Bioinformatics with Python Cookbook - Second Edition

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The preceding pattern has a biological cause that ends up having consequences on sequencing: Anopheles mosquitoes might have a big chromosomal inversion in the middle of arm 2L. Karyotypes that are not the same as the one on the reference genome used to make the calls are harder to call due to evolutionary divergence. These make the number of sequencer reads in that area lower. This is very specific to this species, but you might expect other kinds of features to appear on other organisms.

A more widely-known case is Copy Number Variation (CNV): if a reference genome has only a copy of a feature, but the individual that you are sequencing has n, then you can expect to see a DP of n times the median across the genome.

But, in ...