RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354256.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) = 37,203,698 / 37,186,377 read pairs aligned = 37,183,663 total alignments = 79,228,672 secondary alignments = 4,838,597 non-unique alignments = 8,154,609 aligned to genes = 62,331,193 ambiguous alignments = 207,418 no feature assigned = 8,243,786 not aligned = 2,044,763 >>>>>>> Reads genomic origin exonic = 62,331,193 (88.32%) intronic = 5,469,862 (7.75%) intergenic = 2,773,924 (3.93%) overlapping exon = 2,457,941 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.19 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 19,930,593 ACCT : 5.28% AGGT : 4.82% AGGA : 3.65% ATCT : 3.46% TCCT : 3.4% GCCT : 2.98% AGCT : 2.76% AGGC : 2.48% CCCT : 2.47% AGAT : 2.32% TTCT : 2.09%