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We found that 50-fold coverage is sufficient for genome assembly and for the detection of most sequence variants, although some additional variants are detected at higher coverage depths.
Homozygous or hemizygous variants are detected by prior mixing with wild-type DNA.
When variants are detected, they can be identified in an additional 3 h by rapid cycle sequencing and capillary electrophoresis.
The results show that all PSTVd sequence variants are detected, and that the closely related Mexican papita viroid is also detected, although with a lower efficiency.
It is likely that only a limited number of similar RIFIN variants are detected, making it difficult to draw general conclusions on RIFIN expression patterns during gametocytogenesis, as relevant proteins may not be visualized and assignment of the variant is difficult.
On the one extreme is collecting such an enormous study sample that rare variants are detected sufficiently often to allow for testing each variant individually; for example, Nejentsev et al. [8] discovered a rare variant with minor allele frequency (MAF) 0.46% in Type I Diabetes cases and 0.67% in controls, using 17,730 individuals.
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FS is amenable to current structural variation detection methods, and variants were detected.
For three loci14,17,24 only two allelic variants were detected.
S. Typhimurium and its variants were detected rapidly and accurately.
Twelve variants were detected only in the FFPE data; all were SNVs and indels and 7 of 12 had an AF lower than 0.13.
Copy-number variants were detected with three steps, by comparison with actual coverage of the resequenced A. thaliana reference strain Col-0.
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