RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354339.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) = 32,049,898 / 32,028,457 read pairs aligned = 32,025,030 total alignments = 68,888,402 secondary alignments = 4,810,047 non-unique alignments = 8,288,904 aligned to genes = 53,790,206 ambiguous alignments = 207,994 no feature assigned = 6,377,061 not aligned = 7,175,313 >>>>>>> Reads genomic origin exonic = 53,790,206 (89.4%) intronic = 4,193,484 (6.97%) intergenic = 2,183,577 (3.63%) overlapping exon = 2,130,412 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.17 5'-3' bias = 2.39 >>>>>>> Junction analysis reads at junctions = 18,463,519 ACCT : 5.49% AGGT : 4.67% ATCT : 3.61% AGGA : 3.51% TCCT : 3.48% GCCT : 3.25% AGCT : 2.62% CCCT : 2.42% AGGC : 2.33% AGAT : 2.19% TTCT : 2.11%