Bowtie2 CIGAR value of '*' makes mapping quality in SAM file difficult to interpret

Question

[daewowo]

I aligned 150nt reads to the human mitochondrion NC_012920.1 using bowtie2 with default parameters. Numerous reads have a CIGAR value of '*' and also no not have the 'NM' parameter eg:

Interpretable read:

8959166 153 NC_012920.1 14872   44  150M    =   14872   0   CCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTAT  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  MD:Z:150    PG:Z:MarkDuplicatesXG:i:0   NM:i:0  XM:i:0  XN:i:0  XO:i:0  AS:i:300    YT:Z:UP

Uninterpretable read:

8223405 101 NC_012920.1 15512   0   *   =   15512   0   CATCAAGGTTAGGGTGGAAGAAGAAATTTCTTATATGGGTCCGATAAAATCACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTATTCTCACCTGACCTCCTAGGA  FFFFFFFF,F,FFFFFFFF:FFF:FFF::F:FFFFFFFFFFFFFFFF:FFFF,,FFFFF:FFFFFFFFFFFFFFFFFFFFF,F,FFFFF,F:FFFF,,,,,:FF:FF,FFFFFFFFFFFFFFFFFFFF:FFFFFF:F,FF,FF:FF,,F,  PG:Z:MarkDuplicates YT:Z:UP

Looking at the sam format documentation there is no clear explanation of a '' for CIGAR, just mentions 'set for unavailable'

When I run BLAST for the 'uninterpreable read' I get a 109/110nt mach, indicating soft clippling at one or both ends and just a single nt match after soft clip.

Any idea why bowtie2 is recording these reads with a CIGAR of '*'?

Sam format

Answer 1

[ATpoint]

It is an unmapped read as indicates by the flag 101 (2nd column, see https://broadinstitute.github.io/picard/explain-flags.html for flag decoding). No mapping means no CIGAR.