Bowtie2 Alignment Score Meaning

Question

[biogirl04]

Hi,

I ran an alignment on Bowtie2 and in the output of the SAM file, I understand that there is an AS tag that signifies Alignment Score. I know that 0 is a perfect match but some of the scores I'm getting are -6, -12, -18. How many points exactly are reduced for mismatches, INDELS, and gaps? How are these scores calculated?

Thanks, Reet

Answer 1

[Devon Ryan]

Have a look at the documentation, where they go through an example with an indel. Gap opening is -5 and every base in the gap is then an additional -3. The mismatch penalty is quality dependent, but they go through examples of that I think. A score if -6 is going to be due to a mismatch, since the a single base indel will be -8.