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Table 4 Proportions of opposing homozygous genotypes observed in nine sire-son pairs

From: Accurate sequence variant genotyping in cattle using variation-aware genome graphs

 

SNPs

Indels

Full

Filtered

Full

Filtered

Raw

Imp

Raw

Imp

Raw

Imp

Raw

Imp

Bovine HD SNP array

0.001

GATK

0.73*

0.15*

0.72*

0.13*

0.98*

0.24*

0.99*

0.21*

Graphtyper

0.36

0.11

0.36

0.11

0.54

0.13

0.54

0.13

SAMtools

0.33

0.28*

0.32

0.25*

0.67

0.54*

0.61

0.57*

  1. The ratio (in percentage) was calculated using autosomal sequence variants considering either the raw or imputed (Imp) sequence variant genotypes before (Full) and after (Filtered) variants were filtered based on commonly used criteria. Asterisks denote significant differences (*P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001) with the best value (italic) for a respective parameter
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Genetics Selection Evolution

ISSN: 1297-9686