RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354215.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) = 35,236,109 / 35,216,179 read pairs aligned = 35,211,699 total alignments = 74,819,370 secondary alignments = 4,367,082 non-unique alignments = 7,124,971 aligned to genes = 57,450,195 ambiguous alignments = 187,156 no feature assigned = 9,669,543 not aligned = 3,278,352 >>>>>>> Reads genomic origin exonic = 57,450,195 (85.59%) intronic = 6,841,838 (10.19%) intergenic = 2,827,705 (4.21%) overlapping exon = 2,366,734 (3.53%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.15 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 17,933,348 ACCT : 5.24% AGGT : 4.72% AGGA : 3.75% ATCT : 3.62% TCCT : 3.32% AGCT : 2.8% GCCT : 2.79% AGAT : 2.55% AGGC : 2.37% CCCT : 2.3% TTCT : 2.28%