RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354059.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) = 32,044,222 / 32,024,451 read pairs aligned = 32,020,437 total alignments = 68,564,599 secondary alignments = 4,495,926 non-unique alignments = 6,961,804 aligned to genes = 48,844,279 ambiguous alignments = 202,013 no feature assigned = 12,065,261 not aligned = 1,752,511 >>>>>>> Reads genomic origin exonic = 48,844,279 (80.19%) intronic = 10,083,901 (16.56%) intergenic = 1,981,360 (3.25%) overlapping exon = 2,411,238 (3.96%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.22 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 18,129,667 ACCT : 5.34% AGGT : 4.59% ATCT : 3.62% TCCT : 3.56% AGGA : 3.48% GCCT : 3.06% AGCT : 2.77% AGGC : 2.46% CCCT : 2.42% AGAT : 2.24% TTCT : 2.13%