Comment:

the definition for CIGAR above does not seem to agree with the the format given at this definition does not agree with the specication at the web site below here

From the web site:

Aligning these two:

RefPos: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

Reference: C C A T A C T G A A C T G A C T A A C

Read: A C T A G A A T G G C T

With the alignment above, you get:

POS: 5

CIGAR: 3M1I3M1D5M

http://genome.sph.umich.edu/wiki/SAM