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 mr1504 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
vg0138349324 sf0138348281 1 38349324 1.84E-09 3.57E-07
vg1227310775 sf1227277175 12 27310775 2.23E-09 2.98E-10
vg0605980045 sf0605979046 6 5980045 2.07E-08 NA
vg0810755455 sf0810754460 8 10755455 2.36E-08 NA
vg1109060930 sf1109055543 11 9060930 3.69E-08 NA
vg1109262627 sf1109257204 11 9262627 3.24E-07 1.67E-06
vg1227259456 sf1227225856 12 27259456 1.32E-06 2.49E-06
vg0518432302 sf0518371788 5 18432302 3.46E-06 NA
vg1121670141 sf1121204018 11 21670141 NA 3.46E-06
vg1214626036 sf1214623376 12 14626036 NA 4.93E-06