RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354118.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) = 33,187,357 / 33,167,042 read pairs aligned = 33,164,393 total alignments = 70,848,116 secondary alignments = 4,493,717 non-unique alignments = 7,428,085 aligned to genes = 54,669,429 ambiguous alignments = 216,937 no feature assigned = 8,252,466 not aligned = 1,640,041 >>>>>>> Reads genomic origin exonic = 54,669,429 (86.88%) intronic = 5,905,560 (9.39%) intergenic = 2,346,906 (3.73%) overlapping exon = 2,070,199 (3.29%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.19 5'-3' bias = 2.1 >>>>>>> Junction analysis reads at junctions = 18,586,162 ACCT : 5.22% AGGT : 4.64% ATCT : 3.73% TCCT : 3.55% AGGA : 3.55% GCCT : 3.19% AGCT : 2.69% CCCT : 2.44% AGGC : 2.42% AGAT : 2.29% TTCT : 2.14%