0	2	66	10	0	2	57	17	0	2	78	11	0	2	60	17	0	2	78	10	0	2	57	Y	58	+99.	0
-Contig17_chr31_26433828_26434459	498	T	C	9.79	chr31	26434322	T	18	0	2	81	10	0	2	57	15	0	2	72	13	0	2	66	16	0	2	75	15	0	2	72	Y	137	4.814	0
-Contig9_chr32_19479532_19479735	12	A	G	20.7	chr32	19479544	A	1	0	2	30	2	0	2	33	1	0	2	30	5	0	2	42	3	0	2	36	3	0	2	36	N	17	+99.	0
-Contig30_chr32_25902721_25905783	208	C	G	162.0	chr32	25902927	G	11	0	2	60	13	0	2	66	11	0	2	60	12	0	2	63	7	0	2	48	11	0	2	60	Y	145	0.322	2
-Contig18_chr33_22207246_22209159	1363	G	T	51.5	chr33	22208619	-	16	0	2	75	8	0	2	51	11	0	2	60	10	0	2	57	15	0	2	72	12	0	2	63	Y	59	2.560	0
-Contig170_chr33_26189421_26189940	292	T	C	98.4	chr33	26189703	T	21	0	2	90	13	0	2	66	15	0	2	72	13	0	2	66	19	0	2	84	13	0	2	66	Y	23	0.307	0
-Contig113_chr34_13341080_13341643	236	C	T	90.7	chr34	13341316	C	4	0	2	39	2	0	2	33	8	0	2	51	4	0	2	39	8	0	2	51	3	0	2	36	Y	47	0.412	3
-Contig152_chr34_31794848_31795540	242	G	A	93.2	chr34	31795093	G	11	0	2	60	24	0	2	99	17	0	2	78	15	0	2	72	18	0	2	81	17	0	2	78	Y	123	2.780	0
-Contig47_chr35_3666773_3667898	348	G	T	124.0	chr35	3667121	G	9	0	2	54	20	0	2	87	18	0	2	81	15	0	2	72	12	0	2	63	14	0	2	69	Y	285	0.235	0
-Contig74_chr35_25394343_25394813	303	A	T	221.0	chr35	25394646	G	23	0	2	96	15	0	2	72	25	0	2	105	7	7	1	49	18	0	2	81	16	0	2	75	Y	58	4.298	0
-Contig5_chr36_4562983_4563634	343	C	T	151.0	chr36	4563324	T	20	0	2	87	20	0	2	87	23	0	2	96	24	0	2	99	9	0	2	54	8	0	2	51	Y	40	1.169	0
-Contig133_chr36_32954045_32955409	136	A	G	116.0	chr36	32954182	A	16	0	2	75	15	0	2	72	20	0	2	87	11	0	2	60	18	0	2	81	13	0	2	66	Y	74	3.772	1
-Contig53_chr37_6665763_6665919	116	C	T	111.0	chr37	6665875	C	9	0	2	54	9	0	2	54	5	0	2	42	9	0	2	54	8	0	2	51	10	0	2	57	N	15	10.875	1
-Contig2_chr37_31197993_31198256	182	C	T	39.6	chr37	31198171	T	6	0	2	45	10	0	2	57	7	0	2	48	9	0	2	54	10	0	2	57	12	0	2	63	N	2	0.595	0
-Contig7_chr38_12217200_12218387	1163	A	T	44.4	chr38	12218353	A	11	0	2	60	13	0	2	66	17	0	2	78	10	0	2	57	11	0	2	60	11	0	2	60	Y	67	+99.	0
-Contig265_chrX_2689247_2689484	114	C	G	103.0	chrX	2689356	C	11	0	2	60	9	0	2	54	13	0	2	66	16	0	2	75	14	0	2	69	10	0	2	57	N	2	9.232	1
-Contig113_chrX_26287829_26288398	385	C	T	59.6	chrX	26288213	C	9	0	2	54	9	0	2	54	17	0	2	78	11	0	2	60	3	8	1	44	4	0	2	39	N	13	0.077	0
-Contig90_chrX_57430715_57431566	548	C	T	116.0	chrX	57431266	T	9	0	2	54	18	0	2	81	13	0	2	66	14	0	2	69	8	0	2	54	7	0	2	48	Y	261	0.154	1
-Contig133_chrX_84833782_84834125	182	G	A	69.7	chrX	84833962	G	5	0	2	42	18	0	2	81	12	0	2	63	19	0	2	84	6	3	1	27	7	0	2	48	N	619	0.278	0
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.gdSnp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.gdSnp	Tue Sep 04 12:49:53 2012 -0400
@@ -0,0 +1,10 @@
+#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
+#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
+Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
+Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
+Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
+Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
+Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
+Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
+Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
+Contig64_chr27_34654435_34654621	132	C	A	115.0	chr27	34654567	T	2	0	2	33	2	0	2	33	5	0	2	42	3	0	2	36	3	0	2	36	8	0	2	51	N	12	0.297	1
diff -r 22fe0154fa54 -r 9b92372de9f6 test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp
--- a/test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp	Tue Jul 10 11:41:22 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
-#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
-Contig47_chr2_25470778_25471576	126	G	A	888.0	chr2	25470896	G	12	0	2	63	14	0	2	69	14	0	2	69	10	0	2	57	18	0	2	81	13	0	2	66	N	11	0.289	1
-Contig73_chr9_29451535_29452248	616	A	G	24.7	chr9	29452127	G	4	0	2	39	7	0	2	48	1	0	2	30	4	0	2	39	7	0	2	48	6	0	2	45	N	49	0.448	4
-Contig69_chr10_40547265_40548153	371	G	A	58.1	chr10	40547649	A	9	0	2	54	8	0	2	51	8	0	2	51	9	0	2	54	4	0	2	39	5	0	2	42	Y	20	0.138	4
-Contig99_chr17_26021506_26022200	505	C	T	88.8	chr17	26022017	T	15	0	2	72	13	0	2	66	19	0	2	84	9	0	2	54	10	0	2	57	11	0	2	60	Y	1	0.172	1
-Contig27_chr17_61713766_61716585	1056	G	C	40.0	chr17	61714821	G	4	0	2	39	8	0	2	51	10	0	2	57	6	0	2	45	6	0	2	45	3	0	2	36	N	6	2.200	4
-Contig26_chr22_57817664_57819633	1453	A	G	150.0	chr22	57819121	G	9	0	2	54	9	0	2	54	13	0	2	66	15	0	2	72	11	0	2	60	14	0	2	69	N	15	0.471	1
-Contig103_chr25_38891221_38892140	407	G	A	131.0	chr25	38891644	G	8	0	2	51	14	0	2	69	18	0	2	81	8	0	2	51	8	0	2	51	11	0	2	60	Y	149	0.167	4
-Contig64_chr27_34654435_34654621	132	C	A	115.0	chr27	34654567	T	2	0	2	33	2	0	2	33	5	0	2	42	3	0	2	36	3	0	2	36	8	0	2	51	N	12	0.297	1