36S76M means 36 nucleotides are soft-clipped (nts that are not part of the alignment but present in the read) + 76 alignment matches.

I suggest reading the SAM specifications document. Page 1 and 2 have a good example that addresses your question about alignment and CIGAR operators.

Unmapped information always shows in FLAG with 0x4, with no information in CIGAR.

clipping(S/H) and skipped(N) information shows in CIGAR.

Taking an example,

1. if read A is unmapped, it's FLAG includes 4(Bit) and it's CIGAR is '*'.

2. if read A is mapped, but only part of it is mapped, it's FLAG does not include 4(Bit) and it's CIGAR is like '36S76M'(means 36nts is unmapped to reference but these soft-chipped sequences are stored in SEQ).

• A simaliar concept is hard clipping(H) (clipped sequences NOT present in SEQ).So H can only be present as the first and/or last operation.S may only have H operations between them, or be present as the end of the CIGAR string(such as 3S89M,67M43S,31S56M21S).

1. if read A is mapped, but parts of it are mapped to different position, which include a long gap between each of part,it's CIGAR is like 56M1200N63M.

• For mRNA, an N operation always represents an intron.