RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354235.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) = 44,093,041 / 44,050,564 read pairs aligned = 44,021,315 total alignments = 95,133,010 secondary alignments = 6,989,405 non-unique alignments = 11,001,785 aligned to genes = 73,772,847 ambiguous alignments = 305,748 no feature assigned = 9,195,992 not aligned = 2,631,765 >>>>>>> Reads genomic origin exonic = 73,772,847 (88.92%) intronic = 6,043,231 (7.28%) intergenic = 3,152,761 (3.8%) overlapping exon = 3,703,126 (4.46%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.29 5'-3' bias = 1.64 >>>>>>> Junction analysis reads at junctions = 25,856,141 ACCT : 5.52% AGGT : 4.55% TCCT : 3.87% ATCT : 3.8% GCCT : 3.69% AGGA : 3.05% CCCT : 2.78% AGCT : 2.64% AGGC : 2.37% TTCT : 2.29% AGAT : 1.8%