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 mr1377 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
vg0216800422 sf0216794552 2 16800422 5.32E-27 2.53E-11
vg0216638231 sf0216632361 2 16638231 9.66E-27 1.50E-11
vg0213525745 sf0213525741 2 13525745 1.61E-17 NA
vg0335141986 sf0335134856 3 35141986 2.72E-17 2.37E-06
vg0335142010 sf0335134880 3 35142010 5.00E-17 2.24E-06
vg0218736301 sf0218730432 2 18736301 1.28E-16 NA
vg0213138029 sf0213138025 2 13138029 4.37E-16 1.95E-06
vg0216121800 sf0216115930 2 16121800 4.74E-16 1.32E-06
vg0218866091 sf0218860222 2 18866091 1.89E-15 1.67E-06
vg0217232931 sf0217227061 2 17232931 NA 4.75E-07
vg0335946674 sf0335939543 3 35946674 NA 2.70E-06