RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354390.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) = 40,458,251 / 40,410,282 read pairs aligned = 40,404,029 total alignments = 85,794,485 secondary alignments = 4,925,952 non-unique alignments = 8,237,868 aligned to genes = 67,759,453 ambiguous alignments = 245,849 no feature assigned = 9,227,744 not aligned = 9,399,283 >>>>>>> Reads genomic origin exonic = 67,759,453 (88.01%) intronic = 5,797,112 (7.53%) intergenic = 3,430,632 (4.46%) overlapping exon = 2,845,314 (3.7%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.21 5'-3' bias = 1.8 >>>>>>> Junction analysis reads at junctions = 22,723,999 ACCT : 5.43% AGGT : 4.59% ATCT : 3.5% AGGA : 3.43% TCCT : 3.43% GCCT : 3.36% AGCT : 2.75% CCCT : 2.43% AGGC : 2.4% AGAT : 2.29% TTCT : 2.15%