RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354373.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) = 44,530,709 / 44,460,156 read pairs aligned = 44,455,117 total alignments = 95,735,349 secondary alignments = 6,744,484 non-unique alignments = 10,579,769 aligned to genes = 71,136,528 ambiguous alignments = 262,281 no feature assigned = 12,978,644 not aligned = 7,438,063 >>>>>>> Reads genomic origin exonic = 71,136,528 (84.57%) intronic = 7,488,293 (8.9%) intergenic = 5,490,351 (6.53%) overlapping exon = 2,904,588 (3.45%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.37 5'-3' bias = 1.67 >>>>>>> Junction analysis reads at junctions = 26,188,065 ACCT : 5.31% AGGT : 4.5% TCCT : 3.96% ATCT : 3.64% GCCT : 3.35% AGGA : 3.28% CCCT : 2.79% AGCT : 2.68% AGGC : 2.38% TTCT : 2.15% AGAT : 1.99%