RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354401.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) = 35,161,702 / 35,125,875 read pairs aligned = 35,122,511 total alignments = 74,719,937 secondary alignments = 4,432,360 non-unique alignments = 7,374,221 aligned to genes = 59,352,161 ambiguous alignments = 221,891 no feature assigned = 7,467,863 not aligned = 6,827,319 >>>>>>> Reads genomic origin exonic = 59,352,161 (88.82%) intronic = 4,979,920 (7.45%) intergenic = 2,487,943 (3.72%) overlapping exon = 2,107,115 (3.15%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.22 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 19,942,023 ACCT : 5.25% AGGT : 4.76% ATCT : 3.66% AGGA : 3.54% TCCT : 3.43% GCCT : 3.11% AGCT : 2.74% TTCT : 2.37% AGGC : 2.36% CCCT : 2.36% AGAT : 2.23%