RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354204.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) = 47,007,698 / 46,965,345 read pairs aligned = 46,958,020 total alignments = 99,501,785 secondary alignments = 5,528,742 non-unique alignments = 9,254,356 aligned to genes = 77,630,490 ambiguous alignments = 281,942 no feature assigned = 12,002,980 not aligned = 11,403,601 >>>>>>> Reads genomic origin exonic = 77,630,490 (86.61%) intronic = 7,854,947 (8.76%) intergenic = 4,148,033 (4.63%) overlapping exon = 3,244,181 (3.62%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.18 5'-3' bias = 2.01 >>>>>>> Junction analysis reads at junctions = 25,195,707 ACCT : 5.25% AGGT : 4.94% AGGA : 3.8% TCCT : 3.52% ATCT : 3.45% GCCT : 2.84% AGCT : 2.72% CCCT : 2.45% AGGC : 2.43% AGAT : 2.42% TTCT : 2.15%