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 mr1235 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
vg0216763637 sf0216757767 2 16763637 1.90E-17 2.23E-09
vg0506159272 sf0506159211 5 6159272 9.41E-13 NA
vg1219345800 sf1219317270 12 19345800 1.61E-12 NA
vg0519916493 sf0519853969 5 19916493 3.24E-12 NA
vg0515732737 sf0515675278 5 15732737 7.01E-12 NA
vg1128883554 sf1128360333 11 28883554 1.28E-09 4.91E-06