Additional file 1 of Cotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding

Additional file 1: Table S1. Summary Statistics about Nanopore Sequencing Reads. Table S2. Statistic About Illumina Short Reads for Genome assembly. Table S3. Statistic for Hi-C Reads from 2 Replicates. Table S4. Syntenic Ratios Compared with CRI12. Table S5. Phenotype data of CRI12 pedigree members. Table S6. The summary statistics about Nanopore long reads of 20 CRI12 pedigree members. Table S7. Genomic annotation for pedigree structural variations. Table S8. Transposon Annotation for each SV. Table S9. Basic information about 3 cohorts. Table S10. SRR accession number of 169 samples in Wang_2017 cohort. Table S11. SRR accession number of 145 samples in He_2021 cohort. Table S12. Statistic about functional PAVs. Table S13. Genomic annotation for functional PAVs. Table S14. Functional annotation for genes directly influenced by functional PAVs. Table S15. Transcription abundance of VW-related genes between resistant and susceptible accessions. Table S16. SV-Gene expression-Phenotype triplets underlying non-coding SVs. Table S17. 6 genes in fatty acid elongation pathways. Table S18. Allelic SVs in CRI12 pedigree. Table S19. Regulation networks formed by a pair of allelic deletions. Table S20. Category information about 70 Fusarium wilt resistance segments. Table S21. Category information about fiber-quality segments. Table S22. Chisquare test for fiber-quality segments. Table S23. Source of 195 samples in Wang_2017 cohort. Table S24. Sub-groups in Fusarium wilt resistance-related segments. Table S25. Chisquare test for 4 categories in 2 sub-groups divided from 70 FR segments. Table S26. Distribution of segments in CRI12 pedigree and population with 733 samples. Table S27. Sub-groups in Fiber-quality related segments. Table S28. Genomic annotation about fiber-quality related segments. Table S29. Fingerprint score of 13138 segments. Table S30. Genomic annotation for fingerprint segments in CRI12 pedigree. Table S31. t-test about fiber length of 5 sub-populations in Wang_2017 cohort.