Supplementary Information BeXY

These are all the input files that were used in the publication.

S1 Table: contains a list of all samples, their respective publication and ENA project number analyzed in this paper (there are 3 sheets for whole-genome sequencing (WGS), high-depth subset of WGS and capture samples).

Capture1240k: contains the counts and the number of targets per scaffold for all ancient humans sequenced with 1240k target enrichment capture sequencing (see S1 table)

downsampling_aneuploids: contains all downsampled counts for simulated aneuploid invididuals as well as scripts to generate those. Also contains our implementation of the method seGMM.

downsampling_euploids: contains all downsampled counts for euploid individuals as well as scripts to generate those.

lowQualityReference: contains all downsampled counts for the simulated low-quality reference genome assembly, as well as the scripts that were used to generate such an assembly based on the human reference genome.

WGS_ancient: contains the counts and the chromosome lengths for all ancient humans sequenced with whole-genome shotgun sequencing (see S1 table)

WGS_ancient_samples_lt_2x: contains the counts and the chromosome lengths for the 116 high-depth WGS samples (see S1 table)

non_model_organisms_posterior_probabilities_t: contains the posterior probabilities for each scaffold to be autosomal, Y-linked, X-linked or different as inferred by BeXY, for each of the six non-model organism species published in Nursyifa et al. 2021 ( https://doi.org/10.1111/1755-0998.13491).