RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354163.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) = 43,943,341 / 43,912,079 read pairs aligned = 43,908,556 total alignments = 94,359,579 secondary alignments = 6,504,159 non-unique alignments = 10,156,518 aligned to genes = 72,638,903 ambiguous alignments = 235,389 no feature assigned = 10,570,707 not aligned = 2,723,408 >>>>>>> Reads genomic origin exonic = 72,638,903 (87.3%) intronic = 6,723,580 (8.08%) intergenic = 3,847,127 (4.62%) overlapping exon = 2,866,888 (3.45%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.2 5'-3' bias = 1.79 >>>>>>> Junction analysis reads at junctions = 21,157,869 ACCT : 5.38% AGGT : 4.54% ATCT : 3.57% TCCT : 3.43% GCCT : 3.41% AGGA : 3.4% AGCT : 2.72% CCCT : 2.47% AGGC : 2.42% TTCT : 2.36% AGAT : 2.16%