RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354400.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) = 41,742,648 / 41,709,172 read pairs aligned = 41,684,098 total alignments = 89,817,040 secondary alignments = 6,365,220 non-unique alignments = 10,447,660 aligned to genes = 70,943,514 ambiguous alignments = 291,173 no feature assigned = 7,613,445 not aligned = 1,352,324 >>>>>>> Reads genomic origin exonic = 70,943,514 (90.31%) intronic = 4,472,544 (5.69%) intergenic = 3,140,901 (4%) overlapping exon = 3,352,922 (4.27%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.24 5'-3' bias = 2.03 >>>>>>> Junction analysis reads at junctions = 24,405,704 ACCT : 5.45% TCCT : 4.47% AGGT : 4.33% ATCT : 4.22% GCCT : 3.52% AGGA : 2.86% CCCT : 2.86% AGCT : 2.41% AGGC : 2.32% TTCT : 2.18% TCCC : 2.14%