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 mr1275 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
vg0500632216 sf0500632216 5 632216 5.34E-12 NA
vg0922414567 sf0922414086 9 22414567 1.36E-11 NA
vg0624913214 sf0624912217 6 24913214 1.60E-11 NA
vg0819446140 sf0819443427 8 19446140 1.75E-11 NA
vg0606734750 sf0606733751 6 6734750 2.36E-11 NA
vg0501988258 sf0501988240 5 1988258 2.25E-10 NA
vg1218873031 sf1218844466 12 18873031 8.46E-10 4.12E-07
vg0313119247 sf0313117965 3 13119247 1.30E-09 1.48E-07
vg0308147280 sf0308146218 3 8147280 3.64E-09 NA
vg1218283417 sf1218254853 12 18283417 3.89E-09 NA
vg0211778484 sf0211778480 2 11778484 9.46E-09 2.15E-08
vg0500592900 sf0500592900 5 592900 9.61E-09 1.85E-07
vg0529106995 sf0529044350 5 29106995 1.03E-08 4.30E-08
vg1016663184 sf1016591957 10 16663184 NA 6.59E-08
vg0304018299 sf0304017295 3 4018299 NA 1.12E-07
vg0131782604 sf0131781560 1 31782604 NA 1.95E-07
vg0407782064 sf0407777332 4 7782064 NA 2.01E-07
vg0614873719 sf0614872720 6 14873719 NA 3.60E-07
vg0422565347 sf0422380232 4 22565347 NA 1.12E-06
vg0316098012 sf0316096659 3 16098012 NA 1.20E-06
vg0703278160 sf0703277161 7 3278160 NA 1.21E-06
vg0216328568 sf0216322698 2 16328568 NA 1.34E-06
vg0409862256 sf0409852954 4 9862256 NA 1.39E-06
vg0814029225 sf0814026511 8 14029225 NA 1.42E-06
vg0813601775 sf0813599060 8 13601775 NA 1.51E-06
vg1017231275 sf1017160048 10 17231275 NA 1.97E-06
vg0715358715 sf0715357722 7 15358715 NA 2.02E-06
vg0715640459 sf0715639466 7 15640459 NA 2.20E-06
vg0211759191 sf0211759187 2 11759191 NA 2.32E-06
vg0420839554 sf0420667597 4 20839554 NA 2.53E-06
vg1217631816 sf1217625771 12 17631816 NA 3.28E-06
vg0811931786 sf0811930791 8 11931786 NA 3.75E-06
vg0224428620 sf0224422751 2 24428620 NA 4.24E-06
vg1217611926 sf1217605881 12 17611926 NA 4.59E-06
vg0208268939 sf0208268938 2 8268939 NA 9.17E-06