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 mr1310 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
vg1122897896 sf1122431767 11 22897896 4.59E-12 5.51E-09
vg0408888649 sf0408883926 4 8888649 9.68E-12 7.42E-08
vg0403236974 sf0403232577 4 3236974 2.24E-11 1.97E-07
vg0601277802 sf0601276803 6 1277802 4.38E-11 9.73E-07
vg0106964159 sf0106963159 1 6964159 1.08E-10 2.54E-08
vg0906478875 sf0906477875 9 6478875 1.69E-10 1.87E-06
vg0601571227 sf0601570228 6 1571227 6.17E-10 3.12E-07
vg0601604412 sf0601603413 6 1604412 2.13E-09 3.39E-07
vg0601414570 sf0601413571 6 1414570 2.53E-09 7.15E-07
vg0321300282 sf0321298792 3 21300282 7.01E-09 1.85E-06
vg1218430387 sf1218401823 12 18430387 7.76E-09 2.86E-07
vg1003367906 sf1003366883 10 3367906 1.01E-08 5.21E-08
vg0506796325 sf0506796267 5 6796325 1.88E-07 7.06E-07
vg0210038513 sf0210038511 2 10038513 1.98E-07 1.33E-07
vg0622335108 sf0622334111 6 22335108 2.07E-07 2.47E-06
vg0216601168 sf0216595298 2 16601168 4.53E-07 5.29E-07
vg0803418306 sf0803417309 8 3418306 4.85E-07 1.27E-06
vg0230849830 sf0230843961 2 30849830 1.25E-06 2.15E-06
vg0601059247 sf0601058248 6 1059247 2.42E-06 2.65E-06
vg1102224382 sf1102220240 11 2224382 2.53E-06 8.65E-07
vg0218086395 sf0218080526 2 18086395 NA 1.76E-06