RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354303.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) = 42,000,040 / 41,954,258 read pairs aligned = 41,940,916 total alignments = 89,624,275 secondary alignments = 5,669,977 non-unique alignments = 9,610,238 aligned to genes = 68,407,200 ambiguous alignments = 188,504 no feature assigned = 11,047,995 not aligned = 6,313,842 >>>>>>> Reads genomic origin exonic = 68,407,200 (86.1%) intronic = 7,050,414 (8.87%) intergenic = 3,997,581 (5.03%) overlapping exon = 3,161,492 (3.98%) >>>>>>> Transcript coverage profile 5' bias = 0.19 3' bias = 0.12 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 18,033,825 ACCT : 5.13% AGGT : 4.71% AGGA : 3.84% ATCT : 3.64% TCCT : 3.31% GCCT : 2.89% AGCT : 2.79% AGAT : 2.54% AGGC : 2.35% CCCT : 2.3% TTCT : 2.28%