RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354113.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) = 37,921,046 / 37,905,083 read pairs aligned = 37,901,715 total alignments = 80,826,523 secondary alignments = 5,000,394 non-unique alignments = 7,909,621 aligned to genes = 63,052,001 ambiguous alignments = 210,791 no feature assigned = 9,131,213 not aligned = 1,786,247 >>>>>>> Reads genomic origin exonic = 63,052,001 (87.35%) intronic = 6,706,362 (9.29%) intergenic = 2,424,851 (3.36%) overlapping exon = 2,277,998 (3.16%) >>>>>>> Transcript coverage profile 5' bias = 0.46 3' bias = 0.19 5'-3' bias = 2.09 >>>>>>> Junction analysis reads at junctions = 21,316,452 ACCT : 5.58% AGGT : 4.68% ATCT : 3.51% AGGA : 3.46% TCCT : 3.22% GCCT : 3.22% AGCT : 2.79% CCCT : 2.45% AGGC : 2.41% AGAT : 2.36% TTCT : 2.1%