RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354328.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) = 41,207,039 / 41,077,532 read pairs aligned = 41,055,031 total alignments = 88,617,064 secondary alignments = 6,332,493 non-unique alignments = 10,661,547 aligned to genes = 69,797,539 ambiguous alignments = 262,704 no feature assigned = 7,575,172 not aligned = 7,747,195 >>>>>>> Reads genomic origin exonic = 69,797,539 (90.21%) intronic = 4,926,732 (6.37%) intergenic = 2,648,440 (3.42%) overlapping exon = 2,981,072 (3.85%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.21 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 22,527,070 ACCT : 5.05% AGGT : 4.74% ATCT : 4.3% TCCT : 3.7% AGGA : 3.43% GCCT : 2.93% CCCT : 2.63% AGCT : 2.37% AGGC : 2.23% TTCT : 2.18% AGAA : 1.99%