Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA

Kathryn E. Holt, Yik Y. Teo, Heng Li, Satheesh Nair, Gordon Dougan, John Wain, Julian Parkhill

Research output: Contribution to journalArticlepeer-review

40 Citations (Scopus)


Summary: Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.
Original languageEnglish
Pages (from-to)2074-2075
Number of pages2
Issue number16
Publication statusPublished - 15 Aug 2009

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