Could Any One Explain What Information Inside Sam File?

Question

[M K]

I mapped my rna reads to human genome using Tophat, and I got the binary file accepted_hits.bam. After that I used samtools to convert it to .sam file, but when I looked to this .sam file I didn't got full understand of it. so can any one help me to understand what inside this file and what important information it. This is a small portion of this file:

@HD     VN:1.0  SO:coordinate
@SQ     SN:1    LN:249250621
@SQ     SN:10   LN:135534747
@SQ     SN:11   LN:135006516
@SQ     SN:12   LN:133851895
@SQ     SN:13   LN:115169878
@SQ     SN:14   LN:107349540
@SQ     SN:15   LN:102531392
@SQ     SN:16   LN:90354753
@SQ     SN:17   LN:81195210
@SQ     SN:18   LN:78077248
@SQ     SN:19   LN:59128983
@SQ     SN:2    LN:243199373
@SQ     SN:20   LN:63025520
@SQ     SN:21   LN:48129895
@SQ     SN:22   LN:51304566
@SQ     SN:3    LN:198022430
@SQ     SN:4    LN:191154276
@SQ     SN:5    LN:180915260
@SQ     SN:6    LN:171115067
@SQ     SN:7    LN:159138663
@SQ     SN:8    LN:146364022
@SQ     SN:9    LN:141213431
@SQ     SN:MT   LN:16569
@SQ     SN:X    LN:155270560
@SQ     SN:Y    LN:59373566
@PG     ID:TopHat       VN:2.0.8        CL:/disk2/mm/tophat --library-type fr-firststrand -p 14 -G /disk2/ab/RNAseq/GeneModel/Hs_ensembl_37.gtf -o /disk2/ab/RNA
seq1/Alignment/Human_brain /disk2/ab/RNAseq/Human_genome/Ensembl/GRCh37/Bowtie2Index/genome /disk2/ab/TrimmedData/Human_brain_trimmed.fastq
HWI-ST330:269:D16WHACXX:1:1208:4303:64472       0       1       10563   3       42M     *       0       0       CGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGG      @@@FFDDDBHHBFGEEEHE8@@GGB@D@D
H7@AF@FHBG@CE      AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:42 YT:Z:UU NH:i:2  CC:Z:15 CP:i:102520480  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:1104:14490:56799      0       1       10568   3       37M     *       0       0       CTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGG   CCCDFFFFHHHHGJ@FHIIJJJJII?FHIFGGIJIII
   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU NH:i:2  CC:Z:15 CP:i:102520480  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:1207:13391:25296      256     1       10568   3       37M     *       0       0       CTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGG   CC@FFFFFHHHHHJIIJJJIJJJJJFHGIEHIIJJJJ
   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU NH:i:2  CC:Z:15 CP:i:102520480  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:2203:2048:27099       256     1       10568   3       37M     *       0       0       CTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGG   CCCFFFFFHHGHHJHIGIIIJIIJIHIHIIIIIIEIJ
   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU NH:i:2  CC:Z:15 CP:i:102520480  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:2312:5126:79980       256     1       11605   3       100M    *       0       0       CAGCAATGTCTAGGAGTGCCTGTTTCTCCACAAAGTGTTTACTTTTGGATTTTTGCCAGTCTAACAGGTGAAGCCCT
GGAGATTCTTATTAGTGATTTGG    BBCFFFFFHHHHHJJ9CGGIIJIJJJJJJIGIJGI?EDHGIJIJJJJIIHIIJJJJJHIHHHIJJGJIFHIJJJGEHHHEFDCEEEECEEEECDEFEEDD    AS:i:-4 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:15A84
      YT:Z:UU NH:i:2  CC:Z:15 CP:i:102519466  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:1206:7020:40556       272     1       11695   3       100M    *       0       0       AGTGATTTGGGCTGGGGCCTGGCCATGTGTATTTTTTTAAATTTCCACTGATGATTTTGCTGCATGGCCGGTGTTGA
GAATGACTGCGCAAATTTGCCGG    CC:CC???<@?B?>7@BBBCC8C>:>>C>C?@96A?B@EDEE=)3==CGGHA@GGIGHFB8;=?:@?0:18D?@IG>HHFA?;BF8?8BFBFDD<DD@?@    AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:100
        YT:Z:UU NH:i:2  CC:Z:15 CP:i:102519376  XS:A:+  HI:i:0
HWI-ST330:269:D16WHACXX:1:1208:6372:22787       256     1       11706   1       100M    *       0       0       CTGGGGCCTGGCCATGTGTATTTTTTTAAATTTCCACTGATGATTTTGCTGCATGGCCGGTGTTGAGAATGACTGCG
CAAATTTGCCGGATTTCCTTTGC    @@CFDFFFAFFFHGEGHHAFCHICGIGGJEGHJJJEGGEEHIHIIEHGIIDCFHBHIEH8-9'5;@C?AACCC;;=8?B=BCDDDCDDD@BBCCCDDCCD    AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:100
        YT:Z:UU NH:i:3  CC:Z:15 CP:i:102519365  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:2310:5378:15201       256     1       11706   1       100M    *       0       0       CTGGGGCCTGGCCATGTGTATTTTTTTAAATTTCCACTGATGATTTTGCTGCATGGCCGGTGTTGAGAATGACTGCG
CAAATTTGCCGGATTTCCTTTGC    CCCFFFFFHGHGHJJIGHFHHIJJJJJIJIJJJJJIJJJIIIJJJJIJJGJJ>FGGJIIHBDDBA>CDCA>;@@5;,3=B>CD@:C:<95@BCCACCA3:    AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:100
        YT:Z:UU NH:i:3  CC:Z:15 CP:i:102519365  XS:A:-  HI:i:0
HWI-ST330:269:D16WHACXX:1:2315:14323:51391      256     1       11706   1       100M    *       0       0       CTGGGGCCTGGCCATGTGTATTTTTTTAAATTTCCACTGATGATTTTGCTGCATGGCCGGTGTTGAGAATGACTGCG

[Pierre Lindenbaum]

start with the sam spec: http://samtools.github.io/hts-specs/SAMv1.pdf

Answer 1

[eddie.im]

Have you read the documentation about SAM files? There is a full description of what kind of information you will find inside a bam file.

Answer 2

[Prakki Rama]

I find this tutorial from UC Davis bioinformatics core useful, regarding SAM file explanations and alignment related information.