RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354084.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) = 34,617,799 / 34,576,411 read pairs aligned = 34,570,775 total alignments = 73,699,286 secondary alignments = 4,505,076 non-unique alignments = 7,243,392 aligned to genes = 56,955,623 ambiguous alignments = 175,224 no feature assigned = 8,864,079 not aligned = 6,384,848 >>>>>>> Reads genomic origin exonic = 56,955,623 (86.53%) intronic = 5,356,399 (8.14%) intergenic = 3,507,680 (5.33%) overlapping exon = 2,413,800 (3.67%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.27 5'-3' bias = 1.61 >>>>>>> Junction analysis reads at junctions = 21,066,559 ACCT : 5.01% AGGT : 5% TCCT : 3.73% AGGA : 3.7% ATCT : 3.64% AGCT : 3.08% GCCT : 2.62% AGGC : 2.51% CCCT : 2.33% AGAT : 2.1% TTCT : 1.97%