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 mr1412 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
vg1105788809 sf1105784561 11 5788809 2.06E-09 2.06E-09
vg0826575991 sf0826573277 8 26575991 1.93E-08 1.94E-08
vg1005927955 sf1005944493 10 5927955 2.36E-08 2.36E-08
vg0404085755 sf0404081362 4 4085755 1.21E-07 1.21E-07
vg0702475950 sf0702474951 7 2475950 8.03E-07 8.03E-07
vg0628851752 sf0628850754 6 28851752 9.40E-07 9.40E-07
vg0217388064 sf0217382194 2 17388064 1.19E-06 1.19E-06
vg0114539569 sf0114538543 1 14539569 1.26E-06 1.26E-06
vg0615632961 sf0615631963 6 15632961 1.44E-06 1.44E-06
vg0220195397 sf0220189529 2 20195397 1.46E-06 1.46E-06
vg1002956418 sf1002955395 10 2956418 1.80E-06 1.80E-06
vg0526981252 sf0526918608 5 26981252 1.86E-06 1.86E-06
vg0909719332 sf0909718331 9 9719332 1.98E-06 1.98E-06
vg0511470966 sf0511470896 5 11470966 2.63E-06 2.63E-06
vg1121623328 sf1121157205 11 21623328 3.06E-06 3.05E-06
vg0812017256 sf0812016261 8 12017256 3.96E-06 3.96E-06
vg0622581640 sf0622580643 6 22581640 4.49E-06 4.49E-06