RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354329.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) = 31,873,611 / 31,832,867 read pairs aligned = 31,828,146 total alignments = 67,833,400 secondary alignments = 4,126,922 non-unique alignments = 6,949,009 aligned to genes = 53,035,953 ambiguous alignments = 164,404 no feature assigned = 7,415,634 not aligned = 14,819,606 >>>>>>> Reads genomic origin exonic = 53,035,953 (87.73%) intronic = 4,349,125 (7.19%) intergenic = 3,066,509 (5.07%) overlapping exon = 1,909,839 (3.16%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.16 5'-3' bias = 2.4 >>>>>>> Junction analysis reads at junctions = 16,301,757 ACCT : 5.32% AGGT : 4.78% ATCT : 3.79% AGGA : 3.68% TCCT : 3.41% GCCT : 2.97% AGCT : 2.71% CCCT : 2.45% AGGC : 2.4% AGAT : 2.35% TTCT : 2.22%