RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354315.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) = 50,541,327 / 50,501,007 read pairs aligned = 50,496,485 total alignments = 107,373,695 secondary alignments = 6,331,361 non-unique alignments = 10,718,986 aligned to genes = 87,240,060 ambiguous alignments = 258,539 no feature assigned = 8,719,573 not aligned = 4,942,102 >>>>>>> Reads genomic origin exonic = 87,240,060 (90.91%) intronic = 4,484,289 (4.67%) intergenic = 4,235,284 (4.41%) overlapping exon = 3,319,745 (3.46%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.17 5'-3' bias = 1.9 >>>>>>> Junction analysis reads at junctions = 26,824,098 ACCT : 5.27% AGGT : 4.64% ATCT : 3.55% AGGA : 3.55% TCCT : 3.35% GCCT : 3.14% AGCT : 2.79% AGGC : 2.38% TTCT : 2.28% AGAT : 2.26% CCCT : 2.24%