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 mr1936 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
vg0222740991 sf0222735122 2 22740991 8.59E-35 4.15E-14
vg0222735698 sf0222729829 2 22735698 1.03E-34 3.65E-14
vg0222732157 sf0222726288 2 22732157 1.14E-34 2.38E-14
vg0222679274 sf0222673405 2 22679274 1.09E-33 1.09E-17
vg0526722696 sf0526660054 5 26722696 3.29E-22 NA
vg1009101162 sf1009030023 10 9101162 4.39E-22 NA
vg0906971590 sf0906970590 9 6971590 2.46E-21 NA
vg0500435853 sf0500435853 5 435853 2.30E-19 1.15E-06
vg0907026290 sf0907025290 9 7026290 4.77E-19 3.47E-09
vg0703826736 sf0703825737 7 3826736 7.58E-19 7.74E-08
vg1110425815 sf1110420360 11 10425815 1.10E-18 6.49E-07
vg0616706040 sf0616705042 6 16706040 4.34E-18 2.04E-08
vg0106081038 sf0106080038 1 6081038 8.79E-18 1.93E-07
vg0316147114 sf0316145761 3 16147114 9.03E-18 5.57E-07
vg1218624984 sf1218596420 12 18624984 5.02E-15 5.91E-07
vg0709033301 sf0709032307 7 9033301 5.75E-15 4.69E-08
vg0220977977 sf0220972109 2 20977977 1.04E-14 5.59E-06
vg0223661758 sf0223655889 2 23661758 NA 6.45E-08
vg0820869390 sf0820866677 8 20869390 NA 6.77E-08
vg0311437556 sf0311436274 3 11437556 NA 1.47E-07
vg0222725003 sf0222719134 2 22725003 NA 2.14E-07
vg0421291212 sf0421119266 4 21291212 NA 2.33E-07
vg0431376032 sf0431190928 4 31376032 NA 3.91E-07
vg0224793205 sf0224787336 2 24793205 NA 4.23E-07
vg0626215270 sf0626214273 6 26215270 NA 5.41E-07
vg0222722554 sf0222716685 2 22722554 NA 7.51E-07
vg0819598853 sf0819596140 8 19598853 NA 8.96E-07
vg1204507349 sf1204506337 12 4507349 NA 9.42E-07
vg0222271516 sf0222265647 2 22271516 NA 1.34E-06
vg0804869267 sf0804868270 8 4869267 NA 8.89E-06