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 mr1200 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
vg0610752378 sf0610751379 6 10752378 9.71E-14 3.58E-11
vg0604638246 sf0604637247 6 4638246 7.62E-12 1.24E-07
vg0626895745 sf0626894748 6 26895745 3.73E-11 1.52E-10
vg0813336261 sf0813333816 8 13336261 7.56E-09 7.66E-06
vg0324965295 sf0324963375 3 24965295 8.06E-09 NA
vg0317440767 sf0317439549 3 17440767 2.05E-08 1.69E-06
vg0228232599 sf0228226730 2 28232599 2.10E-08 1.36E-06
vg0113977512 sf0113976486 1 13977512 2.30E-08 4.91E-06
vg0629851797 sf0629850799 6 29851797 2.36E-07 1.13E-06
vg1127529196 sf1127057583 11 27529196 5.13E-07 8.59E-07
vg0235302983 sf0235297114 2 35302983 8.70E-07 2.32E-06
vg1104309736 sf1104305638 11 4309736 6.24E-06 4.42E-06
vg0306976273 sf0306975271 3 6976273 7.53E-06 NA
vg0130953874 sf0130952830 1 30953874 NA 1.75E-07
vg0421799928 sf0421627978 4 21799928 NA 3.15E-06