Journal Article

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 and Julian Parkhill

in Bioinformatics

Volume 25, issue 16, pages 2074-2075
Published in print August 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI:

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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×.

Availability: The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1537 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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