Additional file 4 of A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice

Additional file 4: Table S3. The tandem duplications identified around GL7 loci and the promotor of IPA1. a equal to Average_depthCNV/Average_depthChr. b the read with a insert size close to the length of the CNV. c the region within 500 bp upstream and downstream of the breakpoint were used to detect the discordant reads. Table S4. The copy number matrix of the 10 CNVs identified by qPCT. Table S5. Genes with high copy number (≥10) in more than 5 accessions. Table S6. The copy number matrices of 10 loci in 15 accessions called by CNVnator, Delly, and CtgRef-CNV. The DUP, DEL, and CN1 loci, were marked as yellow, purple, and green, respectively. Table S7. The weighted accuracies of three softwares based on the qPCT results of 10 loci in 15 accessions. Table S8. The comparisons of CNV results generated by three methods. Table S9. The accuracy of the selected 150 CNVs detected by CtgRef-CNV but not detected by CNVnator. Table S10. The accuracy of the selected 150 CNVs detected by CNVnator but not detected by CtgRef-CNV. Table S11. The comparison of CNVs between Yu et al. and present study. Table S12. The comparison of CNVs between Du et al. and present study. Table S13. The comparison of CNVs between Wang et al. (3 K rice genomes) and present study. Table S14. The comparison of CNVs between Fuentes et al. (3 K rice genomes) and present study.