RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354412.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) = 53,141,033 / 53,105,945 read pairs aligned = 53,099,626 total alignments = 113,660,721 secondary alignments = 7,413,743 non-unique alignments = 12,252,572 aligned to genes = 87,299,418 ambiguous alignments = 326,254 no feature assigned = 13,220,336 not aligned = 10,103,186 >>>>>>> Reads genomic origin exonic = 87,299,418 (86.85%) intronic = 8,752,604 (8.71%) intergenic = 4,467,732 (4.44%) overlapping exon = 3,501,089 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.19 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 29,198,266 ACCT : 5.44% AGGT : 4.66% ATCT : 3.66% TCCT : 3.54% AGGA : 3.52% GCCT : 3.25% AGCT : 2.63% CCCT : 2.5% AGGC : 2.38% AGAT : 2.28% TTCT : 2.28%