RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354319.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) = 49,041,933 / 48,986,119 read pairs aligned = 48,978,285 total alignments = 104,078,901 secondary alignments = 6,050,849 non-unique alignments = 10,244,468 aligned to genes = 79,897,812 ambiguous alignments = 251,771 no feature assigned = 13,335,464 not aligned = 9,068,550 >>>>>>> Reads genomic origin exonic = 79,897,812 (85.7%) intronic = 8,661,107 (9.29%) intergenic = 4,674,357 (5.01%) overlapping exon = 3,459,083 (3.71%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.13 5'-3' bias = 2.4 >>>>>>> Junction analysis reads at junctions = 23,721,100 ACCT : 5.39% AGGT : 4.76% AGGA : 3.75% TCCT : 3.54% ATCT : 3.52% GCCT : 2.91% AGCT : 2.71% AGAT : 2.38% AGGC : 2.33% CCCT : 2.27% TTCT : 2.11%