RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354070.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) = 39,418,647 / 39,398,841 read pairs aligned = 39,395,911 total alignments = 84,010,913 secondary alignments = 5,193,425 non-unique alignments = 8,613,591 aligned to genes = 66,857,187 ambiguous alignments = 261,619 no feature assigned = 7,946,159 not aligned = 3,207,988 >>>>>>> Reads genomic origin exonic = 66,857,187 (89.38%) intronic = 5,374,878 (7.19%) intergenic = 2,571,281 (3.44%) overlapping exon = 2,255,456 (3.02%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.21 5'-3' bias = 1.77 >>>>>>> Junction analysis reads at junctions = 22,476,620 ACCT : 5.43% AGGT : 4.65% ATCT : 3.63% TCCT : 3.62% AGGA : 3.41% GCCT : 3.28% AGCT : 2.7% CCCT : 2.49% AGGC : 2.36% AGAT : 2.13% TTCT : 2.1%