RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354082.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) = 43,552,404 / 43,527,084 read pairs aligned = 43,519,417 total alignments = 94,720,534 secondary alignments = 7,641,046 non-unique alignments = 10,881,474 aligned to genes = 73,211,439 ambiguous alignments = 290,581 no feature assigned = 8,947,647 not aligned = 2,262,624 >>>>>>> Reads genomic origin exonic = 73,211,439 (89.11%) intronic = 5,979,141 (7.28%) intergenic = 2,968,506 (3.61%) overlapping exon = 3,178,387 (3.87%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.23 5'-3' bias = 1.71 >>>>>>> Junction analysis reads at junctions = 25,129,896 ACCT : 5.34% AGGT : 4.27% ATCT : 4.21% TCCT : 4.17% GCCT : 3.55% AGGA : 3.06% CCCT : 2.59% AGCT : 2.44% AGGC : 2.31% TTCT : 2.19% TCCC : 1.9%