Format of Marker 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 either H or the two-character format (for example, A/B is represented by AB).

Note for the Linkage Map and QTL processes (Recombination and Linkage Groups , Linkage Map Order, QTL Single Marker Analysis, Build QTL Genotype Probability Data Set, and QTL IM, CIM and MIM Analysis) only:

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For an F2 cross, dominance coding is allowed with Numeric Genotypes. For a marker that is dominant for the A allele (from parental line P), genotypes that are not BB (A/B or A/A) are represented by 3.

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For a dominant marker for the B (P2 line dominance) allele coded as not AA (A/B or B/B), genotypes are represented with a 4. If dominance coding is used for a marker, then only values of 2 and 3 for a P1 dominant marker or only values of 0 and 4 for a P2 should be observed in that column.

Note: When genotypes or alleles are coded in character values, missing values must be represented by a blank value (e.g., when genotypes are coded as A/B, missing values are blank values). When genotypes or alleles are coded in numerical values, missing values must be represented by a dot ".", without the double quote (for example, when genotypes are coded as 0, 1, ..., missing values are ".", without the double quote).

To Specify the Format:

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