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 mr1126 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
vg0610125380 sf0610124381 6 10125380 1.37E-06 1.37E-06
vg1112940954 sf1112477275 11 12940954 1.88E-06 1.88E-06
vg0624726893 sf0624725896 6 24726893 2.05E-06 2.05E-06
vg1121387639 sf1120921516 11 21387639 2.15E-06 2.16E-06
vg1009327905 sf1009256726 10 9327905 3.06E-06 3.06E-06
vg0701536569 sf0701535569 7 1536569 3.36E-06 3.36E-06
vg0610564701 sf0610563702 6 10564701 3.65E-06 3.65E-06
vg1114485005 sf1114021322 11 14485005 4.16E-06 4.17E-06
vg0913080416 sf0913079415 9 13080416 4.49E-06 4.49E-06