RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354060.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) = 34,098,842 / 34,079,141 read pairs aligned = 34,075,658 total alignments = 72,510,309 secondary alignments = 4,332,326 non-unique alignments = 6,931,902 aligned to genes = 54,809,512 ambiguous alignments = 188,763 no feature assigned = 10,190,684 not aligned = 2,861,333 >>>>>>> Reads genomic origin exonic = 54,809,512 (84.32%) intronic = 7,253,630 (11.16%) intergenic = 2,937,054 (4.52%) overlapping exon = 2,187,237 (3.36%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.22 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 17,134,932 ACCT : 5.35% AGGT : 4.74% AGGA : 3.57% ATCT : 3.54% TCCT : 3.45% GCCT : 3.12% AGCT : 2.76% CCCT : 2.38% AGGC : 2.37% AGAT : 2.32% TTCT : 2.16%