RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354053.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) = 51,044,898 / 50,992,946 read pairs aligned = 50,983,671 total alignments = 108,609,243 secondary alignments = 6,571,399 non-unique alignments = 10,895,139 aligned to genes = 83,032,237 ambiguous alignments = 311,458 no feature assigned = 13,934,617 not aligned = 11,688,798 >>>>>>> Reads genomic origin exonic = 83,032,237 (85.63%) intronic = 9,417,872 (9.71%) intergenic = 4,516,745 (4.66%) overlapping exon = 3,492,583 (3.6%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.19 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 25,645,879 ACCT : 5.32% AGGT : 4.78% AGGA : 3.58% TCCT : 3.56% ATCT : 3.53% GCCT : 2.95% AGCT : 2.65% CCCT : 2.4% AGGC : 2.38% AGAT : 2.31% TTCT : 2.31%