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 mr1004 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
vg0220043147 sf0220037279 2 20043147 3.72E-09 1.69E-11
vg0921454670 sf0921454189 9 21454670 4.21E-09 NA
vg0212300877 sf0212300873 2 12300877 7.07E-09 2.88E-07
vg0921446168 sf0921445687 9 21446168 1.36E-08 NA
vg0429014530 sf0428829388 4 29014530 1.95E-08 2.22E-06
vg0614462670 sf0614461671 6 14462670 1.24E-07 NA
vg0501245720 sf0501245704 5 1245720 1.61E-07 8.38E-08
vg0400650174 sf0400649173 4 650174 2.75E-07 1.52E-06
vg0215099729 sf0215093859 2 15099729 3.31E-07 2.48E-06
vg0728961469 sf0728960477 7 28961469 3.91E-07 NA
vg0314683652 sf0314682339 3 14683652 7.31E-07 3.03E-06
vg0627526239 sf0627525241 6 27526239 2.44E-06 3.25E-07
vg0208229343 sf0208229342 2 8229343 3.69E-06 2.70E-07
vg0523485262 sf0523422683 5 23485262 5.06E-06 1.03E-06
vg0600114214 sf0600113214 6 114214 5.81E-06 4.25E-06
vg1001623967 sf1001622944 10 1623967 9.30E-06 1.51E-08
vg0706877418 sf0706876423 7 6877418 NA 3.65E-09
vg0716176808 sf0716175815 7 16176808 NA 7.32E-08
vg0506765429 sf0506765371 5 6765429 NA 1.09E-07
vg0417367372 sf0417195415 4 17367372 NA 4.40E-07
vg0627106092 sf0627105095 6 27106092 NA 9.53E-07
vg0725477178 sf0725476184 7 25477178 NA 2.70E-06
vg0713636558 sf0713635565 7 13636558 NA 4.33E-06
vg1117608756 sf1117142612 11 17608756 NA 4.83E-06