RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354138.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) = 43,715,050 / 43,665,052 read pairs aligned = 43,646,149 total alignments = 94,560,051 secondary alignments = 7,179,949 non-unique alignments = 11,098,380 aligned to genes = 71,866,756 ambiguous alignments = 327,264 no feature assigned = 10,319,834 not aligned = 2,527,784 >>>>>>> Reads genomic origin exonic = 71,866,756 (87.44%) intronic = 7,595,518 (9.24%) intergenic = 2,724,316 (3.31%) overlapping exon = 3,765,337 (4.58%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.22 5'-3' bias = 1.84 >>>>>>> Junction analysis reads at junctions = 30,056,330 ACCT : 5.3% AGGT : 4.76% TCCT : 3.56% ATCT : 3.56% AGGA : 3.34% GCCT : 3.2% AGCT : 2.78% CCCT : 2.71% AGGC : 2.45% TTCT : 2.06% AGAT : 2.03%