Genome and Marker Parameters
CHR
- Description: The number of chromosomes to generate.
- Options: Integer value ranging from 1 to 31
- Usage: 'CHR: 3'.
- Type: Mandatory.
CHR_LENGTH
- Description: The length for each chromosome, in Megabases.
- Option: Integer value.
- Usage: '
CHR_LENGTH: 150 150 150'.
- Type: Mandatory.
- Note:
The number of Chromosome length variables specified has to correspond to chromosome number.
NUM_MARK
- Description: The number of markers within a chromosome. The marker location is generated based on a uniform distribution from 0 to the length of the chromosome.
- Options: Integer value.
- Usage: '
NUM MARK: 4000 4000 4000'.
- Type: Mandatory.
- Note:
Quantitative and fitness mutations cannot be markers. The program will exit if the number of markers is greater than the available number of mutations within a chromosome.
MARKER_MAF
- Description: Minimum allele frequency allowed for markers.
- Option: A double, that can range from 0.0 to 0.50.
- Usage: 'MARKER MAF: 0.05'.
- Type: Optional. Default is 0.05.
QTL
- Description: The number of quantitative trait loci (QTL) for each chromosome. The QTL location is generated based on a uniform distribution from 0 to the length of the chromosome.
- Option: Integer. Number of QTL and fitness trait loci (FTL) can’t exceed 5000.
- Usage: 'QTL: 50 50 50'.
- Type: Optional. Default is 0.
QUANTITATIVE_MAF
- Description: Minimum allele frequency allowed for QTL.
- Option: Range from 0.0 to 0.50.
- Usage: 'QUANTITATIVE_MAF: 0.01'.
- Type: Optional. Default is 0.01.
FIT_LETHAL
- Description: The number of lethal fitness trait loci (FTL) for each chromosome. The lethal FTL location is generated based on a uniform distribution from 0 to the length of the chromosome.
- Option: Integer value. 5000 is max number of QTL and FTL.
- Usage: '
FIT_LETHAL: 25 25 25'.
- Type: Optional. Default is 0.
- Note:
Lethal FTL can not have a covariance with the quantitative trait. The number of lethal FTL variables specified has to correspond to chromosome number.
FIT_SUBLETHAL
- Description: The number of sub-lethal fitness trait loci (FTL) for each chromosome. The sub-lethal FTL location is generated based on a uniform distribution from 0 to the length of the chromosome.
- Option: Integer value. 5000 is max number of QTL and FTL.
- Usage: '
FIT_SUBLETHAL: 25 25 25'.
- Type: Optional. Default is 0.
- Note:
Sub-lethal FTL can have a covariance with the quantitative trait. The number of sub-lethal FTL variables specified has to correspond to chromosome number.
FITNESS_MAF
- Description: Parameters that describe the maximum FTL frequency allowed and the range in lethal FTL allele frequencies. If the parameter is given, the first two are required, while the last one is optional
- Options:
- double (0.0-0.50): Maximum allele frequency for the unfavorable allele allowed for lethal FTL.
- double (0.0-0.50): Maximum allele frequency for the unfavorable allele allowed for sub-lethal FTL.
- double (0.0-0.50): Maximum allele frequency range for the lethal FTL.
- Usage: '
FITNESS MAF: 0.02 0.08 0.01'.
- Type: Optional. Default is 0.02, 0.08 and 0.01.
- Note:
Using the default values, the lethal FTL frequencies range from 0.01 to 0.02 and the sub-lethal frequencies range from 0.0 to 0.08. If the frequency of either lethal or sub-lethal FTL is too high, a large number of founders and progeny may not make it to breeding age. If the number of individuals is too small to generate the founder generation the simulation exits.
FOUNDER_HAPLOTYPES
- Description: The number of haplotypes generated by MaCS.
- Option: Integer value.
- Usage: 'FOUNDER_HAPLOTYPES: 4000'.
- Type: Optional. Default is based on male & female number.
HAPLOTYPE_SIZE
- Description: The number of markers contained within a non-overlapping haplotype window.
- Option: Integer value.
- Usage: 'HAPLOTYPE_SIZE: 50'.
- Type: Optional. Default is 50.
RECOMBINATION
- Description: The type of distribution that generates the location of recombination events along the genome. The number of recombination events is generated from a Poisson distribution. The rate parameter fixed at 1.0 across all chromosomes.
- Options:
- Uniform: Recombination sampled from a Uniform distribution from 0 to 1.0.
- Beta: Recombination sampled from a Beta distribution (0.5, 0.5) from 0 to 1.0. Recombinations occurs more often at the end of the chromosome than towards the middle.
- Usage: '
RECOMBINATION: Uniform'.
- Type: Optional. Default is Uniform.
MUTATION
- Description: Used in the MaCS software to generate scaled mutation parameter and in the simulation to generate new mutations as generations proceed.
- Options:
- Mutation Rate (float) : Probability of a new mutation occurring at a given base pair and follows the infinite-site model. A Poisson distribution with a rate parameter equal to the mutation rate times the length of the chromosome in nucleotides generates the total number of mutations occurring within a new gamete.
- Proportion of mutations that can be QTL (double; 0.0 to 1.0) : The proportion of Mutations that can be QTL: Within the forward-in-time part of the simulation program, represents the number of non-neutral mutations that occurred out of the total number of new mutations. Each type of trait (i.e. quantitative, lethal, sub-lethal) has an equal chance of being chosen.
- Usage: '
MUTATION: 2.5e-8 0.0'.
- Type: Optional. Default is 2.5e-8 0.0.
