Additional file 2 of Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid

Additional file 2: table S1. Whole-Genome Bisulfite Sequencing read statistics (number of reads). Table S2. Bisulfite conversion statistics (%). Table S3. Methylkit data processing (number of cytosines). Table S4. Overall average methylation levels (%). Table S5. Cytosine contexts distribution (%). Table S6. Methylation vs. gene expression. Table S7. DMA results (number of significant hypo-/hyper-methylated regions). Table S8. Proportion of DMRs located in introns containing TEs (%). Table S9. TE composition of the Cabernet Sauvignon genome. Table S10. Intra-cultivar DMA results (number of significant hypo-/hyper-methylated regions). Table S11. Number of mapped reads after bismark mapping on each CS haplotype. Table S12. Number of windows with variants. Table S13. Substitution type distribution. Table S14. Number of SNPs shared between pairs of clones. Table S15. Number of SNPs shared between clones. Table S16. DMRs with polymorphic sites compared to the overall DMRs. Table S17. Average number of SNPs in regions considered DMR or not significant. Table S18. RNA-Seq mapping rates. Table S19. DEA results for the DE alleles. Table S20. Intersection of the DE alleles between the comparisons involving CS and the parental comparison CFvSB. Table S21. Differentially expressed sRNA clusters located within 1 kb of the DMRs and considered inherited (iCF/iSB). Table S22. Bismark results - mapping on phased genomes (number of reads). Table S23. Bismark results - mapping per haplotype (number of reads). Table S24. Bismark deduplication results (number of alignments). Table S25. Bismark results. Table S26. RNA-Seq read filtering. Table S27. Read statistics pos-trimming by ShortStack. Table S28. Read statistics pre- and post-trimming by fastp for the berry samples. Table S29. Read statistics pre- and post-trimming by fastp for the leaf samples.