RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354099.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) = 32,739,446 / 32,707,132 read pairs aligned = 32,701,198 total alignments = 69,858,176 secondary alignments = 4,411,598 non-unique alignments = 6,989,813 aligned to genes = 56,402,585 ambiguous alignments = 215,522 no feature assigned = 5,862,154 not aligned = 4,158,452 >>>>>>> Reads genomic origin exonic = 56,402,585 (90.59%) intronic = 3,593,741 (5.77%) intergenic = 2,268,413 (3.64%) overlapping exon = 2,195,794 (3.53%) >>>>>>> Transcript coverage profile 5' bias = 0.13 3' bias = 0.16 5'-3' bias = 2.05 >>>>>>> Junction analysis reads at junctions = 17,886,348 ATCT : 5.08% ACCT : 4.81% TCCT : 4.62% AGGT : 4.48% CCCT : 3.55% AGGA : 3.04% GCCT : 2.62% TTCT : 2.42% AGCT : 2.12% AGGC : 2.08% AGAA : 1.96%