Genotype probability file

Output file

The .geno_prob.txt file contains genotype probabilities for each individual.

There are three lines per individual, corresponding to probabilities for aa, aA or Aa, and AA genotypes. The first value in each line is the individual ID. The remaining values are genotype probabilities at each locus.

Example with four individuals and four loci:

id1 0.7912 0.0000 0.0000 1.0000
id1 0.2088 0.2179 0.5274 0.0000
id1 0.0000 0.7820 0.4725 0.0000
id2 0.0000 0.0000 0.0000 0.0001
id2 1.0000 1.0000 1.0000 0.9999
id2 0.0000 0.0000 0.0000 0.0000
id3 0.3784 0.2171 0.0000 1.0000
id3 0.4140 0.4329 0.0001 0.0000
id3 0.2076 0.3500 0.9999 0.0000
id4 0.9999 0.0000 0.0000 1.0000
id4 0.0001 0.0001 0.9999 0.0000
id4 0.0000 0.9999 0.0000 0.0000

When working with the X chromosome, for a female individual, the interpretation is as for an autosomal chromosome above. For a male individual, the first line and the last line respectively correspond to a and A genotypes, with the middle line is a placeholder.

Example with four individuals and their X chromosome genotypes at four loci:

id1 and id3 are males, while id2 and id4 are females:

id1 0.7912 0.2179 0.5274 1.0000
id1 0.0000 0.0000 0.0000 0.0000
id1 0.2088 0.7820 0.4725 0.0000
id2 0.0000 0.0000 0.0000 0.0001
id2 1.0000 1.0000 1.0000 0.9999
id2 0.0000 0.0000 0.0000 0.0000
id3 0.3784 0.2171 0.0001 1.0000
id3 0.0000 0.0000 0.0000 0.0000
id3 0.6216 0.7829 0.9999 0.0000
id4 0.9999 0.0000 0.0000 1.0000
id4 0.0001 0.0001 0.9999 0.0000
id4 0.0000 0.9999 0.0000 0.0000