-
Notifications
You must be signed in to change notification settings - Fork 6
/
Copy pathTCGA-55-6543.annotated.vcf
219 lines (219 loc) · 19.1 KB
/
TCGA-55-6543.annotated.vcf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
##fileformat=VCFv4.1
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=PP2,Number=1,Type=String,Description="('PolyPhen2 annotations in the following order:Gene name; UniProt id; Amino acid change; HVar effect category; Strength of var effect (probability); ', 'HDiv effect category; Strength of div effect (probability)')">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=BQ,Number=A,Type=Float,Description="Average base quality for reads supporting alleles">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=FA,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##FILTER=<ID=PASS,Description="Accept as a confident somatic mutation">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TCGA-55-6543-10A-01D-1753-08 TCGA-55-6543-01A-11D-1753-08
1 24397690 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:21,0:.:22:0.0:0 0/1:23,3:30.0:26:0.115:2
1 26134941 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:17,0:.:17:0.0:0 0/1:9,3:33.0:12:0.25:2
1 27537995 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:13,1:.:14:0.071:0 0/1:11,4:24.0:15:0.267:2
1 110280922 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:62,0:.:62:0.0:0 0/1:37,20:31.0:57:0.351:2
1 121484099 rs142367070 G T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:55,1:.:39:0.018:0 0/1:128,6:33.0:134:0.045:2
1 145112313 rs2596302 T C . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:20:0.0:0 0/1:14,4:31.0:18:0.222:2
1 148853906 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:51,1:.:52:0.019:0 0/1:68,4:31.0:72:0.056:2
1 154233344 . T G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:22,3:.:25:0.12:0 0/1:35,7:17.0:43:0.167:2
1 157548366 . G T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:50,0:.:50:0.0:0 0/1:55,5:33.0:60:0.083:2
2 60998828 . T G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:22,0:.:22:0.0:0 0/1:19,9:37.0:28:0.321:2
2 98263950 . C A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:97,0:.:97:0.0:0 0/1:56,32:29.0:88:0.364:2
2 130987344 rs113863640 A G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:39,0:.:39:0.0:0 0/1:34,3:37.0:37:0.081:2
2 165351172 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:11,0:.:11:0.0:0 0/1:3,5:30.0:8:0.625:2
2 179247908 . C G . PASS SOMATIC;VT=SNP;PP2=OSBPL6,Q9BZF3,N593K,probably damaging,0.998,probably damaging,1.0 GT:AD:BQ:DP:FA:SS 0:27,2:.:29:0.069:0 0/1:27,4:28.0:31:0.129:2
2 179631362 rs3816782 A C . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:33,0:.:33:0.0:0 0/1:26,13:37.0:39:0.333:2
2 190788073 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:88,0:.:88:0.0:0 0/1:50,31:31.0:81:0.383:2
2 230312248 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:26,0:.:26:0.0:0 0/1:21,5:31.0:26:0.192:2
3 9775768 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:30,0:.:30:0.0:0 0/1:33,11:30.0:44:0.25:2
3 46593057 . C A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:123,0:.:123:0.0:0 0/1:59,28:34.0:87:0.322:2
5 21882649 . C A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:18,0:.:18:0.0:0 0/1:21,5:31.0:26:0.192:2
5 31526237 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:84,0:.:84:0.0:0 0/1:102,19:33.0:121:0.157:2
5 33630758 . T G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:11,0:.:11:0.0:0 0/1:30,4:38.0:34:0.118:2
5 85592319 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:10,0:.:8:0.0:0 0/1:17,3:37.0:20:0.15:2
5 108924741 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:9,0:.:9:0.0:0 0/1:16,5:30.0:21:0.238:2
5 145477637 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:20:0.0:0 0/1:28,8:37.0:36:0.222:2
5 145477898 . T G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:36,0:.:36:0.0:0 0/1:44,12:33.0:56:0.214:2
5 146030242 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:34,0:.:34:0.0:0 0/1:45,6:30.0:52:0.118:2
6 11233444 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:32,0:.:32:0.0:0 0/1:39,18:37.0:57:0.316:2
6 29384929 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:17,0:.:17:0.0:0 0/1:9,2:39.0:11:0.182:2
7 20180463 rs71839686 G C . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:26,0:.:26:0.0:0 0/1:37,5:23.0:42:0.119:2
7 55832562 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:57,1:.:58:0.017:0 0/1:79,5:37.0:84:0.06:2
7 87785187 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:158,0:.:159:0.0:0 0/1:149,34:37.0:183:0.186:2
7 99796940 . G A . PASS SOMATIC;VT=SNP;PP2=STAG3,Q9UJ98,R508Q,benign,0.0,benign,0.0 GT:AD:BQ:DP:FA:SS 0:37,0:.:37:0.0:0 0/1:49,10:30.0:59:0.169:2
7 100478963 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:55,0:.:55:0.0:0 0/1:58,17:31.0:75:0.227:2
8 7826122 rs367569527 G A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:35,1:.:22:0.028:0 0/1:13,3:32.0:16:0.188:2
8 54141824 rs963549 C T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:52,0:.:52:0.0:0 0/1:25,23:34.0:48:0.479:2
9 33395031 rs72707429 G A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:36,1:.:37:0.027:0 0/1:25,6:31.0:31:0.194:2
9 33395039 rs72707431 C T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:36,1:.:38:0.027:0 0/1:26,4:30.0:30:0.133:2
9 35971954 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:121,1:.:122:0.008197:0 0/1:93,4:32.0:97:0.041:2
9 37692531 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:25,0:.:25:0.0:0 0/1:22,3:32.0:25:0.12:2
9 68433578 rs80303737 A G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:62,1:.:51:0.016:0 0/1:72,4:39.0:76:0.053:2
9 70871793 rs373464207 A G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:108,1:.:55:0.009174:0 0/1:79,5:39.0:84:0.06:2
9 95650487 rs180739891 C T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:126,0:.:126:0.0:0 0/1:89,38:29.0:127:0.299:2
9 134070639 . A T . PASS SOMATIC;VT=SNP;PP2=NUP214,P35658,I1227L,benign,0.046,benign,0.112 GT:AD:BQ:DP:FA:SS 0:139,0:.:139:0.0:0 0/1:91,38:31.0:129:0.295:2
10 12219775 . G T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:28,0:.:28:0.0:0 0/1:26,3:36.0:29:0.103:2
10 26880266 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:38,1:.:39:0.026:0 0/1:26,4:31.0:30:0.133:2
10 42385282 rs4124037 C T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:27,0:.:24:0.0:0 0/1:117,5:32.0:122:0.041:2
10 42385584 rs4462921 T A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:23,0:.:13:0.0:0 0/1:72,4:32.0:76:0.053:2
10 42599767 rs139875229 A C . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:33,0:.:27:0.0:0 0/1:103,6:35.0:110:0.055:2
10 102256138 . C G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:78,0:.:78:0.0:0 0/1:47,23:32.0:70:0.329:2
10 115457383 . A C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:27,1:.:28:0.036:0 0/1:36,6:19.0:42:0.143:2
10 122667993 . C A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:25,0:.:25:0.0:0 0/1:33,3:31.0:36:0.083:2
11 433471 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:37,0:.:37:0.0:0 0/1:49,15:34.0:64:0.234:2
11 3143534 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:15,0:.:15:0.0:0 0/1:15,4:30.0:19:0.211:2
11 51579639 . T G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:18:0.0:0 0/1:115,8:38.0:123:0.065:2
11 118771997 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:32,0:.:32:0.0:0 0/1:46,18:32.0:64:0.281:2
12 11230389 . G C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:51,0:.:51:0.0:0 0/1:67,4:36.0:71:0.056:2
12 44770574 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:17,1:.:18:0.056:0 0/1:26,8:14.0:34:0.235:2
12 94697492 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:15,2:.:17:0.118:0 0/1:3,6:13.0:9:0.667:2
13 19961981 rs199807479 G A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:42,1:.:39:0.023:0 0/1:41,6:33.0:47:0.128:2
13 28903740 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:28,0:.:28:0.0:0 0/1:25,7:33.0:32:0.219:2
13 49345969 . C A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:29,0:.:29:0.0:0 0/1:31,3:32.0:34:0.088:2
13 49761195 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:27,0:.:27:0.0:0 0/1:22,8:38.0:30:0.267:2
13 77625934 rs376292784 T A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:30,0:.:30:0.0:0 0/1:22,13:34.0:35:0.371:2
14 20147746 . C A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:99,0:.:78:0.0:0 0/1:70,7:31.0:77:0.091:2
14 20344588 . C A . PASS SOMATIC;VT=SNP;PP2=OR4K2,Q8NGD2,H54Q,benign,0.017,benign,0.008 GT:AD:BQ:DP:FA:SS 0:268,0:.:268:0.0:0 0/1:158,141:32.0:299:0.472:2
14 20926895 . A T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:19,0:.:19:0.0:0 0/1:16,9:34.0:25:0.36:2
14 22111343 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:9,0:.:9:0.0:0 0/1:10,6:38.0:16:0.375:2
14 22180975 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:170,0:.:170:0.0:0 0/1:203,58:31.0:261:0.222:2
14 24607425 . G C . PASS SOMATIC;VT=SNP;PP2=PSME1,Q06323,M160I,benign,0.306,possibly damaging,0.683 GT:AD:BQ:DP:FA:SS 0:213,0:.:213:0.0:0 0/1:338,15:37.0:353:0.042:2
14 51372344 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:57,0:.:57:0.0:0 0/1:60,15:37.0:75:0.2:2
14 76121073 . A T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:13,0:.:13:0.0:0 0/1:8,18:32.0:26:0.692:2
14 106234188 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:11,0:.:8:0.0:0 0/1:12,3:39.0:15:0.2:2
14 106357543 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:20:0.0:0 0/1:33,10:28.0:43:0.233:2
15 25652270 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:31,0:.:31:0.0:0 0/1:34,9:38.0:43:0.209:2
15 34150088 rs200923286 C A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:35,0:.:35:0.0:0 0/1:38,3:32.0:41:0.073:2
15 40756669 . G T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:13,0:.:13:0.0:0 0/1:20,3:32.0:23:0.13:2
15 76077992 rs61053099 C G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:43,1:.:28:0.023:0 0/1:27,7:37.0:34:0.206:2
16 20168328 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:35,0:.:35:0.0:0 0/1:40,3:37.0:44:0.07:2
16 29332310 rs143769600 C T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:62,0:.:62:0.0:0 0/1:43,9:31.0:52:0.173:2
16 29394822 rs376240593 A G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:35,1:.:25:0.028:0 0/1:27,5:35.0:32:0.156:2
16 33404765 rs7186361 A G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:20:0.0:0 0/1:25,3:31.0:28:0.107:2
16 33404778 . A G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:18,0:.:18:0.0:0 0/1:24,4:32.0:28:0.143:2
16 33784423 rs190376515 T C . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:19,0:.:19:0.0:0 0/1:22,3:30.0:25:0.12:2
17 4623596 . T G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:17,1:.:18:0.056:0 0/1:21,6:16.0:27:0.222:2
17 10436696 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:109,1:.:110:0.009091:0 0/1:71,24:31.0:95:0.253:2
17 20363816 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:26,0:.:21:0.0:0 0/1:33,4:35.0:37:0.108:2
17 33289128 . C A . PASS SOMATIC;VT=SNP;PP2=ZNF830,Q96NB3,S181R,benign,0.024,benign,0.112 GT:AD:BQ:DP:FA:SS 0:15,0:.:15:0.0:0 0/1:18,3:30.0:21:0.143:2
17 39382815 rs71371476 G A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:21,0:.:21:0.0:0 0/1:34,3:36.0:37:0.081:2
17 45105769 . C G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:81,0:.:81:0.0:0 0/1:87,4:36.0:91:0.044:2
17 45234725 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:61,1:.:53:0.016:0 0/1:79,5:31.0:84:0.06:2
17 79952826 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:20:0.0:0 0/1:13,3:39.0:16:0.188:2
18 11610570 rs200091851 C T . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:40,0:.:22:0.0:0 0/1:24,4:32.0:28:0.143:2
18 11610580 rs201205019 T G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:37,0:.:19:0.0:0 0/1:24,3:37.0:27:0.111:2
18 15198461 rs367836376 G A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:20,0:.:8:0.0:0 0/1:15,3:35.0:18:0.167:2
19 4911111 . A C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:8,0:.:8:0.0:0 0/1:7,5:17.0:12:0.417:2
19 11152224 . A G . PASS SOMATIC;VT=SNP;PP2=SMARCA4,P51532,K1471R,possibly damaging,0.472,possibly damaging,0.563 GT:AD:BQ:DP:FA:SS 0:25,0:.:25:0.0:0 0/1:17,10:35.0:27:0.37:2
19 12015959 . A T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:96,0:.:96:0.0:0 0/1:48,28:33.0:76:0.368:2
19 20243385 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:81,1:.:82:0.012:0 0/1:93,4:34.0:97:0.041:2
19 21116811 rs201690956 A G . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:53,1:.:54:0.019:0 0/1:64,6:25.0:70:0.086:2
19 27732093 rs74211273 G A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:44,1:.:36:0.022:0 0/1:147,8:27.0:155:0.052:2
19 49445800 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:33,0:.:33:0.0:0 0/1:29,17:29.0:46:0.37:2
19 55678043 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:27,0:.:27:0.0:0 0/1:32,13:31.0:45:0.289:2
19 56166481 . T A . PASS SOMATIC;VT=SNP;PP2=U2AF2,P26368-2,F4Y,benign,0.002,benign,0.0 GT:AD:BQ:DP:FA:SS 0:12,0:.:12:0.0:0 0/1:17,4:30.0:21:0.19:2
20 34528978 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:29,0:.:29:0.0:0 0/1:26,9:33.0:35:0.257:2
20 57035851 . G T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:25,0:.:25:0.0:0 0/1:28,3:32.0:31:0.097:2
21 10615108 . G A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:10,0:.:9:0.0:0 0/1:3,2:36.0:5:0.4:2
22 25023459 rs138813205 G C . PASS DB;SOMATIC;VT=SNP;PP2=GGT1,P19440,D361H,benign,0.038,benign,0.022 GT:AD:BQ:DP:FA:SS 0:38,1:.:36:0.026:0 0/1:26,3:34.0:29:0.103:2
22 36588021 . T C . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:42,0:.:42:0.0:0 0/1:31,11:37.0:42:0.262:2
22 42339544 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:12,0:.:12:0.0:0 0/1:9,7:30.0:16:0.438:2
X 54497770 . C T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:76,0:.:76:0.0:0 0/1:57,10:32.0:67:0.149:2
X 119664014 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:349,0:.:351:0.0:0 0/1:356,72:33.0:429:0.168:2
X 138630558 . A G . PASS SOMATIC;VT=SNP;PP2=F9,P00740,Q143R,benign,0.373,possibly damaging,0.617 GT:AD:BQ:DP:FA:SS 0:95,0:.:95:0.0:0 0/1:113,32:34.0:145:0.221:2
X 144337081 rs480466 C A . PASS DB;SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:22,0:.:22:0.0:0 0/1:33,3:34.0:36:0.083:2
X 153173206 . C G . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:25,0:.:25:0.0:0 0/1:45,5:36.0:50:0.1:2
X 155252868 . T A . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:8,0:.:5:0.0:0 0/1:8,5:30.0:13:0.385:2
Y 13470717 . A T . PASS SOMATIC;VT=SNP;PP2=.,.,.,.,.,.,. GT:AD:BQ:DP:FA:SS 0:30,0:.:30:0.0:0 0/1:1,3:22.0:4:0.75:2