RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354186.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) = 36,981,862 / 36,963,434 read pairs aligned = 36,960,146 total alignments = 78,337,454 secondary alignments = 4,392,158 non-unique alignments = 7,327,110 aligned to genes = 63,624,762 ambiguous alignments = 230,641 no feature assigned = 6,862,128 not aligned = 4,665,224 >>>>>>> Reads genomic origin exonic = 63,624,762 (90.26%) intronic = 4,222,133 (5.99%) intergenic = 2,639,995 (3.75%) overlapping exon = 2,305,691 (3.27%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.16 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 21,008,843 ACCT : 5.67% AGGT : 4.6% ATCT : 3.76% TCCT : 3.59% GCCT : 3.35% AGGA : 3.3% AGCT : 2.58% CCCT : 2.35% AGGC : 2.33% TTCT : 2.06% AGAT : 2.03%