RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354248.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) = 43,952,706 / 43,935,119 read pairs aligned = 43,910,265 total alignments = 95,208,361 secondary alignments = 7,320,536 non-unique alignments = 11,875,802 aligned to genes = 74,847,809 ambiguous alignments = 278,911 no feature assigned = 7,544,234 not aligned = 3,592,109 >>>>>>> Reads genomic origin exonic = 74,847,809 (90.84%) intronic = 4,301,060 (5.22%) intergenic = 3,243,174 (3.94%) overlapping exon = 3,308,996 (4.02%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.15 5'-3' bias = 1.54 >>>>>>> Junction analysis reads at junctions = 24,602,331 ACCT : 4.85% ATCT : 4.82% TCCT : 4.6% AGGT : 4.41% CCCT : 3.5% AGGA : 2.84% AGGC : 2.5% GCCT : 2.26% AGAC : 2.14% TTCT : 2.03% AGCT : 2.01%