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 mr1113 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
vg1008520987 sf1008449849 10 8520987 1.32E-17 4.37E-11
vg1204314449 sf1204313437 12 4314449 1.35E-14 9.50E-10
vg0905249361 sf0905248361 9 5249361 1.61E-14 NA
vg0407824132 sf0407819400 4 7824132 1.86E-14 9.86E-08
vg1005905764 sf1005922302 10 5905764 4.34E-14 6.23E-09
vg1216843191 sf1216837145 12 16843191 4.96E-14 1.40E-08
vg0501908149 sf0501908131 5 1908149 1.24E-10 7.31E-08
vg0403205910 sf0403201513 4 3205910 5.66E-10 3.23E-08
vg0501809225 sf0501809208 5 1809225 6.01E-10 5.79E-07
vg0708524273 sf0708523278 7 8524273 1.40E-09 1.97E-06
vg1223473790 sf1223440250 12 23473790 1.65E-09 1.64E-06
vg1007445967 sf1007461590 10 7445967 9.07E-08 1.39E-06
vg0315572376 sf0315571023 3 15572376 1.35E-07 4.68E-06
vg0601673777 sf0601672778 6 1673777 1.69E-06 NA
vg0920478307 sf0920477826 9 20478307 2.90E-06 1.27E-06
vg0408965989 sf0408961265 4 8965989 4.67E-06 2.71E-06
vg1010541730 sf1010470551 10 10541730 NA 6.53E-07
vg0417689977 sf0417518018 4 17689977 NA 1.26E-06
vg0718582884 sf0718581891 7 18582884 NA 4.67E-06
vg0427400029 sf0427214893 4 27400029 NA 4.88E-06