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 mr1190 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
vg0223190854 sf0223184985 2 23190854 1.28E-10 NA
vg0505822309 sf0505822247 5 5822309 2.83E-10 7.98E-06
vg0129864706 sf0129863661 1 29864706 4.53E-10 NA
vg0922565216 sf0922564735 9 22565216 6.83E-10 NA
vg0124877078 sf0124876034 1 24877078 1.07E-09 NA
vg0626102263 sf0626101266 6 26102263 4.51E-08 NA
vg0113766179 sf0113765153 1 13766179 2.13E-07 NA
vg0232802493 sf0232796624 2 32802493 2.28E-07 NA
vg0706131395 sf0706130396 7 6131395 NA 2.16E-06
vg1222068437 sf1222034984 12 22068437 NA 3.97E-06
vg0505629606 sf0505629544 5 5629606 NA 6.91E-06
vg1217175426 sf1217169381 12 17175426 NA 8.79E-06