RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354288.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) = 52,671,655 / 52,643,361 read pairs aligned = 52,631,448 total alignments = 113,282,305 secondary alignments = 7,967,289 non-unique alignments = 12,852,428 aligned to genes = 91,808,008 ambiguous alignments = 345,344 no feature assigned = 7,477,225 not aligned = 3,291,346 >>>>>>> Reads genomic origin exonic = 91,808,008 (92.47%) intronic = 4,544,381 (4.58%) intergenic = 2,932,844 (2.95%) overlapping exon = 4,240,469 (4.27%) >>>>>>> Transcript coverage profile 5' bias = 0.11 3' bias = 0.15 5'-3' bias = 1.86 >>>>>>> Junction analysis reads at junctions = 29,203,516 ACCT : 5.58% ATCT : 4.78% TCCT : 4.76% AGGT : 4.28% CCCT : 2.89% AGGA : 2.8% GCCT : 2.74% AGGC : 2.4% TCCC : 2.34% AGCT : 2% CGTA : 1.95%