RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354080.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) = 34,002,932 / 33,975,508 read pairs aligned = 33,968,964 total alignments = 72,131,249 secondary alignments = 4,152,809 non-unique alignments = 6,944,748 aligned to genes = 57,037,667 ambiguous alignments = 177,139 no feature assigned = 7,714,469 not aligned = 6,031,544 >>>>>>> Reads genomic origin exonic = 57,037,667 (88.09%) intronic = 5,294,726 (8.18%) intergenic = 2,419,743 (3.74%) overlapping exon = 2,261,035 (3.49%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.19 5'-3' bias = 1.79 >>>>>>> Junction analysis reads at junctions = 18,601,844 ACCT : 5.34% AGGT : 4.87% ATCT : 3.82% TCCT : 3.59% AGGA : 3.57% GCCT : 3.07% AGCT : 2.89% AGGC : 2.4% CCCT : 2.23% AGAT : 2.11% TTCT : 1.97%