RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354325.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) = 59,848,435 / 59,804,695 read pairs aligned = 59,794,158 total alignments = 129,845,037 secondary alignments = 10,191,907 non-unique alignments = 15,790,042 aligned to genes = 100,950,740 ambiguous alignments = 414,973 no feature assigned = 11,588,553 not aligned = 7,798,324 >>>>>>> Reads genomic origin exonic = 100,950,740 (89.7%) intronic = 6,257,046 (5.56%) intergenic = 5,331,507 (4.74%) overlapping exon = 4,848,282 (4.31%) >>>>>>> Transcript coverage profile 5' bias = 0.05 3' bias = 0.07 5'-3' bias = 2.8 >>>>>>> Junction analysis reads at junctions = 32,715,761 TCCT : 5.61% ACCT : 4.9% AGGT : 4.37% ATCT : 4.18% CCCT : 3.93% AGGA : 3.29% AGGC : 2.08% TGCT : 1.98% AGAC : 1.93% AGCT : 1.83% GTCT : 1.83%