RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354148.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) = 28,838,728 / 28,820,203 read pairs aligned = 28,816,820 total alignments = 61,366,141 secondary alignments = 3,707,210 non-unique alignments = 6,039,514 aligned to genes = 47,425,420 ambiguous alignments = 151,426 no feature assigned = 7,417,694 not aligned = 3,004,879 >>>>>>> Reads genomic origin exonic = 47,425,420 (86.47%) intronic = 5,020,951 (9.16%) intergenic = 2,396,743 (4.37%) overlapping exon = 1,863,526 (3.4%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.21 5'-3' bias = 1.86 >>>>>>> Junction analysis reads at junctions = 15,923,729 ACCT : 5.27% AGGT : 4.82% ATCT : 3.8% AGGA : 3.63% TCCT : 3.46% GCCT : 2.9% AGCT : 2.85% AGGC : 2.38% CCCT : 2.38% AGAT : 2.33% TTCT : 2.22%