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Missing markers are treated as matches.
When X-specific markers are treated as autosomal markers, the resulting genomic relationship matrix reflects sex-linked relationships, but on an incorrect scale because males have one X chromosome while females have two.
Although an AFLP marker locus can have two allelic bands of the opposite haplotype, such allele pairs are not revealed in the potato genetic map, and the AFLP markers are treated as presence/absence (i.e. dominant) markers with only a single allele.
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Each fragment size of the 39 markers was treated as a unique characteristic and scored as present (1) or absent (0).
Each fragment size of the 15 DNA markers was treated as a unique characteristic and scored as present (1) or absent (0).
The eleven prior known SNP markers were treated as the "anchor" markers genotyped on all subjects with the remaining markers sequenced in a portion of the subjects.
The probability from the markers is treated as the prior probability.
Heterozygosity in codominant markers was treated as missing data by MAPMAKER because the 'ri self' configuration does not recognize it.
Utilizing the package PHYLIP-3.69 [ 21] the SPP markers were treated as restriction site markers and scored as 1 or 0. The SeqBoot module was used to create 100 re-samples data sets for bootstrap calculation.
In addition, to reduce the inflation of effect estimation of QTL, effects of each marker are treated as random draws from a common prior density in GWP.
If one of these markers was located within 5,000 bp of a probe, the genotype obtained from this marker was treated as the "true" genotype for this probe.
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