Additional file 5 of Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation

Additional file5: Table S16. Top 100 results from an analysis associating XCI status with genotype. See additional files. There are separate sheets for association with Xi/Xa and 450k based XCI status calls, and for comparing to all chromosomes, and just chromosome X. The adjusted p-value is calculated using the Benjamini-Hochberg method. For the sheet associating DNAme based XCI status calls with loci on all chromosomes, we included all 610 significant loci instead of the top 100. I have also included the amount of samples with each XCI status (E for escapes XCI, S for subject to XCI) and each genotype (ref for reference allele, het for heterozygous, alt for alternate allele) (columns E-J). Columns M-N are the ratio of reference to alternate alleles at samples escaping or subject to XCI, with O being the ratio of these two columns and P being the reciprocal of O if it is less than 1, to make comparison easier. This enrichment column (col P) shows enrichment of reference allele at samples with one XCI status over the other. For the DNAme allChr sheet we have also included a column showing the attributable risk per allele.