RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354132.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) = 40,190,538 / 40,167,626 read pairs aligned = 40,164,887 total alignments = 85,428,938 secondary alignments = 5,070,774 non-unique alignments = 8,256,367 aligned to genes = 67,024,224 ambiguous alignments = 232,030 no feature assigned = 9,463,493 not aligned = 2,767,706 >>>>>>> Reads genomic origin exonic = 67,024,224 (87.63%) intronic = 6,455,871 (8.44%) intergenic = 3,007,622 (3.93%) overlapping exon = 2,779,965 (3.63%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.2 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 21,867,686 ACCT : 5.42% AGGT : 4.66% ATCT : 3.63% AGGA : 3.56% TCCT : 3.49% GCCT : 3.16% AGCT : 2.78% CCCT : 2.49% AGGC : 2.4% AGAT : 2.26% TTCT : 2.07%