Data Files

log_file.txt:
- This file displays a great deal of information on specifics within each generation and it is advisable that one should look over it after you try a new simulation protocol.

Master_DataFrame:
- A file that contains multiple statistics for individuals that survived. If only one quantitative trait is simulated, columns for trait 2 are not displayed.
  ID: ID of individual.
  Sire: Sire Identification of individual.
  Dam: Dam Identification of individual.
  Sex: Sex of individual (0 = male and 1 = female).
  Gen: Generation the animal was born.
  Age: Age the animal was removed from the population.
  Progeny: Number of progeny.
  Dead: Number of dead progeny.
  Ped_F: Pedigree based inbreeding metric.
  Gen_F: Diagonal of genomic based relationship constructed based on Van Raden (2008).
  Hap1 F: Diagonal of haplotype 1 based relationship matrix.
  Hap2_F: Diagonal of haplotype 2 based relationship matrix.
  Hap3_F: Diagonal of ROH based relationship matrix.
  Homolethal: Number of homozygous lethal genotypes.
  Heterlethal: Number of heterozygous lethal genotypes.
  Homosublethal: Number of homozygous sub-lethal genotypes.
  Hetersublethal: Number of heterozygous sub-lethal genotypes.
  Letequiv: Lethal equivalent value.
  Homozy: Proportion of the genome homozygous.
  PropROH: Proportion of the genome in an ROH of a given length.
  Fitness: Multiplicative Fitness value of the individual.
  Phen1: Phenotype for trait 1.
  EBV1: Estimated breeding value for trait 1.
  Acc1: Accuracy of estimated breeding value for trait 1.
  TGV1: True genotypic value for trait 1 (Σ (a + d)).
  TBV1: True breeding value for trait 1 (Σ a).
  TDD1: True dominance deviation for trait 1 (Σ d).
  R1: Residual value for trait 1.
  Phen2: Phenotype for trait 2.
  EBV2: Estimated breeding value for trait 2.
  Acc2: Accuracy of estimated breeding value for trait 2.
  TGV2: True genotypic value for trait 2 (Σ (a + d)).
  TBV2: True breeding value for trait 2 (Σ a).
  TDD2: True dominance deviation for trait 2 (Σ d).
  R2: Residual value for trait 2.

Master_Genotypes.gz:
- A zipped file that contains genotypic information for individuals that survived.
  ID: Identification of individual.
  Marker: Marker genotypes of individual (0-11; 2-22; 3-12; 4-21).
  QTL: QTL genotypes of individual (0-11; 2-22; 3-12; 4-21).

Marker_Map:
- The marker map for SNP that were utilized to create a marker panel.
  chr: Chromosome location.
  pos: Nucleotide position of marker.

QTL_new_old_Class:
- A file that contains information on QTL effects and frequency across generations. If only one quantitative trait is simulated, columns for trait 2 are not displayed.
  Chr: Chromosome location.
  Pos: Nucleotide position of QTL.
  Additive Selective1: If it is a QTL it refers to the additive effect and if it is a FTL it refers to the selection coefficient for trait 1.
  Dominance2: The dominance effect for the QTL or degree of dominance for FTL for trait 1.
  Additive Selective2: If it is a QTL it refers to the additive effect and if it is a FTL it refers to the selection coefficient for trait 2.
  Dominance2: The dominance effect for the QTL or degree of dominance for FTL for trait 2.
  Type: Refers to the type of loci (2 = quantitative trait; 4 = fitness lethal; 5 = fitness sub-lethal).
  Gen: Generation at which the mutation occured.
  Freq: Allele frequency in the progeny. Each generation is separated by a underscore.

Low_Fitness:
- This file has a number of metrics for each individual that did not survive to breeding age and is the primary file to locate useful information when simulating fitness traits.
  Sire: Sire ID of individual.
  Dam: Dam ID of individual.
  Gen: Generation the animal was born.
  Ped_F: Pedigree based inbreeding metric.
  Gen_F: Diagonal of genomic based relationship constructed based on Van Raden (2008).
  Hap3_F: Diagonal of ROH based relationship matrix.
  Homozy: Proportion of the genome homozygous.
  Homolethal: Number of homozygous lethal genotypes.
  Heterlethal: Number of heterozygous lethal genotypes.
  Homosublethal: Number of homozygous sub-lethal genotypes.
  Hetersublethal: Number of heterozygous sub-lethal genotypes.
  Letequiv: Lethal equivalent value.
  Fitness: Multiplicative Fitness value of the individual.
  TGV1: True genotypic value of individual for trait 1 (Σ (a + d)).
  TTBV1: True breeding value of individual for trait 1 (Σ a).
  TTDD1: True dominance deviation of individual for trait 1 (Σ d).
  TTGV2: True genotypic value of individual for trait 2 (Σ (a + d)).
  TTBV2: True breeding value of individual for trait 2 (Σ a).
  TTDD2: True dominance deviation of individual for trait 2 (Σ d).
  QTL_Fitness: QTL genotypes of individual (0-11; 2-22; 3-12; 4-21).

Animal_GenoPheno_Status:
- This file outlines when and if an animal was genotyped along with whether they have a phenotype.
  ID: ID of individual.
  GenoStatus: Genotype Status.
  GenoStage: At what stage an animal was genotyped (i.e. selection candidate or parent).
  Pheno1Status: Phenotype status for trait 1.
  Pheno2Status: Phenotype status for trait 2.
  When_Culled: The stage of animal which includes selection candidate (popselcandidate), parent (popparent), culled as a selection candidated (popculled selcandidate) and culled as a parent (popculled parent).
  Generation_Born: Generation when animal was born.
  Age Culled: Age of an animal when it was culled.
  Progeny: Number of progeny.
  Sex: Sex of individual (0 = male and 1 = female).