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) = 23,011,732 / 22,733,617 read pairs aligned = 20,735,972 total alignments = 48,635,772 secondary alignments = 2,890,423 non-unique alignments = 4,601,142 aligned to genes = 39,103,662 ambiguous alignments = 352,759 no feature assigned = 4,577,916 not aligned = 1,808,371 SSP estimation (fwd/rev) = 0.5 / 0.5 >>>>>>> Reads genomic origin exonic = 39,103,662 (89.52%) intronic = 3,240,596 (7.42%) intergenic = 1,337,320 (3.06%) overlapping exon = 971,103 (2.22%) >>>>>>> Transcript coverage profile 5' bias = 0.64 3' bias = 0.24 5'-3' bias = 1.61 >>>>>>> Junction analysis reads at junctions = 24,666,458 AGGT : 4.53% ACCT : 4.4% AGGA : 3.64% AGGG : 3.01% TCCT : 2.94% AGCT : 2.86% CCCT : 2.68% AGAT : 2.59% AGAA : 2.5% ATCT : 2.41% AGGC : 2.39%