RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354278.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) = 47,216,611 / 47,191,863 read pairs aligned = 47,179,225 total alignments = 101,573,965 secondary alignments = 7,165,491 non-unique alignments = 11,121,565 aligned to genes = 80,856,676 ambiguous alignments = 344,616 no feature assigned = 8,435,569 not aligned = 3,847,554 >>>>>>> Reads genomic origin exonic = 80,856,676 (90.55%) intronic = 5,166,134 (5.79%) intergenic = 3,269,435 (3.66%) overlapping exon = 3,864,103 (4.33%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.13 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 27,218,368 TCCT : 5.73% ACCT : 5.54% ATCT : 4.84% AGGT : 4.02% CCCT : 3.21% AGGA : 2.79% GCCT : 2.44% AGGC : 2.31% TCCC : 2.2% AGCT : 1.97% TTCT : 1.92%