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 mr1889 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
vg0524406503 sf0524343924 5 24406503 5.43E-37 2.85E-22
vg1100512559 sf1100511562 11 512559 1.24E-18 2.48E-07
vg0524373363 sf0524310784 5 24373363 8.07E-18 7.23E-07
vg1122446629 sf1121980500 11 22446629 2.32E-17 2.59E-11
vg0524382156 sf0524319577 5 24382156 6.00E-17 1.84E-07
vg0600822160 sf0600821161 6 822160 1.03E-14 3.71E-06
vg1205231921 sf1205230907 12 5231921 3.16E-14 3.95E-08
vg1120734654 sf1120268557 11 20734654 1.01E-12 7.09E-07
vg0600140599 sf0600139599 6 140599 5.41E-12 2.03E-06
vg1214822893 sf1214820234 12 14822893 1.28E-09 NA
vg1214822906 sf1214820247 12 14822906 1.39E-09 2.32E-06
vg1004850765 sf1004867302 10 4850765 5.84E-09 4.95E-06
vg0135088154 sf0135087111 1 35088154 NA 1.14E-06
vg0515100790 sf0515043332 5 15100790 NA 2.80E-06
vg0205011592 sf0205011589 2 5011592 NA 3.11E-06
vg0702562003 sf0702561004 7 2562003 NA 4.16E-06