Repository navigation
Expand file tree
/
Copy pathtest_simple.sam
More file actions
37 lines (37 loc) · 9.46 KB
/
Copy pathtest_simple.sam
File metadata and controls
37 lines (37 loc) · 9.46 KB
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
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chr1 LN:100000 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:9ebc6df9496613f373e73396d5b3b6b6 SP:Homo sapiens
@RG ID:exampleBAM.bam PL:illumina PU:exampleBAM.bam LB:exampleBAM.bam SM:exampleBAM.bam
@PG ID:0 VN:0.7.1-9 CL:/seq/software/picard/current/3rd_party/maq/maq map -D -s 0 -a 1500 -e 2100 /seq/picard/30PPJAAXX/C1-152_2009-01-25_2009-04-07/1/Solexa-9821/30PPJAAXX.1.0.out.aln.map /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.bfa /seq/picard/30PPJAAXX/C1-152_2009-01-25_2009-04-07/1/Solexa-9821/30PPJAAXX.1.0.1.bfq /seq/picard/30PPJAAXX/C1-152_2009-01-25_2009-04-07/1/Solexa-9821/30PPJAAXX.1.0.2.bfq 2> /seq/picard/30PPJAAXX/C1-152_2009-01-25_2009-04-07/1/Solexa-9821/30PPJAAXX.1.0.out.map.log
30PPJAAXX090125:1:42:512:1817#0 99 chr1 200 0 76M = 255 -130 ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3: PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam ZA:f:2.3 ZB:i:23 ZC:A:t MC:Z:10M
30PPJAAXX090125:1:42:512:1817#0 147 chr1 255 2 76M = 200 -130 CAACCCCAGCCCAAACCCGAACCCAAACCCGAACCCGAACCCTAACCCAACCCCCAACCCCAACCCTAACCCTAAC 2+&:A=4?'8@'%2'=>B3A3<A='A=A9>&>;A?A,@&>A?1A:AAB5=&9>7&:,@A<*70@B=9:0>@@2;=3 PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam MC:Z:2S8M
30PPJAAXX090125:1:60:1109:517#0 73 chr1 257 0 76M = 257 0 ACCCTAACCCTAAACATAAACCTAACCCTAACCTGAACCTTATCCAGAACCCCAACTCGAACAAAAGTCGTAACCT ===<4:67(=>@>B?>BB=;::87=?9@B?=((*>1@6B:)8'85%%=,+(-7923%7<,0)4/'-1(.('02-9' PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam MC:Z:2S4M2D2M
30PPJAAXX090125:1:67:744:1312#0 163 chr1 10399 0 76M = 10479 -155 GGAAATTTACAAGGAACAAATGTGAAGCACAACATTTAGGTTTTAAAAATCAAGCGAATAAATACAGAAGGTGGAG ):CCBAABBBCCBC?=-=CC=@A?ACCB==CCC:ABBBBC=B@BA=ABCCBCCACC-=CCBCCCBCB2>><22BAB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam MC:Z:2H2M4I2M2D2M
30PPJAAXX090125:1:67:744:1312#0 83 chr1 10479 0 76M = 10399 -155 CTTGCTTTAGACACTGTTCATGTGAAGAAAGACCTGGAAACTTCTGTTAACTATAAGCTCAGTAGGGGCTAAAAGC @BC<B@4=CC7>.>,BBAA<1>CCB=C>((C<@=@?CBB:3<C@CA@C=,?B@@A=A?A5B:;CCCC=7CB7<7?< PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam MC:Z:2S10M10N10M10D10I10M10H
30PPJAAXX090125:1:18:14:1047#0 99 chr1 22910 0 76M = 22924 -89 GTGTCCATAGATTAATGAGTGAATACACAAATGGTGATATGGACATACAGTGGAGTATTAGTCATAAAAAGGAAGG ?3><><B<ABBBCBA@BBB>BB@<=9BA@B@AB@0@CB@BAA8':A=><73?=<=,;A><?238A>?=6=>27@=: PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam MC:Z:100I
30PPJAAXX090125:1:18:14:1047#0 147 chr1 22924 0 76M = 22910 -89 ATGAGTGAATACACAAATGGTGATATGGACATACAGTGGAGTATTAGTCATAAAAAGGAAGGCAGAGCTGATCCAC A64>235B;:562<>?;?5588=6'.:09?B@@A@6>7.<:A@@/>9>>@@AB9BA==AB:3>0388<>:?BCC?B PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:54:1146:1815#0 163 chr1 27878 0 76M = 27982 -179 GGGACGGTGGTAGTGTTAGTCCAGTAACACAGCCTAGACCCCGGCTTCCACGCGGGTTTGACCGGCGCCTACTAAA B5*>49)&)(7A=2A2760(=0(>9>*662+2;7',0(934(.(3/90,56A))A?/,*'*('*8%)5/4'=3,0= PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:54:1146:1815#0 83 chr1 27982 0 76M = 27878 -179 CAGACTATTCACACCAGGGAAGCCAGATGCATCCTTAACCATCTCAGATCATCTGGCTCCTCAGCTCAAAGCCTCC BB*,**5<@A.,*)+2.,,=@6.A/CBCCAB44<?;((./@1(8C?+5@AAB,BBCBC7<C7C@+84@=4@<0@?, PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:13:176:419#0 163 chr1 29967 0 76M = 30014 -122 CTGCCATGTGAGCTTGGAAGCAGAGCCATCCACACAGCTGAGCCCTAGATGAGAACGCAGTGCTGGCTGACACCCT B@27@BCCCBCACB=CBBBB9CB@8/BBC@)7AB;ABBC>>>>BACB=?>;BA>@:?>9B9>3?BA=B<B=B'6-@ PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:13:176:419#0 83 chr1 30014 0 76M = 29967 -122 GATGAGAACTCAGTGCTGGCTGACACCCTGATGGCACCTTACAGAGGACCAGTTAGGCTGTGCCAACTCCTGACCT 6:<AA=7+:)??8?5?=5=A@=?A69A4A@BB?(@4@@B?AAA?B87;?AB:BBC6?>?7B=?>B5;AAAB<<BAB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:43:1756:518#0 163 chr1 34825 0 76M = 34871 -121 CATCACTATTTGTCAGGGAAGTACTAATTAAAACAAAAATGAGATGTCCCCTCAAACCTGTTAGAATGGCTATTAT B>3?CBBBBBB?0?BBCBABA4BABBABC@>BB?BA9A?BBAA?BB<<B>BABAA@??=B8@>?>A7>@B;7(:36 PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:43:1756:518#0 83 chr1 34871 0 76M = 34825 -121 TCCCCTCAAACCTGTTAGAATGGCTATTATCAAAAAGATGAAAGATAGCAACTATCAGAGAGGATGATAGAAAAGG :@837468?*>>673397?7'46@5>>3;':@A@@A@@@9AA<<A@@?BB399B6<?<ABBBB>+A>;A?<,3@BB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:19:464:1362#0 99 chr1 44899 0 76M = 44965 -141 AGCCTTCCTCTTTTCAAACCTACTCTTCTTTCAGTGTTCTCAGTCACAATAATTTGTACCAACTAGTTACCTAGTT BBBBBBBBBABCBBAA5A@@BBBABBBBBBB?BB?B@@A/<@B>BB@BABB@A@@?@A??@@@@B>9A@?;@@A:A PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:19:464:1362#0 147 chr1 44965 0 76M = 44899 -141 TTACCTAGTTGCACAACCCAAAATCTGGGAAAAATAATAGATTTCTTTCTCCATAGTACCCCAAAATCAAAAAATC BB><?;A?>B@B@B??BBBBBBB>BAAAABBBCABAB@CBBA>ABBA>BBBCBBBBB@BCCBCCCBABCCCCCCBB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:37:1786:1220#0 163 chr1 46597 22 76M = 46605 -83 AGGTGGAGCCTTTGCACTTTCAGGCCACCATGATAACCTGGAGATTAGATTTTTCTGTGTCTTTATATCAATAATA @A6'>94>7@@89A8@?<32?BB:@@<>54<@/@8:%8BB=6>7@A1>96::<>1<517669'81<;><74<<:8> PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:37:1786:1220#0 83 chr1 46605 13 76M = 46597 -83 CCTTTGCACTTTCAGGCCACCATGATAACCTGGAGATTAGATTTTGCTGTGTCTTTATATCAATAATAAAGCCAAG &.01%)1*-'848'-4@82<8:=<*79%6=:BB@BA<=*8'0=44'=6A>?-??<4;1?)<@:9><4>@1>4@BAA PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:49:164:100#0 163 chr1 52694 0 76M = 52712 -93 AGATTTGTTAATAATAAATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCGT BBBBABB?@AABABBBBBAAB=>A@:>BAA<17AAAB>==@@@A@@@>?<9>@69;@?A7/<@6@:25<:<,2>?@ PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:49:164:100#0 83 chr1 52712 0 76M = 52694 -93 TTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCGTTTCTTTCAGGTTGCTTCA -A>B:@B;8A@@B@C4B9:8:?BBB:AA@2:>BBBABBC?BBBBB<:A=??B@0<ACCBBBBBACBCCCAC@?BCB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:14:920:883#0 163 chr1 57504 0 76M = 57554 -125 TTCACTGCAAAACTTCTTGAAACAGTACTTATTTTCTCTCCTCCATACACAATTGAAATGGCTCTCAACTCATGCC ;@CCCCCBCACC?CACCCACCCCCCCCCBCCCCCCCCCBCCCCB5BCCBBCACCC@BCCCACBCCBBCC?BCCA@< PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:14:920:883#0 83 chr1 57554 0 76M = 57504 -125 AATTGAAATGGCTCTCAACTCATGCCCAGAAGTCAGTGTTCAGTCTCTCACCTGGCAGATAGCAACTTAGAAAGAT A=5:B?A?;A@@<@>@>@B<B@@B?:A?B@?B@A@BABA<B@BA:<>=1:B?;BBBBB:@BBA7?BBB>2BCCBCA PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:99:1772:159#0 99 chr1 59531 0 76M = 59570 -114 TTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCAT BBCCBBBBAAABB<A<BA?5>?AB>@<@@AABBBBB?A<ABABA????B?BAABB==>AA@:>@A9:99=::?@:5 PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:99:1772:159#0 147 chr1 59570 0 76M = 59531 -114 TTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTT 535667;97997835(40899;;2449999999727859:99:9::9:9::::;:8::999:::::::735:::0! PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:24:1388:1031#0 163 chr1 60330 0 76M = 60387 -132 GAAAAACAAACGCCTCCCATTATAAGTTTATACTTCACCTCCCACCACTATAACAACCCAGAATCCATGAGGGCAT BBCBABACB?@5=BABB=>B?=<?=A??0?A?B?>AAAA<AABBBBABBB@BB<AB=@@>@;??A??=,8?=@@== PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:24:1388:1031#0 83 chr1 60387 0 76M = 60330 -132 CCAGAATCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGCCTTCTAGGTCCT ;*44;>(7>A<@3>88A<A?09AA=B:BAA3BBBA<%?>BC@BB6;A>8@8?A?BA;52BBA;039=A89=>A9A? PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:41:1418:1562#0 163 chr1 89147 0 76M = 89245 -173 GAGATGAGGTTTCACTATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCATGATGCACCCACGTTGGCCTCCCAA @9?@BB;?@-B?BBBBBB@BB;>A??@8A@BC@9A?CB@+AA=1:4@@B?9;>A<.:BAC<B@<2?B;6@(>(1(5 PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:41:1418:1562#0 83 chr1 89245 0 76M = 89147 -173 CCCCCCGTCCCGGCCTGGGTGTGTTTTTACAGCCAGTCTTCAGGTGCCCACTGTAGGAACAATGTCATTTAACCCT -+-'&3+-3+)*),%&4:+,%.;(>5%5&:;=@ABABB=9;2;@;@BB?&8?:;??8:)@95>:=B5.7ABBAABA PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:27:120:150#0 99 chr1 89543 13 76M = 89597 -129 TGCCAGGCACCCAGATCCAGTTCTAGAGTTTCACATGATCGTGAGTGTTGGTTAATGAGTCAATGTGAACTGGGAG BB9>99;@536?9<@A688?43AA=@9<%<:?9??3:7.-9>A79):=4;1994.9))6)82)6<6605&6466'< PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:27:120:150#0 147 chr1 89597 0 76M = 89543 -129 ATGAGTCAATGTGAACTGGGAGGGGAGATTTTTCAGGAGTGCCACAGGGCTCTCCCTTTAATCACATACACTCCCT 9))86%9@>760:>43-:AB75=.638%;(:-7-.>9'':089/52<(;<97?3--5@=8<=:A;6?(:/.1=BB? PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:43:556:97#0 99 chr1 94613 0 76M = 94780 -242 AGGGTGTTCTGGATAAAGAAGACTCAGGAAGACAAGTATGAAGCATAATCTGTGACATTCCATGCGGCAGACATTA ABBB>BABCCBBCA:CCB@B?=ABCBCBBBBCCCBB@BCBBBBBBA?>BCAB@B@BAB@BCBABABAB6=0B>@BB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:43:556:97#0 147 chr1 94780 22 76M = 94613 -242 CCATCAGTGAAATGGATTGCAAATACAAAGAGTAATACCATGTCACTTAAGAATAGAATCATGGACGAGGCTGCCA BCCBBCCBCBBCCCCCCCCBCC?A?CCBBCB?6ACCC@CBABCABB?BACCCBCBCCAB?AAAC@CB?BBCCCCCB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:48:836:440#0 99 chr1 97204 0 76M = 97289 -160 GACTAGAGCTACACCAATAATACAAAGGTGTAAACAAATAATGATGAGATGACAAAGGCTGAGTGTTTTCTATTTG )@CBCB==CCBBCBCCC?A=ACC@ACBBCC=CCC@CCABCCCACCCBCCCCCBA?ABCCCCBC=C:?6BCBCBCCC PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
30PPJAAXX090125:1:48:836:440#0 147 chr1 97289 0 76M = 97204 -160 TTGTTGAGTTATTTATGTATATAATTTCATGCAATCTTCATGTTATGGGGATGTTCTAATCCACTGTGACTCTGTC 8BCBCBBBCC@BCBACBCACBCBBCCCBBBBB:BCBBBCACBCC@CC?CCBCBCBBCBBCCB8BCCCBA@ABBCCB PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam