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 mr1922 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
vg0917464960 sf0917463959 9 17464960 1.56E-34 3.10E-06
vg0233645466 sf0233639597 2 33645466 2.39E-34 1.07E-06
vg1227345530 sf1227311930 12 27345530 2.83E-34 5.79E-06
vg0914955409 sf0914954408 9 14955409 5.23E-34 NA
vg0922486189 sf0922485708 9 22486189 1.62E-33 NA
vg0625911134 sf0625910137 6 25911134 1.14E-32 4.46E-06
vg0819251922 sf0819249209 8 19251922 1.93E-31 8.31E-06
vg0919894626 sf0919894145 9 19894626 3.85E-28 1.10E-07
vg1006010925 sf1006027463 10 6010925 NA 1.57E-07
vg0234163711 sf0234157842 2 34163711 NA 3.06E-07
vg1216468379 sf1216465672 12 16468379 NA 1.31E-06
vg1005588645 sf1005605183 10 5588645 NA 1.57E-06
vg1009130986 sf1009059847 10 9130986 NA 1.82E-06
vg0726691050 sf0726690056 7 26691050 NA 2.22E-06
vg0908568026 sf0908567025 9 8568026 NA 3.69E-06
vg1006141936 sf1006158478 10 6141936 NA 4.33E-06