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 mr1031 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
vg1208149893 sf1208147299 12 8149893 3.22E-18 NA
vg0130113615 sf0130112570 1 30113615 3.30E-18 NA
vg1016262709 sf1016191484 10 16262709 2.35E-17 2.04E-06
vg0434000706 sf0433815599 4 34000706 8.78E-17 4.59E-11
vg1222579507 sf1222545946 12 22579507 1.78E-16 NA
vg1216893534 sf1216887488 12 16893534 2.80E-16 2.81E-06
vg0526967577 sf0526904933 5 26967577 3.03E-16 4.59E-07
vg1214995780 sf1214993122 12 14995780 1.16E-14 NA
vg1208263364 sf1208260769 12 8263364 9.09E-14 3.25E-06
vg1216893924 sf1216887878 12 16893924 1.35E-13 6.29E-06
vg1209270443 sf1209267853 12 9270443 5.34E-13 1.36E-06
vg0234867369 sf0234861500 2 34867369 1.72E-12 NA
vg0713442761 sf0713441768 7 13442761 NA 4.21E-07
vg1020760386 sf1020688865 10 20760386 NA 7.93E-07
vg0905473217 sf0905472217 9 5473217 NA 1.06E-06
vg1118299752 sf1117833611 11 18299752 NA 1.86E-06
vg1015803765 sf1015732535 10 15803765 NA 1.94E-06
vg1020694761 sf1020623240 10 20694761 NA 2.88E-06
vg0801514213 sf0801513215 8 1514213 NA 3.65E-06