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 mr1065 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
vg0610559165 sf0610558166 6 10559165 6.13E-69 2.38E-45
vg0610566237 sf0610565238 6 10566237 4.54E-68 3.04E-50
vg0610548932 sf0610547933 6 10548932 3.91E-49 6.58E-30
vg0610412338 sf0610411339 6 10412338 6.21E-38 9.30E-24
vg0610548064 sf0610547065 6 10548064 1.34E-36 3.78E-20
vg0610609112 sf0610608113 6 10609112 5.28E-27 9.95E-18
vg0617319066 sf0617318069 6 17319066 8.22E-25 1.95E-07
vg0610873460 sf0610872461 6 10873460 4.01E-23 7.36E-12
vg0614169262 sf0614168263 6 14169262 2.45E-22 NA
vg0611561542 sf0611560543 6 11561542 2.37E-21 2.11E-13
vg0609889304 sf0609888305 6 9889304 7.71E-20 4.34E-13
vg0611478431 sf0611477432 6 11478431 4.44E-17 1.02E-11
vg0612086046 sf0612085047 6 12086046 3.14E-16 1.43E-11
vg0920309265 sf0920308784 9 20309265 3.67E-16 1.24E-09
vg0610679932 sf0610678933 6 10679932 5.42E-15 2.87E-17
vg0610445215 sf0610444216 6 10445215 6.73E-15 1.69E-12
vg0610589825 sf0610588826 6 10589825 9.70E-15 3.21E-12
vg0610442142 sf0610441143 6 10442142 4.59E-14 3.76E-15
vg0611946117 sf0611945118 6 11946117 1.08E-13 6.13E-10
vg0611303174 sf0611302175 6 11303174 3.53E-13 1.76E-07
vg0615150907 sf0615149908 6 15150907 1.55E-12 1.67E-07
vg0610752419 sf0610751420 6 10752419 4.34E-12 4.43E-10
vg0610127588 sf0610126589 6 10127588 NA 4.16E-12
vg0611646456 sf0611645457 6 11646456 NA 6.82E-10
vg0618988041 sf0618987044 6 18988041 NA 1.84E-09
vg0613809145 sf0613808146 6 13809145 NA 2.13E-08