Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets

Genomics. 2013 Mar;101(3):204-9. doi: 10.1016/j.ygeno.2012.12.001. Epub 2012 Dec 12.


Identification of single nucleotide polymorphisms (SNPs) is a key element in sequence-based genetic analysis. Next generation sequencing offers a cost-effective basis to generate the necessary, large sequence data sets, and bioinformatic methods are being developed to process sequencing machine readouts. We were interested in detection of SNPs in a 350 kb region of an EMS-mutagenized Arabidopsis chromosome 3. The region was selectively analyzed using PCR-generated, overlapping fragments for Solexa sequencing. The ensuing reads provided a high coverage and were processed bioinformatically. In order to assess the SNP candidates obtained with a frequently used alignment program and SNP caller, we developed an additional method that allows the identification of high confidence SNP loci. The method can easily be applied to complete genome sequence data of sufficient coverage.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Base Sequence
  • Chromosome Mapping
  • Computational Biology
  • Ethyl Methanesulfonate / toxicity
  • Genome, Plant / drug effects
  • Genome, Plant / genetics
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Mutagenesis / genetics
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA*


  • Ethyl Methanesulfonate