Additional file 13: Gene expression for XY homologous genes. X chromosome expression for 26 X and Y homologous genes (AMELX, ARSD, ARSE, ARSF, CASK, GYG2, HSFX1, HSFX2, NLGN4X, OFD1, PCDH11X, PRKX, RBMX, RPS4X, SOX3, STS, TBL1X, TGIF2LX, TMSB4X, TSPYL2, USP9X, VCX, VCX2, VCX3A, VCX3B, ZFX). Difference in gene expression for when male XY and female XX samples were aligned to a default and sex chromosome complement informed reference genome for each tissue. Little to no difference in gene expression between default and sex chromosome complement informed reference genome alignment was observed for 25 of the 26 X and Y homologous genes for both male XY and female XX samples using either HISAT or STAR. The log2 fold increase in expression for PCDH11X when aligned using HISAT was 0.4, 0.28, 0.33, 0.16, and 0.16 for whole blood, brain cortex, breast, liver, and thyroid, respectively. The greatest increase in expression was observed for PCDH11X in female whole blood at a log2 fold increase of 0.4.