In 3007ac0, we confirm that HH550 SNP abundances for genes in chromosomes 1-22 did not change. We confirm their consistency.

For chrX, 89% of genes had at least one SNP on HH550 in the revised dataset. For chrY, only 20% of genes had at least one SNP.

I find it unlikely that changes to a small number of genes could have such a drastic effect.

from snplentiful.

SNP abundance distributions before and after the drastic change

As expected, fixing the chrX and chrY bug led to fewer genes with 0 SNPs (notebook). This affected all platforms, so it is unclear why only HH550 would experience drastic change.

For reference, chrX contains 692 genes and chrY contains 20.

from snplentiful.

Expert diagnosis

We recreated the plots from the first post in python using seaborn. First, however we had to diagnose and fix a seaborn bug (mwaskom/seaborn#686) which was drawing scatterplots in addition to curves.

The result is shown below, using lowess curves and with the chrXY-void dataset on the top row and the corrected dataset on the bottom row (notebook):

So... our facets created in ggplot2 were incorrectly labeled. The drastic change from chrXY abundances is real but occurred for HO1 rather than HH550. These findings are consistent with the SNP abundance histograms, where HO1 underwent a drastic change with the chrXY bugfix.

from snplentiful.