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 4 sheets for whole-genome sequencing of ancient humans (WGS), high-depth subset of ancient WGS, 1240k target enrichment capture samples of ancient humans, and modern human WGS from the Simons Genome Diversity Project). 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_trisomy: contains all downsampled counts for simulated invididuals with trisomy 21 (factor21_1.5) and without trisomy 21 (factor_21_1) as well as scripts to generate those. 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) WGS_modern_SGDP: contains the counts and the chromosome lengths for the 276 modern human samples downloaded from the Simons Genome Diversity Project (see S1 table). wgs_modern_SGDP_original_counts_withoutSeqTypes.txt corresponds to the counts obtained from the downloaded CRAM files, without considering differences in sequencing types. wgs_modern_SGDP_original_counts_withSeqTypes.txt corresponds to the same counts, but the sequencing type per sample is specified in the second column. wgs_modern_SGDP_filteredMQ30_counts.txt corresponds to the counts obtained by filtering on a mapping quality of 30. 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).