RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354201.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) = 29,560,511 / 29,543,548 read pairs aligned = 29,540,619 total alignments = 62,870,923 secondary alignments = 3,766,864 non-unique alignments = 6,136,730 aligned to genes = 49,910,603 ambiguous alignments = 180,739 no feature assigned = 6,304,607 not aligned = 3,592,527 >>>>>>> Reads genomic origin exonic = 49,910,603 (88.78%) intronic = 4,244,244 (7.55%) intergenic = 2,060,363 (3.67%) overlapping exon = 1,752,121 (3.12%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.21 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 15,431,333 ACCT : 5.38% AGGT : 4.72% AGGA : 3.55% ATCT : 3.53% TCCT : 3.51% GCCT : 3.22% AGCT : 2.71% CCCT : 2.48% AGGC : 2.38% AGAT : 2.21% TTCT : 2.09%