Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line? I'm working with scATAC-Seq data on the K562 cell line, which is supposed to be derived from a female patient. While following the scATAC-seq data analysis pipeline, after performing bowtie alignment they recommend filtering out all reads aligned to mitochondrial DNA and on the Y chromosome.

Out of curiosity, I decided to count how many reads aligned to chrY and found that it can be quite high - chrY has approximately 10% as many reads as a similarly-sized chromosome (chr19 in hg19).

Is it normal to find reads mapping to chrY when the cell line is female-derived, or did I mess up somehow?
There are homologous regions between X an Y chromosomes: https://en.wikipedia.org/wiki/Pseudoautosomal_region

It is therefore normal to have some female-derived reads mapping in Y chromosome.

You should probably check what proportion of such reads fall in other parts of the Y chromosome than pseudoautosomal regions.