RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354175.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) = 41,245,765 / 41,226,929 read pairs aligned = 41,189,898 total alignments = 88,665,895 secondary alignments = 6,193,201 non-unique alignments = 10,000,213 aligned to genes = 70,358,603 ambiguous alignments = 280,250 no feature assigned = 7,468,405 not aligned = 1,322,076 >>>>>>> Reads genomic origin exonic = 70,358,603 (90.4%) intronic = 4,320,180 (5.55%) intergenic = 3,148,225 (4.05%) overlapping exon = 3,529,453 (4.53%) >>>>>>> Transcript coverage profile 5' bias = 0.21 3' bias = 0.16 5'-3' bias = 2.72 >>>>>>> Junction analysis reads at junctions = 23,143,007 ACCT : 5.33% TCCT : 5.18% ATCT : 4.7% AGGT : 4.17% CCCT : 3.2% GCCT : 3.14% AGGA : 2.77% TTCT : 2.37% AGGC : 2.22% TCCC : 2.16% AGCT : 2.15%