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 mr1435 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 7.42E-65 1.42E-24
vg0216699507 sf0216693637 2 16699507 8.82E-56 3.61E-11
vg0216767790 sf0216761920 2 16767790 1.50E-54 8.91E-12
vg0216627796 sf0216621926 2 16627796 1.85E-45 3.12E-13
vg0217463620 sf0217457750 2 17463620 7.79E-45 1.42E-09
vg0213818897 sf0213813027 2 13818897 6.70E-44 NA
vg0402172640 sf0402168235 4 2172640 1.18E-43 7.34E-07
vg0317478810 sf0317477592 3 17478810 2.37E-43 3.31E-06
vg0520296343 sf0520233816 5 20296343 1.74E-39 4.29E-06
vg0317506741 sf0317505523 3 17506741 9.11E-38 3.27E-06
vg0400014297 sf0400013297 4 14297 1.25E-37 6.30E-07
vg0400005711 sf0400004711 4 5711 1.66E-37 1.63E-06
vg0217232931 sf0217227061 2 17232931 NA 1.20E-12
vg0213525745 sf0213525741 2 13525745 NA 2.79E-08
vg0216576715 sf0216570845 2 16576715 NA 1.58E-07
vg0217327456 sf0217321586 2 17327456 NA 2.73E-07
vg0142085967 sf0142084924 1 42085967 NA 4.00E-07
vg0900337327 sf0900336327 9 337327 NA 9.70E-07
vg0216380390 sf0216374520 2 16380390 NA 1.52E-06
vg1121625049 sf1121158926 11 21625049 NA 3.15E-06
vg0622468172 sf0622467175 6 22468172 NA 4.68E-06