RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354377.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) = 30,554,420 / 30,538,403 read pairs aligned = 30,535,503 total alignments = 64,933,637 secondary alignments = 3,840,814 non-unique alignments = 6,333,335 aligned to genes = 50,371,200 ambiguous alignments = 183,892 no feature assigned = 7,778,469 not aligned = 1,655,197 >>>>>>> Reads genomic origin exonic = 50,371,200 (86.62%) intronic = 5,613,385 (9.65%) intergenic = 2,165,084 (3.72%) overlapping exon = 1,936,644 (3.33%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.19 5'-3' bias = 2.01 >>>>>>> Junction analysis reads at junctions = 16,041,365 ACCT : 5.33% AGGT : 4.68% ATCT : 3.58% AGGA : 3.56% TCCT : 3.4% GCCT : 3.24% AGCT : 2.75% CCCT : 2.41% AGGC : 2.37% AGAT : 2.29% TTCT : 2.17%