RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354354.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) = 31,747,210 / 31,725,434 read pairs aligned = 31,720,308 total alignments = 70,026,674 secondary alignments = 6,554,030 non-unique alignments = 8,632,244 aligned to genes = 54,497,215 ambiguous alignments = 233,717 no feature assigned = 5,214,594 not aligned = 3,049,144 >>>>>>> Reads genomic origin exonic = 54,497,215 (91.27%) intronic = 3,008,902 (5.04%) intergenic = 2,205,692 (3.69%) overlapping exon = 2,105,165 (3.53%) >>>>>>> Transcript coverage profile 5' bias = 0.18 3' bias = 0.18 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 17,886,771 ACCT : 5.23% TCCT : 4.86% ATCT : 4.83% AGGT : 4.25% CCCT : 3.23% AGGA : 3.01% GCCT : 2.88% TTCT : 2.22% AGCT : 2.17% AGGC : 2.13% GTCT : 1.82%