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 mr1825 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
vg1002102348 sf1002101325 10 2102348 9.97E-24 NA
vg0420332785 sf0420160829 4 20332785 2.37E-23 NA
vg0500066576 sf0500066576 5 66576 4.16E-23 NA
vg0313761354 sf0313760071 3 13761354 4.34E-23 NA
vg0520821970 sf0520759411 5 20821970 4.76E-21 NA
vg0130761957 sf0130760913 1 30761957 8.80E-18 NA
vg1001967604 sf1001966581 10 1967604 NA 1.81E-06
vg1000830764 sf1000829740 10 830764 NA 2.71E-06
vg1102854048 sf1102849952 11 2854048 NA 4.23E-06
vg1002144991 sf1002143968 10 2144991 NA 4.65E-06
vg0432863071 sf0432677958 4 32863071 NA 4.77E-06
vg0141568520 sf0141567477 1 41568520 NA 5.72E-06