在bam文件中的第二列有这样一些数字，99，147，83，77，141等等，这些数字表示了这条reads的比对的状态。

samtools view FA51.ht2p.bam|less

ST-E00192:599:HHWGGCCXY:3:1101:1032:12842       99      14      49862576        60      149M    =       49862627        200     CAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG   AAFFAJJJFFJJ<A<AJJJJJJJJFFFJJJJJJFJJJFF<JA7FJFF7FJJFFJAJJJAFJJJJJJJJJFJFAJJJ-FJJFJJ-FJJJJJJJJJJAJJFJJJFFJJJJJFFAJFFJJAFJJ<-AJ<F<JJJJ)FF7<AFJJJ7AAFAJF   AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:149        YS:i:0  YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:12842       147     14      49862627        60      149M    =       49862576        -200    ACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACT   )<<J<<777-<-))A7))-7FAFFA<A<<<-)))FJFJ<<<7)JJJFJJFFFJAJJJJJJJFFF77-FJJFJ<<<JJJA7FJA<AJ7JJJJJFFFJF<FFAFJJJJJJJJFJF<JJJFFFJAJJFJJJJJJFJFF7JJJFJF-FAFAAA   AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:149        YS:i:0  YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:13650       99      12      46365362        60      149M    =       46365521        308     CTAGATGAACATTTACTCAGGTTAGAAGTCGGGTATAAAACAGTGTAACTTTTGTCCTATTACTTGCTCTGGGAAGGCTGCCAGCTGATTCATAACACAAAATGCTTCTCAAAGACTTGATACTAATGCAGGGAACAAAGCTTGTTTGT   AA<AF<FFFJJJ7A-FF77<FJFJJJJJJJJJJ<FJJ-7<FFFFFJJFFJJAFJJJ--<-<FJJJF-F-AAFA7AFFJJJF7<J--FAFJ-JJFFJFJFFFJAJFFAJAFFF7AF-7AJFAAFA7-7FAAFAJ7<AJ-AFA--7AJAJF   AS:i:-6 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:57C1C89    YS:i:-11        YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:13650       147     12      46365521        60      149M    =       46365362        -308    ATCTTATCTTTAAGCACTTTCAGAAAAATTATCCACCAACTTTGAAACAGCTTTAGCATGTAATTTCTAATGCTGGAAACTAAAAAATTTTAAAACAAGTTTTTTTCCAGATGCGTTAGCAAATATTATTAAATATTTCAATGAGGAAA   7------7----A<AFA7<JFA--<7-<---))<JFJF7JJA-7--JJAFA<-<<-AAFA<-7-7A7J7F-FA<7777<--JJAJF--JF<JJFAFAA-<J<AJ--JFFJFJF7-JJFFJJJF<FFFJJJJ<FF7--FFF-7A7AA<AA   AS:i:-11        XN:i:0  XM:i:4  XO:i:0  XG:i:0  NM:i:4  MD:Z:30G1A11G0T103      YS:i:-6 YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:14600       99      14      49862566        60      149M    =       49862682        262     CTATGTTGCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCTTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCAC   AAF<FFJJAF7AJ<JJJJ77<AFJ-7AJ7FJFJ7<<<FJJ-AFJJJJJ<-F-<FFA7FJAJJJFJFA<7<FFFFJFJJJFFJJJFJFJJJJAJAJJ<AJJAJJAJJJJJF-AFAFFFFJFFJFFJJFJ<7F<)-)--JF7JFJAFJ77<   AS:i:-3 ZS:i:-8 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:110C38     YS:i:0  YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:14600       147     14      49862682        60      146M    =       49862566        -262    CAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACTCCTGGGCTCAAGCGATCCTCCCACCTCAGCCTCCCGAGTAGCTGGGACTACA      FJAFF7F77J<-F7JJFF7)JF<<<)J7<7JAF77-F<A)7)JJF-FJA-JAA7-A--JFAJAA7777--7AJF<JJJJAAFJJJF7-A-AAJF<F<A7-<AFA7-A<<-<F7FJ<AF7-JFFJA-JFJF<AJJFA7A-JJF7J<F      AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:146        YS:i:-3 YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:14846       99      14      49853665        60      41M8935N108M    =       49853729        9020    ACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTGGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGAT   AAFFJAJJAJJ7JJJJJ7JJJJJJJJJJJFJJFJJJJ-F<-7AJA7F<FJJJA-FJ-<FJJJJFJJJJJA-7FJJJJJJAAJJJAJJJJJJJJF--7A<FJ7FJJJJJJJFFFJ<FJJJJJJ-7F7-AJFJFFFJJJJJJ<))A-AA))   AS:i:-8 ZS:i:-3 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:8A28T111   YS:i:-5 YT:Z:CP XS:A:-  NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:14846       147     14      49853729        60      46M8935N103M    =       49853665        -9020   GGTTCCCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGAGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACTCCTGGGCTCAAGCGATCCTCCCACCTCAGCCTCCCGA   --7<-))<<7--FFF<7)A7<A777FF-7)JF<<)<-7J<<7-AFF7FF--FF<A---7F-JJFAFA-AJJJJFFA7777<JF<<AF-FF-<AA--FJJFJJJJJFF7JJFAJJA-AJF7JJJJFAA-JFAFFFFJJ<FFJJAAJFAAA   AS:i:-5 ZS:i:-5 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:5A36G106   YS:i:-8 YT:Z:CP XS:A:+  NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:14986       99      14      49862563        60      148M1S  =       49862662        245     TCGCTATGTTGCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCATGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGG   AAF7AJJFJJ<FF7FFJFAFJJJFJ-FJJ--FJJJJJ<F7-AJJ<JJJ-7FJF-FJFJJJ-7F---<--AJAJJJJJJJAJ<JAAJAJFFFJJAJJ7J-77FFJFJJJJ-7A-7FJFJJFFJJAFFJAJJJFFJJJ)7AFJJJJJAJJ-   AS:i:-4 ZS:i:-9 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:65C82      YS:i:-5 YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:14986       147     14      49862662        60      138M79055N8M    =       49862563        -245    CCGGTTCACCCCTCCTTAGACAACCTGGTGGGCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACTCCTGGGCTCAAGCGATCCTCCCACCTCAGCCT      )7<--<-))-A-<-<-<A<-AJAA<7-<-)-)-A-FFJA)7-<)7)<)7--AJJFJFFA-77AJ7-JJFAJJJAJJJJF77FJAFFJAAJFJFFA<AF7AF<JF-<<JFJF-AJAAAA-AJJAJA-7-7F77-FJFFA7AF-AFA-      AS:i:-5 ZS:i:-5 XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:19G11T114  YS:i:-4 YT:Z:CP XS:A:-  NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:15373       83      14      49586700        60      149M    =       49586621        -228    TTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGCGCCTGTGAATAGCCACTGCACTCCA   FJJAFFAAJJJJJJJ<--)JJAJAAAFJA<FAAF7FJJJJJJJJJJJJJJFJJJJJJJJJAA77JJJJJJJJJJFJJFFJFJJJJJJJJJJJJJF-J7JJJJJJJJJ<JJJJFJJJJJAJFJ<<JJJJJJJJJFJJJJ7JJJJJF<AAA   AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:149        YS:i:0  YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:15373       163     14      49586621        60      149M    =       49586700        228     GAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGAACCGGCC   AAAFF<JJJJJFJJJJJJAJJJFFJJJJJJFJJJJJJJJJJJJFJJJJJJJJJFJFJA7FFFJFJJFJA--FFA7AJ<JA7AJA<AAFJJFJFJF<FAJJJJ77FJJ7AAFJJJF--)A<A7AJA<FAA-A7AF<FFJJAJF-7-AF<<   AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:149        YS:i:0  YT:Z:CP NH:i:1
ST-E00192:599:HHWGGCCXY:3:1101:1032:17483       77      *       0       0       *       *       0       0       GAGGAGTTATTGGGGTTGAATTTGCACAAATATTTGCAACCGCAGGAACAAAAGTTACTATTTTACAAAACCTACCATTAATTTTAGCTAACCTTGATAGTGAAATTTCAAAGCAATTAAGTGCTAATTTAGAAAAATTAGGTGTAAAA   AAAFFFAF<FFJAJAF<JJJJJJFJJJJJAJ-JJ-F-<JJJAFJJJJJ-FJJJFJJJ<J<JJJJJJJ---AFJA7JJJJJFJJJJFJJJJJJ<JJJJJJAJJFJAJJJFA<-77FF-FJJJJ7<FFAAAJAJ-7-77AFAFJJJJJJJF   YT:Z:UP
ST-E00192:599:HHWGGCCXY:3:1101:1032:17483       141     *       0       0       *       *       0       0       TCAGATTTAATTCTGTGTTCTTGATTATCAACTGTGTAAACAACTTCATCGTTTTCAAATCTTTGAGTTGTTGCATTTGTAACGATTTTTACACCTAATTTTTCTAAATTAGCACTTACTTGCTTTGAAATTTCACTATCAAGGTTAGC   AAAFJAJJJJFJJJFJJJF-FFF-FFJJJJ-FJJJJFJF<AJJFJJF7F-FFJJJFJJJJ<JJJJ-FFJ-FJAF-AJJJJJJJJJJJJFJFFF--A-7FFFJJAAJJ7FFJJA--7A--<FA-<<FFAF-<7AFJ-7-<-<7F<F-<F-   YT:Z:UP

以下以双末端测序的bam文件为例，这些数字表示的意义分为3种类型：

1.两条reads都比对上

99=1+2+32+64：该对reads都比对到基因组，这是read1，比对到参考基因组正链
147=1+2+16+128：该对reads都比对到基因组，这是read2，比对到参考基因组负链

83=1+2+16+64：该对reads都比对到基因组，这是read1，比对到参考基因组负链
163=1+2+32+128：该对reads都比对到基因组，这是read2，比对到参考基因组正链

2. 两条reads都没有比对上

77=1+4+8+64：该对reads都没有比对到参考基因组，这是read1
141=1+4+8+128：该对reads都没有比对到参考基因组，这是read2

3. 两条reads有一条没有比对上，另一条比对上

69=1+4+64：该对reads中的read1，没有比对到参考基因组，与其配对的read2比对到参考基因组正链
153=1+8+16+128：该对reads中的read2，比对到参考基因组正链，与其配对的read1没有比对到参考基因组

89=1+8+16+64：该对reads中的read1，比对到参考基因组负链，与其配对的read2没有比对到参考基因组
133=1+4+128：该对reads中的read2，没有比对到参考基因组，与其配对的read1比对到参考基因组负链

每个数字都是由2的n次方相加而来，即等号后的数字。可通过samtools flags +数字查看。

samtools flags 1
#0x1    1   PAIRED
samtools flags 2
#0x2    2   PROPER_PAIR
samtools flags 4
#0x4    4   UNMAP
amtools flags 8
#0x8    8   MUNMAP
samtools flags 16
#0x10   16  REVERSE
samtools flags 32
#0x20   32  MREVERSE
samtools flags 64
#0x40   64  READ1
samtools flags 128
#0x80   128 READ2
samtools flags 256
#0x100  256 SECONDARY
samtools flags 512
#0x200  512 QCFAIL
samtools flags 1024
#0x400  1024    DUP
samtools flags 2048
#0x800  2048    SUPPLEMENTARY

解释为：

1：The read is one of a pair
2：The alignment is one end of a proper paired-end alignment
4：The read has no reported alignments
8：The read is one of a pair and has no reported alignments
16：The alignment is to the reverse reference strand
32：The other mate in the paired-end alignment is aligned to the reverse reference strand
64：The read is mate 1 in a pair
128：The read is mate 2 in a pair

翻译如下：

1（1）双末端测序
2（10）paired reads都正确比对到参考序列上
4（100）该read没比对到参考序列上
8（1000）与该read成对的另一条read没有比对到参考序列上
16（10000）该read比对到参考序列负链

32（100000）与该read成对的另一条read比对到参考序列负链
64（1000000）该read是成对reads中的read1
128（10000000）该read是成对reads中的read2

Flags表示的意义可以用下图概括

Flags表示的意义.png