RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354296.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) = 39,150,823 / 39,128,565 read pairs aligned = 39,124,975 total alignments = 83,265,369 secondary alignments = 4,985,981 non-unique alignments = 8,532,303 aligned to genes = 66,420,878 ambiguous alignments = 213,951 no feature assigned = 7,810,287 not aligned = 2,608,366 >>>>>>> Reads genomic origin exonic = 66,420,878 (89.48%) intronic = 4,887,428 (6.58%) intergenic = 2,922,859 (3.94%) overlapping exon = 2,426,467 (3.27%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.19 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 20,003,816 ACCT : 5.35% AGGT : 4.57% ATCT : 3.68% AGGA : 3.5% TCCT : 3.32% GCCT : 3.27% AGCT : 2.74% CCCT : 2.37% AGGC : 2.33% AGAT : 2.22% TTCT : 2.18%