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Table 2 Conditional concordance rates (conditional on microarray genotype; SE in parentheses)

From: Evaluating the concordance between sequencing, imputation and microarray genotype calls in the GAW18 data

Sequence genotype1

Microarray genotype

 

AA

AB

BB

Missing (XX)

AA

NGS

0.998 (0.03)

0.003 (0.03)

0.004 (0.06)

0.52 (0.36)

 

Imp

0.998 (0.02)

0.02 (0.11)

0.0006 (0.02)

0.44 (0.46)

AB

NGS

0.0009 (0.02)

0.996 (0.04)

0.02 (0.08)

0.30 (0.24)

 

Imp

0.002 (0.02)

0.980 (0.12)

0.006 (0.06)

0.38 (0.43)

BB

NGS

0.0007 (0.02)

0.0006 (0.02)

0.98 (0.10)

0.19 (0.28)

 

Imp

8 × 10−5 (0.008)

0.003 (0.05)

0.993 (0.07)

0.18 (0.35)

Missing (XX)

NGS

8 × 10−5 (0.005)

0.0006 (0.02)

0.0007 (0.01)

0.001 (0.02)

 

Imp

8 × 10−5 (0.005)

0.0003 (0.009)

0.0004 (0.01)

0.007 (0.07)