Table 2

Concordance of the sequence-derived genotype calls with genotypes from the MassARRAY genotyping for 19 SNPs

Hardy-Weinberg statistic

SNP rsID

Number matching genotype

Number of under-callsa

Number of over-callsb

Number of N/Nc

Sequencing

MassARRAY

Hidden variant


rs594323

253

1

33

2

1.2

4.2

SNP at 22 bp

rs9759081

272

15

2

0

0

8.6

SNP at 19 bp

rs9852837

276

0

13

0

0.2

0.01

Indel at 38 bp

rs4141964

287

1

0

1

1.6

1.2

-

rs324419

287

2

0

0

0.7

0.9

-

rs17203666

289

0

0

0

0.6

0.6

-

rs11715363

286

3

0

0

0.1

0

-

rs17203659

288

1

0

0

0.2

0

-

rs6778770

287

0

1

0

0.2

0.3

-

rs17282181

283

4

2

0

0

0.2

-

rs497897

287

1

1

0

1.2

0.2

-

rs567384

283

4

2

0

2.3

0.6

-

rs3773155

286

3

0

0

0

0

-

rs3773159

286

1

2

0

2.3

2.1

-

rs13076593

288

1

0

0

0.8

0.1

-

rs936839

288

1

0

0

1.1

1.2

-

rs13066225

289

0

0

0

0.1

0.1

-

rs324420

289

0

0

0

0

0

-

rs7652615

289

0

0

0

0.4

0.4

-


aGenotype called as reference homozygote by sequencing and heterozygote by MassARRAY or heterozygote by sequencing and alternative homozygote by MassARRAY. bGenotype called as heterozygote by sequencing and reference homozygote by MassARRAY or alternative homozygote by sequencing and heterozygote by MassARRAY. cUncalled genotype or tri-allelic in one of the two.

Harismendy et al. Genome Biology 2010 11:R118   doi:10.1186/gb-2010-11-11-r118

Open Data