RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354220.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) = 42,567,660 / 42,543,232 read pairs aligned = 42,539,468 total alignments = 90,586,765 secondary alignments = 5,475,873 non-unique alignments = 9,205,517 aligned to genes = 72,381,119 ambiguous alignments = 274,588 no feature assigned = 8,395,995 not aligned = 3,313,272 >>>>>>> Reads genomic origin exonic = 72,381,119 (89.61%) intronic = 5,539,913 (6.86%) intergenic = 2,856,082 (3.54%) overlapping exon = 2,523,726 (3.12%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.21 5'-3' bias = 1.9 >>>>>>> Junction analysis reads at junctions = 24,057,603 ACCT : 5.28% AGGT : 4.62% ATCT : 3.62% AGGA : 3.51% TCCT : 3.49% GCCT : 3.12% AGCT : 2.75% AGGC : 2.44% CCCT : 2.42% AGAT : 2.23% TTCT : 2.23%