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 mr1510 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
vg1105453065 sf1105448816 11 5453065 1.37E-10 2.63E-06
vg0119495785 sf0119494740 1 19495785 1.56E-09 NA
vg0119476565 sf0119475520 1 19476565 5.51E-09 NA
vg0112126841 sf0112125815 1 12126841 7.42E-09 NA
vg0726931821 sf0726930827 7 26931821 7.67E-09 NA
vg0501179160 sf0501179144 5 1179160 3.00E-08 8.19E-06
vg0119708213 sf0119707168 1 19708213 1.69E-07 NA
vg0919908679 sf0919908198 9 19908679 3.68E-07 NA
vg0139155508 sf0139154465 1 39155508 3.34E-06 NA
vg0806942341 sf0806941346 8 6942341 4.04E-06 NA
vg0803044175 sf0803043178 8 3044175 NA 4.75E-06