RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354299.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) = 44,125,859 / 44,088,221 read pairs aligned = 44,083,363 total alignments = 93,816,858 secondary alignments = 5,602,778 non-unique alignments = 8,541,249 aligned to genes = 70,384,529 ambiguous alignments = 257,424 no feature assigned = 13,836,430 not aligned = 5,094,696 >>>>>>> Reads genomic origin exonic = 70,384,529 (83.57%) intronic = 8,783,178 (10.43%) intergenic = 5,053,252 (6%) overlapping exon = 3,431,241 (4.07%) >>>>>>> Transcript coverage profile 5' bias = 0.51 3' bias = 0.26 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 28,672,667 ACCT : 5.32% AGGT : 4.55% GCCT : 3.68% ATCT : 3.53% TCCT : 3.45% AGGA : 3.33% AGCT : 2.79% CCCT : 2.68% AGGC : 2.42% TTCT : 2.3% AGAT : 2.1%