RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354269.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) = 34,884,078 / 34,870,025 read pairs aligned = 34,866,999 total alignments = 74,741,199 secondary alignments = 4,987,096 non-unique alignments = 7,684,640 aligned to genes = 57,287,424 ambiguous alignments = 199,215 no feature assigned = 8,863,934 not aligned = 1,688,861 >>>>>>> Reads genomic origin exonic = 57,287,424 (86.6%) intronic = 4,992,328 (7.55%) intergenic = 3,871,606 (5.85%) overlapping exon = 2,251,901 (3.4%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.27 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 18,958,295 AGGT : 4.99% ACCT : 4.98% AGGA : 3.6% TCCT : 3.4% ATCT : 3.32% GCCT : 2.88% AGCT : 2.85% AGGC : 2.51% CCCT : 2.45% AGAT : 2.17% TTCT : 2.05%