RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354316.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) = 54,714,946 / 54,636,432 read pairs aligned = 54,618,939 total alignments = 116,346,291 secondary alignments = 6,994,913 non-unique alignments = 11,921,690 aligned to genes = 87,826,865 ambiguous alignments = 272,270 no feature assigned = 15,967,534 not aligned = 7,905,778 >>>>>>> Reads genomic origin exonic = 87,826,865 (84.62%) intronic = 11,152,896 (10.75%) intergenic = 4,814,638 (4.64%) overlapping exon = 4,273,996 (4.12%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.14 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 25,961,223 ACCT : 5.15% AGGT : 4.7% ATCT : 3.72% AGGA : 3.7% TCCT : 3.27% GCCT : 3.07% AGCT : 2.77% AGAT : 2.48% AGGC : 2.38% CCCT : 2.37% TTCT : 2.25%