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 mr1333 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
vg0706513088 sf0706512093 7 6513088 1.20E-18 NA
vg0226148109 sf0226142240 2 26148109 2.81E-18 NA
vg0721760138 sf0721759145 7 21760138 9.20E-18 NA
vg0622253727 sf0622252730 6 22253727 1.45E-17 NA
vg0304933331 sf0304932333 3 4933331 2.61E-17 NA
vg0205434835 sf0205434835 2 5434835 1.86E-14 NA
vg0315250257 sf0315248904 3 15250257 NA 1.83E-07
vg0107647091 sf0107646091 1 7647091 NA 1.93E-07
vg1125281160 sf1124815000 11 25281160 NA 2.29E-06
vg0205031937 sf0205031934 2 5031937 NA 4.55E-06