RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354062.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) = 35,100,543 / 35,078,030 read pairs aligned = 35,074,928 total alignments = 74,441,056 secondary alignments = 4,262,483 non-unique alignments = 7,147,751 aligned to genes = 58,572,335 ambiguous alignments = 206,695 no feature assigned = 8,265,005 not aligned = 3,702,861 >>>>>>> Reads genomic origin exonic = 58,572,335 (87.63%) intronic = 5,749,844 (8.6%) intergenic = 2,515,161 (3.76%) overlapping exon = 2,197,145 (3.29%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.17 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 18,437,877 ACCT : 5.33% AGGT : 4.78% ATCT : 3.64% AGGA : 3.62% TCCT : 3.43% GCCT : 2.86% AGCT : 2.7% TTCT : 2.66% AGAT : 2.39% AGGC : 2.34% CCCT : 2.29%