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 mr1178 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
vg1215854444 sf1215851740 12 15854444 2.04E-64 2.07E-30
vg1209571445 sf1209568854 12 9571445 6.13E-54 1.34E-22
vg1223872806 sf1223839259 12 23872806 5.88E-38 1.27E-09
vg1212726422 sf1212723761 12 12726422 1.70E-28 1.46E-09
vg0410423427 sf0410414126 4 10423427 5.30E-23 3.96E-07
vg1217065644 sf1217059599 12 17065644 1.43E-15 6.41E-08
vg0526374847 sf0526312210 5 26374847 2.07E-15 1.20E-06
vg1216192507 sf1216189803 12 16192507 2.97E-15 5.71E-13
vg1207570300 sf1207567705 12 7570300 6.21E-13 2.38E-10
vg1216261360 sf1216258656 12 16261360 1.66E-12 2.51E-07
vg0527368751 sf0527306107 5 27368751 2.69E-12 NA
vg1215958506 sf1215955802 12 15958506 3.05E-12 6.77E-07
vg1214847524 sf1214844865 12 14847524 1.13E-11 7.63E-10
vg1216261082 sf1216258378 12 16261082 NA 8.42E-08
vg1207838306 sf1207835712 12 7838306 NA 2.32E-07
vg0808847695 sf0808846699 8 8847695 NA 3.67E-07
vg1217055950 sf1217049905 12 17055950 NA 4.02E-07
vg1216679292 sf1216673246 12 16679292 NA 7.16E-07
vg0509418232 sf0509418161 5 9418232 NA 9.92E-07
vg0707363448 sf0707362453 7 7363448 NA 1.11E-06
vg1208194851 sf1208192257 12 8194851 NA 1.37E-06