Hi all ,
One of the record in bam file is :
HWI-ST1162:72:D0PMMACXX:5:1104:10496:88597 16 gi|355477192|ref|NC_007299.5| 1 255 101M * 0 0 TACCCCACTCACACTTATGGATAGATCAACTAAACAGAAAATTAACAAGGAAAAAAAAAACAAAAAAAACATGTATCTATAAAGCTCACTAAAGGAAAGCA 05DDDDCDDCDDDDDDDDDDDCDCCADDDCDDDEDDEDEEEEDDDDDDDDDDHJJJJJJIJJJJJJJJIIJJJJJIJGJJJJJJIIHGHHHHHFFFFFCCC XA:i:1 MD:Z:60A33C6 RG:Z:D0PMMACXX:IT27.48-3 NM:i:2
What does the second field means? What may be the possible values for second field of a bam file. In one paper I read it as a flag. But I could not find the explanation for value 0 and 16 .