简介
SAM是一种序列比对格式标准， 由sanger制定，是以TAB为分割符的文本格式。主要应用于测序序列mapping到基因组上的结果表示，当然也可以表示任意的多重比对结果。
SAM分为两部分，注释信息（header section）和比对结果部分（alignment section），注释信息可有可无，都是以@开头，用不同的tag表示不同的信息，主要有@HD，说明符合标准的版本、对比序列的排列顺序；@SQ，参考序列说明；@RG，比对上的序列（read）说明；@PG，使用的程序说明；@CO，任意的说明信息。
比对结果
比对结果部分（alignment section），每一行表示一个片段（segment）的比对信息，包括11个必须的字段（mandatory fields）和一个可选的字段，字段之间用tag分割。必须的字段有11个，顺序固定，不可用时，根据字段定义，可以为’0‘或者’*‘，12个字段详情如下：
| 1 | QNAME | Query template/pair NAME |
|---|---|---|
| 2 | FLAG | bitwise FLAG |
| 3 | RNAME | Reference sequence NAME |
| 4 | POS | 1-based leftmost POSition/coordinate of clipped sequence |
| 5 | MAPQ | MAPping Quality (Phred-scaled) |
| 6 | CIGAR | extended CIGAR string |
| 7 | MRNM | Mate Reference sequence NaMe (‘=’ if same as RNAME) |
| 8 | MPOS | 1-based Mate POSistion |
| 9 | TLEN | inferred Template LENgth (insert size) |
| 10 | SEQquery | SEQuence on the same strand as the reference |
| 11 | QUAL | query QUALity (ASCII-33 gives the Phred base quality) |
| 12 | +OPT | variable OPTional fields in the format TAG:VTYPE:VALUE |
FLAG详解
Each bit in the FLAG field is defined as:
| 0x0001 | p | the read is paired in sequencing |
|---|---|---|
| 0x0002 | P | the read is mapped in a proper pair |
| 0x0004 | u | the query sequence itself is unmapped |
| 0x0008 | U | the mate is unmapped |
| 0x0010 | r | strand of the query (1 for reverse) |
| 0x0020 | R | strand of the mate |
| 0x0040 | 1 | the read is the first read in a pair |
| 0x0080 | 2 | the read is the second read in a pair |
| 0x0100 | s | the alignment is not primary |
| 0x0200 | f | the read fails platform/vendor quality checks |
| 0x0400 | d | the read is either a PCR or an optical duplicate |
| 0x0800 | S | the alignment is supplementary |
CIGAR格式
A CIGAR string is comprised of a series of operation lengths plus the operations. The conventional CIGAR format allows for three types of operations: M for match or mismatch, I for insertion and D for deletion. The extended CIGAR format further allows four more operations, as is shown in the following table, to describe clipping, padding and splicing:
| Operation | Description |
|---|---|
| M | Alignment match (can be a sequence match or mismatch) |
| I | Insertion to the reference |
| D | Deletion from the reference |
| N | Skipped region from the reference |
| S | Soft clip on the read (clipped sequence present in |
| H | Hard clip on the read (clipped sequence NOT present in |
| P | Padding (silent deletion from the padded reference sequence) |
