RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354409.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) = 56,903,112 / 56,866,497 read pairs aligned = 56,861,803 total alignments = 122,002,576 secondary alignments = 8,232,967 non-unique alignments = 12,661,324 aligned to genes = 88,121,710 ambiguous alignments = 345,631 no feature assigned = 19,886,966 not aligned = 4,511,863 >>>>>>> Reads genomic origin exonic = 88,121,710 (81.59%) intronic = 13,946,910 (12.91%) intergenic = 5,940,056 (5.5%) overlapping exon = 3,942,835 (3.65%) >>>>>>> Transcript coverage profile 5' bias = 0.53 3' bias = 0.33 5'-3' bias = 1.65 >>>>>>> Junction analysis reads at junctions = 36,835,913 ACCT : 5.21% AGGT : 4.66% TCCT : 3.53% AGGA : 3.41% GCCT : 3.36% ATCT : 3.35% AGCT : 2.8% CCCT : 2.59% AGGC : 2.46% AGAT : 2.18% TTCT : 2.09%