RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354071.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) = 43,894,751 / 43,874,614 read pairs aligned = 43,867,255 total alignments = 96,740,860 secondary alignments = 8,971,495 non-unique alignments = 13,305,514 aligned to genes = 74,123,370 ambiguous alignments = 322,227 no feature assigned = 7,631,213 not aligned = 2,457,257 >>>>>>> Reads genomic origin exonic = 74,123,370 (90.67%) intronic = 4,404,924 (5.39%) intergenic = 3,226,289 (3.95%) overlapping exon = 3,787,784 (4.63%) >>>>>>> Transcript coverage profile 5' bias = 0.11 3' bias = 0.13 5'-3' bias = 2.24 >>>>>>> Junction analysis reads at junctions = 26,142,734 TCCT : 5.54% ACCT : 5.18% ATCT : 4.42% AGGT : 4.2% CCCT : 3.37% AGGA : 3.01% GCCT : 2.36% AGGC : 2.25% TTCT : 2.18% TCCC : 1.96% AGCT : 1.91%