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 mr1562 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
vg0114542149 sf0114541123 1 14542149 1.61E-07 1.61E-07
vg0516853388 sf0516793029 5 16853388 3.49E-07 3.49E-07
vg0322731213 sf0322729702 3 22731213 5.54E-07 5.54E-07
vg1225798168 sf1225764562 12 25798168 9.44E-07 9.45E-07
vg0714532415 sf0714531422 7 14532415 1.15E-06 1.15E-06
vg0601434008 sf0601433009 6 1434008 1.26E-06 1.26E-06
vg0504587625 sf0504587602 5 4587625 1.54E-06 1.54E-06
vg0326606264 sf0326599318 3 26606264 1.87E-06 1.87E-06
vg0120129472 sf0120128427 1 20129472 2.00E-06 2.00E-06
vg0518412104 sf0518351590 5 18412104 2.22E-06 2.22E-06
vg1020162838 sf1020091336 10 20162838 2.44E-06 2.44E-06
vg0212840665 sf0212840661 2 12840665 2.58E-06 2.58E-06
vg0911253719 sf0911252718 9 11253719 3.72E-06 3.72E-06
vg0118253541 sf0118252495 1 18253541 3.77E-06 3.77E-06
vg0809419409 sf0809418413 8 9419409 4.47E-06 4.47E-06
vg0434884835 sf0434699725 4 34884835 4.50E-06 4.50E-06
vg0810067400 sf0810066404 8 10067400 4.71E-06 4.71E-06
vg0910719137 sf0910718136 9 10719137 6.95E-06 6.95E-06