RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354410.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) = 32,362,823 / 32,343,261 read pairs aligned = 32,340,369 total alignments = 68,535,463 secondary alignments = 3,829,379 non-unique alignments = 6,275,514 aligned to genes = 54,063,854 ambiguous alignments = 186,998 no feature assigned = 7,689,163 not aligned = 2,331,184 >>>>>>> Reads genomic origin exonic = 54,063,854 (87.55%) intronic = 5,419,613 (8.78%) intergenic = 2,269,550 (3.68%) overlapping exon = 2,085,065 (3.38%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.21 5'-3' bias = 1.9 >>>>>>> Junction analysis reads at junctions = 17,123,116 ACCT : 5.45% AGGT : 4.62% ATCT : 3.54% TCCT : 3.47% AGGA : 3.45% GCCT : 3.33% AGCT : 2.72% CCCT : 2.45% AGGC : 2.38% AGAT : 2.22% TTCT : 2.09%