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 mr1218 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
vg1104144713 sf1104140615 11 4144713 3.96E-13 4.05E-11
vg0608860294 sf0608859295 6 8860294 9.04E-10 1.27E-07
vg0815322514 sf0815319800 8 15322514 3.55E-09 1.64E-07
vg1202732210 sf1202731212 12 2732210 5.57E-09 3.86E-06
vg1217218651 sf1217212606 12 17218651 1.21E-08 1.58E-06
vg1002115213 sf1002114190 10 2115213 1.35E-08 4.22E-07
vg1209341359 sf1209338768 12 9341359 1.76E-08 4.06E-06
vg0812106092 sf0812105097 8 12106092 6.12E-08 8.69E-07
vg0807835171 sf0807834175 8 7835171 1.30E-07 1.53E-06
vg0402328521 sf0402324116 4 2328521 4.20E-06 NA
vg1124274881 sf1123808751 11 24274881 5.55E-06 4.52E-06
vg0600160651 sf0600159651 6 160651 NA 2.69E-06