RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354408.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) = 35,615,661 / 35,584,685 read pairs aligned = 35,581,893 total alignments = 75,220,298 secondary alignments = 4,019,952 non-unique alignments = 6,836,677 aligned to genes = 59,595,720 ambiguous alignments = 198,524 no feature assigned = 8,359,462 not aligned = 4,317,470 >>>>>>> Reads genomic origin exonic = 59,595,720 (87.7%) intronic = 5,676,197 (8.35%) intergenic = 2,683,265 (3.95%) overlapping exon = 2,278,206 (3.35%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.18 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 19,615,740 ACCT : 5.52% AGGT : 4.69% ATCT : 3.56% AGGA : 3.51% TCCT : 3.4% GCCT : 3.28% AGCT : 2.72% AGGC : 2.41% AGAT : 2.35% CCCT : 2.33% TTCT : 2.26%