RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354064.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) = 58,435,666 / 58,324,439 read pairs aligned = 58,315,493 total alignments = 125,651,064 secondary alignments = 8,890,959 non-unique alignments = 13,939,944 aligned to genes = 90,511,023 ambiguous alignments = 337,133 no feature assigned = 19,838,797 not aligned = 16,168,087 >>>>>>> Reads genomic origin exonic = 90,511,023 (82.02%) intronic = 12,266,614 (11.12%) intergenic = 7,572,183 (6.86%) overlapping exon = 3,985,199 (3.61%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.32 5'-3' bias = 1.72 >>>>>>> Junction analysis reads at junctions = 35,141,538 ACCT : 5.07% AGGT : 4.6% TCCT : 3.96% ATCT : 3.74% GCCT : 3.45% AGGA : 3.23% CCCT : 2.77% AGCT : 2.69% AGGC : 2.51% TTCT : 2.21% AGAT : 1.95%