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 mr1007 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
vg0921456056 sf0921455575 9 21456056 1.25E-20 2.64E-16
vg1218024420 sf1217995856 12 18024420 3.16E-11 4.43E-06
vg1218024396 sf1217995832 12 18024396 1.13E-10 6.17E-06
vg0922446085 sf0922445604 9 22446085 1.04E-09 NA
vg0524621673 sf0524559093 5 24621673 1.12E-09 NA
vg0219061231 sf0219055363 2 19061231 3.92E-09 NA
vg0523538514 sf0523475935 5 23538514 3.43E-07 NA
vg1009009289 sf1008938150 10 9009289 NA 7.96E-07
vg0817164286 sf0817161572 8 17164286 NA 9.75E-07
vg0817029761 sf0817027047 8 17029761 NA 1.51E-06
vg0905711629 sf0905710629 9 5711629 NA 3.23E-06
vg0135259527 sf0135258484 1 35259527 NA 4.91E-06