Additional file 2 of Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity

Additional file 2: Table S1. The estimated mash distance of haplotype-resolved assemblies to the reference genome and the order of integrating the assemblies during pangenome construction. Table S2. The predicted genotype of each sample to the two NRUIs derived from alignment of LR sequences to the genome followed SV calling. Table S3. Effect of the two NRUIs on cattle key traits. Table S4. The list of public RNA-Seq data used for expression validation of the novel genes predicted by Augustus. Table S5. Significant enrichment of molecular function terms of cattle genes harboring NRUIs using the Panther enrichment system. Table S6. Significant enrichment of protein class terms of cattle genes harboring NRUIs using the Panther enrichment system. Table S7. Significant enrichment of pathway terms of cattle genes harboring NRUIs using the Panther enrichment system. Table S8. Repeats annotated by RepeatMasker. Table S9. The list of novel genes predicted by Augustus. Table S10. The average TPM estimated from RNA-Seq sequence alignment to the Augustus-predicted novel gene sequences. Table S11. The average TPM estimated from RNA-Seq sequence alignment to the 5 genes without detectable homology.