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 mr1470 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
vg0107645362 sf0107644362 1 7645362 4.98E-09 6.46E-07
vg0805992743 sf0805991746 8 5992743 1.76E-08 2.29E-06
vg0105523729 sf0105522729 1 5523729 1.84E-08 2.15E-06
vg1206186379 sf1206185270 12 6186379 5.26E-08 1.30E-06
vg1011651673 sf1011580488 10 11651673 7.06E-08 4.85E-06
vg0107647091 sf0107646091 1 7647091 8.54E-07 3.02E-07
vg0316549393 sf0316548038 3 16549393 1.06E-06 4.61E-06
vg1208977468 sf1208974876 12 8977468 3.40E-06 3.07E-07
vg0205031937 sf0205031934 2 5031937 NA 8.94E-06