RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354126.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) = 51,731,630 / 51,676,716 read pairs aligned = 51,656,280 total alignments = 114,520,880 secondary alignments = 11,112,534 non-unique alignments = 14,284,182 aligned to genes = 85,322,404 ambiguous alignments = 262,254 no feature assigned = 11,895,006 not aligned = 2,441,810 >>>>>>> Reads genomic origin exonic = 85,322,404 (87.76%) intronic = 8,234,434 (8.47%) intergenic = 3,660,572 (3.77%) overlapping exon = 3,855,580 (3.97%) >>>>>>> Transcript coverage profile 5' bias = 0.47 3' bias = 0.22 5'-3' bias = 1.73 >>>>>>> Junction analysis reads at junctions = 28,099,849 ACCT : 4.88% AGGT : 4.83% ATCT : 3.66% AGGA : 3.59% TCCT : 3.58% GCCT : 3.09% AGCT : 3.01% CCCT : 2.59% AGGC : 2.41% TTCT : 2.14% AGAT : 2.1%