RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354091.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) = 67,086,173 / 67,016,098 read pairs aligned = 67,010,929 total alignments = 143,113,385 secondary alignments = 9,011,114 non-unique alignments = 13,894,813 aligned to genes = 104,235,314 ambiguous alignments = 413,812 no feature assigned = 23,480,715 not aligned = 5,485,655 >>>>>>> Reads genomic origin exonic = 104,235,314 (81.61%) intronic = 15,407,111 (12.06%) intergenic = 8,073,604 (6.32%) overlapping exon = 5,235,592 (4.1%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.28 5'-3' bias = 1.65 >>>>>>> Junction analysis reads at junctions = 44,332,076 ACCT : 5.26% AGGT : 4.62% GCCT : 3.71% TCCT : 3.58% ATCT : 3.43% AGGA : 3.41% CCCT : 2.84% AGCT : 2.81% AGGC : 2.48% AGAT : 2.21% TTCT : 2.12%