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 mr1409 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
vg0216629891 sf0216624021 2 16629891 6.85E-08 NA
vg0528732432 sf0528669787 5 28732432 1.87E-07 3.80E-07
vg0911066866 sf0911065865 9 11066866 2.54E-07 2.30E-07
vg0628269113 sf0628268115 6 28269113 8.79E-07 2.35E-06
vg0817501174 sf0817498460 8 17501174 2.54E-06 5.54E-07
vg1209657474 sf1209654883 12 9657474 3.68E-06 3.53E-06
vg0325763022 sf0325761040 3 25763022 9.42E-06 NA