RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354334.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) = 34,181,836 / 34,128,589 read pairs aligned = 34,122,885 total alignments = 82,606,174 secondary alignments = 14,295,749 non-unique alignments = 13,212,734 aligned to genes = 52,160,391 ambiguous alignments = 226,639 no feature assigned = 11,033,299 not aligned = 8,477,015 >>>>>>> Reads genomic origin exonic = 52,160,391 (82.54%) intronic = 6,898,587 (10.92%) intergenic = 4,134,712 (6.54%) overlapping exon = 2,401,829 (3.8%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.35 5'-3' bias = 1.66 >>>>>>> Junction analysis reads at junctions = 20,706,194 ACCT : 5.41% AGGT : 4.55% TCCT : 3.84% ATCT : 3.52% GCCT : 3.44% AGGA : 3.17% CCCT : 2.82% AGCT : 2.52% AGGC : 2.42% TTCT : 2.15% AGAT : 2%