RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354398.markdup.sorted.bam gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf counting algorithm = uniquely-mapped-reads protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 42,957,175 / 42,665,456 read pairs aligned = 42,627,352 total alignments = 94,883,475 secondary alignments = 9,260,844 non-unique alignments = 12,484,715 aligned to genes = 61,500,583 ambiguous alignments = 217,933 no feature assigned = 18,595,463 not aligned = 21,937,621 >>>>>>> Reads genomic origin exonic = 61,500,583 (76.78%) intronic = 8,650,594 (10.8%) intergenic = 9,944,869 (12.42%) overlapping exon = 3,573,068 (4.46%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.24 5'-3' bias = 1.86 >>>>>>> Junction analysis reads at junctions = 20,779,013 ACCT : 5.17% AGGT : 4.7% TCCT : 3.79% ATCT : 3.74% GCCT : 3.42% AGGA : 3.27% CCCT : 2.63% AGCT : 2.61% TTCT : 2.33% AGGC : 2.31% AGAT : 1.95%