Additional file 2 of Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Additional file 2: Table S1. Inversion detect by sniffles in the Nipponbare reference genome. Table S2. The 78 circum-basmati samples with Illumina sequencing result used in this study. Table S3. Names of the Basmati 334 and Dom Sufid genome gene models that had a deletion frequency of zero across the population. Table S4. Names of the Basmati 334 and Dom Sufid genome gene models that had a deletion frequency of above 0.3 and omitted from down stream analysis. Table S5. Orthogroup status for the Basmati 334, Dom Sufid, R498, Nipponbare, and N22 genome gene models. Table S6. Count and repeat types of the presence-absence variation (PAV) in the Basmati 334 or Dom Sufid genome in comparison to the Nipponbare genome. Table S7. Gene ontology results for orthogroups where gene members from the circum-basmati are missing. Table S8. Gene ontology results for orthogroups where gene members from circum-aus, indica, and japonica are missing. Table S9. Population frequency across the 78 circum-basmati samples for orthogroups that were specifically missing a gene in the Basmati 334 and Dom Sufid genome gene models. Table S10. Genome coordinates of the LTR retrotransposons of the Basmati 334 genomes. Table S11. Genome coordinates of the LTR retrotransposons of the Dom Sufid genomes. Table S12. Genome coordinates of the Gypsy elements indicated with a single star in Fig. 3. Table S13. Genome coordinates of the Copia elements indicated with a single star in Fig. 3. Table S14. Genome coordinates of the Gypsy elements indicated with a double star in Fig. 3. Table S15. Genome coordinates of the Copia elements indicated with a triple star in Fig. 3. Table S16. The 82 Oryza population samples with Illumina sequencing result used in this study. Table S17. a i parameter estimates for the 13 different demographic models. See Additional file 1: Figure S9 for visualization of the estimating parameters.