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 mr1219 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
vg0605274340 sf0605273341 6 5274340 9.51E-38 3.03E-24
vg0605049749 sf0605048750 6 5049749 3.99E-18 1.81E-09
vg0605049951 sf0605048952 6 5049951 5.28E-18 1.98E-11
vg0605437555 sf0605436556 6 5437555 6.05E-18 2.87E-09
vg0605433695 sf0605432696 6 5433695 1.68E-17 6.90E-10
vg0605270755 sf0605269756 6 5270755 2.28E-17 1.08E-08
vg0605306584 sf0605305585 6 5306584 3.37E-16 7.42E-17
vg0605311849 sf0605310850 6 5311849 2.58E-13 2.69E-18
vg0605205203 sf0605204204 6 5205203 1.03E-11 4.06E-07
vg0605481649 sf0604784202 6 5481649 1.32E-10 1.15E-06
vg0605181590 sf0605180591 6 5181590 2.05E-10 2.17E-06
vg0605330241 sf0605329242 6 5330241 1.60E-08 1.21E-08
vg0125462906 sf0125461862 1 25462906 1.68E-06 1.71E-07
vg0234516971 sf0234511102 2 34516971 4.49E-06 3.99E-07
vg0200067614 sf0200067614 2 67614 5.06E-06 4.88E-08
vg0605259601 sf0605258602 6 5259601 NA 3.24E-09
vg0125383093 sf0125382049 1 25383093 NA 3.01E-07
vg0234360827 sf0234354958 2 34360827 NA 3.23E-07
vg1003005565 sf1003004542 10 3005565 NA 3.50E-07
vg1201219940 sf1201218940 12 1219940 NA 1.04E-06
vg0920825892 sf0920825411 9 20825892 NA 1.42E-06
vg0713012318 sf0713011325 7 13012318 NA 1.85E-06
vg0728437840 sf0728436848 7 28437840 NA 2.42E-06
vg1218161219 sf1218132655 12 18161219 NA 3.12E-06
vg0431357155 sf0431172049 4 31357155 NA 4.06E-06
vg0309810939 sf0309809875 3 9810939 NA 4.51E-06
vg1224593986 sf1224560440 12 24593986 NA 4.58E-06