RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354061.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) = 44,847,581 / 44,822,597 read pairs aligned = 44,813,520 total alignments = 96,368,813 secondary alignments = 6,698,635 non-unique alignments = 10,701,358 aligned to genes = 76,980,781 ambiguous alignments = 307,655 no feature assigned = 7,756,371 not aligned = 3,137,260 >>>>>>> Reads genomic origin exonic = 76,980,781 (90.85%) intronic = 4,954,938 (5.85%) intergenic = 2,801,433 (3.31%) overlapping exon = 3,403,529 (4.02%) >>>>>>> Transcript coverage profile 5' bias = 0.15 3' bias = 0.15 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 23,887,359 ACCT : 5.23% TCCT : 4.86% AGGT : 4.53% ATCT : 4.31% AGGA : 3.23% CCCT : 2.96% GCCT : 2.64% AGGC : 2.2% TTCT : 2.19% AGCT : 2.13% AGAA : 1.89%