RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354075.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) = 46,237,060 / 46,207,369 read pairs aligned = 46,199,620 total alignments = 101,510,585 secondary alignments = 9,066,156 non-unique alignments = 12,903,017 aligned to genes = 79,998,365 ambiguous alignments = 390,426 no feature assigned = 6,630,267 not aligned = 2,564,031 >>>>>>> Reads genomic origin exonic = 79,998,365 (92.35%) intronic = 3,902,471 (4.5%) intergenic = 2,727,796 (3.15%) overlapping exon = 3,592,599 (4.15%) >>>>>>> Transcript coverage profile 5' bias = 0.11 3' bias = 0.12 5'-3' bias = 2.14 >>>>>>> Junction analysis reads at junctions = 26,631,656 TCCT : 5.95% ACCT : 5.33% ATCT : 4.65% AGGT : 4.16% CCCT : 3.67% AGGA : 2.87% GCCT : 2.23% AGGC : 2.21% GTCT : 2.07% TCCC : 1.97% AGCT : 1.93%