RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354266.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) = 28,143,212 / 28,129,061 read pairs aligned = 28,127,383 total alignments = 59,965,308 secondary alignments = 3,693,035 non-unique alignments = 6,163,320 aligned to genes = 46,711,974 ambiguous alignments = 157,367 no feature assigned = 6,676,428 not aligned = 1,250,291 >>>>>>> Reads genomic origin exonic = 46,711,974 (87.49%) intronic = 4,314,540 (8.08%) intergenic = 2,361,888 (4.42%) overlapping exon = 1,784,953 (3.34%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.2 5'-3' bias = 2.04 >>>>>>> Junction analysis reads at junctions = 14,102,502 ACCT : 5.3% AGGT : 4.85% AGGA : 3.7% ATCT : 3.59% TCCT : 3.38% GCCT : 2.89% AGCT : 2.8% AGAT : 2.43% CCCT : 2.41% AGGC : 2.39% TTCT : 2.2%