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 mr1158 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
vg0700103970 sf0700102970 7 103970 2.99E-15 2.68E-07
vg0700013531 sf0700012531 7 13531 7.24E-15 1.45E-07
vg0104860223 sf0104859223 1 4860223 5.19E-12 NA
vg0406169990 sf0406165430 4 6169990 1.76E-10 NA
vg1000093149 sf1000092149 10 93149 2.41E-10 1.36E-06
vg0528095084 sf0528032439 5 28095084 4.66E-10 NA
vg0421038480 sf0420866534 4 21038480 4.63E-09 2.02E-06
vg1000091714 sf1000090714 10 91714 7.89E-09 4.78E-07
vg1000060841 sf1000059841 10 60841 3.79E-08 6.34E-07
vg1126339132 sf1125867545 11 26339132 4.45E-08 3.29E-06
vg0421227235 sf0421055287 4 21227235 2.39E-07 NA
vg1126452884 sf1125981297 11 26452884 5.46E-07 NA
vg0604453219 sf0604452220 6 4453219 1.12E-06 3.64E-06