RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354305.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) = 48,357,489 / 48,321,369 read pairs aligned = 48,307,671 total alignments = 105,170,663 secondary alignments = 8,491,805 non-unique alignments = 12,842,435 aligned to genes = 82,044,639 ambiguous alignments = 342,911 no feature assigned = 8,856,386 not aligned = 3,282,692 >>>>>>> Reads genomic origin exonic = 82,044,639 (90.26%) intronic = 5,437,612 (5.98%) intergenic = 3,418,774 (3.76%) overlapping exon = 4,056,545 (4.46%) >>>>>>> Transcript coverage profile 5' bias = 0.11 3' bias = 0.14 5'-3' bias = 1.84 >>>>>>> Junction analysis reads at junctions = 30,145,166 ACCT : 5.34% TCCT : 5.06% AGGT : 4.47% ATCT : 4.08% AGGA : 3.02% CCCT : 2.91% GCCT : 2.35% AGGC : 2.22% AGCT : 2.03% TTCT : 1.9% TCCC : 1.89%