RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354087.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) = 65,372,906 / 65,284,004 read pairs aligned = 65,276,619 total alignments = 138,820,358 secondary alignments = 8,163,448 non-unique alignments = 13,084,272 aligned to genes = 101,575,831 ambiguous alignments = 363,951 no feature assigned = 22,957,720 not aligned = 10,776,242 >>>>>>> Reads genomic origin exonic = 101,575,831 (81.57%) intronic = 13,699,127 (11%) intergenic = 9,258,593 (7.43%) overlapping exon = 5,146,393 (4.13%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.3 5'-3' bias = 1.69 >>>>>>> Junction analysis reads at junctions = 33,498,862 ACCT : 4.99% AGGT : 4.79% TCCT : 3.69% ATCT : 3.57% AGGA : 3.45% GCCT : 3.17% CCCT : 2.79% AGCT : 2.76% AGGC : 2.53% TTCT : 2.01% AGAT : 2.01%