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 mr1090 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
vg0610609054 sf0610608055 6 10609054 7.48E-29 1.48E-22
vg0610752378 sf0610751379 6 10752378 1.91E-25 6.68E-21
vg0403922278 sf0403917884 4 3922278 6.88E-14 1.36E-09
vg0610370985 sf0610369986 6 10370985 1.76E-11 2.84E-08
vg0132765829 sf0132764785 1 32765829 1.85E-11 NA
vg1006614973 sf1006630596 10 6614973 2.06E-11 7.06E-06
vg0626895745 sf0626894748 6 26895745 1.45E-10 1.25E-09
vg0610358655 sf0610357656 6 10358655 2.01E-10 1.15E-08
vg0901474384 sf0901473384 9 1474384 2.06E-10 2.43E-06
vg0701068994 sf0701067994 7 1068994 2.61E-10 6.17E-07
vg0629851797 sf0629850799 6 29851797 3.47E-10 4.16E-08
vg0135554286 sf0135553243 1 35554286 1.32E-09 4.59E-06
vg1004377181 sf1004393719 10 4377181 2.04E-09 8.86E-07
vg1222906823 sf1222873262 12 22906823 2.19E-09 4.62E-06
vg0316691399 sf0316690045 3 16691399 2.32E-09 1.71E-06
vg0910025779 sf0910024778 9 10025779 8.29E-09 1.07E-07
vg1202381362 sf1202380363 12 2381362 2.11E-08 7.05E-07
vg0307412350 sf0307411288 3 7412350 2.49E-08 4.67E-07
vg0523792337 sf0523729758 5 23792337 4.35E-08 9.54E-07
vg0609451875 sf0609450876 6 9451875 6.16E-08 NA
vg0717838198 sf0717837205 7 17838198 2.97E-07 1.10E-06
vg0610453711 sf0610452712 6 10453711 NA 2.42E-07
vg1120970935 sf1120504812 11 20970935 NA 1.93E-06
vg0610071263 sf0610070264 6 10071263 NA 4.79E-06
vg1004371908 sf1004388446 10 4371908 NA 4.87E-06