bam/sam 数据格式的介绍 （二）
5.详解
举例：
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名称 如：E00606:11:H2CC3CCXY:8:1101:7172:14195
/*! @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 ： 代表这个序列采用的是PE双端测序
2： 代表这个序列和参考序列完全匹配，没有错配和插入缺失
4： 代表这个序列没有mapping到参考序列上
8： 代表这个序列的另一端序列没有比对到参考序列上，比如这条序列是R1,它对应的R2端序列没有比对到参考序列上
16：代表这个序列比对到参考序列的负链上
32 ：代表这个序列对应的另一端序列比对到参考序列的负链上
64 ： 代表这个序列是R1端序列， read1;
128 : 代表这个序列是R2端序列，read2；
256： 代表这个序列不是主要的比对，一条序列可能比对到参考序列的多个位置，只有一个是首要的比对位置，其他都是次要的
512： 代表这个序列在QC时失败了，被过滤不掉了（# 这个标签不常用）
1024: 代表这个序列是PCR重复序列（#这个标签不常用）
2048: 代表这个序列是补充的比对（#这个标签具体什么意思，没搞清楚，但是不常用）
上面的这几个标签都是2的n次方，这样的数列有一个特点，就是随机挑选其中的几个，它们的和是唯一的，比如65 只能是1 和 64 组成，代表这个序列是双端测序，而且是read1
samtools 中flag 可以查看flags详细信息：如：
$samtools flags 77
0x4d 77 PAIRED,UNMAP,MUNMAP,READ1
flags值为77
PAIRED表示这条序列采用双端测序， 其值为1；
UNMAP表示这个序列没有mapping到参考序列上， 其值为4；
MUNMAP表示这个序列的另一端序列没有比对到参考序列上， 其值为8；
READ1表示这条序列是R1端序列，其值为64.
以上数值相加和为77
$samtools flags 141
0x8d 141 PAIRED,UNMAP,MUNMAP,READ2
flags值为141
PAIRED表示这条序列采用双端测序， 其值为1；
UNMAP表示这个序列没有mapping到参考序列上， 其值为4；
MUNMAP表示这个序列的另一端序列没有比对到参考序列上， 其值为8；
READ1表示这条序列是R1端序列，其值为128.
以上数值相加和为141
3）RNAME
reference sequence name
举例：
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名称 如：E00606:11:H2CC3CCXY:8:1101:7172:14195
2）FLAG
/*! @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 ： 代表这个序列采用的是PE双端测序
2： 代表这个序列和参考序列完全匹配，没有错配和插入缺失
4： 代表这个序列没有mapping到参考序列上
8： 代表这个序列的另一端序列没有比对到参考序列上，比如这条序列是R1,它对应的R2端序列没有比对到参考序列上
16：代表这个序列比对到参考序列的负链上
32 ：代表这个序列对应的另一端序列比对到参考序列的负链上
64 ： 代表这个序列是R1端序列， read1;
128 : 代表这个序列是R2端序列，read2；
256： 代表这个序列不是主要的比对，一条序列可能比对到参考序列的多个位置，只有一个是首要的比对位置，其他都是次要的
512： 代表这个序列在QC时失败了，被过滤不掉了（# 这个标签不常用）
1024: 代表这个序列是PCR重复序列（#这个标签不常用）
2048: 代表这个序列是补充的比对（#这个标签具体什么意思，没搞清楚，但是不常用）
上面的这几个标签都是2的n次方，这样的数列有一个特点，就是随机挑选其中的几个，它们的和是唯一的，比如65 只能是1 和 64 组成，代表这个序列是双端测序，而且是read1
samtools 中flag 可以查看flags详细信息：如：
$samtools flags 77
0x4d 77 PAIRED,UNMAP,MUNMAP,READ1
flags值为77
PAIRED表示这条序列采用双端测序， 其值为1；
UNMAP表示这个序列没有mapping到参考序列上， 其值为4；
MUNMAP表示这个序列的另一端序列没有比对到参考序列上， 其值为8；
READ1表示这条序列是R1端序列，其值为64.
以上数值相加和为77
$samtools flags 141
0x8d 141 PAIRED,UNMAP,MUNMAP,READ2
flags值为141
PAIRED表示这条序列采用双端测序， 其值为1；
UNMAP表示这个序列没有mapping到参考序列上， 其值为4；
MUNMAP表示这个序列的另一端序列没有比对到参考序列上， 其值为8；
READ1表示这条序列是R1端序列，其值为128.
以上数值相加和为141
3）RNAME
reference sequence name
一般是参考基因组染色体名称，如果没有比对上，用*表示