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 mr1109 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
vg0216840888 sf0216835018 2 16840888 5.96E-101 2.48E-31
vg0217039117 sf0217033247 2 17039117 3.39E-99 5.11E-33
vg0525733901 sf0525671322 5 25733901 1.03E-72 1.32E-07
vg0220354869 sf0220349001 2 20354869 2.18E-68 NA
vg0221164625 sf0221158757 2 21164625 7.78E-67 2.20E-07
vg0520578454 sf0520515895 5 20578454 2.26E-66 NA
vg0317985175 sf0317983957 3 17985175 8.74E-65 NA
vg0524409418 sf0524346839 5 24409418 5.58E-61 6.40E-08
vg0524719942 sf0524657362 5 24719942 9.75E-60 8.06E-09
vg0217228197 sf0217222327 2 17228197 NA 5.59E-18
vg0524368371 sf0524305792 5 24368371 NA 5.76E-11
vg0524388914 sf0524326335 5 24388914 NA 3.07E-10
vg0217027146 sf0217021276 2 17027146 NA 3.39E-10
vg0213525745 sf0213525741 2 13525745 NA 6.27E-10
vg0900336799 sf0900335799 9 336799 NA 1.43E-08
vg0812023942 sf0812022947 8 12023942 NA 1.48E-08
vg1005364864 sf1005381401 10 5364864 NA 7.17E-08
vg0216474066 sf0216468196 2 16474066 NA 7.23E-08
vg0216633239 sf0216627369 2 16633239 NA 2.28E-07
vg0221192069 sf0221186201 2 21192069 NA 2.90E-07
vg0526174872 sf0526112292 5 26174872 NA 3.49E-07
vg0217327456 sf0217321586 2 17327456 NA 3.75E-07
vg0609171483 sf0609170484 6 9171483 NA 4.35E-07
vg0217845805 sf0217839936 2 17845805 NA 5.47E-07
vg0216763637 sf0216757767 2 16763637 NA 1.20E-06
vg1114596727 sf1114133045 11 14596727 NA 1.29E-06
vg0908235149 sf0908234149 9 8235149 NA 1.46E-06
vg0631235279 sf0631234281 6 31235279 NA 1.85E-06
vg0216383410 sf0216377540 2 16383410 NA 2.79E-06
vg0215905928 sf0215900058 2 15905928 NA 3.16E-06
vg0217940314 sf0217934445 2 17940314 NA 4.05E-06