RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354216.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) = 51,764,901 / 51,736,782 read pairs aligned = 51,731,811 total alignments = 109,966,485 secondary alignments = 6,464,802 non-unique alignments = 10,731,538 aligned to genes = 85,062,383 ambiguous alignments = 252,777 no feature assigned = 13,403,655 not aligned = 5,357,543 >>>>>>> Reads genomic origin exonic = 85,062,383 (86.39%) intronic = 8,339,899 (8.47%) intergenic = 5,063,756 (5.14%) overlapping exon = 3,572,316 (3.63%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.2 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 23,881,708 ACCT : 5.38% AGGT : 4.78% AGGA : 3.65% ATCT : 3.51% TCCT : 3.47% GCCT : 2.98% AGCT : 2.72% CCCT : 2.39% AGGC : 2.39% AGAT : 2.35% TTCT : 2.12%