RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354252.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) = 35,471,962 / 35,452,961 read pairs aligned = 35,448,832 total alignments = 75,473,531 secondary alignments = 4,548,608 non-unique alignments = 6,852,702 aligned to genes = 59,821,288 ambiguous alignments = 230,140 no feature assigned = 7,929,610 not aligned = 1,912,663 >>>>>>> Reads genomic origin exonic = 59,821,288 (88.3%) intronic = 5,414,463 (7.99%) intergenic = 2,515,147 (3.71%) overlapping exon = 2,360,782 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.19 5'-3' bias = 2.04 >>>>>>> Junction analysis reads at junctions = 21,408,486 ACCT : 5.57% AGGT : 4.71% ATCT : 3.55% AGGA : 3.5% TCCT : 3.47% GCCT : 3.32% AGCT : 2.63% CCCT : 2.37% AGGC : 2.37% AGAT : 2.17% TTCT : 2.16%