OutputFiles

• 1 Introduction
• 2 Sync file (--output-sync)
  • order of the populations in the sync file
• 3 Output haplotypes (--output-dir)
• 4 Genotype/phenotype/fitness (--output-gpf)

1 Introduction

This section introduces output files of MimicrEE2

2 Sync file (--output-sync)

The sync file contains the allele frequency counts for the base population and the evolved populations. The sync file summarizes the counts from all replicates and all generations for which an output was requested. To save disc space, the file will be zipped.
It can directly be used with tools such as PoPoolationTE2, for example to compute the significance of allele frequency changes for SNPs.

2L  79  G   0:0:0:15:0:0    0:0:0:38:0:0
2L  80  A   12:0:0:0:0:0    38:0:0:0:0:0
2L  81  A   14:0:0:0:0:0    43:0:0:0:0:0
2L  82  A   14:0:0:0:0:0    42:0:0:0:0:0

• col1: reference contig
• col2: position in reference contig
• col3: reference character
• col4: allele frequency counts of population 1
• col5: allele frequency counts of population 2
• ....
• col-n: allelel frequency counts of population n-3

The allelele frequency counts are in the format
A-count:T-count:C-count:G-count:N-count:deletion-count;
For example the following entry

4:10:0:0:0:0

states that allele A was counted 4-times, allele T 10-times and all others zero times

order of the populations in the sync file

The sync file contains the allele frequency counts for population 1, population 2, ...., population n.
The order of these populations is best explained by an example.
Lets assume that we perform simulations for 3 replicates and request an output for the generations 10,20,30 (--snapshots 10,20,30). Than MimicrEE2 provides the populations in the following order:

base   r1-g10   r1-g20    r1-g30   base   r2-g10   r2-g20   r2-g30   base   r3-g10   r3-g20   r3-g30

• base: the base population
• r1-g10: replicate 1, generation 10
• ...
• r3-g30: replicate 3, generation 30

3 Output haplotypes (--output-dir)

It is possible to output the haplotypes of evolved haplotypes. A distinct MimicrEE2 haplotype file will be generated for the haplotypes of each requested population (see [HaplotypeFile] for the MimicrEE2 haplotype format). A separate file will thus be generated for the haplotypes of each replicate at each of the requested generations (--snapshots). A folder needs to be provided since many files may be generated. Existing files will be overwritten. All output files will be zipped.

For example if we perform simulations for 3 replicates and request an output at generations 10,20,30, than the following files will be generated in the provided folder (--output-dir).

haplotypes.r1.g0.mimhap.gz
haplotypes.r1.g10.mimhap.gz
haplotypes.r1.g20.mimhap.gz
haplotypes.r1.g30.mimhap.gz
haplotypes.r2.g0.mimhap.gz
haplotypes.r2.g10.mimhap.gz
haplotypes.r2.g20.mimhap.gz
haplotypes.r2.g30.mimhap.gz
haplotypes.r3.g0.mimhap.gz
haplotypes.r3.g10.mimhap.gz
haplotypes.r3.g20.mimhap.gz
haplotypes.r3.g30.mimhap.gz

• r1.. replicate 1
• g10.. generation 10; the base population is generation g0

Note the output folder will not be generated, i.e. the outpuf folder has to exist
Note the haplotypes of the base population (g0) are always stored
Note existing files will be overwritten

4 Genotype/phenotype/fitness (--output-gpf)

The gpf file contains the genotype/phenotype/fitness for all individuals of the base and the evolved populations. The file contains the results from all replicates for all requested generations. Every individual will be written in a separate line.

1   0   F   9.0 10.023949655996946  1.34
1   0   M   7.5 7.989310010279259   1.03
1   0   F   6.5 8.566069549227915   1.23
1   0   H   6.5 4.489143719014003   0.83

• col1: replicate
• col2: generation (0 is the not evolved base population)
• col3: sex; M=male, F=female, H=hermaphrodite
• col4: genotype of an individual
• col5: phenotpye of an individual
• col6: fitness of an individual

Note all three measures are provided for each mode; measures that are not ignored in a mode (e.g. fitness in truncating selection; truncating selection acts on the phenotypic value) are set to 1.0