Mercurial > repos > miller-lab > genome_diversity
changeset 16:be0e2223c531
Deleted selected files
| author | miller-lab |
|---|---|
| date | Fri, 28 Sep 2012 11:56:42 -0400 |
| parents | 4a8beb08d1b9 |
| children | a3af29edcce2 |
| files | aggregate_gd_indivs.xml commits.log filter_gd_snp.xml specify.xml test-data/test_in/a.gd_indivs test-data/test_in/b.gd_indivs test-data/test_in/c.gd_indivs test-data/test_in/sample.gd_sap test-data/test_in/sample.gd_snp test-data/test_out/add_fst_column/add_fst_column.gd_snp test-data/test_out/modify_snp_table/modify.gd_snp test-data/test_out/pca/admix.gd_indivs test-data/test_out/pca/admix.gd_snp test-data/test_out/select_snps/select_snps.gd_snp test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.gd_snp |
| diffstat | 15 files changed, 0 insertions(+), 1885 deletions(-) [+] |
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--- a/aggregate_gd_indivs.xml Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,86 +0,0 @@ -<tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.0.0"> - <description>: Append summary columns for a population</description> - - <command interpreter="python"> - modify_snp_table.py "$input" "$p1_input" "$output" "-1" "-1" "-1" "-1" - #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) - #set $arg = '%s:%s' % ($individual_col, $individual) - "$arg" - #end for - </command> - - <inputs> - <param name="input" type="data" format="gd_snp" label="SNP dataset" /> - <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> - </inputs> - - <outputs> - <data name="output" format="gd_snp" metadata_source="input" /> - </outputs> - - <tests> - <test> - <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> - <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> - <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.gd_snp" /> - </test> - </tests> - - <help> - -**Dataset formats** - -The input datasets are in gd_snp_ and gd_indivs_ formats. -The output dataset is in gd_snp_ format. (`Dataset missing?`_) - -.. _gd_snp: ./static/formatHelp.html#gd_snp -.. _gd_indivs: ./static/formatHelp.html#gd_indivs -.. _Dataset missing?: ./static/formatHelp.html - ------ - -**What it does** - -The user specifies that some of the individuals in a gd_snp dataset form a -"population", by supplying a list that has been previously created using the -Specify Individuals tool. The program appends a -new "entity" (set of four columns) to the gd_snp table, analogous to the columns -for an individual but containing summary data for the population as a group. -These four columns give the total counts for the two alleles, the "genotype" for -the population, and the maximum quality value, taken over all individuals in the -population. If all defined genotypes in the population are 2 (agree with the -reference), then the population's genotype is 2, and similarly for 0; otherwise -the genotype is 1 (unless all individuals have undefined genotype, in which case -it is -1). - ------ - -**Example** - -- input gd_snp:: - - 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 - etc. - -- input individuals:: - - 9 PB1 - 13 PB2 - 17 PB3 - -- output:: - - 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 29 0 2 72 - 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 3 0 2 30 - 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 13 0 2 42 - etc. - - </help> -</tool>
--- a/commits.log Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ - -:7b775e5b68b4 -cathy 2012-09-28 00:55 -Galaxy didn't like my RST syntax. :-/ - -:9b5b4f73bd98 -cathy 2012-09-28 00:08 -Tweaks by Cathy, e.g. adjusting text where renamed tools are mentioned. -Also riemerized through first section, "Initial Analysis". - -:93eeef51be96 -cathy 2012-09-27 14:03 -Fixed datatype bugs in the Filter SNPs and Aggregate Individuals tools. - -:119e1e904cc4 -cathy 2012-09-26 15:38 -Restored modify_snp_table.py from the archive, since it's still used by the -Filter SNPs and Aggregate Individuals tools. - -:cc508d55cc9d -cathy 2012-09-26 15:16 -Tweaked description for the Prepare Input tool. - -:cdb8430b1659 -cathy 2012-09-26 15:10 -Added ": " at the beginning of each description to separate it from the name. - -:3286bdea6b3d -cathy 2012-09-26 13:01 -Clarified tool names and descriptions. - -:8a9bdfc0d31f -cathy 2012-09-19 17:15 -Edited docs in aggregate_gd_indivs.xml: clarified "What it does", reformatted -example data. - -:f7c6a18af605 -cathy 2012-09-19 11:31 -Edited docs in specify.xml: clarified "What it does", reformatted example data. -
--- a/filter_gd_snp.xml Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -<tool id="gd_filter_gd_snp" name="Filter SNPs" version="1.0.0"> - <description>: Discard some SNPs based on coverage or quality</description> - - <command interpreter="python"> - modify_snp_table.py "$input" "$p1_input" "$output" "$lo_coverage" "$hi_coverage" "$low_ind_cov" "$lo_quality" - #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) - #set $arg = '%s:%s' % ($individual_col, $individual) - "$arg" - #end for - </command> - - <inputs> - <param name="input" type="data" format="gd_snp" label="SNP dataset" /> - <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> - <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" /> - <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" /> - <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" /> - <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" /> - </inputs> - - <outputs> - <data name="output" format="gd_snp" metadata_source="input" /> - </outputs> - - <tests> - <test> - <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> - <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> - <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.gd_snp" /> - </test> - </tests> - - <help> - -**Dataset formats** - -The input datasets are in gd_snp_ and gd_indivs_ formats. -The output dataset is in gd_snp_ format. (`Dataset missing?`_) - -.. _gd_snp: ./static/formatHelp.html#gd_snp -.. _gd_indivs: ./static/formatHelp.html#gd_indivs -.. _Dataset missing?: ./static/formatHelp.html - ------ - -**What it does** - -The user specifies that some of the individuals in a gd_snp dataset form a -"population", by supplying a list that has been previously created using the -Specify Individuals tool. SNPs are then discarded if their total coverage -for the population is too low or too high, or if their coverage or quality -score for any individual in the population is too low. - ------ - -**Example** - -- input gd_snp:: - - 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 - etc. - -- input individuals:: - - 9 PB1 - 13 PB2 - 17 PB3 - -- output when the lower bound on individual coverage is "3":: - - 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 - etc. - - </help> -</tool>
--- a/specify.xml Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -<tool id="gd_specify" name="Specify Individuals" version="1.0.0"> - <description>: Define a collection of individuals from a gd_snp dataset</description> - - <command interpreter="bash"> - echo.bash "$input" "$output" - #for $individual in str($individuals).split(',') - #set $individual_idx = $input.dataset.metadata.individual_names.index($individual) - #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] ) - #set $arg = '\t'.join([$individual_col, $individual, '']) - "$arg" - #end for - </command> - - <inputs> - <param name="input" type="data" format="gd_snp" label="SNP dataset"/> - <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include"> - <options> - <filter type="data_meta" ref="input" key="individual_names" /> - </options> - <validator type="no_options" message="You must select at least one individual."/> - </param> - <param name="outname" type="text" size="20" label="Label for this collection"> - <validator type="empty_field" message="You must enter a label."/> - #used to be "Individuals from ${input.hid}" - </param> - </inputs> - - <outputs> - <data name="output" format="gd_indivs" label="${outname}" /> - </outputs> - - <tests> - <test> - <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> - <param name="individuals" value="PB1,PB2" /> - <output name="output" file="test_in/a.gd_indivs" /> - </test> - </tests> - - <help> - -**Dataset formats** - -The input dataset is in gd_snp_ format; -the output is in gd_indivs_ format. (`Dataset missing?`_) - -.. _gd_snp: ./static/formatHelp.html#gd_snp -.. _gd_indivs: ./static/formatHelp.html#gd_indivs -.. _Dataset missing?: ./static/formatHelp.html - ------ - -**What it does** - -This tool makes a list of selected entities (the sets of four columns -representing individuals or groups) from a gd_snp dataset. It does not copy -the SNP data; it just records which entities should be considered as belonging -to some collection or population. The label you specify is used to name the -output dataset in your history. This list can then be used to instruct other -tools to work on just part of the original gd_snp dataset. - ------ - -**Example** - -- input:: - - 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 - etc. - -- input metadata:: - - #{"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"} - -- output when individuals PB1, PB2, and PB3 are selected:: - - 9 PB1 - 13 PB2 - 17 PB3 - - </help> -</tool>
--- a/test-data/test_in/a.gd_indivs Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -9 PB1 -13 PB2
--- a/test-data/test_in/b.gd_indivs Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -17 PB3 -21 PB4
--- a/test-data/test_in/c.gd_indivs Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -25 PB6 -29 PB8
--- a/test-data/test_in/sample.gd_sap Fri Sep 28 11:48:38 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
--- a/test-data/test_in/sample.gd_snp Fri Sep 28 11:48:38 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
--- a/test-data/test_out/add_fst_column/add_fst_column.gd_snp Fri Sep 28 11:48:38 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
--- a/test-data/test_out/modify_snp_table/modify.gd_snp Fri Sep 28 11:48:38 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
--- a/test-data/test_out/pca/admix.gd_indivs Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -PB1 M All_Individuals -PB2 M All_Individuals -PB3 M All_Individuals -PB4 M All_Individuals -PB6 M All_Individuals -PB8 M All_Individuals
--- a/test-data/test_out/pca/admix.gd_snp Fri Sep 28 11:48:38 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,303 +0,0 @@ - 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 - snp29 11 0.002 2000 A T - snp30 11 0.002 2000 A T - snp31 11 0.002 2000 A T - snp33 11 0.002 2000 A T - snp34 11 0.002 2000 A T - snp37 11 0.002 2000 A T - snp38 11 0.002 2000 A T - snp39 11 0.002 2000 A T - snp40 11 0.002 2000 A T - snp41 11 0.002 2000 A T - snp42 11 0.002 2000 A T - snp43 11 0.002 2000 A T - snp45 11 0.002 2000 A T - snp46 11 0.002 2000 A T - 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snp288 11 0.002 2000 A T - snp289 11 0.002 2000 A T - snp290 11 0.002 2000 A T - snp291 11 0.002 2000 A T - snp292 11 0.002 2000 A T - snp293 11 0.002 2000 A T - snp294 11 0.002 2000 A T - snp297 11 0.002 2000 A T - snp298 11 0.002 2000 A T - snp299 11 0.002 2000 A T - snp300 11 0.002 2000 A T - snp301 11 0.002 2000 A T - snp302 11 0.002 2000 A T - snp303 11 0.002 2000 A T - snp304 11 0.002 2000 A T - snp307 11 0.002 2000 A T - snp308 11 0.002 2000 A T - snp309 11 0.002 2000 A T - snp310 11 0.002 2000 A T - snp312 11 0.002 2000 A T - snp313 11 0.002 2000 A T - snp316 11 0.002 2000 A T - snp317 11 0.002 2000 A T - snp320 11 0.002 2000 A T - snp321 11 0.002 2000 A T - snp322 11 0.002 2000 A T - snp323 11 0.002 2000 A T - snp324 11 0.002 2000 A T - snp325 11 0.002 2000 A T - snp328 11 0.002 2000 A T - snp329 11 0.002 2000 A T - snp331 11 0.002 2000 A T - snp332 11 0.002 2000 A T - snp333 11 0.002 2000 A T - snp334 11 0.002 2000 A T - snp335 11 0.002 2000 A T - snp336 11 0.002 2000 A T - snp338 11 0.002 2000 A T - 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--- a/test-data/test_out/select_snps/select_snps.gd_snp Fri Sep 28 11:48:38 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
--- a/test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.gd_snp Fri Sep 28 11:48:38 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