RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354171.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) = 27,293,282 / 27,267,676 read pairs aligned = 27,263,053 total alignments = 58,166,001 secondary alignments = 3,605,043 non-unique alignments = 5,893,126 aligned to genes = 46,193,349 ambiguous alignments = 170,118 no feature assigned = 5,617,542 not aligned = 5,049,338 >>>>>>> Reads genomic origin exonic = 46,193,349 (89.16%) intronic = 2,905,566 (5.61%) intergenic = 2,711,976 (5.23%) overlapping exon = 1,943,327 (3.75%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.21 5'-3' bias = 1.74 >>>>>>> Junction analysis reads at junctions = 15,887,057 ACCT : 6.04% ATCT : 4.38% TCCT : 4.32% AGGT : 4.23% GCCT : 3.79% AGGA : 2.87% CCCT : 2.77% TTCT : 2.32% TCCC : 2.31% AGCT : 2.16% AGGC : 2.13%