RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354270.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) = 43,202,493 / 43,174,046 read pairs aligned = 43,168,864 total alignments = 92,494,107 secondary alignments = 6,117,568 non-unique alignments = 10,020,271 aligned to genes = 63,940,017 ambiguous alignments = 235,535 no feature assigned = 17,759,121 not aligned = 4,295,981 >>>>>>> Reads genomic origin exonic = 63,940,017 (78.26%) intronic = 10,038,079 (12.29%) intergenic = 7,721,042 (9.45%) overlapping exon = 2,938,616 (3.6%) >>>>>>> Transcript coverage profile 5' bias = 0.44 3' bias = 0.21 5'-3' bias = 2.14 >>>>>>> Junction analysis reads at junctions = 25,502,424 ACCT : 5.06% AGGT : 4.81% AGGA : 3.54% ATCT : 3.53% TCCT : 3.5% GCCT : 3.23% AGCT : 2.7% CCCT : 2.62% AGGC : 2.44% TTCT : 2.29% AGAT : 2.19%