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 mr1599 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
vg0216562778 sf0216556908 2 16562778 4.40E-84 2.10E-13
vg0216891914 sf0216886044 2 16891914 7.25E-83 1.40E-16
vg0216763637 sf0216757767 2 16763637 1.69E-81 2.18E-16
vg0719352448 sf0719351455 7 19352448 1.59E-66 NA
vg0216800422 sf0216794552 2 16800422 3.74E-66 1.02E-24
vg0213818897 sf0213813027 2 13818897 7.86E-66 NA
vg1101092613 sf1101091614 11 1092613 1.08E-65 NA
vg0216822884 sf0216817014 2 16822884 1.43E-65 1.07E-24
vg0402172640 sf0402168235 4 2172640 9.34E-62 3.76E-07
vg0217232931 sf0217227061 2 17232931 NA 2.77E-11
vg0213525745 sf0213525741 2 13525745 NA 1.51E-09
vg0525571168 sf0525508589 5 25571168 NA 4.47E-07
vg0526133789 sf0526071209 5 26133789 NA 4.81E-07
vg0900337327 sf0900336327 9 337327 NA 5.80E-07
vg0217266536 sf0217260666 2 17266536 NA 2.81E-06
vg0216761078 sf0216755208 2 16761078 NA 3.52E-06
vg0217364866 sf0217358996 2 17364866 NA 4.95E-06