Qualimap general alignment error rate

Question

[celine.petitjean]

Hello,

I am using qualimap to estimate the quality of some assemblies, and I am not sure to understand exactly what means the "general alignment error rate" given?

Thank you in advance if anyone could help me with that! Celine

[celine.petitjean]

Hi Genomax, thank you for your answer. I have read the description of the parameter in qualimap, but I still don't understand exactly how it is calculated. It does not correspond exactly to the number of mismatches and indels reported to the number of bases in my reads, so I wanted to know exactly how it was calculated. thank you! Celine

Answer 1

[GenoMax]

Did you mean to say alignments?

From qualimap help:

Mismatches and indels

The section reports general alignment error rate (computed as a ratio of total collected edit distance to the number of mapped bases), total number of mismatches and total number of indels (computed from the CIGAR values). Additionally fraction of the homopolymer indels among total indels is provided. Note, the error rate and mismatches metrics are based on optional fields of a SAM record (NM for edit distance, MD for mismatches). The features are not reported if these fields are missing in the SAM file.