RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354254.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) = 20,470,536 / 20,459,383 read pairs aligned = 20,451,092 total alignments = 44,328,505 secondary alignments = 3,398,586 non-unique alignments = 5,389,091 aligned to genes = 34,901,129 ambiguous alignments = 128,952 no feature assigned = 3,548,316 not aligned = 1,762,095 >>>>>>> Reads genomic origin exonic = 34,901,129 (90.77%) intronic = 1,761,391 (4.58%) intergenic = 1,786,925 (4.65%) overlapping exon = 1,580,357 (4.11%) >>>>>>> Transcript coverage profile 5' bias = 0.12 3' bias = 0.13 5'-3' bias = 2.26 >>>>>>> Junction analysis reads at junctions = 10,648,434 ACCT : 5.66% TCCT : 4.94% ATCT : 4.39% AGGT : 4.31% CCCT : 2.96% AGGA : 2.89% GCCT : 2.73% TCCC : 2.44% AGGC : 2.26% TTCT : 1.98% AGCT : 1.93%