Supplementary_Table_S1.csv Supplementary Table S1. Diverse characteristics of human sequencing data used by the Blacklist software. "bam_accession_table" – Accession numbers of 1,255 BAM files and the associated FASTQ files ("R1 FASTQs", "R2 FASTQs"), their paired-end status, and indicators of whether the data was cropped, pooled, duplicated, or restricted. Also includes BAM read length and the number of mapped and unmapped reads. "donor_accession_table" – Accession numbers of 250 donors and the associated BAM files, total mapped and unmapped reads per donor, number of BAM files per donor, read length, and tissue ontology. "fastq_accession_table" – Characteristics of the original FASTQ files used to generate sample-specific BAM files.
Supplementary_Table_S2.xlsx Supplementary Table S2. Dominant High Signal annotation counts and proportions in exclusion sets generated by the Blacklist software. The "Corrected List" refers to exclusion sets generated using our modified version of the Blacklist software, which enables dual high-signal and low-mappability annotations.
Supplementary_Table_S3.csv Supplementary Table S3. Characteristics of exclusion sets aligned with different aligners. Total number and average width of the regions, number of regions overlapping gaps, and proportion of gap coverage.
Supplementary_Table_S4.csv Supplementary Table S4. Characteristics of exclusion sets generated with different parameters. Total number and average width of the regions, number of regions overlapping gaps, and proportion of gap coverage. The list names include the bridge parameter (e.g., b1000), the k-mer parameter (e.g., k36), and the number of files (e.g., n50).
Supplementary_Table_S5.xlsx Supplementary Table S5. Genes affected by exclusion sets. Protein-coding genes, sorted alphabetically, are listed first, followed by lncRNAs and other categories.
Supplementary_Table_S6.xlsx Supplementary Table S6. Oncogenes and tumor suppressors affected by exclusion sets. "Cancer Association" results from the oncoEnrichR analysis are shown for each list, sorted by oncogenic and tumor suppressor confidence levels.
Supplementary_Table_S7.csv Supplementary Table S7. Alignment statistics of ChIP-seq input sequencing data to the "sponge" sequences and other contigs comprising the human genome reference.
Supplementary_Table_S8.csv Supplementary Table S8. Differentially expressed genes between samples aligned to the hg38 autosomal reference and to the hg38 reference with the "sponge" sequences.