RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354407.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) = 52,372,451 / 52,318,207 read pairs aligned = 52,310,149 total alignments = 111,082,708 secondary alignments = 6,392,050 non-unique alignments = 10,618,652 aligned to genes = 87,946,642 ambiguous alignments = 342,128 no feature assigned = 11,752,448 not aligned = 8,777,822 >>>>>>> Reads genomic origin exonic = 87,946,642 (88.21%) intronic = 8,038,926 (8.06%) intergenic = 3,713,522 (3.72%) overlapping exon = 3,548,548 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.18 5'-3' bias = 1.88 >>>>>>> Junction analysis reads at junctions = 31,453,401 ACCT : 5.34% AGGT : 4.74% AGGA : 3.58% ATCT : 3.52% TCCT : 3.39% GCCT : 3.05% AGCT : 2.78% AGGC : 2.39% CCCT : 2.3% AGAT : 2.26% TTCT : 2.19%