RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354195.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) = 46,433,556 / 46,396,691 read pairs aligned = 46,384,014 total alignments = 99,423,538 secondary alignments = 6,593,291 non-unique alignments = 10,511,485 aligned to genes = 79,160,797 ambiguous alignments = 285,822 no feature assigned = 8,829,560 not aligned = 3,948,711 >>>>>>> Reads genomic origin exonic = 79,160,797 (89.97%) intronic = 5,443,469 (6.19%) intergenic = 3,386,091 (3.85%) overlapping exon = 3,464,192 (3.94%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.18 5'-3' bias = 2.09 >>>>>>> Junction analysis reads at junctions = 25,141,832 ACCT : 5.38% AGGT : 4.69% TCCT : 3.95% ATCT : 3.79% AGGA : 3.37% GCCT : 2.95% CCCT : 2.52% AGCT : 2.38% AGGC : 2.3% TTCT : 2.04% AGAT : 1.93%