coverage in chr19 of mm39 lower than other chromosomes

[lablancoberdugo]

Hello,
I am currelty running insilicoseq_1.5.3 to generate simulated reads from the mm39 mouse genome. I am running the program using the coverage_file option with a 30 coverage in chr1-19 and once reads are generated and mapped back to the mm39 reference genome the average coverage is significantly lower in chr19 compared to those of the other chromosomes.
overall coverage ends up being 29x and the coverage in chr19 is 3x

have you seen this issue before?

[HadrienG]

Hi!

I have never used InSilicoSeq with eukaryotes. Are there regions in chr19 of the mouse genome that are notoriously hard to map to?

/Hadrien