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 mr1114 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 2.38E-13 3.96E-10
vg0700863821 sf0700862821 7 863821 1.79E-11 7.97E-08
vg0141320383 sf0141319340 1 41320383 1.89E-11 4.84E-08
vg1117137503 sf1116671355 11 17137503 3.40E-11 1.53E-10
vg0108582948 sf0108581948 1 8582948 1.37E-10 8.39E-07
vg1201867679 sf1201866676 12 1867679 1.96E-10 5.00E-08
vg0728000317 sf0727999324 7 28000317 2.37E-10 2.98E-07
vg0136191693 sf0136190650 1 36191693 2.64E-10 1.07E-08
vg1016339056 sf1016267832 10 16339056 5.00E-10 1.47E-07
vg0515214258 sf0515156800 5 15214258 8.71E-10 1.48E-07
vg0336193973 sf0336186899 3 36193973 1.29E-09 6.15E-07
vg0127078208 sf0127077164 1 27078208 3.34E-09 1.69E-06
vg0225199712 sf0225193843 2 25199712 4.42E-09 4.67E-07
vg1002009944 sf1002008921 10 2009944 1.55E-08 7.83E-07
vg0910734256 sf0910733255 9 10734256 3.24E-08 7.18E-07
vg0224173859 sf0224167990 2 24173859 3.81E-08 7.32E-08
vg0432825867 sf0432640753 4 32825867 5.98E-08 1.54E-07
vg0709675216 sf0709674222 7 9675216 1.55E-07 3.08E-07
vg0432345183 sf0432160072 4 32345183 2.99E-07 3.51E-08
vg0621728622 sf0621727625 6 21728622 3.95E-06 6.21E-07
vg0123425063 sf0123424019 1 23425063 5.02E-06 6.59E-07
vg0710900359 sf0710899365 7 10900359 NA 7.90E-07