RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354363.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) = 34,741,126 / 34,709,660 read pairs aligned = 34,704,178 total alignments = 74,030,807 secondary alignments = 4,580,021 non-unique alignments = 7,514,933 aligned to genes = 57,238,542 ambiguous alignments = 191,903 no feature assigned = 8,707,180 not aligned = 4,389,570 >>>>>>> Reads genomic origin exonic = 57,238,542 (86.8%) intronic = 5,554,891 (8.42%) intergenic = 3,152,289 (4.78%) overlapping exon = 2,179,623 (3.31%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.2 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 16,977,865 ACCT : 5.57% AGGT : 4.66% ATCT : 3.56% AGGA : 3.53% TCCT : 3.42% GCCT : 3.34% AGCT : 2.67% CCCT : 2.48% AGGC : 2.34% AGAT : 2.23% TTCT : 2.14%