Additional file 2 of Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment

Additional file 2: Table S1. Samples collected for genome assembly. Table S2. Quality evaluation of the assembled genomes using BUSCO (v3.0.2) software with the “mammalia_odb9” dataset. Table S3. Mapping ratio of Illumina reads to Hainan_v1 and Mongolian_v1 genomes. Table S4. Repeat annotation in the Mongolian_v1 genome. Table S5. Repeat annotation in the Hainan_v1 genome. Table S6. Polymorphism statistics. Table S7. SNP and Indel statistics of 373 Illumina data mapping to Hainan_v1, Mongolian_v1 and ARS_UCD1.2 genomes, respectively. Table S8. Genomic landscape of SVs (insertions and deletions) in the Hainan_v1 (Qry) and Mongolian_v1 (Ref) genomes. Table S9. Mapping ratio of Nanopore long reads to the Mongolian_v1 genome. Table S10. SVs statistics of different sets. Table S11. Population stratified structural variations (SVs) detected by LRS between Hainan and Mongolian cattle. Table S12. Distribution of LRS-based SV in different functional regions of the genome. Table S13. Summary of Illumina short-read sequencing data (mapping to Mongolian_v1 only chromosome scaffolds) used in this study. Table S14. Significantly enriched KEGG pathways and GO terms (adjusted P < 0.05) in genes affected by significant population stratification SVs. Table S15. Structural variations (SVs) that overlapped with ATAC peak. Table S16. North‒south stratified SVs that may be derived from banteng introgression. Table S17. The information of RT-PCR primers. Table S18. Summary of ATAC-seq and ChIP-seq data used in this study.