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 mr1237 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
vg0610567030 sf0610566031 6 10567030 4.69E-25 8.55E-14
vg0719259692 sf0719258699 7 19259692 3.49E-13 NA
vg0617319066 sf0617318069 6 17319066 3.90E-13 NA
vg0612996928 sf0612995929 6 12996928 7.01E-12 NA
vg0402394027 sf0402389622 4 2394027 9.41E-12 NA
vg0617629311 sf0617628314 6 17629311 2.65E-10 4.78E-06
vg0610684949 sf0610683950 6 10684949 3.36E-09 1.75E-07
vg0622250564 sf0622249567 6 22250564 9.72E-09 NA
vg0610419183 sf0610418184 6 10419183 3.66E-08 2.68E-08
vg0610661282 sf0610660283 6 10661282 1.36E-07 4.65E-06
vg1209051637 sf1209049046 12 9051637 2.89E-07 NA