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Table 4 Example of preprocessing step 1, loading genotype data into the six n-locus bit variables (n = 5).

From: Haplotype association analyses in resources of mixed structure using Monte Carlo testing

 

M1

M2

M3

M4

M5

Genotype values*

12

00

11

12

22

Variables

Haplotype pair

Homozygous†

0

0

1

0

1

Heterozygous§

1

0

0

1

0

Unphased**

1

0

0

1

0

Haplotype 1

Set‡

0

0

1

0

1

Missing††

0

1

0

0

0

Value§§

0

0

0

0

1

Haplotype 2

Set

0

0

1

0

1

Missing

0

1

0

0

0

Value

0

0

0

0

1

  1. *11 indicates a homozygous genotype for the major allele; 12 a heterozygous genotype, and 22 a homozygous genotype for the minor allele; 00 indicates missing genotype.
  2. †Homozygous 0 indicates the positions that are heterozygous or missing and 1 indicates the homozygous positions.
  3. §Heterozygous 0 indicates the positions that are homozygous or missing and 1 indicates the heterozygous positions.
  4. **Unphased 0 indicates the positions that are phased or missing and 1 indicates a heterozygous position without known phase.
  5. ‡Set 0 indicates the positions that have not been assigned an allele (i.e. unphased or missing) and 1 indicates the allele value and phase is known.
  6. ††Missing 0 indicates the positions that have an observed allele value and 1 indicates positions that are missing.
  7. §§Value 0 indicates the positions that have the major allele or unknown and 1 indicates positions that have the minor allele.