期刊
VIRUS EVOLUTION
卷 5, 期 1, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/ve/vey041
关键词
virus diversity; sequence data; polymorphism; entropy
类别
资金
- Sir Henry Dale Fellowship - Wellcome Trust [101239/Z/13/Z]
- Sir Henry Dale Fellowship - Royal Society [101239/Z/13/Z]
Viruses exist within hosts at large population sizes and are subject to high rates of mutation. As such, viral populations exhibit considerable sequence diversity. A variety of summary statistics have been developed which describe, in a single number, the extent of diversity in a viral population; such measurements allow the diversities of different populations to be compared, and the effect of evolutionary forces on a population to be assessed. Here we highlight statistical artefacts underlying some common measures of sequence diversity, whereby variation in the depth of genome sequencing may substantially affect the extent of diversity measured in a viral population, making comparisons of population diversity invalid. Specifically, naive estimation of sequence entropy provides a systematically biased metric, a lower read depth being expected to produce a lower estimate of diversity. The number of polymorphic loci per kilobase of genome is more unpredictably affected by read depth, giving potentially flawed results at lower sequencing depths. We show that the nucleotide diversity statistic pi provides an unbiased estimate of diversity in the sense that the expected value of the statistic is equal to the correct value of the property being measured. Our results are of importance for studies interpreting genome sequence data; we describe how diversity may be assessed in viral populations in a fair and unbiased manner.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据