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 mr1116 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
vg0421387824 sf0421215877 4 21387824 4.72E-09 2.17E-07
vg0225214236 sf0225208367 2 25214236 1.38E-08 4.63E-08
vg0812524957 sf0812522509 8 12524957 3.18E-08 1.33E-06
vg1201867679 sf1201866676 12 1867679 3.25E-08 4.71E-07
vg1001348300 sf1001347277 10 1348300 4.99E-08 3.30E-06
vg0432747868 sf0432562754 4 32747868 5.46E-08 1.42E-06
vg0136191693 sf0136190650 1 36191693 5.52E-08 3.23E-07
vg0727970899 sf0727969906 7 27970899 7.45E-08 1.41E-06
vg0139756098 sf0139755055 1 39756098 9.94E-08 8.05E-07
vg0504720198 sf0504720175 5 4720198 1.01E-07 3.83E-06
vg0515214258 sf0515156800 5 15214258 1.06E-07 3.45E-06
vg0432825867 sf0432640753 4 32825867 1.20E-07 2.67E-07
vg1016339056 sf1016267832 10 16339056 1.57E-07 1.57E-06
vg0127078208 sf0127077164 1 27078208 2.05E-07 2.00E-06
vg0220479498 sf0220473630 2 20479498 2.64E-07 4.20E-06
vg1117137503 sf1116671355 11 17137503 3.07E-07 1.63E-06
vg0432345183 sf0432160072 4 32345183 5.25E-07 8.43E-08
vg0726032754 sf0726031760 7 26032754 8.72E-07 4.65E-06
vg1015833216 sf1015761986 10 15833216 1.44E-06 4.29E-06
vg0224173859 sf0224167990 2 24173859 1.66E-06 4.53E-06
vg0710900359 sf0710899365 7 10900359 NA 1.82E-06
vg1006914384 sf1006930007 10 6914384 NA 5.48E-06