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 mr1715 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
vg0315534358 sf0315533005 3 15534358 9.95E-10 5.51E-06
vg0527125919 sf0527063275 5 27125919 7.41E-09 NA
vg1226380204 sf1226346598 12 26380204 1.16E-08 NA
vg0403563096 sf0403558698 4 3563096 2.54E-08 NA
vg1005530195 sf1005546732 10 5530195 3.70E-08 NA
vg0526119802 sf0526057222 5 26119802 7.03E-08 NA
vg0825565228 sf0825562514 8 25565228 1.31E-07 1.26E-06
vg0600926009 sf0600925010 6 926009 5.69E-07 1.11E-06
vg1121944084 sf1121477955 11 21944084 2.62E-06 4.77E-06
vg1004195671 sf1004142537 10 4195671 3.02E-06 NA
vg0705673479 sf0705672480 7 5673479 NA 2.27E-06
vg0422049007 sf0421895582 4 22049007 NA 4.58E-06