sequence data
Mus_musculus.GRCm38.74.dna.toplevel.fa>1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
It supports multiple sequences in a file (used in inputs for multiple alignment program or in reference genome toplevel)
>seq1 ..... >seq2 ..... >seq3 .....
sequence data with quality scores
4 lines/read
DRR028646_1.fastq@DRR028646.1 HISEQ:63:H9B95ADXX:1:1101:1486:1977 length=151 NTTTTGTCTTATTGACGCTGTCTTTGGCCTTACAGAAGCTTTGCAGTTTCATGAGGTCCCATTTGTCAATTCTAGATCTTACAGCACAAGCCATTGCTGTTCTATTCAGGAATTTTTCCCCTGTGCCAATATCTTCGAGGCTTTTCCCCAC +DRR028646.1 HISEQ:63:H9B95ADXX:1:1101:1486:1977 length=151 #1:BDDDBBCFBBHG?GHIEEDDGH>@GGEEHFGEIDF9DFGHDDFBFGHAHHIDF8BFGEGIIIDFGGHGIICGGHEHEHHDEECD@AC?B3;@CCCC:>@A@DDCDCCC?CCCCCCCCCCBCCCCCACCCA:@:88?BBBCCC@:ACC@ @DRR028646.2 HISEQ:63:H9B95ADXX:1:1101:1339:1991 length=151 NTTGTGATTTTCAGTTTTCTCGCCATATTTCAGGTCCTACAGTGTGCATTTCTCATTTTTCACGTTTTTCAGTGATTTCGTCATTTTTCAATTCGTCAAGTGGATGTGTCTCGTTTTCCATGATTTTCAGTTTTCTTGCNNNNNNNNNNNN +DRR028646.2 HISEQ:63:H9B95ADXX:1:1101:1339:1991 length=151 #11B==DDFHBFDEA@B>GG?EGBCGEEH>CFECDFH@GHCB*?0?FBFFDEGH>BGGEIA:<;BBFH;=FHI>7=E)=7(;ADDEECEC;A>35(5=3>5:>>>:55>@(5(8?B@AC@@3(4>CC@>:4:(4:>C@############# @DRR028646.3 HISEQ:63:H9B95ADXX:1:1101:1466:1996 length=151 NACTTAACGACTTGAAAAATGAAGAAATCACTAAAAAACGTGAAAAATGAGAAATGCACACTGAAGGACCTGGACTATGGCGAGAAAACTGAAAATCTCGGAAAATGAGAAATACACACTTTAGGACGTGAAATATGGCGAGGAAAACTTA ...
The SAM/BAM Format Specification
a result of bwa sampe... DRR028646.1 99 X 132463361 60 151M = 132463667 457 NTTTTGTCTTATTGACGCTGTCTTTGGCCTTACAGAAGCTTTGCAGTTTCATGAGGTCCCATTTGTCAATTCTAGATCTTACAGCACAAGCCATTGCTGTTCTATTCAGGAATTTTTCCCCTGTGCCAATATCTTCGAGGCTTTTCCCCAC #1:BDDDBBCFBBHG?GHIEEDDGH>@GGEEHFGEIDF9DFGHDDFBFGHAHHIDF8BFGEGIIIDFGGHGIICGGHEHEHHDEECD@AC?B3;@CCCC:>@A@DDCDCCC?CCCCCCCCCCBCCCCCACCCA:@:88?BBBCCC@:ACC@ XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T150 DRR028646.1 147 X 132463667 60 151M = 132463361 -457 NCAATGTTAAGTTTTAAGTGTGAACCACTATCTCATTTCTAAAATTTAGCATCCCCTTCACGCACTAGCATCTGCAGTCATAAGAATATAGAAATAAGAATTCAGAGTAAATGCAATAAATTAATGTTATTGCTTTTGATTTTCTTTTTCA #ADDC@CDDDCCCDCCDCCCDCDDBC>ADDDDDDDCCA?:CDDCACDC?88/?:CACDDEFFDEHECEE>GGIGGHGF@HCIJHGGHFHBEEIGEEFBGHJIIGIJJIGIJGJJIIIGIJIJJIHIGEJIEIJJJIGIDFFFDFFFDF@@@ XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A150 DRR028646.2 77 * 0 0 * * 0 0 NTTGTGATTTTCAGTTTTCTCGCCATATTTCAGGTCCTACAGTGTGCATTTCTCATTTTTCACGTTTTTCAGTGATTTCGTCATTTTTCAATTCGTCAAGTGGATGTGTCTCGTTTTCCATGATTTTCAGTTTTCTTGCNNNNNNNNNNNN #11B==DDFHBFDEA@B>GG?EGBCGEEH>CFECDFH@GHCB*?0?FBFFDEGH>BGGEIA:<;BBFH;=FHI>7=E)=7(;ADDEECEC;A>35(5=3>5:>>>:55>@(5(8?B@AC@@3(4>CC@>:4:(4:>C@############# DRR028646.2 141 * 0 0 * * 0 0 TGAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN <<<?@################################################################################################################################################## DRR028646.3 77 * 0 0 * * 0 0 NACTTAACGACTTGAAAAATGAAGAAATCACTAAAAAACGTGAAAAATGAGAAATGCACACTGAAGGACCTGGACTATGGCGAGAAAACTGAAAATCTCGGAAAATGAGAAATACACACTTTAGGACGTGAAATATGGCGAGGAAAACTTA #+1=AD;AD:8:DE3:22A3<9A?A<E9:*1??9?DBD6@D?;/88(=.).)8.).==@A;A;C37?@AD################################################################################# DRR028646.3 141 * 0 0 * * 0 0 TTTTTCAGTTATCCTCGCCATATTTCACGTCCTAAAGTGGGTGTTTCTCATTTTCCGTGATTTTCATTTTTCTCGCCGTGTTCCAGGTCCTTCAATGTGCATTTCTCATTTTTCACGTTTTTTAGTGATTTCTTCATTTTTCAAGTCGTCN -751-2>):=:8)2:8(3@?;1:?############################################################################################################################### DRR028646.4 77 * 0 0 * * 0 0 NAAAATAATAAGGAATAAGGGACCATGGAAATNTANCACNAGNNNNTNNNNNNNNNNNTANNNNNNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN #1=DDFFFHHHHHJJJJJJHIJJJJJJJJJJJ#1?#1?F#0?############################################################################################################# DRR028646.4 141 * 0 0 * * 0 0 AAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN <<<@@################################################################################################################################################## DRR028646.5 99 1 139944851 60 151M = 139945139 439 NTATACAAACAGGACCCAACATTTTGCTGCTTATAGGAAACTCATCTCAGAGAAAAAGATAGACACTACCTCAGTATGAAAGGCTAGAAAACAATTTTCAAAGCAAATGGTAGGAAGAAACAAGCTGGAGTAGCCATCCTAATATCTAATA #1=DDFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJIJJJJJJJIJJJJGFGHIJJJJJJJJJHHHHHGFFFFFFEECEDDDDDDCDDDDDDEDDDDDDDDDDD@DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDEEEEDED XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0C150 DRR028646.5 147 1 139945139 60 151M = 139944851 -439 GATAATTTAGTAAAGCTCAAAGCACACATTGCACCTCAAAAATAATAGTGGGAGACTTCAACACACCACTTTCACTACTGGACAGATCATGGAAACAGAAACTAAACAGGGACACAGGGAAACTAACAGAAGTTATGAAACAAATGGATCT DEDEDDDEDDCDDCC@>CCC@DDCDCDDDDDA>C@<BDEEEEDEDCDDCCEDDCCDC??DBA?EDGCGHGEHF@C@@D@EGIGG@GHIIBJJJJIHG@IHEHGHGDIJIGHHIGJJJJIJIIJIJIIJIJJIIJJJJIFHHHHFFFFF@C@ XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:151 DRR028646.6 99 16 81441870 60 151M = 81442137 418 NCAAAATTAATAAATTCTGCATCTATTTTAGTAAATAAAATATCCTAAATAGAATAGCTAGTCAAAAGTTGACATTTTTGTCATATATAGGGCTTGATAGTCAGTGAATAAATGAATGCGACAATTCAGATATTGATTGAGAAAGATGAAA #1=DDBD?=DFHBACEHICBHDCEFHHFHAFHDF@EF<F?EBDDCDCF?GDG*:?F@G?BB???FDHGFFH==BFGAHI<E;7=7C;C;?AA;@DA;A@>@@>>@C@DEDCCCCCCDCCB?@>>A@ACCCCCCD@CDCC@C?CCCACCCC@ XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T150 DRR028646.6 147 16 81442137 60 151M = 81441870 -418 TAATATATATATGCATATATATATATATAGTTTAAAAAAAAAGAAACCTTTGACACTATAAAGTTTCTTTGATAATGCTACTAAAAGAGATGTTGCTAAGGTATCTCAGATAATTATACACGTCACTTCATAACACTTTTAATCCCATTCA >EDCDDDA@CDDCEEEEDC@DDDEDCCCCA@>BBBBBCCCCCCCCCC@>DC@6>;C>CEDC>BDCHFEEHGE@@@AGEEHIHGIIIIDIHFD?IIIIHGGHDHCFBIIHIHIHHIIHGGIGFF@CHGHEIGHHE?GGGHHHD3DDDBA;@? XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:151 DRR028646.7 83 9 100578847 60 151M = 100578357 -641 GCAACATAAGAAAAATAGACCAGTGGCACTTTATTAAAATTAAATGTCTTGTGTGCCTCAAAGGCTGAGAGTGGGCTGGGGTGATGAAGCAGCCGGTCGGAACCCTGTGCACAGACCTGACCTGAGTCTGACCCCGTGAACCCCTGCTGGN CCDDDDCDDCDEDEEDDDCDDCC@DCCCDCDEDCDDDDDDCEDCACCA??B?ABDA<:CDDDDDDDDCCAD?DDB@@DDDDDEEDDDDDBBBDDFHHGGDGCGIGIJIIIJJIGJIGGIIJIJIHGFGEEGIJJJIIIHHHHHFDFDD=4# XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:150A0 DRR028646.7 163 9 100578357 60 151M = 100578847 641 CACACTCTCCACACGGATGATGGAAGCAGGAAGACACGCTATGCTCAGCAACTCTGCGAGTTCAAAACCAGCCTGGTTATAGTCAACACTCTCAAAACCAAAACAAACAAAACATTCTCGAAGATATAGTTGGAGGCTCCCTACTTCTTAG @;?BDDDDD?FFHGHIEGH>HHEFDGGICBCGGBGHIGIIAHAFCCE3=4;FCCC>)5->55?DCC>BCB?===A?3>>AACCDD>:>?@>:::ACCB@AA8<?BABB@BBBB@CCCECB@CBBCADECB@AC:9?BBBBB<><CCCCCCC XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:151 ...
VCF (Variant Call Format) Specification
describes variations (SNPs, short INDELs, ...) relative to the reference genome
an example result of samtools mpileup##fileformat=VCFv4.1 ##samtoolsVersion=0.1.19-96b5f2294a ... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DRR028646_1_caggs.bam caggs 472 . C G 31 . DP=11;VDB=3.555881e-02;RPB=-8.293682e-01;AF1=0.5032;AC1=1;DP4=0,1,0,4;MQ=60;FQ=-8.63;PV4=1,0.053,1,1 GT:PL:GQ 0/1:61,0,19:22 ...
FAQs: Data File Format in UCSC Genome Bioinformatics