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 mr1037 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
vg0402389835 sf0402385430 4 2389835 5.32E-17 5.45E-14
vg0205658378 sf0205658378 2 5658378 1.16E-09 2.38E-08
vg0403108372 sf0403103975 4 3108372 1.46E-09 3.05E-06
vg0404314509 sf0404310115 4 4314509 4.49E-09 5.19E-07
vg1010719593 sf1010648414 10 10719593 9.64E-09 1.23E-07
vg0404309404 sf0404305010 4 4309404 1.02E-08 8.98E-07
vg0205889382 sf0205889382 2 5889382 1.26E-08 5.89E-07
vg0921454670 sf0921454189 9 21454670 1.44E-08 NA
vg0205633844 sf0205633844 2 5633844 5.96E-08 1.05E-06
vg1215004734 sf1215002076 12 15004734 8.01E-08 2.58E-06
vg0402048808 sf0402044404 4 2048808 1.17E-07 2.40E-08
vg0313463686 sf0313462404 3 13463686 1.52E-07 2.65E-07
vg0912507153 sf0912506152 9 12507153 3.90E-07 1.19E-06
vg0402701254 sf0402696859 4 2701254 5.28E-07 2.12E-06
vg0421287077 sf0421115131 4 21287077 3.10E-06 3.06E-06
vg0918096355 sf0918095354 9 18096355 NA 1.11E-06
vg0323551151 sf0323549325 3 23551151 NA 1.31E-06
vg0107832208 sf0107831208 1 7832208 NA 2.33E-06
vg1208405606 sf1208403012 12 8405606 NA 4.91E-06
vg0620936633 sf0620935636 6 20936633 NA 9.25E-06