RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354391.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) = 40,672,443 / 40,633,648 read pairs aligned = 40,629,590 total alignments = 86,572,214 secondary alignments = 5,266,123 non-unique alignments = 8,869,574 aligned to genes = 66,829,164 ambiguous alignments = 223,123 no feature assigned = 10,346,323 not aligned = 3,911,155 >>>>>>> Reads genomic origin exonic = 66,829,164 (86.59%) intronic = 6,700,508 (8.68%) intergenic = 3,645,815 (4.72%) overlapping exon = 2,555,439 (3.31%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.2 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 20,668,773 ACCT : 5.42% AGGT : 4.57% ATCT : 3.65% AGGA : 3.49% TCCT : 3.46% GCCT : 3.4% AGCT : 2.7% CCCT : 2.36% AGGC : 2.34% AGAT : 2.21% TTCT : 2.11%