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 mr1038 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
vg1000256952 sf1000255952 10 256952 5.73E-08 5.73E-08
vg1127077047 sf1126605434 11 27077047 1.06E-07 1.06E-07
vg0526356740 sf0526294103 5 26356740 1.41E-07 1.41E-07
vg1224006854 sf1223973307 12 24006854 6.64E-07 6.64E-07
vg0105850195 sf0105849195 1 5850195 1.20E-06 1.20E-06
vg0623074199 sf0623073202 6 23074199 1.25E-06 1.25E-06
vg0906217253 sf0906216253 9 6217253 1.57E-06 1.57E-06
vg0106177750 sf0106176750 1 6177750 1.67E-06 1.67E-06
vg1119756808 sf1119290496 11 19756808 2.34E-06 2.34E-06
vg0233356353 sf0233350484 2 33356353 3.07E-06 3.07E-06
vg0603087867 sf0603086868 6 3087867 3.26E-06 3.26E-06
vg0107178303 sf0107177303 1 7178303 4.35E-06 4.35E-06
vg0819069416 sf0819066703 8 19069416 4.78E-06 4.78E-06
vg1223900974 sf1223867427 12 23900974 8.23E-06 8.23E-06