RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354318.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) = 52,502,071 / 52,458,507 read pairs aligned = 52,441,709 total alignments = 115,565,285 secondary alignments = 10,604,707 non-unique alignments = 16,821,063 aligned to genes = 88,349,820 ambiguous alignments = 386,456 no feature assigned = 8,902,341 not aligned = 3,468,956 >>>>>>> Reads genomic origin exonic = 88,349,820 (90.85%) intronic = 4,775,809 (4.91%) intergenic = 4,126,532 (4.24%) overlapping exon = 3,990,766 (4.1%) >>>>>>> Transcript coverage profile 5' bias = 0.08 3' bias = 0.12 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 29,041,321 TCCT : 6.42% ACCT : 5.13% ATCT : 4.69% AGGT : 3.96% CCCT : 3.88% AGGA : 2.76% GCCT : 2.33% GTCT : 2.24% AGGC : 2.23% TTCT : 2.18% TCCC : 2.07%