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 mr1668 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
vg1119206802 sf1118740490 11 19206802 1.53E-09 NA
vg1119228700 sf1118762388 11 19228700 1.86E-09 NA
vg1117693473 sf1117227329 11 17693473 5.54E-08 NA
vg0331670849 sf0331663726 3 31670849 2.64E-07 2.44E-06
vg0607113275 sf0607112276 6 7113275 3.65E-06 NA
vg0319678890 sf0319677401 3 19678890 5.24E-06 2.85E-06
vg1102616547 sf1102612451 11 2616547 NA 1.38E-06
vg0434677023 sf0434491913 4 34677023 NA 2.30E-06