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 mr1247 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 7.48E-17 5.60E-13
vg0336193973 sf0336186899 3 36193973 1.47E-13 3.39E-10
vg0727970899 sf0727969906 7 27970899 5.10E-13 7.55E-09
vg0728000317 sf0727999324 7 28000317 6.21E-13 3.47E-09
vg1001348300 sf1001347277 10 1348300 1.29E-12 2.95E-08
vg0504720198 sf0504720175 5 4720198 1.33E-12 1.37E-08
vg0308535729 sf0308534667 3 8535729 2.67E-11 2.89E-07
vg1126461419 sf1125989832 11 26461419 3.65E-11 8.34E-08
vg1016339056 sf1016267832 10 16339056 9.09E-11 1.23E-07
vg0334827866 sf0334820736 3 34827866 1.19E-10 3.99E-08
vg1117137503 sf1116671355 11 17137503 5.19E-10 2.91E-08
vg1201867679 sf1201866676 12 1867679 7.45E-10 2.14E-07
vg0424049928 sf0423864789 4 24049928 1.05E-09 9.68E-07
vg0906313471 sf0906312471 9 6313471 1.54E-09 1.79E-07
vg1204507349 sf1204506337 12 4507349 2.55E-09 6.77E-07
vg0819421680 sf0819418967 8 19421680 2.46E-08 1.28E-07
vg0224540597 sf0224534728 2 24540597 5.45E-08 1.71E-06
vg1205542061 sf1205541047 12 5542061 9.66E-08 1.51E-06
vg0219292377 sf0219286509 2 19292377 8.40E-07 1.02E-06
vg0714480545 sf0714479552 7 14480545 1.22E-06 1.17E-06
vg1204323457 sf1204322445 12 4323457 1.40E-06 8.51E-07