Author: Folarin, Onikepe A.; Ehichioya, Deborah; Schaffner, Stephen F.; Winnicki, Sarah M.; Wohl, Shirlee; Eromon, Philomena; West, Kendra L.; Gladden-Young, Adrianne; Oyejide, Nicholas E.; Matranga, Christian B.; Deme, Awa Bineta; James, Ayorinde; Tomkins-Tinch, Christopher; Onyewurunwa, Kenneth; Ladner, Jason T.; Palacios, Gustavo; Nosamiefan, Iguosadolo; Andersen, Kristian G.; Omilabu, Sunday; Park, Daniel J.; Yozwiak, Nathan L.; Nasidi, Abdusallam; Garry, Robert F.; Tomori, Oyewale; Sabeti, Pardis C.; Happi, Christian T.
Title: Ebola Virus Epidemiology and Evolution in Nigeria Document date: 2016_10_15
ID: 2g9ggwog_26
Snippet: As noted in the Discussion, new single-nucleotide polymorphisms (SNPs) were observed to be clustered, with 6 SNPs appearing in 1 sample, 2 in another, and none in the remaining 9 samples. To determine whether this was unlikely given a uniform mutation rate per transmission, a P value was calculated as follows. From the transmission tree, the sequenced cases represent a minimum of 11 transmissions from the index case. Assume that new SNPs in a tra.....
Document: As noted in the Discussion, new single-nucleotide polymorphisms (SNPs) were observed to be clustered, with 6 SNPs appearing in 1 sample, 2 in another, and none in the remaining 9 samples. To determine whether this was unlikely given a uniform mutation rate per transmission, a P value was calculated as follows. From the transmission tree, the sequenced cases represent a minimum of 11 transmissions from the index case. Assume that new SNPs in a transmission occur in a Poisson process at an unknown rate, µ s . For a given µ s , we calculate the probability of seeing 4 new SNPs in ≥1 case and then integrate over all values of µ s , weighting by the probability of observing 6 SNPs in 11 transmissions. That is,
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