RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354095.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) = 31,744,963 / 31,719,529 read pairs aligned = 31,716,232 total alignments = 67,734,611 secondary alignments = 4,270,119 non-unique alignments = 7,274,880 aligned to genes = 52,251,375 ambiguous alignments = 195,967 no feature assigned = 7,764,798 not aligned = 5,742,492 >>>>>>> Reads genomic origin exonic = 52,251,375 (87.06%) intronic = 4,626,728 (7.71%) intergenic = 3,138,070 (5.23%) overlapping exon = 2,006,490 (3.34%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.23 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 16,313,785 ACCT : 5.44% AGGT : 4.68% ATCT : 3.61% TCCT : 3.49% AGGA : 3.46% GCCT : 3.35% AGCT : 2.72% CCCT : 2.66% AGGC : 2.41% AGAT : 2.21% TTCT : 2.14%