Question: 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

Answer: Have you read [the documentation][1] about SAM files? There is a full description of what kind of information you will find inside a bam file.

[1]: http://samtools.github.io/hts-specs/SAMv1.pdf