RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = /dev/stdin gff file = /home/bayegy/Databases/transcriptome/references/mmu/GCF_000001635.27_GRCm39_genomic.gtf counting algorithm = uniquely-mapped-reads protocol = non-strand-specific 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 22,924,073 / 22,929,526 read pairs aligned = 21,068,745 total alignments = 54,245,244 secondary alignments = 8,391,645 non-unique alignments = 11,855,082 aligned to genes = 37,238,999 ambiguous alignments = 295,437 no feature assigned = 4,855,627 not aligned = 1,245,497 SSP estimation (fwd/rev) = 0.5 / 0.5 >>>>>>> Reads genomic origin exonic = 37,238,999 (88.46%) intronic = 2,327,913 (5.53%) intergenic = 2,527,714 (6%) overlapping exon = 825,965 (1.96%) >>>>>>> Transcript coverage profile 5' bias = 0.63 3' bias = 0.31 5'-3' bias = 1.46 >>>>>>> Junction analysis reads at junctions = 25,800,335 ACCT : 4.57% AGGT : 4.22% ATCT : 3.48% AGCT : 3.44% TCCT : 3.29% AGGG : 3.24% AGGC : 3.14% GCCT : 3.02% AGGA : 2.97% CCCT : 2.28% AGAT : 2.09%