RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354221.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) = 36,503,748 / 36,481,069 read pairs aligned = 36,477,526 total alignments = 77,082,466 secondary alignments = 4,097,649 non-unique alignments = 6,695,566 aligned to genes = 60,699,706 ambiguous alignments = 223,256 no feature assigned = 9,153,955 not aligned = 3,474,061 >>>>>>> Reads genomic origin exonic = 60,699,706 (86.9%) intronic = 6,317,388 (9.04%) intergenic = 2,836,567 (4.06%) overlapping exon = 2,454,342 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.18 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 19,739,845 ACCT : 5.43% AGGT : 4.8% AGGA : 3.59% ATCT : 3.55% TCCT : 3.37% GCCT : 3.06% AGCT : 2.78% AGGC : 2.44% CCCT : 2.35% AGAT : 2.29% TTCT : 2.27%