# HG changeset patch # User greg # Date 1676923010 0 # Node ID 52a9e19ae58815f4ab85aeb11ede07b6fc940400 # Parent 64999b5b58fe3aab79d544cf2d3a4d7ba0716074 Uploaded diff -r 64999b5b58fe -r 52a9e19ae588 call_amr_mutations.xml --- a/call_amr_mutations.xml Fri Feb 10 17:35:04 2023 +0000 +++ b/call_amr_mutations.xml Mon Feb 20 19:56:50 2023 +0000 @@ -9,8 +9,8 @@ #if $os.path.getsize(str($varscan_raw)) > 0: cat '$varscan_raw' | awk '(NR > 1 && $9 == 2 && $5 + $6 >= 15){OFS = "\t";f = $6 / ($5 + $6); gsub(/.*\//, "", $4);s = $4;gsub(/[+\\-]/, "", s);$7 = sprintf("%.2f%%", f * 100);min = 1 / log(length(s) + 2) / log(10) + 2/10;if(f > min){print}}' > varscan_snp && - cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > varscan_snp_vcf && - cat varscan_snp_vcf | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_vcf' + cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > varscan_snp_tsv && + cat varscan_snp_tsv | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_tsv' #end if ]]> @@ -18,13 +18,13 @@ - + - + - + diff -r 64999b5b58fe -r 52a9e19ae588 test-data/input1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.vcf Mon Feb 20 19:56:50 2023 +0000 @@ -0,0 +1,112 @@ +Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele +chromosome 6848 C T 0 46 100% 0 2 0 18 2.434301551680221E-27 0 1 0 0 14 32 T +chromosome 28975 G A 0 19 100% 0 2 0 16 2.829233375250701E-11 0 1 0 0 16 3 A +chromosome 64632 T C 1 20 95.24% 1 2 17 17 4.087260223157705E-11 1 1 1 0 9 11 C +chromosome 73738 T C 0 15 100% 0 2 0 16 6.446725037893782E-9 0 1 0 0 12 3 C +chromosome 122896 G A 0 29 100% 0 2 0 21 3.325875998788469E-17 0 1 0 0 3 26 A +chromosome 171823 C T 1 20 90.91% 1 2 15 19 4.087260223157705E-11 1 1 1 0 17 3 T +chromosome 182106 C T 0 15 100% 0 2 0 16 6.446725037893782E-9 0 1 0 0 6 9 T +chromosome 200731 C T 2 47 95.92% 1 2 22 20 5.0043936105136293E-26 1 1 2 0 21 26 T +chromosome 240050 T C 0 30 93.75% 0 2 0 19 8.455616946072207E-18 0 1 0 0 14 16 C +chromosome 243867 C T 0 33 100% 0 2 0 19 1.3851512057218843E-19 0 1 0 0 24 9 T +chromosome 245190 C T 0 42 93.33% 0 2 0 18 5.9562436962098315E-25 0 1 0 0 24 18 T +chromosome 274236 C A 0 59 100% 0 2 0 20 4.105646544903784E-35 0 1 0 0 21 38 A +chromosome 317131 G T 1 7 87.5% 1 1 21 18 6.993006993006951E-4 1 1 1 0 7 0 T +chromosome 318187 C T 0 39 100% 0 2 0 21 3.6741722220670473E-23 0 1 0 0 17 22 T +chromosome 337241 T C 0 39 95.12% 0 2 0 20 3.6741722220670473E-23 0 1 0 0 19 20 C +chromosome 359536 G A 0 18 100% 0 2 0 16 1.1019119461502356E-10 0 1 0 0 5 13 A +chromosome 387637 G A 0 27 100% 0 2 0 19 5.136266628670978E-16 0 1 0 0 15 12 A +chromosome 433277 G T 0 19 100% 0 2 0 19 2.829233375250701E-11 0 1 0 0 10 9 T +chromosome 513052 C T 0 16 100% 0 2 0 18 1.6636709775210046E-9 0 1 0 0 2 14 T +chromosome 521963 A G 1 57 91.94% 1 2 19 21 9.60721291507612E-33 1 1 1 0 26 31 G +chromosome 571199 G A 3 17 85% 1 2 16 21 1.2847621301458368E-8 1 1 0 3 7 10 A +chromosome 644625 T C 1 21 95.45% 1 2 22 18 1.093104478286346E-11 1 1 0 1 10 11 C +chromosome 665308 T C 1 16 94.12% 1 2 17 17 7.713383623051864E-9 1 1 1 0 7 9 C +chromosome 692932 C T 1 20 95.24% 1 2 19 17 4.087260223157705E-11 1 1 0 1 5 15 T +chromosome 702761 G C 0 20 95.24% 0 2 0 18 7.254444551924877E-12 0 1 0 0 13 7 C +chromosome 706839 C T 0 7 100% 0 2 0 20 2.9137529137529E-4 0 1 0 0 4 3 T +chromosome 732173 A T 0 20 100% 0 2 0 18 7.254444551924877E-12 0 1 0 0 10 10 T +chromosome 765499 A C 0 27 100% 0 2 0 18 5.136266628670978E-16 0 1 0 0 24 3 C +chromosome 789298 G A 0 18 100% 0 2 0 16 1.1019119461502356E-10 0 1 0 0 9 9 A +chromosome 814684 T G 4 22 81.48% 1 2 18 17 5.52610926578708E-11 1 1 4 0 11 11 G +chromosome 852207 T G 0 13 100% 0 2 0 17 9.614829913658729E-8 0 1 0 0 8 5 G +chromosome 867050 A C 0 14 93.33% 0 2 0 18 2.4927336813189342E-8 0 1 0 0 9 5 C +chromosome 1023150 A G 0 27 100% 0 2 0 17 5.136266628670978E-16 0 1 0 0 11 16 G +chromosome 1120096 C T 0 55 100% 0 2 0 20 1.0149479655659631E-32 0 1 0 0 19 36 T +chromosome 1131906 T C 0 27 100% 0 2 0 17 5.136266628670978E-16 0 1 0 0 11 16 C +chromosome 1181950 A G 1 36 97.3% 1 2 16 18 2.176240469993604E-20 1 1 0 1 21 15 G +chromosome 1184347 G A 1 18 90% 1 2 15 21 5.658466750501197E-10 1 1 0 1 5 13 A +chromosome 1223198 C T 0 27 100% 0 2 0 20 5.136266628670978E-16 0 1 0 0 6 21 T +chromosome 1270555 G T 0 15 93.75% 0 2 0 18 6.446725037893782E-9 0 1 0 0 4 11 T +chromosome 1306861 C T 0 31 100% 0 2 0 19 2.148558404330002E-18 0 1 0 0 17 14 T +chromosome 1377487 G A 1 12 92.31% 1 2 18 20 1.3460761879122365E-6 1 1 0 1 8 4 A +chromosome 1385721 G A 0 38 100% 0 2 0 19 1.4508269799957698E-22 0 1 0 0 18 20 A +chromosome 1406212 C T 0 28 100% 0 2 0 19 1.3074133236616653E-16 0 1 0 0 15 13 T +chromosome 1423420 A G 0 16 94.12% 0 2 0 18 1.6636709775210046E-9 0 1 0 0 1 15 G +chromosome 1481095 C T 0 9 100% 0 1 0 22 2.056766762649123E-5 0 1 0 0 9 0 T +chromosome 1481116 C T 0 12 100% 0 1 0 18 3.6980115052534125E-7 0 1 0 0 12 0 T +chromosome 1592398 C A 0 26 100% 0 2 0 20 2.016460231996677E-15 0 1 0 0 1 25 A +chromosome 1621512 C A 0 27 100% 0 2 0 19 5.136266628670978E-16 0 1 0 0 4 23 A +chromosome 1631941 G T 0 24 100% 0 2 0 18 3.101005612159882E-14 0 1 0 0 14 10 T +chromosome 1728049 G A 1 17 94.44% 1 2 15 17 2.0936326976854063E-9 1 1 1 0 8 9 A +chromosome 1774177 C T 0 27 100% 0 2 0 17 5.136266628670978E-16 0 1 0 0 16 11 T +chromosome 1781207 C T 0 6 85.71% 0 2 0 22 0.0010822510822510842 0 1 0 0 3 3 T +chromosome 1797708 T C 0 21 100% 0 2 0 19 1.8578455559807287E-12 0 1 0 0 8 13 C +chromosome 1798769 G T 1 22 95.65% 1 2 22 18 2.914945275430307E-12 1 1 0 1 9 13 T +chromosome 1867996 T C 0 15 100% 0 2 0 17 6.446725037893782E-9 0 1 0 0 7 8 C +chromosome 1982986 C T 0 26 100% 0 2 0 20 2.016460231996677E-15 0 1 0 0 15 11 T +chromosome 2067935 G A 0 17 100% 0 2 0 19 4.2852131239177147E-10 0 1 0 0 6 11 A +chromosome 2133680 G T 0 24 100% 0 2 0 18 3.101005612159882E-14 0 1 0 0 13 11 T +chromosome 2179870 T C 2 12 85.71% 1 2 18 19 2.9912804175827393E-6 1 1 2 0 5 7 C +chromosome 2280814 A C 1 7 87.5% 1 2 15 18 6.993006993006951E-4 1 1 1 0 6 1 C +chromosome 2299647 A G 0 8 100% 0 2 0 20 7.770007770007759E-5 0 1 0 0 4 4 G +chromosome 2371243 T C 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 9 8 C +chromosome 2423657 A G 1 19 90.48% 1 2 16 18 1.5234333559041912E-10 1 1 1 0 6 13 G +chromosome 2694862 G A 2 15 88.24% 1 1 16 19 7.327714441899113E-8 1 1 0 2 15 0 A +chromosome 2749671 A G 0 27 96.43% 0 2 0 20 5.136266628670978E-16 0 1 0 0 8 19 G +chromosome 2834318 G A 0 20 100% 0 2 0 18 7.254444551924877E-12 0 1 0 0 4 16 A +chromosome 2956135 G A 0 15 100% 0 2 0 18 6.446725037893782E-9 0 1 0 0 8 7 A +chromosome 2989856 G A 0 28 100% 0 2 0 23 1.3074133236616653E-16 0 1 0 0 12 16 A +chromosome 3038888 T C 2 21 87.5% 2 2 15 18 3.643681594287794E-11 1 1 1 1 9 12 C +chromosome 3163858 A G 0 21 100% 0 2 0 17 1.8578455559807287E-12 0 1 0 0 8 13 G +chromosome 3306423 C T 0 19 100% 0 2 0 18 2.829233375250701E-11 0 1 0 0 12 7 T +chromosome 3364887 G A 0 15 100% 0 2 0 20 6.446725037893782E-9 0 1 0 0 1 14 A +chromosome 3382079 C T 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 6 11 T +chromosome 3457902 C T 2 12 80% 1 1 18 22 2.9912804175827393E-6 1 1 2 0 12 0 T +chromosome 3460779 T C 0 24 100% 0 2 0 19 3.101005612159882E-14 0 1 0 0 14 10 C +chromosome 3568849 A G 1 27 93.1% 1 2 18 17 3.7914986386187776E-15 1 1 0 1 17 10 G +chromosome 3696168 C T 0 27 100% 0 2 0 18 5.136266628670978E-16 0 1 0 0 14 13 T +chromosome 3712048 T C 0 28 100% 0 2 0 20 1.3074133236616653E-16 0 1 0 0 15 13 C +chromosome 3739850 A G 0 19 100% 0 2 0 17 2.829233375250701E-11 0 1 0 0 6 13 G +chromosome 3758015 A G 0 29 100% 0 2 0 19 3.325875998788469E-17 0 1 0 0 13 16 G +chromosome 3841816 G A 0 20 100% 0 2 0 19 7.254444551924877E-12 0 1 0 0 11 9 A +chromosome 4035203 T C 0 19 100% 0 2 0 17 2.829233375250701E-11 0 1 0 0 10 9 C +chromosome 4145299 C T 1 27 96.43% 1 2 17 21 3.7914986386187776E-15 1 1 0 1 15 12 T +chromosome 4147376 C T 1 25 96.15% 1 2 15 19 5.4444426263911445E-14 1 1 1 0 19 6 T +chromosome 4158968 C T 0 25 100% 0 2 0 20 7.910728602448565E-15 0 1 0 0 7 18 T +chromosome 4212929 G T 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 16 1 T +chromosome 4232753 C T 0 29 100% 0 2 0 16 3.325875998788469E-17 0 1 0 0 17 12 T +chromosome 4345557 T A 1 23 95.83% 1 2 15 18 7.752514030399528E-13 1 1 1 0 21 2 A +chromosome 4456896 G A 0 17 100% 0 2 0 18 4.2852131239177147E-10 0 1 0 0 12 5 A +chromosome 4501001 G A 0 34 100% 0 2 0 19 3.5145627607868225E-20 0 1 0 0 12 22 A +chromosome 4519053 A G 2 24 92.31% 2 2 15 19 7.622219676947252E-13 1 1 1 1 8 16 G +chromosome 4519433 C A 0 16 100% 0 2 0 17 1.6636709775210046E-9 0 1 0 0 5 11 A +chromosome 4698084 T C 4 41 91.11% 2 2 18 20 2.040655516360998E-21 1 1 3 1 15 26 C +chromosome 4867375 G A 0 37 97.37% 0 1 0 22 5.726948605246429E-22 0 1 0 0 0 37 A +chromosome 4906423 C A 0 5 83.33% 0 1 0 17 0.003968253968253951 0 1 0 0 5 0 A +chromosome 4929312 T G 1 18 94.74% 1 2 23 17 5.658466750501197E-10 1 1 0 1 9 9 G +chromosome 4951610 G A 0 49 98% 0 2 0 19 3.925014596481366E-29 0 1 0 0 19 30 A +chromosome 5040523 C T 3 12 80% 1 2 17 19 5.2605276309212935E-6 1 1 3 0 9 3 T +chromosome 5077771 G A 0 30 96.77% 0 2 0 20 8.455616946072207E-18 0 1 0 0 19 11 A +chromosome 5140491 G A 0 26 100% 0 2 0 16 2.016460231996677E-15 0 1 0 0 19 7 A +chromosome 5157810 G A 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 10 7 A +pXO1 7452 C T 1 14 87.5% 1 2 15 16 1.0314760060630275E-7 1 1 1 0 9 5 T +pXO1 28077 G A 3 13 81.25% 1 2 17 21 1.6120971772178452E-6 1 1 0 3 3 10 A +pXO1 31308 A C 1 6 85.71% 1 2 16 18 0.0023310023310023167 1 1 1 0 4 2 C +pXO1 55873 A T 0 34 100% 0 1 0 22 3.5145627607868225E-20 0 1 0 0 0 34 T +pXO1 55874 A T 0 40 100% 0 2 0 21 9.301701828018192E-24 0 1 0 0 1 39 T +pXO1 77518 A G 0 23 82.14% 0 2 0 18 1.214560531429256E-13 0 1 0 0 8 15 G +pXO1 141921 T G 1 20 95.24% 1 2 17 17 4.087260223157705E-11 1 1 1 0 7 13 G +pXO1 141922 T A 1 35 94.59% 1 2 21 19 8.361344963659992E-20 1 1 1 0 10 25 A +pXO1 141923 T A 1 52 96.3% 1 2 15 22 8.6089731799244E-30 1 1 1 0 18 34 A +pXO1 150892 C A 0 87 100% 0 2 0 19 6.914158005458386E-52 0 1 0 0 24 63 A diff -r 64999b5b58fe -r 52a9e19ae588 test-data/mutation_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutation_regions.bed Mon Feb 20 19:56:50 2023 +0000 @@ -0,0 +1,44 @@ +#contig start stop name type drug note +chromosome 6843 6862 gyrA QRDR snp quinolone gyrA QRDR mutation is the most common quinolone resistance mutation. It has not been observed in naturally occuring isolates. +chromosome 5664 6166 gyrB QRDR snp quinolone gyrB QRDR mutation is less a less common quinolone resistance mutation. It has not been observed in naturally occuring isolates. +chromosome 124092 124443 rplV any macrolide rplV alteration has been associated with macrolide resistance. +chromosome 3365449 3365459 parC QRDR 1 snp quinolone parC QRDR mutation is less a less common quinolone resistance mutation. It has not been observed in naturally occuring isolates. +chromosome 3365231 3365648 parC QRDR 2 snp quinolone parC QRDR mutation is less a less common quinolone resistance mutation. It has not been observed in naturally occuring isolates. +chromosome 3366159 3366605 parE QRDR snp quinolone parE QRDR mutation is less a less common quinolone resistance mutation. It has not been observed in naturally occuring isolates. +chromosome 842403 842981 tetR any quinolone terR inactivation has been shown to confer quinolone resistance in a lab setting. It has not been observed in natually ocurring isolates. +chromosome 2323274 2323294 rsip poly-A any beta-lactam rsiP inactivation has been shown to confer penicillin resistance in a lab setting. It has not been observed in naturally ocurring isolates. +chromosome 2323269 2324096 rsip broad-gene any beta-lactam rsiP inactivation has been shown to confer penicillin resistance in a lab setting. It has not been observed in naturally ocurring isolates. +chromosome 2421872 2421877 abc-f poly-A indel lincosamide Restoration of the abc-f ORF has been associated with lincosamide resistance in a lab setting. It has not been observed in naturally ocurring isolates. +chromosome 9307 10861 16S.1 point NA NA +chromosome 11230 14158 23S.1 point NA NA +chromosome 14203 14318 5S.1 point NA NA +chromosome 29101 30655 16S.2 point NA NA +chromosome 31024 33952 23S.2 point NA NA +chromosome 33997 34112 5S.2 point NA NA +chromosome 82423 83977 16S.3 point NA NA +chromosome 84119 87047 23S.3 point NA NA +chromosome 87093 87208 5S.3 point NA NA +chromosome 145487 147041 16S.4 point NA NA +chromosome 147183 150111 23S.4 point NA NA +chromosome 150194 150309 5S.4 point NA NA +chromosome 246207 247761 16S.5 point NA NA +chromosome 247903 250831 23S.5 point NA NA +chromosome 250877 250992 5S.5 point NA NA +chromosome 266786 268340 16S.6 point NA NA +chromosome 268482 271410 23S.6 point NA NA +chromosome 271456 271571 5S.6 point NA NA +chromosome 280084 281638 16S.7 point NA NA +chromosome 281780 284708 23S.7 point NA NA +chromosome 284755 284870 5S.7 point NA NA +chromosome 290057 291611 16S.8 point NA NA +chromosome 291753 294681 23S.8 point NA NA +chromosome 294728 294843 5S.8 point NA NA +chromosome 532435 533988 16S.9 point NA NA +chromosome 534123 537051 23S.9 point NA NA +chromosome 537148 537263 5S.9 point NA NA +chromosome 741537 743091 16S.10 point NA NA +chromosome 743233 746161 23S.10 point NA NA +chromosome 746259 746374 5S.10 point NA NA +chromosome 4652034 4652149 5S.11 point NA NA +chromosome 4652247 4655175 23S.11 point NA NA +chromosome 4655317 4656870 16S.11 point NA NA diff -r 64999b5b58fe -r 52a9e19ae588 test-data/output1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.tsv Mon Feb 20 19:56:50 2023 +0000 @@ -0,0 +1,95 @@ +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE +chromosome 6848 . C T 0 PASS . GT 1|1 +chromosome 28975 . G A 0 PASS . GT 1|1 +chromosome 64632 . T C 0 PASS . GT 1|1 +chromosome 73738 . T C 0 PASS . GT 1|1 +chromosome 122896 . G A 0 PASS . GT 1|1 +chromosome 171823 . C T 0 PASS . GT 1|1 +chromosome 182106 . C T 0 PASS . GT 1|1 +chromosome 200731 . C T 0 PASS . GT 1|1 +chromosome 240050 . T C 0 PASS . GT 1|1 +chromosome 243867 . C T 0 PASS . GT 1|1 +chromosome 245190 . C T 0 PASS . GT 1|1 +chromosome 274236 . C A 0 PASS . GT 1|1 +chromosome 318187 . C T 0 PASS . GT 1|1 +chromosome 337241 . T C 0 PASS . GT 1|1 +chromosome 359536 . G A 0 PASS . GT 1|1 +chromosome 387637 . G A 0 PASS . GT 1|1 +chromosome 433277 . G T 0 PASS . GT 1|1 +chromosome 513052 . C T 0 PASS . GT 1|1 +chromosome 521963 . A G 0 PASS . GT 1|1 +chromosome 571199 . G A 0 PASS . GT 1|1 +chromosome 644625 . T C 0 PASS . GT 1|1 +chromosome 665308 . T C 0 PASS . GT 1|1 +chromosome 692932 . C T 0 PASS . GT 1|1 +chromosome 702761 . G C 0 PASS . GT 1|1 +chromosome 732173 . A T 0 PASS . GT 1|1 +chromosome 765499 . A C 0 PASS . GT 1|1 +chromosome 789298 . G A 0 PASS . GT 1|1 +chromosome 814684 . T G 0 PASS . GT 1|1 +chromosome 1023150 . A G 0 PASS . GT 1|1 +chromosome 1120096 . C T 0 PASS . GT 1|1 +chromosome 1131906 . T C 0 PASS . GT 1|1 +chromosome 1181950 . A G 0 PASS . GT 1|1 +chromosome 1184347 . G A 0 PASS . GT 1|1 +chromosome 1223198 . C T 0 PASS . GT 1|1 +chromosome 1270555 . G T 0 PASS . GT 1|1 +chromosome 1306861 . C T 0 PASS . GT 1|1 +chromosome 1385721 . G A 0 PASS . GT 1|1 +chromosome 1406212 . C T 0 PASS . GT 1|1 +chromosome 1423420 . A G 0 PASS . GT 1|1 +chromosome 1592398 . C A 0 PASS . GT 1|1 +chromosome 1621512 . C A 0 PASS . GT 1|1 +chromosome 1631941 . G T 0 PASS . GT 1|1 +chromosome 1728049 . G A 0 PASS . GT 1|1 +chromosome 1774177 . C T 0 PASS . GT 1|1 +chromosome 1797708 . T C 0 PASS . GT 1|1 +chromosome 1798769 . G T 0 PASS . GT 1|1 +chromosome 1867996 . T C 0 PASS . GT 1|1 +chromosome 1982986 . C T 0 PASS . GT 1|1 +chromosome 2067935 . G A 0 PASS . GT 1|1 +chromosome 2133680 . G T 0 PASS . GT 1|1 +chromosome 2371243 . T C 0 PASS . GT 1|1 +chromosome 2423657 . A G 0 PASS . GT 1|1 +chromosome 2749671 . A G 0 PASS . GT 1|1 +chromosome 2834318 . G A 0 PASS . GT 1|1 +chromosome 2956135 . G A 0 PASS . GT 1|1 +chromosome 2989856 . G A 0 PASS . GT 1|1 +chromosome 3038888 . T C 0 PASS . GT 1|1 +chromosome 3163858 . A G 0 PASS . GT 1|1 +chromosome 3306423 . C T 0 PASS . GT 1|1 +chromosome 3364887 . G A 0 PASS . GT 1|1 +chromosome 3382079 . C T 0 PASS . GT 1|1 +chromosome 3460779 . T C 0 PASS . GT 1|1 +chromosome 3568849 . A G 0 PASS . GT 1|1 +chromosome 3696168 . C T 0 PASS . GT 1|1 +chromosome 3712048 . T C 0 PASS . GT 1|1 +chromosome 3739850 . A G 0 PASS . GT 1|1 +chromosome 3758015 . A G 0 PASS . GT 1|1 +chromosome 3841816 . G A 0 PASS . GT 1|1 +chromosome 4035203 . T C 0 PASS . GT 1|1 +chromosome 4145299 . C T 0 PASS . GT 1|1 +chromosome 4147376 . C T 0 PASS . GT 1|1 +chromosome 4158968 . C T 0 PASS . GT 1|1 +chromosome 4212929 . G T 0 PASS . GT 1|1 +chromosome 4232753 . C T 0 PASS . GT 1|1 +chromosome 4345557 . T A 0 PASS . GT 1|1 +chromosome 4456896 . G A 0 PASS . GT 1|1 +chromosome 4501001 . G A 0 PASS . GT 1|1 +chromosome 4519053 . A G 0 PASS . GT 1|1 +chromosome 4519433 . C A 0 PASS . GT 1|1 +chromosome 4698084 . T C 0 PASS . GT 1|1 +chromosome 4929312 . T G 0 PASS . GT 1|1 +chromosome 4951610 . G A 0 PASS . GT 1|1 +chromosome 5040523 . C T 0 PASS . GT 1|1 +chromosome 5077771 . G A 0 PASS . GT 1|1 +chromosome 5140491 . G A 0 PASS . GT 1|1 +chromosome 5157810 . G A 0 PASS . GT 1|1 +pXO1 7452 . C T 0 PASS . GT 1|1 +pXO1 28077 . G A 0 PASS . GT 1|1 +pXO1 55874 . A T 0 PASS . GT 1|1 +pXO1 77518 . A G 0 PASS . GT 1|1 +pXO1 141921 . T G 0 PASS . GT 1|1 +pXO1 141922 . T A 0 PASS . GT 1|1 +pXO1 141923 . T A 0 PASS . GT 1|1 +pXO1 150892 . C A 0 PASS . GT 1|1