RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354239.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) = 34,649,226 / 34,625,806 read pairs aligned = 34,622,944 total alignments = 73,954,372 secondary alignments = 4,679,340 non-unique alignments = 7,872,920 aligned to genes = 58,862,729 ambiguous alignments = 217,610 no feature assigned = 6,725,420 not aligned = 2,842,106 >>>>>>> Reads genomic origin exonic = 58,862,729 (89.75%) intronic = 4,435,457 (6.76%) intergenic = 2,289,963 (3.49%) overlapping exon = 1,952,698 (2.98%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.18 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 19,287,984 ACCT : 5.68% AGGT : 4.99% AGGA : 3.72% TCCT : 3.48% ATCT : 3.47% GCCT : 3.06% AGCT : 2.74% CCCT : 2.44% AGGC : 2.41% AGAT : 2.27% TTCT : 2.14%