RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354206.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) = 48,798,369 / 48,759,299 read pairs aligned = 48,753,247 total alignments = 103,147,508 secondary alignments = 5,589,840 non-unique alignments = 9,139,498 aligned to genes = 81,187,506 ambiguous alignments = 236,505 no feature assigned = 12,088,249 not aligned = 5,523,314 >>>>>>> Reads genomic origin exonic = 81,187,506 (87.04%) intronic = 7,517,512 (8.06%) intergenic = 4,570,737 (4.9%) overlapping exon = 3,503,395 (3.76%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.16 5'-3' bias = 1.97 >>>>>>> Junction analysis reads at junctions = 24,540,697 ACCT : 5.41% AGGT : 4.95% AGGA : 3.73% ATCT : 3.62% TCCT : 3.47% GCCT : 2.96% AGCT : 2.74% AGGC : 2.5% CCCT : 2.37% AGAT : 2.33% TTCT : 2.2%