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Variants that failed to be called in all individuals were excluded.
At this same coverage only 9/31 of variants that failed previous verification by capillary sequencing showed the SNV, and of these, 7 showed the reference base.
Ad hoc qPCR experiments would confirm or refute the existence of the variants that failed NimbleGen validation and also determine the accuracy of the genotyping step.
Of these patients, 44 of 103 were infected with non-B subtypes, including 4 variants that failed to group within known subtypes in phylogenetic analyses (6 ).
A series of filtering steps removed variants that failed to pass filters and those with greater than 30% of samples missing data.
The mitochondrial chaperone mortalin was implicated in Parkinson's disease (PD) because of its reduced levels in the brains of PD patients and disease-associated rare genetic variants that failed to rescue impaired mitochondrial integrity in cellular knockdown models.
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SpoIIE variants that fail to accumulate in the forespore are marked in blue.
Missing variants and directly typed variants that fail pre-imputation QC checks are imputed and these data are used for downstream analyses.
For those variants that fail to map, new mappings are obtained using ssaha2, an improved version of SSAHA http://www.sanger.ac.uk/resources/software/ssaha2/ [ 24].
Our work suggests that any argument on partner recognition in a system that is intrinsically spatial (such as legume and rhizobia and fig and colonizing fig wasp) will require identifying variants that fail to distinguish cooperators from cheaters.
Indeed, mutation of the Cyt c axial His residue to Met, Lys, or Arg generates variants that fail to attach heme, further establishing the necessity of His in Cyt c biogenesis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com