Determine if qualimap results are misleading, if so remove/replace it

[pansapiens]

It's not clear how to interpret the qualimap (2.2.2b) report. The total number of mapped reads reported by qualimap seems to be <~ 10 % of the mapped reads, and the number of reads reported by qualimap as mapping to "Intergenic" features are < ~10% of the number of reads that featureCounts reports mapping to "Unassigned_NoFeatures", even though these would be expected to be similar values.

Maybe it's subsampling ?