Additional file 2 of Pig pangenome graph reveals functional features of non-reference sequences

Additional file 2: Table S1. The information of samples used for population-based NRS analysis. Table S2. he enrichment analysis of genes affected by deleterious variants for SWT and TC pig. Table S3. rchored ratio of 15 pig assemblies. Table S4. The distance between Sus scrofa 11.1 and other 20 assemblies calculated using Mash. Table S5. The information of Non-reference nodes (NRNs) in 20 assemblies. Table S6. The information of NRSs in each step of filtering. Table S7. GO enrichment analysis of genes whose CDS regions were affected by pNRS insertion events. Table S8. Enrichment analysis of QTLs where the pNRS insertion occurred. Table S9. Enrichment analysis of QTLs where the cNRS insertion occurred. Table S10. The information of low-quality reads mapping to NRSs. Table S11. The classification of 23,831 NRSs. Table S12. Fisher’s exact test for the difference of NRS frequencies between Asian pigs and European pigs. Table S13. Fisher’s exact test for the difference of NRS frequencies between cold-resistant pigs and heat-resistant pigs. Table S14. Fisher’s exact test for the difference of NRS frequencies between high-altitude pigs and low-altitude pigs. Table S15. Genes residing in the 11.6 Mb region of Chromosome X (ChrX: 45,231,666:56,875,949) enriched by 47 significantly different NRS between cold-resistant pigs and heat-resistant pigs. Table S16. Repeats annotated by RepeatMasker. Table S17. Novel genes annotated by Interproscan, Swissprot and KOBAS. Table S18. Significant terms (corrected P value < 0.05) of functional enrichment analysis of novel genes using KOBAS.