RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354078.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) = 41,877,628 / 41,860,470 read pairs aligned = 41,849,209 total alignments = 89,570,424 secondary alignments = 5,832,326 non-unique alignments = 9,407,928 aligned to genes = 71,624,947 ambiguous alignments = 239,266 no feature assigned = 7,744,382 not aligned = 2,623,862 >>>>>>> Reads genomic origin exonic = 71,624,947 (90.24%) intronic = 4,815,318 (6.07%) intergenic = 2,929,064 (3.69%) overlapping exon = 2,970,831 (3.74%) >>>>>>> Transcript coverage profile 5' bias = 0.21 3' bias = 0.17 5'-3' bias = 2.04 >>>>>>> Junction analysis reads at junctions = 22,607,454 ACCT : 5.51% ATCT : 4.43% AGGT : 4.4% TCCT : 4.01% GCCT : 3.44% AGGA : 3.14% CCCT : 2.67% AGCT : 2.26% AGGC : 2.18% TTCT : 2.1% TCCC : 2.03%