Additional file 9 of Impact of short-read sequencing on the misassembly of a plant genome

Additional file 9: Table S1. Performance of 3-class or binary prediction models. Table S2. Importance values and Kruskal test of features in Model 34. Table S3. Correlation among densities of HC/LC/BG regions and genomic features. Table S4. Importance values of features in Model 35.Table S5. Importance values of features in Model 34B. Table S6. Importance values of features in Model 35B. Table S7. Number of annotated sequences in HC regions and 10,000 randomly sampled BG regions (based on the number and length distribution of HC regions). Table S8. Gene set enrichment analysis for Pfam domains for HC regions vs. whole genome. Table S9. Gene set enrichment analysis for GO terms for HC regions vs. whole genome. Table S10. Gene set enrichment analysis for metabolic pathways for HC regions vs. whole genome. Table S11. Gene set enrichment analysis for Pfam domains for HC regions vs. BG regions. Table S12. Gene set enrichment analysis for GO terms for HC regions vs. BG regions. Table S13. Gene set enrichment analysis for metabolic pathways for HC regions vs. BG regions. Table S14. Aligned regions between Short-read assembly and Long-read assembly. Table S15. Categories of regions in Short-read assembly. Table S16. Corresponding variable coverage regions between two assemblies. Table S17. HC regions in Short-read assembly and corresponding variable coverage regions in Long-read assembly. Table S18. Importance values of features in Model 37. Table S19. Importance values of features in Model 38. Table S20. Choice of bin size.