RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354130.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) = 31,335,323 / 31,316,968 read pairs aligned = 31,314,576 total alignments = 67,496,646 secondary alignments = 4,844,355 non-unique alignments = 7,645,990 aligned to genes = 50,352,379 ambiguous alignments = 166,880 no feature assigned = 8,825,825 not aligned = 1,353,825 >>>>>>> Reads genomic origin exonic = 50,352,379 (85.09%) intronic = 6,488,200 (10.96%) intergenic = 2,337,625 (3.95%) overlapping exon = 1,978,654 (3.34%) >>>>>>> Transcript coverage profile 5' bias = 0.46 3' bias = 0.22 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 15,526,091 ACCT : 5.14% AGGT : 4.59% ATCT : 3.68% AGGA : 3.49% TCCT : 3.41% GCCT : 2.96% AGCT : 2.88% CCCT : 2.47% AGGC : 2.34% TTCT : 2.23% AGAT : 2.22%