RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354284.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) = 30,942,860 / 30,912,396 read pairs aligned = 30,903,913 total alignments = 65,593,417 secondary alignments = 3,738,161 non-unique alignments = 6,107,027 aligned to genes = 53,030,121 ambiguous alignments = 177,837 no feature assigned = 5,976,943 not aligned = 6,618,840 >>>>>>> Reads genomic origin exonic = 53,030,121 (89.87%) intronic = 3,390,613 (5.75%) intergenic = 2,586,330 (4.38%) overlapping exon = 2,033,187 (3.45%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.15 5'-3' bias = 2.28 >>>>>>> Junction analysis reads at junctions = 16,695,825 ACCT : 5.94% AGGT : 4.48% ATCT : 3.9% TCCT : 3.88% GCCT : 3.43% AGGA : 3.24% CCCT : 2.5% AGCT : 2.37% AGGC : 2.33% TTCT : 2.11% AGAT : 1.95%