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 mr1422 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
vg0506207863 sf0506207802 5 6207863 6.72E-13 8.95E-10
vg1215227027 sf1215224324 12 15227027 1.07E-10 1.66E-07
vg0612076142 sf0612075143 6 12076142 3.04E-10 1.08E-06
vg0209789548 sf0209789546 2 9789548 3.84E-10 1.67E-06
vg0904668868 sf0904667868 9 4668868 4.12E-10 3.13E-07
vg0107079944 sf0107078944 1 7079944 5.41E-10 2.63E-06
vg0608860294 sf0608859295 6 8860294 2.09E-09 1.22E-06
vg0229293828 sf0229287959 2 29293828 3.36E-09 9.84E-07
vg1208079291 sf1208076697 12 8079291 5.67E-09 4.78E-06
vg1104144721 sf1104140623 11 4144721 8.41E-09 4.85E-06
vg0502976477 sf0502976453 5 2976477 1.14E-08 4.89E-06
vg0335559333 sf0335552202 3 35559333 1.26E-08 2.54E-06
vg0316786220 sf0316785094 3 16786220 1.70E-08 2.30E-06
vg0720205040 sf0720204047 7 20205040 1.96E-08 NA
vg0819769034 sf0819766321 8 19769034 4.97E-08 4.54E-07
vg0800558745 sf0800557745 8 558745 7.57E-08 1.90E-06