RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354295.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) = 49,861,222 / 49,840,990 read pairs aligned = 49,836,748 total alignments = 107,394,066 secondary alignments = 7,691,854 non-unique alignments = 12,470,032 aligned to genes = 76,243,711 ambiguous alignments = 235,128 no feature assigned = 17,668,982 not aligned = 2,796,648 >>>>>>> Reads genomic origin exonic = 76,243,711 (81.19%) intronic = 8,596,107 (9.15%) intergenic = 9,072,875 (9.66%) overlapping exon = 3,213,557 (3.42%) >>>>>>> Transcript coverage profile 5' bias = 0.57 3' bias = 0.28 5'-3' bias = 1.84 >>>>>>> Junction analysis reads at junctions = 24,698,259 ACCT : 5.02% AGGT : 4.64% TCCT : 3.58% ATCT : 3.47% AGGA : 3.44% GCCT : 3.34% AGCT : 2.82% CCCT : 2.69% AGGC : 2.36% TTCT : 2.24% AGAT : 2.12%