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Jianbo He edited this page Oct 25, 2019 · 7 revisions

RTM-GWAS-SNPLDB

  • (.vcf) The SNPLDB genotype data file in VCF format

  • (.block) The estimated genomic block information

  • (.allele) The haplotype code for each marker

RTM-GWAS-GSC

  • (.mat) The symmetric genetic similarity coefficient (GSC) matrix

  • (.eval) The engenvalues of the GSC matrix

  • (.evec) The eigenvectors of the GSC matrix

RTM-GWAS-ASSOC

  • (.loc) A list of detected loci (marker names) for each trait
>Trait-1
LDB_1_1000
LDB_2_2000
>Trait-2
LDB_3_3000
LDB_4_4000
  • (.aov1) (.aov3) Type I and type III ANOVA table of the final multi-locus model
>Trait-1
Source DF SS MS F p
...

Calculate phenotypic variation explained (PVE, R^2)

R^2_i = SSQ_i / SST

where

SST = SSQ_1 + SSQ_2 + ... + SSQ_n + SSE

SSQ_i, the sum of squares of i-th locus

SST, the total sum of squares

SSE, the sum of squares of error

  • (.est) Model effect estimates (including allele effect)
>Trait-1
Parameter Estimate
...
  • (.pval) P-value of each marker at the forward selection and backward elimination procedure for QTL detection

This p-value is different from the final multi-QTL model in .aov1 and .aov3. When genotype-by-environment effect is considered, this p-value is from statistical hypothesis testing for the model (QTL + QTLxEnv.).

NOTE: as the total genetic contribution of detected loci is limited by specifying the option Max. model R-square (--rsq), the resulting p-value of a non-QTL marker may be less than significance level.
Locus Chromosome Position ft
...
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