5.詳解

舉例：

E00606:11:H2CC3CCXY:8:1101:7172:1419577*0 0**00 CTACGAGTCATTTAGCACCGGGTTCTCCACAAACTTGCGGTGCGTCTCCAGAGAGGGGCGGCACTCGTTCGGCCGCACCCCGGTCCAGTCACGAACGGCTCTCCACACCGGCCGGCCCCGGGGGGTCGACCGGCTATCCCAGGCCAATCAAAFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JFJJJJ<FJJJJJJJJJJJJJJJJJ)FJ<JJJJJJFJJJJJJJJJJFJJ<XM:i:0
E00606:11:H2CC3CCXY:8:1101:7172:14195 2:N:0:ATCACG 141*00* *00AGACATTTGGTGCGTGTGCTTGGCTGAGGAGCCACTGGTGCGAAGCTACCATCTGTGGGATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCTAAACGTAACGATACCGCAGCGCCGCGGGACTTTGATTGGCCTGGGATAGCCGGTCAAAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJ<JAJJJJJJJ<JJJJJ<JJJJJJJJJF7JJFFFJJJJJFJAJJJAJFJJJJ7JJFJJFFA-A7FFJJJJF-AFJJJJJJJJXM:i:0
E00606:11:H2CC3CCXY:8:1101:6400:1419577*0 0**00 GCGGGATGCAGGCCGCTCACCATGGCGACGGAGCTGGAGGCGTGGCTCATGTATGAGGATGTCTGGGGCAGCGGATACGTCACCACCTCCAGTACATCATGAGAGCTGCGCTTGAAGCGGTTATTACTGGGCAGCGGCAGCAGGGGGCAGAAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJXM:i:0
E00606:11:H2CC3CCXY:8:1101:7963:14195 2:N:0:ATCACG 141*00* *00GAGTCTAACGCACGCGCGAGTCAAAGGGTGTCTCCGAGCCCCCACGGCGCAATGAAGGTGAAGGCCGGCGCTCGCCGGCCCAGGTGGGATCCCCCCGCCCCGGCGGGGGGCGCACCACCGGCCCGTCTCGCCCGCACCGCCGGGCAGGTGAAAFFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJFJFJJFJJJJJ<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  

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

/*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
#define BAM_FPAIRED        1
/*! @abstract the read is mapped in a proper pair */
#define BAM_FPROPER_PAIR   2
/*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
#define BAM_FUNMAP         4
/*! @abstract the mate is unmapped */
#define BAM_FMUNMAP        8
/*! @abstract the read is mapped to the reverse strand */
#define BAM_FREVERSE      16
/*! @abstract the mate is mapped to the reverse strand */
#define BAM_FMREVERSE     32
/*! @abstract this is read1 */
#define BAM_FREAD1        64
/*! @abstract this is read2 */
#define BAM_FREAD2       128
/*! @abstract not primary alignment */
#define BAM_FSECONDARY   256
/*! @abstract QC failure */
#define BAM_FQCFAIL      512
/*! @abstract optical or PCR duplicate */
#define BAM_FDUP        1024
/*! @abstract supplementary alignment */
#define BAM_FSUPPLEMENTARY 2048

1 ： 代表這個序列採用的是PE雙端測序

2： 代表這個序列和參考序列完全匹配，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鏈上

32 ：代表這個序列對應的另一端序列比對到參考序列的負鏈上

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，只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（# 這個標籤不常用）

1024: 代表這個序列是PCR重複序列（#這個標籤不常用）

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

上面的這幾個標籤都是2的n次方，這樣的數列有一個特點，就是隨機挑選其中的幾個，它們的和是唯一的，比如65 只能是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表示這條序列採用雙端測序， 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表示這條序列採用雙端測序， 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