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 mr1636 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
vg0205292054 sf0205292052 2 5292054 2.44E-11 2.44E-07
vg0205306560 sf0205306559 2 5306560 3.40E-11 1.26E-07
vg0726964336 sf0726963342 7 26964336 3.63E-10 NA
vg0916342758 sf0916341757 9 16342758 4.51E-09 NA
vg0131564206 sf0131563162 1 31564206 4.74E-09 NA
vg1104966259 sf1104962070 11 4966259 1.76E-08 NA
vg0300249514 sf0300248514 3 249514 1.02E-07 1.51E-06
vg0709448532 sf0709447538 7 9448532 1.23E-07 1.57E-06
vg0902200100 sf0902199100 9 2200100 9.87E-07 3.12E-06
vg0714622950 sf0714621957 7 14622950 1.72E-06 NA
vg0714470576 sf0714469583 7 14470576 NA 3.54E-06