Format of SNP Variables

Parameters | Genetics | Format of SNP Variables

Format of SNP Variables

This required feature enables you to specify the format of the marker data in the input data set.

Genotypic information for sets of alleles or markers is frequently listed using combinations of letters and numbers. Data sets can present these genotypes in one of several formats. In the two column allelic format, each of the two alleles that make up a genotype is listed in a separate column. In the one column format, both alleles are listed in a single column. Alleles might or not be delimited and might be coded using either character or numeric values.

Select:

When:

Alleles

The data is in the two-column allelic format.

In the example shown below, each allele for the locus is presented in a separate column: ma1 and ma2. This individual is heterozygous for the A and B alleles.

Genotypes

Marker data is in the one-column genotypic format, and the alleles are delimited by some character (such as a “/”).

The individual represented in this example is heterozygous at the ma1 locus. The two alleles are delimited by a “/”.

Nondelimited Genotypes

Marker data are in the one-column genotypic format and the genotypes are not delimited.

The individual represented in this example is heterozygous for the A and B alleles at the ma1 locus. The two alleles are not delimited.

Numeric Genotypes

Numeric Genotypes is selected only for SNP markers for which the two homozygotes are represented by 0 and 2, and the heterozygous genotype is represented by 1.

There are three individuals represented in this example. The first is heterozygous at the ma1 locus. The second and third are homozygous, but for different alleles, at the ma1 locus.

Single-Character Homozygous Genotypes¹

The homozygotes are represented by one letter only (for example, A/A is represented by A).

Note: Heterozygotes are still represented using the two-character format (for example, A/B is represented by AB).

1

This format may or may not be available for specification, depending on the process.

To Specify the Format:

Select the desired format by clicking within the appropriate radio button.

Select:	When:
Alleles	The data is in the two-column allelic format. In the example shown below, each allele for the locus is presented in a separate column: ma1 and ma2. This individual is heterozygous for the A and B alleles.
Genotypes	Marker data is in the one-column genotypic format, and the alleles are delimited by some character (such as a “/”). The individual represented in this example is heterozygous at the ma1 locus. The two alleles are delimited by a “/”.
Nondelimited Genotypes	Marker data are in the one-column genotypic format and the genotypes are not delimited. The individual represented in this example is heterozygous for the A and B alleles at the ma1 locus. The two alleles are not delimited.
Numeric Genotypes	Numeric Genotypes is selected only for SNP markers for which the two homozygotes are represented by 0 and 2, and the heterozygous genotype is represented by 1. There are three individuals represented in this example. The first is heterozygous at the ma1 locus. The second and third are homozygous, but for different alleles, at the ma1 locus.
Single-Character Homozygous Genotypes¹	The homozygotes are represented by one letter only (for example, A/A is represented by A). Note: Heterozygotes are still represented using the two-character format (for example, A/B is represented by AB).