RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354065.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) = 32,712,900 / 32,684,729 read pairs aligned = 32,677,521 total alignments = 70,794,072 secondary alignments = 5,396,443 non-unique alignments = 8,255,744 aligned to genes = 55,185,983 ambiguous alignments = 226,148 no feature assigned = 6,438,792 not aligned = 5,318,069 >>>>>>> Reads genomic origin exonic = 55,185,983 (89.55%) intronic = 3,242,435 (5.26%) intergenic = 3,196,357 (5.19%) overlapping exon = 2,250,811 (3.65%) >>>>>>> Transcript coverage profile 5' bias = 0.15 3' bias = 0.16 5'-3' bias = 1.95 >>>>>>> Junction analysis reads at junctions = 18,471,170 ACCT : 5.53% TCCT : 5.39% ATCT : 4.95% AGGT : 4.06% CCCT : 3.58% GCCT : 2.93% AGGA : 2.83% TTCT : 2.37% GTCT : 2.14% AGGC : 2.03% AGCT : 1.96%