RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354200.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) = 70,763,736 / 70,727,345 read pairs aligned = 70,717,475 total alignments = 159,175,093 secondary alignments = 17,684,012 non-unique alignments = 24,785,780 aligned to genes = 118,555,157 ambiguous alignments = 477,697 no feature assigned = 11,663,749 not aligned = 4,230,557 >>>>>>> Reads genomic origin exonic = 118,555,157 (91.04%) intronic = 5,711,363 (4.39%) intergenic = 5,952,386 (4.57%) overlapping exon = 6,272,873 (4.82%) >>>>>>> Transcript coverage profile 5' bias = 0.19 3' bias = 0.18 5'-3' bias = 2.08 >>>>>>> Junction analysis reads at junctions = 37,769,335 ACCT : 4.89% AGGT : 4.76% ATCT : 4.62% TCCT : 4.04% CCCT : 3.12% AGGA : 3.07% GCCT : 2.65% AGGC : 2.48% AGCT : 2.22% TTCT : 2.06% AGAA : 2.03%