RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354111.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) = 42,412,643 / 42,348,916 read pairs aligned = 42,330,798 total alignments = 89,880,843 secondary alignments = 5,119,284 non-unique alignments = 8,634,169 aligned to genes = 69,555,711 ambiguous alignments = 203,488 no feature assigned = 11,161,044 not aligned = 8,982,627 >>>>>>> Reads genomic origin exonic = 69,555,711 (86.17%) intronic = 7,213,353 (8.94%) intergenic = 3,947,691 (4.89%) overlapping exon = 3,015,251 (3.74%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.16 5'-3' bias = 2.09 >>>>>>> Junction analysis reads at junctions = 18,322,302 ACCT : 5.32% AGGT : 4.73% ATCT : 3.79% AGGA : 3.61% TCCT : 3.48% GCCT : 2.89% AGCT : 2.64% AGAT : 2.47% CCCT : 2.44% AGGC : 2.42% TTCT : 2.21%