Off topic:In what cases, does Padded Alignment apply?

Question

[2012secondseason]

Hi. I'am so curious about Padded Alignment. In situation like this,

REF: CACGATCAGACCGATACGTCCGA READ1: CGATCAGAGACCGATA READ2: ATCA*AGACCGATAC READ3: GATCAGACCG The padded CIGAR are different:

READ1: 6M2I8M READ2: 4M1P1I9M READ3: 5M2P5M In what cases, READ2 is not just 4M1I9M but 4M1P1I9M ?

Thanks.