RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354352.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) = 44,298,364 / 44,234,181 read pairs aligned = 44,223,683 total alignments = 95,914,859 secondary alignments = 7,382,314 non-unique alignments = 12,667,803 aligned to genes = 73,658,809 ambiguous alignments = 287,580 no feature assigned = 8,925,165 not aligned = 3,816,697 >>>>>>> Reads genomic origin exonic = 73,658,809 (89.19%) intronic = 5,536,302 (6.7%) intergenic = 3,388,863 (4.1%) overlapping exon = 3,360,899 (4.07%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.23 5'-3' bias = 1.78 >>>>>>> Junction analysis reads at junctions = 22,470,791 ACCT : 5.17% AGGT : 4.54% TCCT : 4.04% ATCT : 3.93% GCCT : 3.35% AGGA : 3.26% CCCT : 2.84% AGCT : 2.49% AGGC : 2.34% TTCT : 2.21% AGAT : 1.86%