Skip to main content

Table 1 NGS error rate and imputation error matrices

From: Sequence- vs. chip-assisted genomic selection: accurate biological information is advised

Real

Called (NGS)

Imputed

 

RR

RA

AA

RR

RA

AA

RR

1 − λ/5

λ/5

0

1 − α

α/2

α/2

RA

λ

1 − 2λ

λ

α/2

1 − α

α/2

AA

0

λ/5

1 − λ/5

α/2

α/2

1 − α

  1. R: reference allele; A: alternative allele; λ: base NGS genotyping error rate; α: imputation error rate. The Table shows the probability of a true genotype being called or imputed for each of the three possible genotypes; for instance, under this model, a true heterozygous genotype RA has a probability λ of being called as homozygous RR or AA and 2λ of being wrongly called.
Back to article page

Genetics Selection Evolution

ISSN: 1297-9686