Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1192 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0303329795 sf0303328791 3 3329795 5.88E-11 1.61E-06
vg0328555824 sf0328548877 3 28555824 7.58E-10 NA
vg0819798927 sf0819796214 8 19798927 9.60E-09 NA
vg0139783926 sf0139782883 1 39783926 1.25E-08 NA
vg0421455278 sf0421283329 4 21455278 1.63E-08 9.05E-06
vg0328874978 sf0328868031 3 28874978 1.10E-07 3.81E-06
vg0101302139 sf0101301139 1 1302139 7.22E-06 NA
vg0333682687 sf0333675557 3 33682687 NA 1.67E-06