bam/sam 資料格式的介紹 （二）

5.詳解

舉例：

E00606:11:H2CC3CCXY:8:1101:7172:14195 77 * 0 0 * * 0 0 CTACGAGTCATTTAGCACCGGGTTCTCCACAAACTTGCGGTGCGTCTCCAGAGAGGGGCGGCACTCGTTCGGCCGCACCCCGGTCCAGTCACGAACGGCTCTCCACACCGGCCGGCCCCGGGGGGTCGACCGGCTATCCCAGGCCAATCA AAFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JFJJJJ<FJJJJJJJJJJJJJJJJJ)FJ<JJJJJJFJJJJJJJJJJFJJ< XM:i:0

E00606:11:H2CC3CCXY:8:1101:7172:14195 2:N:0:ATCACG 141 * 0 0 * * 0 0 AGACATTTGGTGCGTGTGCTTGGCTGAGGAGCCACTGGTGCGAAGCTACCATCTGTGGGATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCTAAACGTAACGATACCGCAGCGCCGCGGGACTTTGATTGGCCTGGGATAGCCGGTC AAAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJ<JAJJJJJJJ<JJJJJ<JJJJJJJJJF7JJFFFJJJJJFJAJJJAJFJJJJ7JJFJJFFA-A7FFJJJJF-AFJJJJJJJJ XM:i:0

E00606:11:H2CC3CCXY:8:1101:6400:14195 77 * 0 0 * * 0 0 GCGGGATGCAGGCCGCTCACCATGGCGACGGAGCTGGAGGCGTGGCTCATGTATGAGGATGTCTGGGGCAGCGGATACGTCACCACCTCCAGTACATCATGAGAGCTGCGCTTGAAGCGGTTATTACTGGGCAGCGGCAGCAGGGGGCAG AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ XM:i:0

E00606:11:H2CC3CCXY:8:1101:7963:14195 2:N:0:ATCACG 141 * 0 0 * * 0 0 GAGTCTAACGCACGCGCGAGTCAAAGGGTGTCTCCGAGCCCCCACGGCGCAATGAAGGTGAAGGCCGGCGCTCGCCGGCCCAGGTGGGATCCCCCCGCCCCGGCGGGGGGCGCACCACCGGCCCGTCTCGCCCGCACCGCCGGGCAGGTG AAAFFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJFJFJJFJJJJJ<JJJJJJJ<FJJJFJJJFFFJJJJFJJJFJJJJJJJJJJJJJ)AFFJJJJFJJJFFJJJJJJJJ)7<JF--<FJFJ)< XM:i:0

1）QNAME

query name 一般就是read名稱 如：E00606:11:H2CC3CCXY:8:1101:7172:14195

2）FLAG  

以下資訊來自于：http://www.cnblogs.com/xudongliang/p/5437850.html

#define BAM_FPAIRED        1

#define BAM_FPROPER_PAIR   2

#define BAM_FUNMAP         4

#define BAM_FMUNMAP        8

#define BAM_FREVERSE      16

#define BAM_FMREVERSE     32

#define BAM_FREAD1        64

#define BAM_FREAD2       128

#define BAM_FSECONDARY   256

#define BAM_FQCFAIL      512

#define BAM_FDUP        1024

#define BAM_FSUPPLEMENTARY 2048

1 ： 代表這個序列采用的是PE雙端測序

2： 代表這個序列和參考序列完全比對，沒有錯配和插入缺失

4： 代表這個序列沒有mapping到參考序列上

8： 代表這個序列的另一端序列沒有比對到參考序列上，比如這條序列是R1,它對應的R2端序列沒有比對到參考序列上

16：代表這個序列比對到參考序列的負鍊上

32 ：代表這個序列對應的另一端序列比對到參考序列的負鍊上

64 ： 代表這個序列是R1端序列， read1;

128 : 代表這個序列是R2端序列，read2；

256： 代表這個序列不是主要的比對，一條序列可能比對到參考序列的多個位置，隻有一個是首要的比對位置，其他都是次要的

512： 代表這個序列在QC時失敗了，被過濾不掉了（# 這個标簽不常用）

1024: 代表這個序列是PCR重複序列（#這個标簽不常用）

2048: 代表這個序列是補充的比對（#這個标簽具體什麼意思，沒搞清楚，但是不常用）

上面的這幾個标簽都是2的n次方，這樣的數列有一個特點，就是随機挑選其中的幾個，它們的和是唯一的，比如65 隻能是1 和 64 組成，代表這個序列是雙端測序，而且是read1

samtools 中flag 可以檢視flags詳細資訊：如：

$samtools flags 77

0x4d    77      PAIRED,UNMAP,MUNMAP,READ1

flags值為77 

PAIRED表示這條序列采用雙端測序， 其值為1；

UNMAP表示這個序列沒有mapping到參考序列上， 其值為4；

MUNMAP表示這個序列的另一端序列沒有比對到參考序列上， 其值為8；

READ1表示這條序列是R1端序列，其值為64.

以上數值相加和為77

$samtools flags 141

0x8d    141     PAIRED,UNMAP,MUNMAP,READ2

flags值為141

PAIRED表示這條序列采用雙端測序， 其值為1；

UNMAP表示這個序列沒有mapping到參考序列上， 其值為4；

MUNMAP表示這個序列的另一端序列沒有比對到參考序列上， 其值為8；

READ1表示這條序列是R1端序列，其值為128.

以上數值相加和為141

3）RNAME

reference sequence name

一般是參考基因組染色體名稱，如果沒有比對上，用*表示