Dear Users,

Recently I have aligned my Illumina reads to my reference genome. I have gone through sam file specifications but, it is quiet difficult to understand.

It would be great help if some one could explain the bam flags below.

A few lines of my aligned bam file:

```
HISEQ:115:C49JYACXX:4:1114:10901:17520  163     scaffold1       1       7       4M2I94M =       208     307     GCACAGAACTTTTTATTGAACAATTGGGCTACTAAATATGCTTACCAAACTCTATGGTAGTGTAGTCACAGTCTCTTAGTAGTAGTATCGATATATTGTA    CC@FFFFFFHHHHJJJJIJJJIJJJIJJJGJIJIIJIJIIIJIJJGIJIIHIIJJJJFHIGHGBHCGIJIJIJJJGIJJCEHHHHHHFFFFDDDEFEEEE    AS:i:-21        XS:i:0  XN:i:0  XM:i:2  XO:i:1  XG:i:2  NM:i:4  MD:Z:0A2G94     YS:i:-11        YT:Z:CP
```

Thank you
There is a neat app to explain the SAM flags: http://broadinstitute.github.io/picard/explain-flags.html
