RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354108.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) = 44,274,461 / 44,246,543 read pairs aligned = 44,240,878 total alignments = 95,743,417 secondary alignments = 7,222,413 non-unique alignments = 10,808,642 aligned to genes = 73,419,021 ambiguous alignments = 314,130 no feature assigned = 10,102,820 not aligned = 2,139,304 >>>>>>> Reads genomic origin exonic = 73,419,021 (87.9%) intronic = 7,539,952 (9.03%) intergenic = 2,562,868 (3.07%) overlapping exon = 3,333,188 (3.99%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.23 5'-3' bias = 1.62 >>>>>>> Junction analysis reads at junctions = 24,174,681 ACCT : 5.26% AGGT : 4.66% ATCT : 3.8% TCCT : 3.69% GCCT : 3.4% AGGA : 3.36% CCCT : 2.68% AGCT : 2.65% AGGC : 2.42% TTCT : 2.11% AGAT : 2.1%