RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354177.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) = 85,815,572 / 85,668,977 read pairs aligned = 85,661,074 total alignments = 182,304,534 secondary alignments = 10,819,985 non-unique alignments = 15,660,330 aligned to genes = 135,504,293 ambiguous alignments = 482,450 no feature assigned = 28,797,845 not aligned = 6,300,089 >>>>>>> Reads genomic origin exonic = 135,504,293 (82.47%) intronic = 20,074,711 (12.22%) intergenic = 8,723,134 (5.31%) overlapping exon = 7,551,578 (4.6%) >>>>>>> Transcript coverage profile 5' bias = 0.57 3' bias = 0.19 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 63,886,526 ACCT : 5.32% AGGT : 4.72% GCCT : 3.57% AGGA : 3.56% TCCT : 3.39% ATCT : 3.37% AGCT : 2.91% CCCT : 2.56% AGGC : 2.43% AGAT : 2.3% TTCT : 2.22%