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 mr1659 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
vg0623234685 sf0623233688 6 23234685 6.45E-12 2.63E-06
vg0622963063 sf0622962066 6 22963063 1.53E-11 9.14E-07
vg0623220810 sf0623219813 6 23220810 2.10E-11 4.31E-06
vg1104978992 sf1104974803 11 4978992 2.79E-10 2.33E-07
vg0302286724 sf0302285720 3 2286724 6.25E-10 NA
vg1101926914 sf1101925914 11 1926914 3.06E-09 NA
vg0130689494 sf0130688450 1 30689494 1.09E-08 NA
vg0101547765 sf0101546765 1 1547765 2.24E-07 3.98E-06
vg1210390475 sf1210387888 12 10390475 6.48E-07 4.12E-06
vg0431614108 sf0431429003 4 31614108 1.92E-06 2.48E-06
vg0215095083 sf0215089213 2 15095083 2.92E-06 1.41E-06
vg0404316759 sf0404312365 4 4316759 9.20E-06 1.47E-06
vg0816119916 sf0816117202 8 16119916 NA 3.62E-06
vg0404315449 sf0404311055 4 4315449 NA 4.67E-06