RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354238.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) = 27,802,942 / 27,787,881 read pairs aligned = 27,785,923 total alignments = 59,008,272 secondary alignments = 3,417,449 non-unique alignments = 5,663,668 aligned to genes = 47,674,732 ambiguous alignments = 168,739 no feature assigned = 5,248,034 not aligned = 3,010,313 >>>>>>> Reads genomic origin exonic = 47,674,732 (90.08%) intronic = 3,351,826 (6.33%) intergenic = 1,896,208 (3.58%) overlapping exon = 1,579,212 (2.98%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.17 5'-3' bias = 2.01 >>>>>>> Junction analysis reads at junctions = 15,769,843 ACCT : 5.54% AGGT : 4.59% ATCT : 3.58% AGGA : 3.49% GCCT : 3.43% TCCT : 3.42% AGCT : 2.67% AGGC : 2.32% CCCT : 2.28% AGAT : 2.21% TTCT : 2.2%