Additional file 2 of Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice

Additional file 2: Table S1. Summary of quantity and quality of genome re-sequencing data. Table S2. Genome coverage of sequencing reads to MSU7 and R498 reference genome. Table S3. Number of genomic variations against MSU7 and R498 reference genome. Table S4. Number of genomic variations from different effect levels against MSU7 reference genome. Table S5. Variation density of different types of autotetraploid rice against MSU7 and R498 reference genome. Table S6. Cross-validation error of different k values in ADMIXTURE analysis. Table S7. GO enrichment analysis of zero-diversity genes in tetraploid rice population. Table S8. Annotation of 717 agronomically important genes that previously reported in diploid rice. Table S9. Haplotype patterns of 717 agronomically important genes in autotetraploid rice (ATR) and neo-tetraploid rice (NTR) lines. Table S10. Neo-tetraploid rice (NTR) specific haplotypes compared with 30 diploid rice cultivars. Table S11. Validation of neo-tetraploid rice specific variation in HSP101–1 using Sanger sequencing. Table S12. The genomic variations in 3024 diploid rice accessions of HSP101 from rice functional genomics and breeding (RFGB) database. Table S13. The genomic variations in diploid rice accessions of HSP101 from RiceVarMap2 database. Table S14. Two target-site primers for NTR specific gene, HSP101–1. Table S15. Mutations of HSP101–1 knockout plants.