RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354260.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) = 51,903,999 / 51,867,385 read pairs aligned = 51,855,078 total alignments = 109,821,579 secondary alignments = 6,050,195 non-unique alignments = 10,073,428 aligned to genes = 85,488,259 ambiguous alignments = 262,474 no feature assigned = 13,528,892 not aligned = 5,658,446 >>>>>>> Reads genomic origin exonic = 85,488,259 (86.34%) intronic = 9,367,011 (9.46%) intergenic = 4,161,881 (4.2%) overlapping exon = 4,194,168 (4.24%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.16 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 27,726,423 ACCT : 5.55% AGGT : 4.67% ATCT : 3.55% AGGA : 3.53% GCCT : 3.25% TCCT : 3.21% AGCT : 2.78% AGAT : 2.39% AGGC : 2.39% CCCT : 2.29% TTCT : 2.18%