RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354079.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) = 50,951,465 / 50,874,826 read pairs aligned = 50,867,287 total alignments = 110,182,154 secondary alignments = 8,355,863 non-unique alignments = 14,510,627 aligned to genes = 83,973,803 ambiguous alignments = 284,278 no feature assigned = 10,995,644 not aligned = 11,835,941 >>>>>>> Reads genomic origin exonic = 83,973,803 (88.42%) intronic = 6,604,481 (6.95%) intergenic = 4,391,163 (4.62%) overlapping exon = 3,995,089 (4.21%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.24 5'-3' bias = 1.78 >>>>>>> Junction analysis reads at junctions = 27,214,838 ACCT : 5.45% AGGT : 4.49% GCCT : 3.65% ATCT : 3.64% TCCT : 3.41% AGGA : 3.31% AGCT : 2.68% TTCT : 2.51% CCCT : 2.49% AGGC : 2.35% AGAT : 2.1%