ArticleMolecular biology and evolution2009
Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences.
Article in Molecular biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- Characterizing bias in population genetic inferences from low-coverage sequencing data.Molecular biology and evolution · 2014Article
- Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications.BMC genomics · 2013Article
- jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.Methods in ecology and evolution · 2012Article
- Atypical at skew in Firmicute genomes results from selection and not from mutation.PLoS genetics · 2011Article
- Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error.Genome research · 2010Article
- Measuring the rates of spontaneous mutation from deep and large-scale polymorphism data.Genetics · 2009Article
- Site frequency spectra from genomic SNP surveys.Theoretical population biology · 2009Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
One challenge of analyzing samples of DNA sequences is to account for the nonnegligible polymorphisms produced by error when the sequencing error rate is high or the sample size is large. Specifically, those artificial sequence variations will bias the observed single nucleotide polymorphism (SNP) frequency spectrum, which in turn may further bias the estimators of the population mutation rate theta =4N mu for diploids. In this paper, we propose a new approach based on the generalized least squares (GLS) method to estimate theta, given a SNP frequency spectrum in a random sample of DNA sequences from a population. With this approach, error rate epsilon can be either known or unknown. In the latter case, epsilon can be estimated given an estimation of theta. Using coalescent simulation, we compared our estimators with other estimators of theta. The results showed that the GLS estimators are more efficient than other theta estimators with error, and the estimation of epsilon is usable in practice when the theta per bp is small. We demonstrate the application of the estimators with 10-kb noncoding region sequence sampled from a human population and provide suggestions for choosing theta estimators with error.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.