Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

annotate test-data/convert.vcf @ 0:ff65d6e0809b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:51:04 -0400
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 ##fileformat=VCFv4.1
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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2 ##FILTER=<ID=PASS,Description="All filters passed">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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3 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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4 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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5 ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype Probability">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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6 ##contig=<ID=X,assembly=b37,length=155270560>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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7 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 NA00006 NA00007 NA00008 NA00009 NA00010
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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9 X 2698630 . A G 537 . . GT:PL:GP 0|0:0,21,186:1,0,0 0|0:0,21,176:1,0,0 0|0:0,15,106:1,0,0 0|0:0,18,127:1,0,0 0|0:0,6,62:1,0,0 0|0:0,15,146:1,0,0 0|0:0,18,141:1,0,0 0|0:0,21,173:1,0,0 0|0:0,12,119:1,0,0 0|0:0,15,145:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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10 X 2698758 . CAA C 999 . . GT:PL:GP 0|0:0,6,16:0.8292,0.1708,0 0|1:0,0,0:0.0278,0.5743,0.3979 0|0:0,0,0:0.6336,0.3664,0 0|0:0,3,8:0.8611,0.1389,0 0|0:0,0,8:0.7628,0.2372,0 0|0:0,9,18:1,0,0 0|0:0,9,23:1,0,0 0|0:0,9,15:0.9855,0.0145,0 0|0:0,6,10:1,0,0 0|0:0,21,33:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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11 X 2698769 . AAG A 999 . . GT:PL:GP 1|0:17,0,7:0.0069,0.9931,0 1|1:0,0,0:0.0004,0.0892,0.9104 0|1:17,3,0:0.0045,0.9954,0.0001 1|0:11,0,2:0.0085,0.9915,0 1|0:11,0,15:0.0003,0.9997,0 0|0:0,15,40:1,0,0 0|0:0,9,23:1,0,0 0|0:0,15,25:0.8474,0.1526,0 0|0:0,15,34:1,0,0 0|0:0,33,56:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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12 X 2698770 . AG A,AAGG 999 . . GT:PL:GP 0|0:0,12,103,12,103,103:0.925,0.0717,0,0.0033,0,0 0|1:0,3,21,3,21,21:0.4944,0.368,0.0018,0.1343,0.0013,0.0002 0|0:0,0,0,0,0,0:0.5458,0.4085,0,0.0457,0,0 0|0:0,3,36,3,36,36:0.8126,0.1758,0,0.0116,0,0 1|0:37,0,86,49,92,130:0,1,0,0,0,0 0|0:0,15,125,15,125,125:1,0,0,0,0,0 0|0:0,9,105,9,105,105:1,0,0,0,0,0 0|0:0,15,109,15,109,109:0.9964,0.0034,0,0.0002,0,0 0|0:0,15,137,15,137,137:1,0,0,0,0,0 0|0:0,33,215,33,215,215:1,0,0,0,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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13 X 2698789 . C G 153 . . GT:PL:GP 0|0:0,21,152:1,0,0 0|0:0,21,131:1,0,0 0|0:0,12,113:1,0,0 0|0:0,12,104:1,0,0 0|0:0,21,137:1,0,0 0|0:0,15,118:0.9999,0.0001,0 0|0:0,15,111:1,0,0 0|0:0,24,152:1,0,0 0|0:0,18,147:1,0,0 0|0:0,33,183:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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14 X 2698822 . A C 85.2 . . GT:PL:GP 0|0:0,21,167:1,0,0 0|0:0,21,171:1,0,0 0|0:0,21,158:1,0,0 0|0:0,18,154:1,0,0 0|0:0,15,135:1,0,0 0|0:0,15,132:1,0,0 0|0:0,21,168:1,0,0 0|0:0,21,175:1,0,0 0|0:0,15,142:1,0,0 0|0:0,21,172:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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15 X 2698831 . G A 303 . . GT:PL:GP 0|0:0,15,129:1,0,0 0|0:0,27,179:1,0,0 0|0:0,24,196:1,0,0 0|0:0,21,158:1,0,0 0|0:0,18,154:1,0,0 0|0:0,12,112:1,0,0 0|0:0,24,162:1,0,0 0|0:0,21,168:1,0,0 0|0:0,9,95:1,0,0 0|0:0,21,164:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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16 X 2698889 . T C 74.4 . . GT:PL:GP 0|0:0,27,193:1,0,0 0|0:0,45,255:1,0,0 0|0:0,21,190:1,0,0 0|0:0,36,254:1,0,0 0|0:0,30,226:1,0,0 0|0:0,36,253:1,0,0 0|0:0,18,156:1,0,0 0|0:0,9,87:1,0,0 0|0:0,9,98:1,0,0 0|0:0,24,205:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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17 X 2698923 . G A 999 . . GT:PL:GP 1|0:62,0,133:0,1,0 0|1:164,0,91:0,1,0 0|1:35,0,73:0,1,0 1|0:91,0,108:0,1,0 1|0:67,0,71:0,1,0 0|0:0,30,187:1,0,0 0|0:0,9,73:1,0,0 0|0:0,12,99:1,0,0 0|0:0,18,153:1,0,0 0|0:0,18,138:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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18 X 2698953 . A AGG 267 . . GT:PL:GP 0|0:0,27,111:1,0,0 0|0:0,33,124:1,0,0 0|0:0,12,62:1,0,0 0|0:0,15,86:1,0,0 0|0:0,12,58:1,0,0 0|0:0,15,69:1,0,0 0|0:0,6,34:1,0,0 0|0:0,18,83:1,0,0 0|0:0,18,80:1,0,0 0|0:0,15,74:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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19 X 2698954 . G A 999 . . GT:PL:GP 1|0:69,0,139:0,1,0 1|1:199,24,0:0,0,1 0|1:15,0,82:0,1,0 1|0:32,0,76:0,1,0 1|0:16,0,80:0,1,0 0|0:0,15,131:1,0,0 0|0:0,6,58:1,0,0 0|1:99,0,39:0,1,0 0|0:0,18,163:1,0,0 0|0:0,15,136:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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20 X 2699002 . C A 65.1 . . GT:PL:GP 0|0:0,18,144:1,0,0 0|0:0,12,115:1,0,0 .|.:0,12,120:1,0,0 0|0:0,15,131:1,0,0 0|0:0,6,29:1,0,0 0|0:0,9,95:1,0,0 0|0:0,9,79:1,0,0 0|0:0,24,188:1,0,0 0|0:0,15,124:1,0,0 0|0:0,9,93:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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21 X 2699025 . T C 44.9 . . GT:PL:GP 0|0:0,24,189:1,0,0 0|0:0,12,98:1,0,0 0|0:0,15,130:1,0,0 0|0:0,15,113:1,0,0 0|0:0,6,63:1,0,0 0|0:0,24,198:1,0,0 0|0:0,12,92:1,0,0 0|0:0,24,197:1,0,0 0|0:0,9,97:1,0,0 0|0:0,12,108:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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22 X 2699091 . G A 45 . . GT:PL:GP 0|0:0,18,162:1,0,0 0|0:0,21,153:1,0,0 0|0:0,12,101:1,0,0 0|0:0,12,97:1,0,0 0|0:0,24,188:1,0,0 0|0:0,24,194:1,0,0 0|0:0,15,127:1,0,0 0|0:0,21,169:1,0,0 0|0:0,15,129:1,0,0 0|0:0,21,171:1,0,0
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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26 X 2699217 . C T 60.3 . . GT:PL:GP 0|0:0,18,158:1,0,0 0|0:0,18,119:1,0,0 0|0:0,21,152:1,0,0 0|0:0,21,162:1,0,0 0|0:0,12,102:1,0,0 0|0:0,18,144:1,0,0 0|0:0,12,108:1,0,0 0|0:0,18,146:1,0,0 0|0:0,12,98:1,0,0 0|0:0,18,155:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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27 X 2699246 . C A 999 . . GT:PL:GP 1|0:128,0,15:0,0.9998,0.0002 1|1:147,21,0:0,0.0001,0.9999 0|1:130,0,5:0,0.9977,0.0023 1|1:237,33,0:0,0,1 1|0:45,0,75:0,1,0 0|1:145,0,49:0,1,0 0|0:0,15,109:1,0,0 0|1:13,0,63:0.0002,0.9998,0 0|0:0,30,178:0.9953,0.0047,0 1|0:120,0,57:0,1,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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28 X 2699275 . T G 999 . . GT:PL:GP 0|0:0,18,165:0.9998,0.0002,0 0|0:0,18,152:1,0,0 1|0:0,9,95:0.0023,0.9977,0 0|0:0,33,239:1,0,0 0|1:125,0,40:0,1,0 1|1:205,27,0:0,0,1 1|0:69,0,43:0,1,0 0|0:0,15,139:1,0,0 0|0:0,30,219:1,0,0 0|1:96,0,54:0,1,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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31 X 2699450 . A C 999 . . GT:PL:GP 0|0:0,12,124:1,0,0 0|0:0,6,55:0.9976,0.0024,0 1|0:99,0,42:0,1,0 0|0:0,21,186:0.9999,0.0001,0 0|1:64,0,100:0,1,0 1|0:38,0,177:0,1,0 1|0:16,0,103:0,1,0 0|0:0,24,202:1,0,0 0|0:0,12,119:1,0,0 0|1:75,0,115:0,1,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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33 X 2699555 . C A 999 . . GT:PL:GP 0:0,156:1,0 1:58,19:0,1 1:51,0:0,1 0:0,91:1,0 1:89,0:0,1 1|1:132,15,0:0,0,1 1|0:99,0,68:0,1,0 0|1:101,0,101:0,1,0 0|0:0,18,161:0.9998,0.0002,0 0|1:118,0,72:0,1,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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34 X 2699645 . G T 999 . . GT:PL:GP 0:0,95:1,0 1:49,0:0,1 0:0,58:1,0 0:0,64:1,0 0:0,113:1,0 0|0:0,18,158:1,0,0 0|0:0,18,146:1,0,0 0|1:68,0,136:0,1,0 0|0:0,30,210:1,0,0 0|0:0,27,186:1,0,0
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35 X 2699676 . G A 999 . . GT:PL:GP 0:0,84:1,0 0:0,87:1,0 1:35,0:0,1 0:0,28:1,0 1:114,0:0,1 1|0:99,0,72:0,1,0 1|0:48,0,89:0,1,0 0|0:0,18,155:1,0,0 0|0:0,24,191:1,0,0 0|1:99,0,61:0,1,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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36 X 2699728 . C T 69.7 . . GT:PL:GP 0:0,58:1,0 0:0,64:1,0 0:0,33:1,0 0:0,69:1,0 0:0,81:1,0 0|0:0,27,183:1,0,0 0|0:0,45,220:1,0,0 0|0:0,30,161:1,0,0 0|0:0,15,110:1,0,0 0|0:0,21,156:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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37 X 2699775 . C A 71.1 . . GT:PL:GP 0:0,62:1,0 0:0,101:1,0 0:0,130:1,0 0:0,141:1,0 0:0,54:1,0 0|0:0,30,203:1,0,0 0|0:0,39,208:1,0,0 0|0:0,30,177:1,0,0 0|0:0,18,132:1,0,0 0|0:0,15,103:1,0,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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38 X 2699898 . C CT 999 . . GT:PL:GP 0:0,32:1,0 0:0,11:1,0 1:11,0:0,1 0:0,11:1,0 1:31,0:0,1 1|0:11,0,24:0.0438,0.9562,0 1|0:8,0,17:0,1,0 0|0:0,33,72:1,0,0 0|0:0,27,69:1,0,0 0|1:11,4,12:0.0003,0.9997,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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39 X 2699968 . A G 999 . . GT:PL:GP .:0,84:1,0 0:0,32:1,0 0:0,57:1,0 1:131,0:0,1 0:0,66:1,0 0|1:89,0,44:0,1,0 0|0:0,18,157:1,0,0 0|0:0,45,255:1,0,0 0|1:75,0,109:0,1,0 1|0:98,0,62:0,1,0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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40 X 2699970 . T C 55.3 . . GT:PL:GP 0:0,68:1,0 0:0,34:1,0 0:0,32:1,0 0:0,162:1,0 0:0,63:1,0 0|0:0,15,149:1,0,0 0|0:0,21,181:1,0,0 0|0:0,45,255:1,0,0 0|0:0,27,207:1,0,0 0|0:0,24,196:1,0,0