RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354103.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) = 37,170,068 / 37,146,201 read pairs aligned = 37,143,179 total alignments = 79,857,218 secondary alignments = 5,540,949 non-unique alignments = 9,187,419 aligned to genes = 60,000,519 ambiguous alignments = 203,725 no feature assigned = 10,046,243 not aligned = 2,332,131 >>>>>>> Reads genomic origin exonic = 60,000,519 (85.66%) intronic = 7,126,699 (10.17%) intergenic = 2,919,544 (4.17%) overlapping exon = 2,252,447 (3.22%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.18 5'-3' bias = 2.3 >>>>>>> Junction analysis reads at junctions = 17,992,106 ACCT : 5.27% AGGT : 4.7% ATCT : 3.76% AGGA : 3.59% TCCT : 3.52% GCCT : 3.03% AGCT : 2.64% CCCT : 2.5% AGGC : 2.37% AGAT : 2.3% TTCT : 2.24%