Fig. 4

X chromosome RNA-Seq alignment differences in the brain cortex. We plot log₂ fold change (FC) across a the entire X chromosome and b the first 5 million bases (Mb) and show c the average fold change in large genomic regions on the X chromosome between the aligning brain cortex using HISAT to the default genome and aligning to a sex chromosome complement informed reference genome. For log₂ FC, a value less than zero indicates that the gene showed higher expression when aligned to a default reference genome, while values above zero indicate that the gene shows higher expression when aligned to a reference genome informed by the sex chromosome complement of the sample. Samples from genetic females are plotted in orange circles, while samples from males are plotted in blue squares. Darker shades indicate which gene points are in PAR1, XTR, and PAR2 while lighter shades are used for genes outside of those regions