/
insert_size_metrics_test.sam
159 lines (159 loc) · 57.3 KB
/
insert_size_metrics_test.sam
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
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:1 LN:249250621 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens
@SQ SN:2 LN:243199373 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens
@SQ SN:3 LN:198022430 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens
@SQ SN:4 LN:191154276 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapiens
@SQ SN:5 LN:180915260 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapiens
@SQ SN:6 LN:171115067 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapiens
@SQ SN:7 LN:159138663 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapiens
@SQ SN:8 LN:146364022 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:96f514a9929e410c6651697bded59aec SP:Homo Sapiens
@SQ SN:9 LN:141213431 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapiens
@SQ SN:10 LN:135534747 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapiens
@SQ SN:11 LN:135006516 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapiens
@SQ SN:12 LN:133851895 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapiens
@SQ SN:13 LN:115169878 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapiens
@SQ SN:14 LN:107349540 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapiens
@SQ SN:15 LN:102531392 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapiens
@SQ SN:16 LN:90354753 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapiens
@SQ SN:17 LN:81195210 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapiens
@SQ SN:18 LN:78077248 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapiens
@SQ SN:19 LN:59128983 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapiens
@SQ SN:20 LN:63025520 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapiens
@SQ SN:21 LN:48129895 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapiens
@SQ SN:22 LN:51304566 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapiens
@SQ SN:X LN:155270560 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapiens
@SQ SN:Y LN:59373566 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo Sapiens
@SQ SN:MT LN:16569 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:c68f52674c9fb33aef52dcf399755519 SP:Homo Sapiens
@SQ SN:GL000207.1 LN:4262 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo Sapiens
@SQ SN:GL000226.1 LN:15008 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo Sapiens
@SQ SN:GL000229.1 LN:19913 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Homo Sapiens
@SQ SN:GL000231.1 LN:27386 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Homo Sapiens
@SQ SN:GL000210.1 LN:27682 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:851106a74238044126131ce2a8e5847c SP:Homo Sapiens
@SQ SN:GL000239.1 LN:33824 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:99795f15702caec4fa1c4e15f8a29c07 SP:Homo Sapiens
@SQ SN:GL000235.1 LN:34474 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Homo Sapiens
@SQ SN:GL000201.1 LN:36148 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Homo Sapiens
@SQ SN:GL000247.1 LN:36422 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7de00226bb7df1c57276ca6baabafd15 SP:Homo Sapiens
@SQ SN:GL000245.1 LN:36651 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:89bc61960f37d94abf0df2d481ada0ec SP:Homo Sapiens
@SQ SN:GL000197.1 LN:37175 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Homo Sapiens
@SQ SN:GL000203.1 LN:37498 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:96358c325fe0e70bee73436e8bb14dbd SP:Homo Sapiens
@SQ SN:GL000246.1 LN:38154 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Homo Sapiens
@SQ SN:GL000249.1 LN:38502 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1d78abec37c15fe29a275eb08d5af236 SP:Homo Sapiens
@SQ SN:GL000196.1 LN:38914 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Homo Sapiens
@SQ SN:GL000248.1 LN:39786 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:5a8e43bec9be36c7b49c84d585107776 SP:Homo Sapiens
@SQ SN:GL000244.1 LN:39929 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:0996b4475f353ca98bacb756ac479140 SP:Homo Sapiens
@SQ SN:GL000238.1 LN:39939 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:131b1efc3270cc838686b54e7c34b17b SP:Homo Sapiens
@SQ SN:GL000202.1 LN:40103 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:06cbf126247d89664a4faebad130fe9c SP:Homo Sapiens
@SQ SN:GL000234.1 LN:40531 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:93f998536b61a56fd0ff47322a911d4b SP:Homo Sapiens
@SQ SN:GL000232.1 LN:40652 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:3e06b6741061ad93a8587531307057d8 SP:Homo Sapiens
@SQ SN:GL000206.1 LN:41001 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Homo Sapiens
@SQ SN:GL000240.1 LN:41933 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Homo Sapiens
@SQ SN:GL000236.1 LN:41934 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Homo Sapiens
@SQ SN:GL000241.1 LN:42152 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo Sapiens
@SQ SN:GL000243.1 LN:43341 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:cc34279a7e353136741c9fce79bc4396 SP:Homo Sapiens
@SQ SN:GL000242.1 LN:43523 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo Sapiens
@SQ SN:GL000230.1 LN:43691 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo Sapiens
@SQ SN:GL000237.1 LN:45867 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo Sapiens
@SQ SN:GL000233.1 LN:45941 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7fed60298a8d62ff808b74b6ce820001 SP:Homo Sapiens
@SQ SN:GL000204.1 LN:81310 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:efc49c871536fa8d79cb0a06fa739722 SP:Homo Sapiens
@SQ SN:GL000198.1 LN:90085 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:868e7784040da90d900d2d1b667a1383 SP:Homo Sapiens
@SQ SN:GL000208.1 LN:92689 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Homo Sapiens
@SQ SN:GL000191.1 LN:106433 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Homo Sapiens
@SQ SN:GL000227.1 LN:128374 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:a4aead23f8053f2655e468bcc6ecdceb SP:Homo Sapiens
@SQ SN:GL000228.1 LN:129120 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Homo Sapiens
@SQ SN:GL000214.1 LN:137718 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:46c2032c37f2ed899eb41c0473319a69 SP:Homo Sapiens
@SQ SN:GL000221.1 LN:155397 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:3238fb74ea87ae857f9c7508d315babb SP:Homo Sapiens
@SQ SN:GL000209.1 LN:159169 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo Sapiens
@SQ SN:GL000218.1 LN:161147 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo Sapiens
@SQ SN:GL000220.1 LN:161802 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens
@SQ SN:GL000213.1 LN:164239 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens
@SQ SN:GL000211.1 LN:166566 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens
@SQ SN:GL000199.1 LN:169874 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:569af3b73522fab4b40995ae4944e78e SP:Homo Sapiens
@SQ SN:GL000217.1 LN:172149 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo Sapiens
@SQ SN:GL000216.1 LN:172294 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:642a232d91c486ac339263820aef7fe0 SP:Homo Sapiens
@SQ SN:GL000215.1 LN:172545 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:5eb3b418480ae67a997957c909375a73 SP:Homo Sapiens
@SQ SN:GL000205.1 LN:174588 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo Sapiens
@SQ SN:GL000219.1 LN:179198 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens
@SQ SN:GL000224.1 LN:179693 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens
@SQ SN:GL000223.1 LN:180455 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens
@SQ SN:GL000195.1 LN:182896 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:5d9ec007868d517e73543b005ba48535 SP:Homo Sapiens
@SQ SN:GL000212.1 LN:186858 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:563531689f3dbd691331fd6c5730a88b SP:Homo Sapiens
@SQ SN:GL000222.1 LN:186861 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo Sapiens
@SQ SN:GL000200.1 LN:187035 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo Sapiens
@SQ SN:GL000193.1 LN:189789 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens
@SQ SN:GL000194.1 LN:191469 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens
@SQ SN:GL000225.1 LN:211173 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens
@SQ SN:GL000192.1 LN:547496 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens
@SQ SN:NC_007605 LN:171823 AS:NC_007605.1 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus
@RG ID:62A79.1 PL:ILLUMINA PU:62A79AAXX100907.1 LB:Solexa-41739 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.2 PL:ILLUMINA PU:62A79AAXX100907.2 LB:Solexa-41739 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.3 PL:ILLUMINA PU:62A79AAXX100907.3 LB:Solexa-41734 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.5 PL:ILLUMINA PU:62A79AAXX100907.5 LB:Solexa-41734 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.6 PL:ILLUMINA PU:62A79AAXX100907.6 LB:Solexa-41748 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.7 PL:ILLUMINA PU:62A79AAXX100907.7 LB:Solexa-41748 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@RG ID:62A79.8 PL:ILLUMINA PU:62A79AAXX100907.8 LB:Solexa-41753 DT:2010-09-07T00:00:00-0400 SM:NA12878 CN:BI
@PG ID:GATK IndelRealigner VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/6/Solexa-41748/62A79AAXX.6.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/3/Solexa-41734/62A79AAXX.3.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1.1 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/7/Solexa-41748/62A79AAXX.7.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@31884174 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@31884174 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@31884174 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1.2 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/5/Solexa-41734/62A79AAXX.5.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@68814013 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.1.3 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/1/Solexa-41739/62A79AAXX.1.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.2 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/2/Solexa-41739/62A79AAXX.2.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@2565a3c2 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@2565a3c2 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@2565a3c2 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK IndelRealigner.3 VN:1.0.4256 CL:analysis_type=IndelRealigner DBSNP=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/8/Solexa-41753/62A79AAXX.8.aligned.duplicates_marked.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.1kg_pilot_indels.vcf, dbsnp,dbsnp,/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.rod] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION SNPsFileForDebugging=null targetIntervals=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.indel_cleaner.intervals output=null useOnlyKnownIndels=true maxReadsForConsensuses=120 maxConsensuses=30 entropyThreshold=0.15 out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@691e0c13 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@691e0c13 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@691e0c13 indelsFileForDebugging=null noOriginalAlignmentTags=false realignReadsWithBadMates=false maxReadsForRealignment=20000 noPGTag=false LODThresholdForCleaning=0.4 maxReadsInRam=500000 targetIntervalsAreNotSorted=false sortInCoordinateOrderEvenThoughItIsHighlyUnsafe=false statisticsFileForDebugging=null
@PG ID:GATK TableRecalibration VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/6/Solexa-41748/62A79AAXX.6.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@7f92c8d9 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@7f92c8d9 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@7f92c8d9 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/6/Solexa-41748/62A79AAXX.6.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.1 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/7/Solexa-41748/62A79AAXX.7.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@f9da4fc bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@f9da4fc index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@f9da4fc output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/7/Solexa-41748/62A79AAXX.7.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.1.1 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/5/Solexa-41734/62A79AAXX.5.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5097eded bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5097eded index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5097eded output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/5/Solexa-41734/62A79AAXX.5.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.1.2 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/1/Solexa-41739/62A79AAXX.1.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/1/Solexa-41739/62A79AAXX.1.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.2 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/3/Solexa-41734/62A79AAXX.3.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@77d2b01b bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@77d2b01b index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@77d2b01b output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/3/Solexa-41734/62A79AAXX.3.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.3 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/2/Solexa-41739/62A79AAXX.2.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@5b976011 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/2/Solexa-41739/62A79AAXX.2.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
@PG ID:GATK TableRecalibration.4 VN:1.0.4256 CL:analysis_type=TableRecalibration DBSNP=null downsample_to_fraction=null input_file=[/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/8/Solexa-41753/62A79AAXX.8.indel_cleaned.bam] interval_merging=ALL read_buffer_size=null unsafe=ALL num_threads=1 read_filter=[] rodToIntervalTrackName=null rodBind=[] read_group_black_list=null validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=true phone_home=NO_ET intervals=null downsampling_type=null BTI_merge_rule=UNION out=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 bam_compression=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 index_output_bam_on_the_fly=org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub@6f878144 output_bam=null window_size_nqs=5 force_read_group=null smoothing=1 default_platform=null exception_if_no_tile=false homopolymer_nback=7 recal_file=/seq/picardnew/62A79AAXX/C1-202_2010-09-07_2010-09-17/8/Solexa-41753/62A79AAXX.8.recal_data.csv no_pg_tag=false skipUQUpdate=false default_read_group=null max_quality_score=40 fail_with_no_eof_marker=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION force_platform=null preserve_qscores_less_than=5 Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate] pQ=5 maxQ=40 smoothing=1
62A79AAXX100907:6:22:12941:18509 163 1 10001 0 36M65S = 10007 41 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTACCAGGAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA :=H;:;>AI=;;>AI><<?@I><<?AI=:887>.**69C54467B634357536=/,;?14245;50367@33247?53347@53357A53347@52237@ RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIIIIIIIIIIIHIIIIIIIIIIHIIIIHHIIHHHGFHIEHBBEEE3C1*<;8=:<<<B<B=@?9@:<@@B@@>BBBBD@BDB@B7?B@AA8@= UQ:i:0
62A79AAXX100907:8:109:17192:16752 99 1 10001 0 36M65S = 10010 44 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC >>I<:;?AI=<;>AI><<?BI?==<BI=:888>.*)69B64468C53458B52258A53358A32357>53357>5335###################### RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:HIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIIIIIIIHIHGIGIBEHFHHECFEEEDBEBEEC;BBB@@BBB@@B@@@###################### UQ:i:0
62A79AAXX100907:5:4:15479:18365 73 1 10002 0 36M65S = 10002 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC =C?AB@FHCDDAFI?=?AFHDAEAGIDDD@DE=;95@D???<BD<>?:AC=;;<>@8898>@99747<.58############################## RG:Z:62A79.5 NM:i:0 OQ:Z:HHHHHHHHHHHHHHDBDGGGHFHGHHHHHHHHHHHHEHHHHHHHDGHEGGEDDGCB;@B@==?=?8<>2>@############################## UQ:i:0
62A79AAXX100907:5:4:15479:18365 133 1 10002 0 * = 10002 0 CTGCTGTACGGCCAAGGCGGATGTACGGTACAGCAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTG 79;;;>EEC@HADHHII>AI=G@EAB?GCD@C@7=;DDBC<ABB4<><B>>C>CAD>@<@@B=@<A>@=@9A@@=<><>?=<<@??5?>?########### RG:Z:62A79.5 OQ:Z:HHHGFHHHHHGHHHGHHDGH<GEEBGGGCGGGGGFGGGFGACEE-A?AEA@GBGDG@DADCE=C@CAC;C>CCC=A=AA?>A@DB?/?=?###########
62A79AAXX100907:8:73:4240:3224 133 1 10002 0 * = 10002 0 GGGTTAGGGTTAGGGTTAGCCTGGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGCTAGGGTGAGGGTTAGGG 8@@CH>GCCEI?GCDGIAI<<>CD9=GCBAA6;532B7?<;7=7?::9A7=:;:48=:;:938662=5=:############################### RG:Z:62A79.8 OQ:Z:GEGGGEGEEGGGGEGHHHHHGGDG8BGGGDCAEDE@G@GGE8AAECC9E@CCE>8=??B:91<<<-@<?@###############################
62A79AAXX100907:8:73:4240:3224 73 1 10002 0 36M65S = 10002 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCCAACCCCAACCCTAAACCCAAACCCAAACC >G::;=@I=<<=@I=;=>AI><=>@I:897:A0,+-7?52258A50357?33337############################################## RG:Z:62A79.8 NM:i:0 OQ:Z:HHHHHHHHHHHHHHHGHGHHHGHGGGBDGBGE<EG<AA=?FBDEB<B@AB>@D6A############################################## UQ:i:0
62A79AAXX100907:6:105:5519:16017 99 1 10003 0 36M65S = 10006 38 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAAACACAACCAC >:9:<?I=<<==I=;<>@I=<<9AI<9:;<D40-,.B43337?42367@52326?433########################################### RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:HHGHGHGHHHHBHHGHHHHGGG>GGEFGGGHEHHHHH>@E8AA??D=BB@A@0>@;@@########################################### UQ:i:0
62A79AAXX100907:6:51:2857:17932 101 1 10003 0 * = 10003 0 TGGCTTATGGATGCCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACTCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCT >AB><I@IDEIID@<>DEC@G@>>H><<<<D40--.B54458B54458B55758B54468B54458B53446?41458A43346@513%>310036?322# RG:Z:62A79.6 OQ:Z:HHHHHHHHHHHHHHHHHHBGEGGCCHHHHHHHHHFHHHHHDGGGGGEGGGDHDHGHHHHHGEGGBGGBDGACA>CGBDD>@@>>C@C@+C34976>A<AA#
62A79AAXX100907:8:93:2828:16974 99 1 10003 0 36M65S = 10012 44 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCTAACCCTAACCCTAACCCAAACCCACACACA >:8:<?I=<<<@I=;=<AI>==;AI<;8:;C4/,..B53357A32######################################################## RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:HHGHHHHHHHDHHHEHBHGHHH@HHEGDEDGGGG@EGEEEB@E>C######################################################## UQ:i:0
62A79AAXX100907:6:51:2857:17932 153 1 10003 0 65S36M = 10003 0 GGCTTATGGATGCCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACTCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA 37>@7@@37@=7<?A45848?7A<<<?7B;<<?7@<<<?7A<<<?7C<@B@8C<==?8B<<=@9C435;7DBCDHAIDEEH@IEDDG@IDDDHAIHCBE=: RG:Z:62A79.6 NM:i:0 OQ:Z:BFBBEBEEEC>EGDGGEDCDDECBGFGEE@GGDBB;GGGEFBGGEEIEIDIGIEIIGDGBGIIIIHGGGGGFIIIIIEIIIGGFGGGGGFGIIIIIIIIII UQ:i:0
62A79AAXX100907:6:117:11919:16423 163 1 10004 0 36M65S = 10009 40 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAGATCGGCAGAGCGTCGTGTAGGG :78;>I=<<=@I=;<<@I>==;?I<=<<9G730//853468B54455=53241@34457.52256;53457@5+15-@>:?5:################## RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:BDGGHHHHHHHHGGHEHHHHH@DGDHHG?HHHHEGHHEHHHHHHGD<>GDFC3BCGGB@,EFA@C<GBGD?CG3C?,==8;CA################## UQ:i:0 XT:i:78
62A79AAXX100907:6:13:15155:6154 165 1 10004 0 * = 10004 0 AACCCTCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA :G:9:=?>A=;IHD?>AI><=?BI><<=?G72/./864469C64469C54468B54469B53468B54468B53353B53347@53347?23469@22+26 RG:Z:62A79.6 OQ:Z:IIIIIIIIIIIIIHIIIIIIHIIIIIIIIIIIIIIIIIIHIIIHIHIIHIIHHHGIHHIHGEHGHGEGGGHGGEEB8EBBB>BBB@B>BA6@===?6?229
62A79AAXX100907:6:13:15155:6154 89 1 10004 0 65S36M = 10004 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA #######################:;=9@:::=7?<::=7A<:8:5;=<<?7B<<<?7B;<<?8B<2384A=@BF>IDEEH@IEDDG@ICCCHAIIDCF?H? RG:Z:62A79.6 NM:i:0 OQ:Z:#######################A=?==9A???@=C@A?C;?>><>?GGGAGBGGGBG@GGGDGBGGGFGBGGGDGEGGGGGDGGGGGEGGIIIIIIIIII UQ:i:0
62A79AAXX100907:6:73:2424:1293 163 1 10005 0 36M65S = 10015 45 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTGGTAGCTAACCCTAACCCTAACCCTAAACCTAACCCTAACCCTAACCCTAAACCCAACCCCAA :8;>I<<<>AI=<<>AI><<>AI><<<@I:53119,35<<;8>757A53357@53355@50043;)3037@############################## RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIIIIIIIIIIIIGIIIIIDIIHIHGIHDEEID@DB@EBDBBDBBBB@DB<B=<<<8<'<<8;?############################## UQ:i:0
62A79AAXX100907:7:119:15783:6171 163 1 10005 0 36M65S = 10011 41 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTGGAAACTAACCCC :8;>I<<<>AI=;;>AI><<?AI><<>@H:53219+4458C54468A52458C53347B53357@53349@322########################### RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIIIIIIHIIIIIIGIIIIIIGIIHFIIIHIDGIGHHGHFEFHBHIHEE>EEDBD@AA@BD<=A<AA########################### UQ:i:0
62A79AAXX100907:7:63:15400:7094 163 1 10005 0 36M65S = 10006 36 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACTACCAGGCTA :8;>I<<<>?I=;;>@I><<>@I><<=@I:52119+4459C44457C44448A52257A54458B32257B3234;7A5.35-?4################ RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:IIIIIIIIIFIIIIIHIIIIHHIIIIGIIIIIIIIHIIFIIFHGFFIFHICDFEFFFEFEHHDDGCCFBBECCB<>??@8@?,@?################ UQ:i:0
62A79AAXX100907:8:69:9249:5472 165 1 10005 0 * = 10005 0 CGCGCCGGCGCAGGCGCAGAGACCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACAGATCGGAAGAGCGTCGT 8;5<=:B@?B>HA?5A?GG?HI><<:<:19344:.*358?32347:5234624+368B53.46?4#################################### RG:Z:62A79.8 OQ:Z:EB<BGGGBGG=G@@4FEEFEGGGGB5;7/97AAC><BBFBCCD>A7=CBA>3?1=GDGDB8>CCA#################################### XT:i:84
62A79AAXX100907:8:69:9249:5472 89 1 10005 0 65S36M = 10005 0 CCCCCCCTCCCCGCCTCCCGCCCGGGGACGGGCGCAGAGCCCTGGTAGCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ##########################################################################@<AAE>HFBCF>HACCF=GCCBC=FB= RG:Z:62A79.8 NM:i:0 OQ:Z:##########################################################################@7BBB=C??DDBF@FFF@FEFDBCFFF UQ:i:0 XT:i:84
62A79AAXX100907:6:62:15066:3015 163 1 10006 0 36M65S = 10012 41 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACCAACCCCAACCCCCACCCCACCCCAAACAACCCA :;>H;;<>AI=;<>AI><<=AI><<>AI<8554;,)459A53357B31158?5.337############################################ RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:IIIIHIIIIIIIIIIIHIIEIIIIIHIIIIIHIDIIHBIFEEDBEEC>C@D@@8B8?############################################ UQ:i:0
62A79AAXX100907:6:105:5519:16017 147 1 10006 0 65S36M = 10003 -38 TACGCCCACCCCTAACCCTACCCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC ###########################################>8::=7@<:;=7@6<<?7B=<<40:8;?A9?@CDG@I@EDG@IDCCF=H@CCF>GB@: RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:###########################################A4AAA?==?B@?B1GGGEGDGGGAB;EFB?>;DGGEG@GGGGGAFFFCF@DFFGGGGD UQ:i:0
62A79AAXX100907:7:63:15400:7094 83 1 10006 0 65S36M = 10005 -36 ACCCCGAACCCTACCCCTACCCCTACCCCTACCCCTAACCCTAACCCTTAACCCTAACCCTAACTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACC #######################################################################?7E9BCG>IADDG?IBDCF?IBDDF>HDA> RG:Z:62A79.7 NM:i:5 MQ:i:0 OQ:Z:#######################################################################B?D8DFECF@GGGCGBGGGGGBGGGHHHHH UQ:i:10
62A79AAXX100907:5:27:16532:6367 99 1 10007 0 36M65S = 10013 41 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCCACCCCAAACCCACCC ;?B>@8?EGBDDAGIDEEAGIDEE=GIDDC<BB:989@D???9BD;;;6>A;;;6<?68777<878/9>597############################# RG:Z:62A79.5 NM:i:0 MQ:i:0 OQ:Z:GGGGG@GGGGHHHHHHHHHHHHHHEHHHHHDHHHHHFFHHHHBHHBDD<BDBDD<@@>CA74>;?;)5;7=?############################# UQ:i:0
62A79AAXX100907:6:22:12941:18509 83 1 10007 0 65S36M = 10001 -41 CCCTAACCCCTACCAGGTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ##########################::=7?<::=7@:::=9><::?7@=<<?8C<<<?7B;<<?.958;A:H?CDG?IEEDG@IEDDF?IFEEH@IDCB? RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:##########################A@@?@;A@A??9AAA=A=AAGAD?DFFDIBGGGBG@GGGEGBGGGDGBGGGDGDGGGGGFGGGGGHIIIIIHIII UQ:i:0
62A79AAXX100907:6:25:3117:6332 165 1 10008 0 * = 10008 0 AATGGAACGCCTGGTAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT :FFAAII=>?;=CDD@HII>=;>?I=;9;<C40--.B54468B54256A53458@41457@53357B53458A54347=53367@50347########### RG:Z:62A79.6 OQ:Z:GGGGDFGGBEGGGGEHHHHHHDGDFGGFFGGHHHEHHHHHHHHGHFB>FFEHBHCA>G@BCEBE@EEEBHDDDDGEAE>B@B=@B@<@<@###########
62A79AAXX100907:8:27:12846:20680 165 1 10008 0 * = 10008 0 CCTTTCCTTTATGCTGCTCTACCAGGACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC 88:GH=<>II@ID@>DA>@:A>=IGCI=:887=.+*58B53468B54368B54448B53468B53458B53348B33358:.02/8?4*027>11+46;50 RG:Z:62A79.8 OQ:Z:HHHHHGHHGHHGHHHHHHHHHHHHGEHHHGHEDHGHDHHH@HHHHHHBGGGGGG>HHGBGGEGBBGBDGB@D<GG<D@BD62<;*==:090?;8>27;>=<
62A79AAXX100907:6:25:3117:6332 89 1 10008 0 65S36M = 10008 0 ACCCTAGCCCTAACCCTACCCCTACCCCTAACCCTACCCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ###############################;:=7;*;7>6@6::=5;;::<6;&:;66B=;:=76558:6E@CCF=D@AAF;GCADF@IDDCG@IDBAC= RG:Z:62A79.6 NM:i:0 OQ:Z:###############################B@?:@.=<=7?0AAA6>:AA:5:+@B8CGAB??:?CFF>?FCFFF:A>BBC>B=BGGGGDGEGGGGGGGG UQ:i:0
62A79AAXX100907:8:27:12846:20680 89 1 10008 0 65S36M = 10008 0 ACCCCAACCCCTACCCCAACCCCAACCCCTACCCCAACCCCAAACCCAACCCCAAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ###########################################################?/9;>04345;3?1>8B3?6ABE/DEA<F?CD@9B>BB@9B. RG:Z:62A79.8 NM:i:0 OQ:Z:###########################################################?':==2=0B?=8?*=7=3>1==B-;DB>?D:D@<@B;DD>D4 UQ:i:0
62A79AAXX100907:8:107:1555:6623 101 1 10009 0 * = 10009 0 TCCGCCTTCGCAGTACCCCTGGTAGCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCTAC >;9A>;>I?B?GGE@>===?CEDAG>:<>F73/./752245@42247342################################################### RG:Z:62A79.8 OQ:Z:HHHHHHHHHGGGGGGHHHHHDGAGGEEGGGHHGHDGHFF><?AAA<A/A?###################################################
62A79AAXX100907:6:117:11919:16423 83 1 10009 0 65S36M = 10004 -40 CCTGCTGAACCCCTCTTCCGACCTCCCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ######################################################::=7?;;895=03595?=ACF=IEEEG@IDDDG@IECEH@IFCCE=> RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:######################################################A??:@:B><6;)CA?:A>EFECGDGGGGGEGGGGGGGHHHHHHHHHH UQ:i:0 XT:i:78
62A79AAXX100907:8:107:1555:6623 153 1 10009 0 65S36M = 10009 0 ACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ##############:=09/;9>505;;:2837:345::?7=<:;>6?::;?5976:?7A:;<?79335;7CABCG:HEEEH3GADDG@IDCDH@EECBD<8 RG:Z:62A79.8 NM:i:0 OQ:Z:##############??25(=:=532==>/78>>882ACE@AAAEB;?@CEE<>89AE?E@BGGB>>GGGGGDGGG>FCGGGA?BGGGGGDGGHGBHHHHHH UQ:i:0
62A79AAXX100907:8:109:17192:16752 147 1 10010 0 65S36M = 10001 -44 CCCCCCCCCCAACCCCTCCCCCTACCCCCACCCCTACCCCCCCCCCAACCCAACCCAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA ##########################################################;<<?8B=2385A@ACGAIDDEG@FEDDG@IDCCHAIEDCF>G9 RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:##########################################################BGGGEGFDIIFIHIIIIIEGGGFGDGGGGGDGGIIIFIIIIII UQ:i:0
62A79AAXX100907:3:113:16808:6267 163 1 10011 0 36M65S = 10012 36 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACACCAGAGATAAGCCTGTTATATTTAGGGTGTCATGTGTGCATTACGAATGCCGC 7;9@C@A??EIABDAGIDEDAGEDDCADGBB?8<=6>+4A>8########################################################### RG:Z:62A79.3 NM:i:0 MQ:i:0 OQ:Z:GGEGGGGEGGHFGHHHHHHHHHDHHGHEGHHHBHGGG28G:@########################################################### UQ:i:0
62A79AAXX100907:7:18:8574:19050 99 1 10011 0 36M65S = 10014 38 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCACCCCCAA ?9<?I=<<>AI<<<>AI><<>BI><<9@I:52119+4458A54448B54447@53357@53226?33257############################### RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:IIIIIIHIIIIGIIIIIIIIGIIHIIBIIIIIIIIIIGFHFHHHCHHGGG>@BB@B@BBBEC0C@A@A?A############################### UQ:i:0
62A79AAXX100907:7:43:12512:9027 99 1 10011 0 36M65S = 10012 36 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAAACCTCACCCTAA >9;>I=<<>@I=;<=@I===?@I>=;>?H962109+3458A53258@51347?31347@53369@43245@42149<,3###################### RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:HHHHHHHHHHHHGHEHHGHHHHHHHGHHHFHDHHFHEHEHFBBFBDBB>B9@@9>B>@A@@B==B;@;49=;;>7=6-@###################### UQ:i:0
62A79AAXX100907:7:119:15783:6171 83 1 10011 0 65S36M = 10005 -41 ACCCCTCACCCTACCCCTAACCCTACCCCTAACCCCACCCCCTGGTACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ##############################################################@4:161;5<<@9D=AAD=FEDDG?IDCCF@IGEDF>HC> RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:##############################################################?/AA?:A5CBB>B7CCA;AAGGGCGEGGGHHHHHHHHHH UQ:i:0
62A79AAXX100907:3:113:16808:6267 83 1 10012 0 65S36M = 10011 -36 TAACCCTAACCCTACCCCAAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC ###################################################################;4==9<82<@7+<4AC@<;>GGGHFDFGEBCAB< RG:Z:62A79.3 NM:i:0 MQ:i:0 OQ:Z:###################################################################?,??<47(4;8+5+;B@7>>EEECECEEE?E?EE UQ:i:0
62A79AAXX100907:6:62:15066:3015 83 1 10012 0 65S36M = 10006 -41 CCCTAACCCTACCCCTACCCCTAGCCCTAACCCTAACCCTACCCCTACCCCTAACCCTAACCCCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACC #######################################################################C>I@DDG?IBDEG?ICDDF?IEDDF>HCA= RG:Z:62A79.6 NM:i:5 MQ:i:0 OQ:Z:#######################################################################GGGBGGGDGBGGECGEGGGGGFGGGGGFGG UQ:i:10
62A79AAXX100907:7:43:12512:9027 147 1 10012 0 65S36M = 10011 -36 CTACCCTGGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC #####################::=5@8::=7@<::>5?:::>6@::;?7@<<<?7@<<<?6@<<<4/:8;>C;IADDI?IEEDG@IBCCF>IDDDE?H?A: RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:#####################??@6?4@?A;?;@??9=<???>?7@BD@B=DGDBDBFFGCDBGGGBD@DGGBGBGGIDIDGGGGGBGGGDGEGGGIIBII UQ:i:0
62A79AAXX100907:8:93:2828:16974 147 1 10012 0 65S36M = 10003 -44 CCCCGCCCTACCCCTACCCCTAACCCTAACCCTAACCCTACCCCTCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC #####################################################?8@;<<?8B;<<5/;:<?C=ICDEI>IG@DG@IDDDF?ICBDF>GA@8 RG:Z:62A79.8 NM:i:0 MQ:i:0 OQ:Z:#####################################################GDDBGGGDGBGGGHHHHHGEGEGHHBHHGGGGGEGGGEGEDGGGGDGG UQ:i:0
62A79AAXX100907:6:90:1828:20961 73 1 10013 0 36M65S = 10013 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCAAACCCCAACCCAAAACCCAACACCCACCCACCCC >=H;;:>>I=<;=@E=<;=;G4999@G;5734;-*)58@13357@412##################################################### RG:Z:62A79.6 NM:i:0 OQ:Z:HHHHHGHDHHHGHG@GGED>B8@B?GDEBE8?@?:GDDB8DBBBBA>A##################################################### UQ:i:0
62A79AAXX100907:6:90:1828:20961 133 1 10013 0 * = 10013 0 GGTTAGGGTTAGGGTTAGGGTTAGCTACCAGGAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTGGGG :@BG>FDDDG<FDDDI@GAD?I@G:;:7*>B;;53################################################################## RG:Z:62A79.6 OQ:Z:GGGGGEGGFD@GGGDGGGBE>GGG>=::0:FE;<C##################################################################
62A79AAXX100907:7:32:5399:2634 101 1 10013 0 * = 10013 0 AGGCGCACAGTCACACGCCACCGGGACAGGAGCGCGGGGGCTACCAGGCTAACCCTAACCCCCAAACCCTAACCCTCACCCCAACCCAAAACCCACCCACA ?EB>A?I=IHF>H>I>C@<I><C@AI;IF<D?33/1::<:############################################################# RG:Z:62A79.7 OQ:Z:IIHIIIHHIIHHGIIIIHIIIIG@BHDIHBFHHGBCCCDC#############################################################
62A79AAXX100907:8:101:5724:10556 101 1 10013 0 * = 10013 0 AACCCTAACCCTAACCTACCAGGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC >H;::>BI><<>AI><?B?=IIF@>AI=;887>.+*58B53359A53358B53458A53358A53356?33358?53258?50247?43357>50346>43 RG:Z:62A79.8 OQ:Z:IIIIIIIIIIIIIIIIIIIIIIHIGHHHHIIHIHHHFGHFEEEIFEEEEFGDDGEFEDBEEHDBBBBCB>BBBDCB@;BDBB7C>BBA@B@B@@7B>>@:@
62A79AAXX100907:5:27:16532:6367 147 1 10013 0 65S36M = 10007 -41 CACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ###############?4077$?9899??90<?>@A9<?>@A>@>ADC?C?AEC>E@DDC@C?DDC8<=ADDDHDIIIFIEIIIHIHHHGEGEIIHBECD@7 RG:Z:62A79.5 NM:i:0 MQ:i:0 OQ:Z:###############?8341)=>7<6==>2:?ACC>A?ACCBD@DGGDGBDIGBICGGGFGBGGGDGFGGGGIEIIIGIEIIIIIIGGGGGFIIIGIFIGG UQ:i:0
62A79AAXX100907:7:32:5399:2634 153 1 10013 0 65S36M = 10013 0 GGGACAGGAGCGCGGGGGCTACCAGGCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC ############833337?6=:9536>7>6;<?6>=<<;?7@;<<<?8@<<<?6B<<<?7@<<<?.:78;A<HCDDG@IDDEG?IECCF>IBDDG?HBA@: RG:Z:62A79.7 NM:i:0 OQ:Z:############B=@@@BDCACCB@>BB@2BDEC@AFDEEEB@DGDGDB=GGGCGBDGGBDBGGGEEDIGIEGEGGGGGEGGGDGDFGGCGBGGGGGEGGG UQ:i:0
62A79AAXX100907:8:101:5724:10556 153 1 10013 0 65S36M = 10013 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 98::=3A<;;?7?;<<<8=;;:=3A:::?8?9:;?7B;<<?8A;<<?6B<;<?8B;<<?8B<<<?.968;A<HCDDG@IDEAI?IGDCG?IDDDG?HCAA8 RG:Z:62A79.8 NM:i:0 OQ:Z:<7???8EEEEGBBBGGA=A=BCC8E@?AE=B9CEEAGBGGGDEBGGGCGAEGGDGBGGGDGEGGGBGEGGGDGDGGGEGEGHHDHHGFGGGFGGGGHHHHH UQ:i:0
62A79AAXX100907:8:13:11880:18982 165 1 10014 0 * = 10014 0 GTTTACATTTTACATGGATAAGGCCCTGCCTGGTAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 9EHH?=IIIIIA=IIDEII@IIE@<<>C=88:8705BC64468C64469C64469C54469C64459A64469A54359B54469B54468B54357B533 RG:Z:62A79.8 OQ:Z:IIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIGIIHIIIIIHIIHIIIIIIIIIIHIIIIIIHHEIFIHHHIFGGDDIHHHHGIGEHGHHGEGBEBHEED
62A79AAXX100907:7:18:8574:19050 147 1 10014 0 65S36M = 10011 -38 ACCCTACCCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ##########################:>1;9::=5=6::>9@;<<?5B;<<=6A;<;?8B<<<?87558>:FBCDG@IEEDG?IDBDF?IEDDF@FDAAC: RG:Z:62A79.7 NM:i:0 MQ:i:0 OQ:Z:##########################A?3>5?AA<;1?CB=?:DDE<E>GGCCF@FBGDGBGGGGGGGGGGGDGGGGGDGGEFFECGGGGGGGDGDGGGGG UQ:i:0
62A79AAXX100907:8:13:11880:18982 89 1 10014 0 65S36M = 10014 0 GGTAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT #######:;=7=::;=7A;;:?79;;<?7B;;;?7A<<<?8B<<<?8B=;<?8B<<<?8B<<<?87558>:FCCCG@IFEEG?IFDDG@IADDG@IBBAC= RG:Z:62A79.8 NM:i:0 OQ:Z:#######AB??@:CECAE;ECEA>=EGGBGBEEE?ECGGGFGEGGGGGDEGGGGEGGGGGEGGGGGDGGGGGGGGGGGGGGGDGGGGGGGBGGGGGEGGGG UQ:i:0
62A79AAXX100907:8:74:13340:18350 73 1 10015 0 36M65S = 10015 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCC >;9:=AI><<>AI><<?BI>==>BI><;<=E4/,-.B53458A53258A32468A50348?50347A53316>1+257@###################### RG:Z:62A79.8 NM:i:0 OQ:Z:IIIIIIIIIIIIIIIIIIIIIIGIIIIIHIIIIIIIGGEIDGD@BFDEFCFHHDFB<ECEBB<D>BDBB@2;;82????###################### UQ:i:0
62A79AAXX100907:8:74:13340:18350 133 1 10015 0 * = 10015 0 TTGTCATTGTAGAAAGTCTGAACCTGGTAGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGG 9G@F=HIICHAHIIIHI??BII><?DEE?D?7;534C9@==<C8@<<<B8?<<<B8?<<;B8?<<;96?<;7988;:;?6998797<::84359819553: RG:Z:62A79.8 OQ:Z:IIIIIIIIIIIIIIIIIIIIHIIIIIIGIIGBGGGFIIIIIEIHIGGCGEGGGCGFGGGBGFGGGB>>DD=5<=<B?=?;5:;59?@AA6888:;+5688?
62A79AAXX100907:6:73:2424:1293 83 1 10015 0 65S36M = 10005 -45 CCCTACCCCTACCCCTACCCCTAACCCTACCCTGGTAGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ######################################=9@4::=9@4:::9@8::=5@<::=7A234;4A<BCF=ICDEG>IBDDG>IBCDF?IDBBD== RG:Z:62A79.6 NM:i:0 MQ:i:0 OQ:Z:######################################?=?.???==/??>=?4AA?<?=ACCAC8EBE?B<GGGBEAEGGBGBGGGDGBGGGFGFGGGGG UQ:i:0