RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354389.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) = 51,309,619 / 51,280,118 read pairs aligned = 51,246,964 total alignments = 109,799,601 secondary alignments = 7,209,864 non-unique alignments = 12,063,631 aligned to genes = 86,784,590 ambiguous alignments = 424,955 no feature assigned = 10,142,573 not aligned = 1,963,701 >>>>>>> Reads genomic origin exonic = 86,784,590 (89.54%) intronic = 6,592,713 (6.8%) intergenic = 3,549,860 (3.66%) overlapping exon = 4,623,846 (4.77%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.19 5'-3' bias = 1.73 >>>>>>> Junction analysis reads at junctions = 33,614,555 ACCT : 5.18% TCCT : 4.84% ATCT : 4.76% AGGT : 4.21% CCCT : 3.36% GCCT : 3.19% AGGA : 2.91% TTCT : 2.36% AGGC : 2.3% AGCT : 2.16% GTCT : 1.99%