RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354054.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) = 27,832,575 / 27,813,922 read pairs aligned = 27,810,680 total alignments = 58,945,548 secondary alignments = 3,299,051 non-unique alignments = 5,345,654 aligned to genes = 47,396,075 ambiguous alignments = 166,979 no feature assigned = 5,729,011 not aligned = 1,993,029 >>>>>>> Reads genomic origin exonic = 47,396,075 (89.22%) intronic = 3,666,499 (6.9%) intergenic = 2,062,512 (3.88%) overlapping exon = 1,909,329 (3.59%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.18 5'-3' bias = 2.2 >>>>>>> Junction analysis reads at junctions = 14,714,661 ACCT : 5.54% AGGT : 4.61% ATCT : 3.81% TCCT : 3.55% GCCT : 3.51% AGGA : 3.34% CCCT : 2.5% AGCT : 2.49% TTCT : 2.36% AGGC : 2.34% AGAT : 2.01%