Additional file 1 of Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus

Additional file 1: Table S1. Data statistics of five Bos indicus de novo pseudohaplotype assemblies. Table S2. NUI occurrence matrix from NUI discovery pipeline. Table S3. NUI breakpoints in the UOA_Brahman_1 reference genome overlapping with B. taurus introgressed segments. Table S4. NUI in common with published pangenomes. Table S5. Transcriptome read mapping (%) to reference vs. pangenome. Table S6. Comparison of top gene expression under heat stress as reported by Sajjanar et al. (2023) and identified in the pangenome. Table S7. BLASTx results of NUI novel genes against the NCBI non-redundant (nr) chordata database. Table S8. BICIs occurrence matrix. Table S9. Overall repeat content in BICIs. Table S10. BICIs annotation in genic and non-genic region. Table S11. BICIs supported by transcript. Table S12. BICIs supported by AUGUSTUS and transcript. Table S13. Assembly accessions ID. Table S14. WGS accessions included in the study. Table S15. Transcriptome accessions included in the study.