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 mr1253 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
vg0216732271 sf0216726401 2 16732271 3.67E-24 4.00E-20
vg0812023942 sf0812022947 8 12023942 2.03E-12 6.42E-08
vg0216372846 sf0216366976 2 16372846 3.66E-10 3.08E-06
vg0216510941 sf0216505071 2 16510941 3.81E-09 2.99E-07
vg0212179963 sf0212179959 2 12179963 5.20E-09 1.98E-06
vg0216104235 sf0216098365 2 16104235 5.55E-09 3.78E-06
vg0900337327 sf0900336327 9 337327 6.17E-09 1.85E-06
vg0117778414 sf0117777368 1 17778414 1.60E-08 1.60E-06
vg1114473442 sf1114009759 11 14473442 2.13E-08 3.55E-06
vg1008865540 sf1008794402 10 8865540 6.82E-08 9.13E-07
vg1005364262 sf1005380799 10 5364262 1.47E-07 2.74E-07
vg0216814133 sf0216808263 2 16814133 2.15E-07 2.60E-06
vg0217242774 sf0217236904 2 17242774 3.23E-07 1.09E-07
vg0224385108 sf0224379239 2 24385108 NA 2.32E-06
vg0706644677 sf0706643682 7 6644677 NA 6.87E-06