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 mr1251 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
vg0216800422 sf0216794552 2 16800422 7.45E-65 1.22E-24
vg0216699507 sf0216693637 2 16699507 4.28E-56 2.14E-11
vg0216767790 sf0216761920 2 16767790 7.62E-55 5.43E-12
vg0216627796 sf0216621926 2 16627796 1.31E-45 2.40E-13
vg0217463620 sf0217457750 2 17463620 6.01E-45 7.77E-10
vg0213818897 sf0213813027 2 13818897 1.16E-43 NA
vg0402172640 sf0402168235 4 2172640 1.52E-43 7.26E-07
vg0317478810 sf0317477592 3 17478810 4.41E-43 3.86E-06
vg0520296343 sf0520233816 5 20296343 3.07E-39 4.73E-06
vg0400014297 sf0400013297 4 14297 1.53E-37 6.46E-07
vg0317506741 sf0317505523 3 17506741 1.53E-37 3.69E-06
vg0400005711 sf0400004711 4 5711 2.01E-37 1.62E-06
vg0217232931 sf0217227061 2 17232931 NA 1.54E-12
vg0213525745 sf0213525741 2 13525745 NA 2.63E-08
vg0216576715 sf0216570845 2 16576715 NA 1.73E-07
vg0217327456 sf0217321586 2 17327456 NA 2.35E-07
vg0142085967 sf0142084924 1 42085967 NA 4.17E-07
vg0900337327 sf0900336327 9 337327 NA 9.23E-07
vg0216380390 sf0216374520 2 16380390 NA 1.70E-06
vg1121625049 sf1121158926 11 21625049 NA 2.84E-06
vg0622468172 sf0622467175 6 22468172 NA 4.65E-06