RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354074.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) = 91,252,929 / 91,043,857 read pairs aligned = 91,027,741 total alignments = 195,027,732 secondary alignments = 12,730,946 non-unique alignments = 20,435,273 aligned to genes = 145,789,904 ambiguous alignments = 573,821 no feature assigned = 27,080,025 not aligned = 23,316,472 >>>>>>> Reads genomic origin exonic = 145,789,904 (84.34%) intronic = 16,343,125 (9.45%) intergenic = 10,736,900 (6.21%) overlapping exon = 6,816,246 (3.94%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.32 5'-3' bias = 1.62 >>>>>>> Junction analysis reads at junctions = 57,521,364 ACCT : 5.07% AGGT : 4.7% TCCT : 3.93% ATCT : 3.73% GCCT : 3.28% AGGA : 3.16% CCCT : 2.8% AGCT : 2.56% AGGC : 2.52% TTCT : 2.19% AGAT : 1.89%