RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354129.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) = 37,846,508 / 37,803,185 read pairs aligned = 37,797,570 total alignments = 81,001,076 secondary alignments = 5,351,383 non-unique alignments = 8,965,612 aligned to genes = 61,492,000 ambiguous alignments = 187,081 no feature assigned = 9,965,995 not aligned = 5,564,533 >>>>>>> Reads genomic origin exonic = 61,492,000 (86.05%) intronic = 7,076,652 (9.9%) intergenic = 2,889,343 (4.04%) overlapping exon = 3,149,678 (4.41%) >>>>>>> Transcript coverage profile 5' bias = 0.44 3' bias = 0.18 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 21,948,690 ACCT : 5.07% AGGT : 4.74% ATCT : 3.84% TCCT : 3.7% AGGA : 3.53% AGCT : 2.86% GCCT : 2.78% AGGC : 2.44% CCCT : 2.24% TTCT : 2.21% AGAT : 2.17%