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 mr1174 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
vg0429956113 sf0429770980 4 29956113 9.38E-29 1.58E-16
vg0430000326 sf0429815193 4 30000326 1.51E-28 7.79E-17
vg0430595523 sf0430410398 4 30595523 9.55E-12 NA
vg0910273304 sf0910272303 9 10273304 4.25E-11 NA
vg0431259186 sf0431074076 4 31259186 2.53E-10 NA
vg0321827246 sf0321825756 3 21827246 5.10E-10 1.79E-06
vg0810358913 sf0810357917 8 10358913 4.06E-06 1.08E-06
vg1200189916 sf1200188916 12 189916 6.06E-06 NA
vg0429797838 sf0429612709 4 29797838 NA 2.24E-06
vg0312560070 sf0312558788 3 12560070 NA 3.00E-06