RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354225.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) = 44,234,746 / 44,210,880 read pairs aligned = 44,206,827 total alignments = 93,544,680 secondary alignments = 5,099,054 non-unique alignments = 8,442,016 aligned to genes = 74,519,159 ambiguous alignments = 280,473 no feature assigned = 9,917,955 not aligned = 1,869,158 >>>>>>> Reads genomic origin exonic = 74,519,159 (88.25%) intronic = 5,910,718 (7%) intergenic = 4,007,237 (4.75%) overlapping exon = 3,165,349 (3.75%) >>>>>>> Transcript coverage profile 5' bias = 0.4 3' bias = 0.25 5'-3' bias = 1.72 >>>>>>> Junction analysis reads at junctions = 28,864,540 ACCT : 5.41% AGGT : 4.58% TCCT : 3.76% ATCT : 3.65% GCCT : 3.65% AGGA : 3.08% AGCT : 2.56% CCCT : 2.5% AGGC : 2.45% TTCT : 2.24% TCCC : 2.04%