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 mr1052 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
vg0921456103 sf0921455622 9 21456103 1.63E-24 7.56E-18
vg0921456056 sf0921455575 9 21456056 7.04E-24 1.92E-19
vg0921456248 sf0921455767 9 21456248 2.99E-13 4.98E-06
vg1218024420 sf1217995856 12 18024420 4.64E-13 1.62E-06
vg0623453825 sf0623452828 6 23453825 1.59E-11 NA
vg0922446085 sf0922445604 9 22446085 3.57E-11 NA
vg1123023188 sf1122557059 11 23023188 2.21E-08 NA
vg0911617740 sf0911616739 9 11617740 2.34E-07 NA
vg0817164286 sf0817161572 8 17164286 NA 8.66E-07
vg0135237418 sf0135236375 1 35237418 NA 4.15E-06
vg0817111129 sf0817108415 8 17111129 NA 4.53E-06
vg0114089932 sf0114088906 1 14089932 NA 4.82E-06