RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354267.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) = 40,060,454 / 40,027,193 read pairs aligned = 40,022,528 total alignments = 84,078,041 secondary alignments = 3,990,394 non-unique alignments = 6,962,113 aligned to genes = 68,709,732 ambiguous alignments = 189,588 no feature assigned = 8,022,791 not aligned = 5,885,935 >>>>>>> Reads genomic origin exonic = 68,709,732 (89.54%) intronic = 3,954,970 (5.15%) intergenic = 4,067,821 (5.3%) overlapping exon = 2,899,092 (3.78%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.14 5'-3' bias = 2.32 >>>>>>> Junction analysis reads at junctions = 20,594,690 ACCT : 5.57% AGGT : 4.8% AGGA : 3.68% ATCT : 3.62% TCCT : 3.45% GCCT : 2.91% AGCT : 2.69% AGGC : 2.4% AGAT : 2.34% CCCT : 2.23% TTCT : 2.17%