RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354213.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) = 28,048,816 / 28,021,102 read pairs aligned = 28,017,984 total alignments = 59,352,689 secondary alignments = 3,282,771 non-unique alignments = 5,465,685 aligned to genes = 47,217,192 ambiguous alignments = 147,918 no feature assigned = 6,316,598 not aligned = 8,007,288 >>>>>>> Reads genomic origin exonic = 47,217,192 (88.2%) intronic = 4,011,286 (7.49%) intergenic = 2,305,312 (4.31%) overlapping exon = 1,813,484 (3.39%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.16 5'-3' bias = 2.22 >>>>>>> Junction analysis reads at junctions = 16,740,286 ACCT : 5.21% AGGT : 5.07% AGGA : 3.72% ATCT : 3.7% TCCT : 3.42% AGCT : 2.82% GCCT : 2.77% AGGC : 2.48% CCCT : 2.38% AGAT : 2.24% TTCT : 2.16%