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 mr1007 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
vg0921454415 sf0921453934 9 21454415 2.86E-21 9.83E-16
vg0921456056 sf0921455575 9 21456056 4.45E-21 2.05E-16
vg0921374162 sf0921373681 9 21374162 2.13E-10 1.54E-07
vg0922455577 sf0922455096 9 22455577 7.40E-09 NA
vg0915237973 sf0915236972 9 15237973 9.29E-09 NA
vg0808243581 sf0808242585 8 8243581 2.54E-08 NA
vg0504038203 sf0504038180 5 4038203 1.42E-07 1.78E-07
vg0205646080 sf0205646080 2 5646080 NA 3.93E-06
vg0913080416 sf0913079415 9 13080416 NA 4.55E-06
vg0328906605 sf0328899657 3 28906605 NA 7.25E-06