RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354411.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) = 36,469,457 / 36,447,898 read pairs aligned = 36,443,652 total alignments = 77,026,752 secondary alignments = 4,109,397 non-unique alignments = 6,722,927 aligned to genes = 60,459,420 ambiguous alignments = 215,088 no feature assigned = 9,307,519 not aligned = 3,068,627 >>>>>>> Reads genomic origin exonic = 60,459,420 (86.66%) intronic = 6,604,193 (9.47%) intergenic = 2,703,326 (3.87%) overlapping exon = 2,522,699 (3.62%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.2 5'-3' bias = 1.71 >>>>>>> Junction analysis reads at junctions = 19,423,659 ACCT : 5.35% AGGT : 4.66% ATCT : 3.6% AGGA : 3.58% TCCT : 3.38% GCCT : 3.22% AGCT : 2.76% CCCT : 2.37% AGGC : 2.32% AGAT : 2.26% TTCT : 2.05%