RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354224.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) = 47,798,095 / 47,763,019 read pairs aligned = 47,740,269 total alignments = 102,482,624 secondary alignments = 6,921,510 non-unique alignments = 11,496,742 aligned to genes = 79,276,531 ambiguous alignments = 295,038 no feature assigned = 10,879,073 not aligned = 1,311,686 >>>>>>> Reads genomic origin exonic = 79,276,531 (87.93%) intronic = 8,138,793 (9.03%) intergenic = 2,740,280 (3.04%) overlapping exon = 3,862,876 (4.28%) >>>>>>> Transcript coverage profile 5' bias = 0.53 3' bias = 0.19 5'-3' bias = 2.1 >>>>>>> Junction analysis reads at junctions = 31,681,594 ACCT : 5.15% AGGT : 4.85% AGGA : 3.57% ATCT : 3.35% TCCT : 3.27% AGCT : 2.87% GCCT : 2.82% AGGC : 2.47% CCCT : 2.44% AGAT : 2.2% TTCT : 2.13%