SAM文件

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SAM file format
The Sequence Alignment/Map (SAM) is a file format to save alignment information of short reads mapped against reference sequences. It usually starts with a header section followed by alignment information as tab separated lines for each read.

Header section
@HD VN:1.3 SO:coordinate
@SQ SN:conticA LN:443
@SQ SN:contigB LN:1493
@SQ SN:contigC LN:328

Tab-delimited read alignment information lines
readID43GYAX15:7:1:1202:19894/1 256 contig43 613960 1 65M * 0 0 CCAGCGCGAACGAAATCCGCATGCGTCTGGTCGTTGCACGGAACGGCGGCGGTGTGATGCACGGC EDDEEDEE=EE?DE??DDDBADEBEFFFDBEFFEBCBC=?BEEEE@=:?::?7?:8-6?7?@??# AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:65 YT:Z:UU

readID43GYAX15:7:1:1202:19894/1 272 contig32 21001 1 65M * 0 0 GCCGGACGTCACACGGCCGCCGGGCCGGTCTACGACCAGACGCATGCGGATTTCGTTAGAGCCGG #??@?7?6-8:?7?::?:=@EEEEB?=CBCBEFFEBDFFFEBEDABDDD??ED?EE=EEDEEDDE AS:i:-5 XS:i:0 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:42T22 YT:Z:UU

readID43GYAX15:7:1:1202:19894/1 256 contig87 540849 1 65M * 0 0 CCTGCACGAACGAAATCCGCATGCGTCTGGTCGTTGTACGGAACGGCGGTTGTGTGACGAACGGC EDDEEDEE=EE?DE??DDDBADEBEFFFDBEFFEBCBC=?BEEEE@=:?::?7?:8-6?7?@??# AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:65 YT:Z:UU

Meaning of columns

QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL TAGS
Read Name
SAM flag --> decode
contig name or * for unmapped
mapped position of base 1 of a read on the reference sequence
MAPQ mapping quality
CIGAR string describing insertions and deletions
Name of mate
Position of mate
Template length
Read Sequence
Read Quality
Additional information in TAG:TYPE:VALUE format

一些思考：
SAM作为比对的结果文件，里面也包含了原始序列，这种会很浪费存储空间。fastq加载到数据库后，每一次比对，可以建立一些中间表进行存储，原始序列只保存一份。可以认为比对只是在给原始序列打标签。

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http://www.metagenomics.wiki/tools/samtools/bam-sam-file-format#:~:text=The Sequence Alignment%2FMap (SAM,separated%20lines%20for%20each%20read.

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SAMv1.pdf