ArticlePloS one2013
Assessing the effect of sequencing depth and sample size in population genetics inferences.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it.
- CMDB: the comprehensive population genome variation database of China.Nucleic acids research · 2023Pooled it
- Identification of rare maternal copy number variants by genome-wide analysis of noninvasive prenatal screening data in 113,017 pregnant women.Annals of medicine · 2026Article
- Comparing methods to estimate time-varying reproduction numbers using genomic and epidemiological data.Infectious Disease Modelling · 2026Article
- Pan-Continental Genomic Analysis of Eurasian Perch Uncovers Global Diversity Hotspots and Postglacial Recolonization Patterns.Ecology and evolution · 2026Article
- Adaptive Genetic Variation in Black-and-White Snub-Nosed Monkeys (Ecology and evolution · 2026Article
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- A low-coverage skim-sequencing and imputation pipeline for genomic selection.The plant genome · 2025Article
- Construction of a Genome-Wide Copy Number Variation Map and Association Analysis of Black Spot in Jujube.Plants (Basel, Switzerland) · 2025Article
- Genotype imputation from low-coverage data for medical and population genetic analyses.Genome research · 2025Article
- Screening of triploid in miscarriage tissues using medium-coverage whole genome sequencing with a three-algorithm integrated approach.Journal of assisted reproduction and genetics · 2025Article
- Haploblocks contribute to parallel climate adaptation following global invasion of a cosmopolitan plant.Nature ecology & evolution · 2025Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- Genome-environment association analysis reveals climate-driven adaptation of chickens.Genetics, selection, evolution : GSE · 2025Article
- Integrating population genomics and environmental data to predict adaptation to climate change in post-bottleneck Tibetan macaques.Science advances · 2025Article
- Periodontal diseases in Africa.Periodontology 2000 · 2025Review
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- The Eastern Fox Squirrel (Journal of mammalogy · 2025Article
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.Molecular biology and evolution · 2025Article
- Population structure of Desmophyllum pertusum found along the United States eastern continental margin.BMC research notes · 2024Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-Generation Sequencing (NGS) technologies have dramatically revolutionised research in many fields of genetics. The ability to sequence many individuals from one or multiple populations at a genomic scale has greatly enhanced population genetics studies and made it a data-driven discipline. Recently, researchers have proposed statistical modelling to address genotyping uncertainty associated with NGS data. However, an ongoing debate is whether it is more beneficial to increase the number of sequenced individuals or the per-sample sequencing depth for estimating genetic variation. Through extensive simulations, I assessed the accuracy of estimating nucleotide diversity, detecting polymorphic sites, and predicting population structure under different experimental scenarios. Results show that the greatest accuracy for estimating population genetics parameters is achieved by employing a large sample size, despite single individuals being sequenced at low depth. Under some circumstances, the minimum sequencing depth for obtaining accurate estimates of allele frequencies and to identify polymorphic sites is [Formula: see text], where both alleles are more likely to have been sequenced. On the other hand, inferences of population structure are more accurate at very large sample sizes, even with extremely low sequencing depth. This all points to the conclusion that under various experimental scenarios, in cost-limited population genetics studies, large sample sizes at low sequencing depth are desirable to achieve high accuracy. These findings will help researchers design their experimental set-ups and guide further investigation on the effect of protocol design for genetic research.
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