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 mr1291 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
vg0902058823 sf0902057823 9 2058823 1.24E-08 2.12E-06
vg0200469050 sf0200469050 2 469050 1.68E-08 9.08E-06
vg0225470163 sf0225464294 2 25470163 4.54E-08 NA
vg0201096822 sf0201096822 2 1096822 5.77E-08 NA
vg1121671958 sf1121205835 11 21671958 8.16E-08 NA
vg0903263501 sf0903262501 9 3263501 4.91E-07 1.05E-06
vg1126878291 sf1126406678 11 26878291 1.09E-06 3.82E-06
vg0721855491 sf0721854498 7 21855491 1.53E-06 NA
vg0630585467 sf0630584469 6 30585467 3.16E-06 NA
vg0225218022 sf0225212153 2 25218022 6.15E-06 NA
vg0828075962 sf0828073248 8 28075962 7.70E-06 NA