Additional file 4: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Figure S1. Edit distance of lost human reads. Figure S2. Profile of repeat elements based on repeat sequences inferred from mapped and unmapped reads (lost repeat reads). Figure S3. Profile of DNA repeats based on repeat sequences inferred from mapped and unmapped reads (lost repeat reads). Figure S4. Profile of SVA retrotransposons based on repeat sequences inferred from mapped and unmapped reads (lost repeat reads). Figure S5. Profile of repeat elements across poly(A) enrichment and ribodepletion libraries. Figure S6. Average number of SVA-F reads across GTEx tissues. Figure S7. Co-expression of Alu and L1 elements across GTEx tissues. Figure S8. Distribution 77 of hyper-edited reads. Figure S9. The sequence context of Figure S8. Figure S10. Distribution of NCL events across 10,641 samples. Figure S11. Number of NCL events across in-house tissues and library preparation protocols. Figure S12. Percentage of NCL reads across GTEx tissues (n = 54). Figure S13. An example of coverage plot of EBV virus. Figure S14. Number of VJ recombinations across GTEx human tissues for IGK chain. Figure S15. Number of VJ recombinations across GTEx human tissues for IGL chain. Figure S16. Association between microbial load and immune diversity. Figure S17. Combinatorial diversity of IGL locus differentiates disease status. Figure S18. Combinatorial diversity of TCRB locus differentiates disease status. Figure S19. Combinatorial diversity of TCRG locus differentiates disease status. Figure S20. The effect of RNA-seq aligner on the fraction of reads accounted by ROP. Figure S21. Relationship between the number of soft clipped RNA-seq reads (partially mapped reads) and the total number of reads. Figure S22. Number of the RNA-seq reads mapped to the human reference genome across five state-of-the-art RNA-seq aligners. (PDF 2344 kb)