Table 3

Concordance of genotypes and SNPs

Concordance with 1 M bead genotyping data

Concordance with WGSS data

Replicatea

All genotypes

SNPs in 1 M chip

SNPs in exome capture

Homs in 1 M chip

Homs in exome capture

Hets in 1 M chip

Hets in exome capture

All genotypes

SNPs in WGSS

SNPs in exome capture

Homs in WGSS

Homs in exome capture

Hets in WGSS

Hets in exome capture


NA-r1

99.846

99.641

99.826

99.649

99.987

99.633

99.687

99.999

99.216

98.636

99.951

99.868

98.683

97.750

NA-r2

99.854

99.670

99.835

99.708

99.975

99.637

99.714

99.999

99.264

98.616

99.943

99.850

98.768

97.724

NS-r1

99.854

99.679

99.819

99.682

99.951

99.676

99.707

99.998

99.211

98.396

99.974

99.747

98.657

97.426

NS-r2

99.849

99.660

99.841

99.684

99.987

99.640

99.716

99.999

99.197

98.706

99.979

99.752

98.629

97.949

AS-r1

99.816

99.526

99.823

99.571

99.948

99.486

99.712

99.998

98.783

98.021

99.917

99.824

97.945

96.703

AS-r2

99.815

99.514

99.805

99.556

99.880

99.477

99.738

99.998

98.762

97.972

99.927

99.771

97.893

96.645


For each replicate, the 30-fold data set used for Table 2 analyses was also used for the analyses. aAS, Agilent solution; NA, NimbleGen array; NS, NimbleGen solution; r1 and r2 are two replicate experiments for each platform. Hets, heterozygotes; Homs, homozygotes.

Asan et al. Genome Biology 2011 12:R95   doi:10.1186/gb-2011-12-9-r95

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