RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354360.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) = 57,893,283 / 57,820,585 read pairs aligned = 57,805,463 total alignments = 124,582,113 secondary alignments = 8,868,245 non-unique alignments = 14,727,861 aligned to genes = 98,164,991 ambiguous alignments = 410,652 no feature assigned = 10,618,281 not aligned = 6,784,698 >>>>>>> Reads genomic origin exonic = 98,164,991 (90.24%) intronic = 6,190,393 (5.69%) intergenic = 4,427,888 (4.07%) overlapping exon = 4,275,585 (3.93%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.19 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 30,641,264 ACCT : 5.32% ATCT : 4.61% AGGT : 4.4% TCCT : 4.3% GCCT : 3.31% AGGA : 3.12% CCCT : 2.93% AGCT : 2.26% TTCT : 2.18% AGGC : 2.15% AGAA : 1.79%