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 mr1226 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
vg0719007567 sf0719006574 7 19007567 1.36E-25 1.04E-12
vg0719011406 sf0719010413 7 19011406 3.13E-24 1.27E-13
vg0719147285 sf0719146292 7 19147285 6.18E-21 4.34E-10
vg0719242112 sf0719241119 7 19242112 2.59E-19 1.13E-09
vg1201654412 sf1201653412 12 1654412 3.05E-19 3.53E-07
vg1201345845 sf1201344845 12 1345845 NA 3.60E-08
vg1201512648 sf1201511648 12 1512648 NA 1.52E-07
vg0304916753 sf0304915755 3 4916753 NA 2.43E-07
vg0718998483 sf0718997490 7 18998483 NA 3.14E-07
vg0503738341 sf0503738318 5 3738341 NA 5.03E-07
vg0719140875 sf0719139882 7 19140875 NA 8.36E-07
vg1202504415 sf1202503417 12 2504415 NA 8.68E-07
vg0706547098 sf0706546103 7 6547098 NA 9.61E-07
vg0707515285 sf0707514290 7 7515285 NA 9.98E-07
vg0421119918 sf0420947970 4 21119918 NA 1.46E-06
vg1119409590 sf1118943278 11 19409590 NA 2.04E-06
vg0714370352 sf0714369359 7 14370352 NA 4.97E-06
vg0315225430 sf0315224077 3 15225430 NA 6.40E-06