Different counts of mapped bases between Samtools coverage and Qualimap bamqc

Question

[pauline10albert]

Hello!

I mapped contigs on a reference genome. I used both Samtools (v1.21) coverage and Qualimap (v2.3) bamqc tools to get my mapping statistics (reads mapped, bases mapped, coverage, depth...).

samtools coverage sorted.bam -o coverage.out

qualimap bamqc -bam sorted.bam -outdir ./qualimap

However, I don't get the same count at all, with Samtools coverage counting 36Mbp mapped and Qualimap bamqc 45Mbp. In the details of each scaffold, I can see more bases mapped each time according to Qualimap bamqc compared to Samtools coverage.

I know that Samtools coverage doesn't apply any quality or length filter if you don't ask it to do so. Then why does it give a smaller count? Did I miss any filter or trimming process? Is any of the tool more reliable for mapping statistics?

Thank you!