SAM/BAM Format

https://samtools.github.io/hts-specs/SAMv1.pdf

HANNIBAL_4_FC308YYAAXX:5:19:697:1715    0       Chr1    3698    50      39M     *       0       0       GAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCAT -BBB9=;@B@9A>8>>@??7BB>;AA@9,96(6?9019? MD:Z:39 PG:Z:MarkDuplicates     XG:i:0  NH:i:1  NM:i:0  XM:i:0  XN:i:0  XO:i:0  AS:i:0  XS:A:+  YT:Z:UU
HANNIBAL_4_FC308YYAAXX:5:5:898:1878     0       Chr1    3744    50      39M     *       0       0       GGACGGTTTAGTGAAAATGGAGGATCAAGTTGGGTTTGG @;ABBBBBA@;?2?AAAA3,;<7<;06@?BB9(9BB9(6 MD:Z:39 PG:Z:MarkDuplicates     XG:i:0  NH:i:1  NM:i:0  XM:i:0  XN:i:0  XO:i:0  AS:i:0  XS:A:+  YT:Z:UU
HANNIBAL_4_FC308YYAAXX:5:75:552:187     0       Chr1    4070    50      40M     *       0       0       CAGAGCAGGACAACGGTTTCTGGTAAATGGAAGCTTACCG        BBBBBBB9BBBBBBBBBBBBBB6<??BB9&1<7?BBA@?=        MD:Z:40 PG:Z:MarkDuplicates     XG:i:0  NH:i:1  NM:i:0  XM:i:0  XN:i:0  XO:i:0  AS:i:0  XS:A:+  YT:Z:UU
HANNIBAL_4_FC308YYAAXX:5:27:463:1527    0       Chr1    4086    50      40M     *       0       0       TTTCTGGTAAATGGAAGCTTACCGGAGAATCTGTTTAGCT        BBCCBBBBBBBA>>@@6@BBBBA<9?6;9<B???<(.7<<        MD:Z:35G2G1     PG:Z:MarkDuplicates     XG:i:0  NH:i:1  NM:i:2  XM:i:2  XN:i:0  XO:i:0  AS:i:-6 XS:A:+  YT:Z:UU

Applications and Tools that use it:

1. Output of sequence aligners

   1. bwa, bowtie, etc.

2. Processing, sorting, and indexing

   1. Samtools,Picardtools

3. Input for SNP detection

   1. Samtools, GATK

4. RNA-seq and CHIP-seq analysis

   1. Cufflinks, DESEQ2, EDGER, MACS, etc.