Mercurial > repos > iuc > bcftools_plugin_missing2ref

comparison test-data/cnv.vcf @ 8:ed003195e914 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:08:08 -0400
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7:31c096c6b156 8:ed003195e914
1 ##fileformat=VCFv4.2
2 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
3 ##FORMAT=<ID=GC,Number=1,Type=Float,Description="GenCall score">
4 ##FORMAT=<ID=IA,Number=1,Type=Float,Description="Intensity of the A Allele">
5 ##FORMAT=<ID=IB,Number=1,Type=Float,Description="Intensity of the B Allele">
6 ##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">
7 ##FORMAT=<ID=LRR,Number=1,Type=Float,Description="Log R Ratio">
8 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test
9 10 135656 rs10904561 T G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.0415:0.5176:0.543:0.661:0.9477
10 10 135708 rs7917054 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:0.2441:0.501:0.742:0.659:0.9604
11 10 178434 rs7089889 T G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1440:0.4833:0.836:0.827:0.8884
12 10 188805 rs12146291 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.2144:0.4715:0.776:0.743:0.9610
13 10 203471 rs10903451 A G . . . GT:LRR:BAF:IA:IB:GC 0/0:0.4201:0.0000:0.619:0.022:0.9337
14 10 252693 rs2379078 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.2673:0.0068:0.806:0.081:0.9018
15 10 273344 rs2448378 A C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.7407:0.0000:0.497:0.012:0.9411
16 10 279248 rs2496278 C A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.4228:0.6268:0.285:0.958:0.6772
17 10 291134 rs10508201 T C . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1085:0.4723:0.317:0.444:0.9106
18 10 293358 exm2249181 A C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0097:0.0044:1.507:0.061:0.3992
19 10 313504 rs4880568 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.5836:0.9803:0.017:0.321:0.9547
20 10 317501 rs2018975 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.3392:0:1.069:0.039:0.7852
21 10 323283 rs3740304 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1836:0.5588:1.053:1.110:0.8640
22 10 326894 rs3125027 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0517:0.0005:1.300:0.026:0.8916
23 10 327162 exm805022 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1197:0:0.995:0.015:0.5328
24 10 329493 rs3815985 C A . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0480:0.5187:0.824:0.794:0.9109
25 10 338553 rs3125031 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.3387:0.4696:0.777:1.004:0.7901
26 10 354301 rs35198327 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.1338:0.4929:0.903:0.996:0.8546
27 10 375475 variant.11341 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0747:0.000199999999999978:1.132:0.012:0.4773
28 10 377161 rs7070654 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1388:0:0.582:0.020:0.9458
29 10 387060 rs7904155 G A . . . GT:LRR:BAF:IA:IB:GC 1/1:0.0615:0.9945:0.080:1.883:0.8310
30 10 390962 exm805090 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0087:9.9999999999989e-05:1.226:0.063:0.6950
31 10 390983 exm805091 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.3606:0:0.398:0.035:0.4585
32 10 394615 exm805105 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0170:0:1.345:0.020:0.4108
33 10 402390 exm805131 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0341:0.0000:1.127:0.023:0.8735
34 10 403792 exm805136 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1428:0.0000:0.908:0.019:0.8483
35 10 410501 exm805166 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0189:0:1.162:0.050:0.4628
36 10 413010 rs9787422 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0871:0.5334:0.908:0.961:0.8338
37 10 423555 rs12245012 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1264:0.00149999999999995:1.658:0.040:0.8015
38 10 423671 rs10904067 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.3622:0.5566:0.326:0.370:0.9306
39 10 431161 exm2271240 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.0175:0.4838:0.935:1.004:0.8308
40 10 435971 exm2249233 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.2716:0.0000:1.217:0.042:0.3992
41 10 435990 exm805214 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1427:0:1.107:0.031:0.4295
42 10 453567 rs4881254 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.1831:0.5079:1.032:1.425:0.8149
43 10 462885 rs10904173 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.0930:0.4819:0.568:0.489:0.9332
44 10 465046 exm805254 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1108:0:1.041:0.038:0.8704
45 10 468599 rs12415961 T C . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1647:0.5021:1.192:0.825:0.8051
46 10 486935 exm805280 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1369:0.0186:0.643:0.060:0.4804
47 10 487973 rs4881313 T C . . . GT:LRR:BAF:IA:IB:GC 0/1:0.0644:0.5628:0.747:0.992:0.8463
48 10 521431 exm2271370 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:0.0436:0.9952:0.028:1.491:0.8545
49 10 521723 rs4881336 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.2056:1:0.055:1.228:0.8344
50 10 547567 rs816599 A G . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.0079:1.0000:0.023:1.101:0.9490
51 10 554186 rs12251997 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1537:0.00309999999999999:1.565:0.032:0.8228
52 10 556129 rs10466270 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.0014:0.5142:0.709:0.732:0.9257
53 10 566379 rs11252926 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0211:0.5024:0.559:0.493:0.9438
54 10 588406 rs10904450 A G . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0834:0.0006:1.837:0.066:0.8107
55 10 592283 rs816646 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.3907:0.5006:0.268:0.158:0.8540
56 10 601089 rs816650 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0897:0:1.053:0.009:0.9557
57 10 615782 rs17221309 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.2800:0.00319999999999998:1.764:0.035:0.7820
58 10 635857 rs7069611 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0450:0.0013:0.593:0.017:0.9595
59 10 669358 rs7898821 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1257:0:1.694:0.067:0.7270
60 10 673037 rs816563 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:0.1368:0.9065:0.167:0.495:0.4895
61 10 680428 rs2124585 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.0590:0.5212:0.660:1.123:0.7133
62 10 712617 rs17136372 A C . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.0174:0.9992:0.028:0.975:0.9556
63 10 738630 rs1750792 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0269:0:1.575:0.025:0.8126
64 10 749238 rs553326 G T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1758:0.00229999999999997:0.955:0.019:0.9300
65 10 754033 rs2265090 C A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1347:0:1.181:0.025:0.9176
66 10 757222 rs10904546 A G . . . GT:LRR:BAF:IA:IB:GC 0/0:0.3035:0.0000:1.975:0.056:0.8047
67 10 766105 rs7906313 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1672:0.0116:0.960:0.062:0.9381
68 10 776027 rs11253377 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.1474:0.9964:0.046:1.017:0.9087
69 10 787896 rs1769242 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:0.2049:0.0000:0.965:0.029:0.9107
70 10 800213 rs2254501 G A . . . GT:LRR:BAF:IA:IB:GC 1/1:0.2422:0.9918:0.027:0.612:0.9374
71 10 802445 rs1769215 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0188:0.00370000000000004:0.859:0.024:0.9303
72 10 803721 rs2790381 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.0421:0.9798:0.029:0.485:0.9700
73 10 811876 rs12414585 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0717:0.516:0.374:0.276:0.9351
74 10 813426 rs11253424 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.5256:0:0.333:0.000:0.8993
75 10 815149 rs7084027 A G . . . GT:LRR:BAF:IA:IB:GC 1/1:0.3183:0.9944:0.037:1.547:0.8419
76 10 820868 rs10752019 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0749:0.0118:1.349:0.070:0.8882
77 10 833528 exm2271241 T G . . . GT:LRR:BAF:IA:IB:GC 0/1:-0.0329:0.4896:0.569:0.681:0.9348
78 10 834736 rs4881530 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0453:0.00249999999999995:1.578:0.040:0.8076
79 10 836115 rs11253444 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:-0.1380:0.5199:0.596:0.670:0.9248
80 10 838179 rs1536337 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0534:0.0000:1.318:0.095:0.7967
81 10 858022 rs9124 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.5565:0:0.715:0.012:0.9397
82 10 858924 exm805329 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0866:0:0.873:0.021:0.9056
83 10 859047 exm805338 C A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1868:0:0.917:0.007:0.5296
84 10 860687 exm805350 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1509:0:1.172:0.059:0.3777
85 10 860726 exm805354 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0224:0.0000:2.255:0.138:0.3747
86 10 860970 exm805360 A G . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1069:0.0000:1.859:0.070:0.7352
87 10 871110 exm805378 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0701:0.0000:1.373:0.002:0.4607
88 10 871746 exm805386 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1743:0.00239999999999996:0.597:0.017:0.5312
89 10 875350 exm805392 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1814:0:0.924:0.018:0.5191
90 10 888899 exm805400 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0585:0.00470000000000004:1.182:0.028:0.5116
91 10 888916 exm805401 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1408:0.0000:1.480:0.041:0.4128
92 10 894838 rs12249828 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.2119:0.4839:1.145:1.256:0.8432
93 10 903950 rs11253471 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:-0.0047:0.4747:0.562:0.549:0.9470
94 10 909757 exm805413 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0614:0:1.538:0.027:0.4097
95 10 909766 exm805415 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0578:0:1.502:0.023:0.4128
96 10 910074 exm805420 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0503:0.0071:1.001:0.057:0.5002
97 10 910081 exm805421 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1352:0.002:1.125:0.033:0.4254
98 10 927331 rs11253489 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0370:0.5325:0.976:1.435:0.7729
99 10 931618 exm805430 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0474:0:1.222:0.009:0.4871
100 10 931631 exm805431 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0819:0.00390000000000001:0.827:0.023:0.5296
101 11 135656 rs10904561 T G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.0415:0.5176:0.543:0.661:0.9477
102 11 135708 rs7917054 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:0.2441:0.501:0.742:0.659:0.9604
103 11 178434 rs7089889 T G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1440:0.4833:0.836:0.827:0.8884
104 11 188805 rs12146291 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.2144:0.4715:0.776:0.743:0.9610
105 11 203471 rs10903451 A G . . . GT:LRR:BAF:IA:IB:GC 0/0:0.4201:0.0000:0.619:0.022:0.9337
106 11 252693 rs2379078 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.2673:0.0068:0.806:0.081:0.9018
107 11 273344 rs2448378 A C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.7407:0.0000:0.497:0.012:0.9411
108 11 279248 rs2496278 C A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.4228:0.6268:0.285:0.958:0.6772
109 11 291134 rs10508201 T C . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1085:0.4723:0.317:0.444:0.9106
110 11 293358 exm2249181 A C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0097:0.0044:1.507:0.061:0.3992
111 11 313504 rs4880568 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.5836:0.9803:0.017:0.321:0.9547
112 11 317501 rs2018975 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.3392:0:1.069:0.039:0.7852
113 11 323283 rs3740304 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1836:0.5588:1.053:1.110:0.8640
114 11 326894 rs3125027 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0517:0.0005:1.300:0.026:0.8916
115 11 327162 exm805022 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1197:0:0.995:0.015:0.5328
116 11 329493 rs3815985 C A . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0480:0.5187:0.824:0.794:0.9109
117 11 338553 rs3125031 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.3387:0.4696:0.777:1.004:0.7901
118 11 354301 rs35198327 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.1338:0.4929:0.903:0.996:0.8546
119 11 375475 variant.11341 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0747:0.000199999999999978:1.132:0.012:0.4773
120 11 377161 rs7070654 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1388:0:0.582:0.020:0.9458
121 11 387060 rs7904155 G A . . . GT:LRR:BAF:IA:IB:GC 1/1:0.0615:0.9945:0.080:1.883:0.8310
122 11 390962 exm805090 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0087:9.9999999999989e-05:1.226:0.063:0.6950
123 11 390983 exm805091 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.3606:0:0.398:0.035:0.4585
124 11 394615 exm805105 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0170:0:1.345:0.020:0.4108
125 11 402390 exm805131 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0341:0.0000:1.127:0.023:0.8735
126 11 403792 exm805136 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1428:0.0000:0.908:0.019:0.8483
127 11 410501 exm805166 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0189:0:1.162:0.050:0.4628
128 11 413010 rs9787422 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0871:0.5334:0.908:0.961:0.8338
129 11 423555 rs12245012 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1264:0.00149999999999995:1.658:0.040:0.8015
130 11 423671 rs10904067 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.3622:0.5566:0.326:0.370:0.9306
131 11 431161 exm2271240 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.0175:0.4838:0.935:1.004:0.8308
132 11 435971 exm2249233 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.2716:0.0000:1.217:0.042:0.3992
133 11 435990 exm805214 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1427:0:1.107:0.031:0.4295
134 11 453567 rs4881254 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.1831:0.5079:1.032:1.425:0.8149
135 11 462885 rs10904173 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.0930:0.4819:0.568:0.489:0.9332
136 11 465046 exm805254 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1108:0:1.041:0.038:0.8704
137 11 468599 rs12415961 T C . . . GT:LRR:BAF:IA:IB:GC 0/1:0.1647:0.5021:1.192:0.825:0.8051
138 11 486935 exm805280 G C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1369:0.0186:0.643:0.060:0.4804
139 11 487973 rs4881313 T C . . . GT:LRR:BAF:IA:IB:GC 0/1:0.0644:0.5628:0.747:0.992:0.8463
140 11 521431 exm2271370 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:0.0436:0.9952:0.028:1.491:0.8545
141 11 521723 rs4881336 C T . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.2056:1:0.055:1.228:0.8344
142 11 547567 rs816599 A G . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.0079:1.0000:0.023:1.101:0.9490
143 11 554186 rs12251997 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.1537:0.00309999999999999:1.565:0.032:0.8228
144 11 556129 rs10466270 A G . . . GT:LRR:BAF:IA:IB:GC 0/1:0.0014:0.5142:0.709:0.732:0.9257
145 11 566379 rs11252926 C T . . . GT:LRR:BAF:IA:IB:GC 1/0:0.0211:0.5024:0.559:0.493:0.9438
146 11 588406 rs10904450 A G . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0834:0.0006:1.837:0.066:0.8107
147 11 592283 rs816646 G A . . . GT:LRR:BAF:IA:IB:GC 1/0:-0.3907:0.5006:0.268:0.158:0.8540
148 11 601089 rs816650 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0897:0:1.053:0.009:0.9557
149 11 615782 rs17221309 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:0.2800:0.00319999999999998:1.764:0.035:0.7820
150 11 635857 rs7069611 T C . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.0450:0.0013:0.593:0.017:0.9595
151 11 669358 rs7898821 G A . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1257:0:1.694:0.067:0.7270
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154 11 712617 rs17136372 A C . . . GT:LRR:BAF:IA:IB:GC 1/1:-0.0174:0.9992:0.028:0.975:0.9556
155 11 738630 rs1750792 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:0.0269:0:1.575:0.025:0.8126
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167 11 815149 rs7084027 A G . . . GT:LRR:BAF:IA:IB:GC 1/1:0.3183:0.9944:0.037:1.547:0.8419
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176 11 860687 exm805350 C T . . . GT:LRR:BAF:IA:IB:GC 0/0:-0.1509:0:1.172:0.059:0.3777
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