RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354116.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) = 62,220,897 / 62,153,948 read pairs aligned = 62,128,381 total alignments = 132,928,405 secondary alignments = 8,553,560 non-unique alignments = 14,003,856 aligned to genes = 102,131,318 ambiguous alignments = 380,936 no feature assigned = 15,642,160 not aligned = 2,091,043 >>>>>>> Reads genomic origin exonic = 102,131,318 (86.72%) intronic = 11,342,494 (9.63%) intergenic = 4,299,666 (3.65%) overlapping exon = 5,197,728 (4.41%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.21 5'-3' bias = 1.86 >>>>>>> Junction analysis reads at junctions = 37,027,422 ACCT : 5.33% AGGT : 4.74% ATCT : 3.65% AGGA : 3.54% TCCT : 3.48% GCCT : 3.34% AGCT : 2.64% CCCT : 2.62% AGGC : 2.39% AGAT : 2.26% TTCT : 2.12%