Edit 1: The following is Y/Auto depth versus age in a cohort. Individuals in this cohort are not known to be cancer patients.
In WGS/WES studies I read and studies I participated in analyzing, I notice that the average sequencing depth on Y chromosome vary a lot more than X chromosome, and the depth is mostly less than the average depth on autosomes (see the figure for an example; from Turro et al. 2020). Most individuals that got sampled do not have diseases involving large deletion of Y chromosome.
What causes the variability in the sequencing depth on Y chromosome? Why is the average depth on Y almost always less than that on autosomes?