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 mr1925 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
vg0110290364 sf0110289340 1 10290364 3.87E-11 1.78E-07
vg0106765973 sf0106764973 1 6765973 8.88E-11 6.78E-09
vg0819206665 sf0819203952 8 19206665 3.93E-10 7.33E-07
vg0906684964 sf0906683964 9 6684964 5.48E-10 1.32E-06
vg0107115494 sf0107114494 1 7115494 8.40E-10 1.29E-07
vg0123927216 sf0123926172 1 23927216 1.23E-09 8.39E-08
vg1021478171 sf1021406648 10 21478171 1.76E-09 5.88E-07
vg0106716872 sf0106715872 1 6716872 6.32E-09 8.49E-08
vg1125082946 sf1124616786 11 25082946 2.98E-08 3.71E-07
vg0814185346 sf0814182632 8 14185346 3.87E-08 5.50E-07
vg1215226859 sf1215224156 12 15226859 3.91E-08 9.75E-07
vg1125850665 sf1125384584 11 25850665 3.91E-08 4.49E-07
vg0104297093 sf0104296093 1 4297093 4.51E-08 9.64E-07
vg0812954188 sf0812952013 8 12954188 5.01E-08 4.07E-07
vg0310513409 sf0310512325 3 10513409 1.47E-07 8.89E-09
vg1018616939 sf1018545496 10 18616939 1.10E-06 7.82E-07
vg0416168444 sf0415996477 4 16168444 2.46E-06 1.81E-07
vg0619257211 sf0619256214 6 19257211 5.77E-06 NA
vg0416594329 sf0416422372 4 16594329 9.19E-06 4.33E-07
vg1018608957 sf1018537514 10 18608957 NA 5.62E-10
vg1125402847 sf1124936686 11 25402847 NA 9.98E-08
vg1125087670 sf1124621510 11 25087670 NA 3.36E-07
vg0134197545 sf0134196501 1 34197545 NA 4.27E-07
vg0621171940 sf0621170943 6 21171940 NA 4.50E-07
vg0416593529 sf0416421572 4 16593529 NA 5.87E-07
vg0100911990 sf0100910990 1 911990 NA 7.45E-07
vg0401578564 sf0401574113 4 1578564 NA 7.61E-07