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Table 3 The genotype frequencies in different scenarios in the presence of MCB or genotyping errors.

From: Missing call bias in high-throughput genotyping

Scenarios Missing Call Bias Genotyping Errors for No-Calls
Scenario I p A A o b s = c p A A / ( c p A A + p A a + p a a ) p A a o b s = p A a / ( c p A A + p A a + p a a ) p a a o b s = p a a / ( c p A A + p A a + p a a ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@8906@ p A A o b s = c p A A + c o n f ( 1 c ) p A A p A a o b s = p A a + ( 1 c o n f ) ( 1 c ) p A A p a a o b s = p a a MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@75B7@
Scenario II p A A o b s = p A A / ( p A A + c p A a + p a a ) p A a o b s = c p A a / ( p A A + c p A a + p a a ) p a a o b s = p a a / ( p A A + c p A a + p a a ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@8906@ p A A o b s = p A A + ( 1 c o n f ) ( 1 c ) p A a p A a o b s = c p A a + c o n f ( 1 c ) p A a p a a o b s = p a a MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@7637@
Scenario III p A A o b s = p A A / ( p A A + c p A a + p a a ) p A a o b s = c p A a / ( p A A + c p A a + p a a ) p a a o b s = p a a / ( p A A + c p A a + p a a ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@8906@ p A A o b s = p A A p A a o b s = c p A a + c o n f ( 1 c ) p A a p a a o b s = p a a + ( 1 c o n f ) ( 1 c ) p A a MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@7637@
Scenario IV p A A o b s = p A A / ( p A A + p A a + c p a a ) p A a o b s = p A a / ( p A A + p A a + c p a a ) p a a o b s = c p a a / ( p A A + p A a + c p a a ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@8906@ p A A o b s = p A A p A a o b s = p A a + ( 1 c o n f ) ( 1 c ) p a a p a a o b s = c p a a + c o n f ( 1 c ) p a a MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@76B7@