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Table 1 Low performing SNPs within the core and additional ISAG-ICAR panel

From: Analytical and statistical consideration on the use of the ISAG-ICAR-SNP bovine panel for parentage control, using the Illumina BeadChip technology: example on the German Holstein population

SNP-name

Panel

Average GC-score (50k)

Average GC-score (10k)

Censored SNP (%)

ARS-USMARC-Parent-DQ786762-rs29010772

C

0.62

0.66

26.4

ARS-USMARC-Parent-EF093511-rs29012316

C

0.66

0.79

7.2

ARS-BFGL-NGS-11383

A

0.79

0.78

6.2

Hapmap52240-rs29013844

A

0.64

0.96

3.6

ARS-USMARC-Parent-DQ837645-rs29015870

C

0.75

0.55

3.2

Hapmap46653-BTA-47447

A

0.87

0.64

2.9

ARS-USMARC-Parent-DQ404150-rs29012530

C

0.84

0.82

2.3

ARS-USMARC-Parent-EF034083-rs29018286

C

0.74

0.79

2.0

ARS-BFGL-NGS-42505

A

0.85

0.92

1.9

ARS-USMARC-Parent-DQ404151-rs29019282

C

0.59

0.69

1.8

ARS-USMARC-Parent-DQ846693-rs29017621

C

0.85

0.83

1.3

ARS-BFGL-NGS-118319

A

0.64

0.74

1.2

Hapmap46550-BTA-103548

A

0.96

0.85

1.1

ARS-USMARC-Parent-DQ839235-rs29012691

C

0.86

0.86

1.0

UA-IFASA-5034

A

0.83

0.75

1.0

ARS-USMARC-Parent-DQ837644-rs29010468

C

0.83

0.89

0.4

  1. SNPs that were most often censored in parentage analysis on both chip types ranked in order of censored parentages (highest first); SNPs that performed poorly on both chip types are marked by bold/italic characters; GC score = GenCall score; 50k = BovineSNP50v2 BeadChip; 10k = EuroG10kv2 BeadChip; C = core panel; A: additional panel.