RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354242.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) = 65,926,347 / 65,890,423 read pairs aligned = 65,878,050 total alignments = 142,754,241 secondary alignments = 10,937,471 non-unique alignments = 16,920,087 aligned to genes = 112,579,920 ambiguous alignments = 559,353 no feature assigned = 11,290,516 not aligned = 6,626,484 >>>>>>> Reads genomic origin exonic = 112,579,920 (90.89%) intronic = 5,675,082 (4.58%) intergenic = 5,615,434 (4.53%) overlapping exon = 5,488,616 (4.43%) >>>>>>> Transcript coverage profile 5' bias = 0.13 3' bias = 0.13 5'-3' bias = 2.21 >>>>>>> Junction analysis reads at junctions = 43,454,013 TCCT : 5.25% ACCT : 4.9% ATCT : 4.55% AGGT : 4.38% CCCT : 3.6% AGGA : 2.93% AGGC : 2.5% GCCT : 2.3% AGAC : 2.12% TTCT : 2.02% AGCT : 2%