Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal
Article first published online: 23 JUN 2012
© 2012 Blackwell Publishing Ltd
Molecular Ecology Resources
Volume 12, Issue 5, pages 861–872, September 2012
How to Cite
HOFFMAN, J. I., TUCKER, R., BRIDGETT, S. J., CLARK, M. S., FORCADA, J. and SLATE, J. (2012), Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources, 12: 861–872. doi: 10.1111/j.1755-0998.2012.03158.x
- Issue published online: 16 AUG 2012
- Article first published online: 23 JUN 2012
- Received 24 February 2012; revision received 30 March 2012; accepted 4 April 2012
Table S1 Details of 144 GoldenGate SNP assays developed from the Antarctic fur seal transcriptome assembly (see Materials and methods for details). ‘Chromosome in the dog’ refers to the genomic location inferred by mapping each isotig to the dog (Canis familaris) genome. Basic Local Alignment Search Tool (BLAST) results indicate the top match of each isotig to the non-redundant (nr) database. Gene Ontology (GO) codes are given only for isotigs that recovered functional annotations relating to growth or immunity. In silico Minor Allele Frequency (MAF) and depth of coverage refer to the exact site of each SNP and are given only for reads accepted as unambiguous by the program SWAP454 (Brockman et al. 2008). Assay Design Tool (ADT) scores vary between 0 and 1, with values of 0.6 or above indicating a high probability of conversion into a successful genotyping assay.
Table S2 Polymorphism characteristics of 102 polymorphic SNP assays in 440 Antarctic fur seals individuals (see Materials and methods for details). The GenTrain score takes into account the quality, shape and degree of separation of the genotype clusters, with higher values indicating improved clustering (Fan et al. 2003).
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