RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354115.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) = 29,838,298 / 29,818,055 read pairs aligned = 29,814,529 total alignments = 63,476,624 secondary alignments = 3,820,271 non-unique alignments = 6,156,535 aligned to genes = 47,510,332 ambiguous alignments = 198,770 no feature assigned = 9,281,809 not aligned = 3,143,329 >>>>>>> Reads genomic origin exonic = 47,510,332 (83.66%) intronic = 6,498,077 (11.44%) intergenic = 2,783,732 (4.9%) overlapping exon = 2,202,608 (3.88%) >>>>>>> Transcript coverage profile 5' bias = 0.54 3' bias = 0.29 5'-3' bias = 1.78 >>>>>>> Junction analysis reads at junctions = 18,577,065 ACCT : 5.09% AGGT : 4.78% AGGA : 3.48% TCCT : 3.43% ATCT : 3.33% GCCT : 3.13% AGCT : 2.83% CCCT : 2.55% AGGC : 2.42% TTCT : 2.21% AGAT : 2.19%