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 mr1629 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
vg0206752992 sf0206752992 2 6752992 1.07E-112 1.12E-06
vg0228271226 sf0228265357 2 28271226 6.24E-112 2.33E-12
vg0331844988 sf0331837865 3 31844988 2.89E-110 NA
vg0228275399 sf0228269530 2 28275399 1.98E-109 1.84E-13
vg0221215158 sf0221209290 2 21215158 3.07E-104 NA
vg0216255973 sf0216250103 2 16255973 3.12E-104 NA
vg0215917784 sf0215911914 2 15917784 3.45E-102 9.58E-06
vg0228193045 sf0228187176 2 28193045 NA 1.31E-07
vg0142227444 sf0142226400 1 42227444 NA 3.75E-06
vg0510321290 sf0510321219 5 10321290 NA 4.46E-06