RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354086.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) = 34,872,588 / 34,842,289 read pairs aligned = 34,838,712 total alignments = 74,179,474 secondary alignments = 4,464,597 non-unique alignments = 7,493,199 aligned to genes = 59,860,018 ambiguous alignments = 203,261 no feature assigned = 6,390,709 not aligned = 5,433,491 >>>>>>> Reads genomic origin exonic = 59,860,018 (90.35%) intronic = 4,484,950 (6.77%) intergenic = 1,905,759 (2.88%) overlapping exon = 2,069,530 (3.12%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.19 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 22,134,805 ACCT : 5.29% AGGT : 5.03% AGGA : 3.69% TCCT : 3.62% ATCT : 3.61% AGCT : 2.83% AGGC : 2.44% GCCT : 2.4% CCCT : 2.26% AGAT : 2.18% AGGG : 2.08%