RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354320.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) = 30,429,675 / 30,410,992 read pairs aligned = 30,406,980 total alignments = 64,907,002 secondary alignments = 4,066,335 non-unique alignments = 6,801,018 aligned to genes = 50,778,741 ambiguous alignments = 169,429 no feature assigned = 6,879,064 not aligned = 2,218,915 >>>>>>> Reads genomic origin exonic = 50,778,741 (88.07%) intronic = 4,870,302 (8.45%) intergenic = 2,008,762 (3.48%) overlapping exon = 1,891,562 (3.28%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.21 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 17,660,136 ACCT : 5.16% AGGT : 4.96% ATCT : 3.77% AGGA : 3.73% TCCT : 3.55% AGCT : 2.84% GCCT : 2.83% AGGC : 2.4% CCCT : 2.3% AGAT : 2.25% TTCT : 2.05%