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 mr1533 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
vg1013524745 sf1013453515 10 13524745 5.51E-42 4.10E-32
vg1013528269 sf1013457039 10 13528269 6.95E-42 3.07E-32
vg1013686061 sf1013614830 10 13686061 7.73E-16 1.29E-10
vg0723699536 sf0723698543 7 23699536 8.46E-15 NA
vg1013767614 sf1013696383 10 13767614 1.22E-13 3.51E-08
vg1013082033 sf1013010848 10 13082033 1.73E-13 4.50E-06
vg1013084355 sf1013013170 10 13084355 5.26E-13 1.58E-06
vg1013687229 sf1013615998 10 13687229 8.87E-13 5.45E-08
vg0723603381 sf0723602388 7 23603381 1.84E-12 1.91E-06
vg1013680813 sf1013609582 10 13680813 2.47E-12 1.04E-06
vg0301975407 sf0301974403 3 1975407 1.10E-08 6.07E-06
vg1013596120 sf1013524890 10 13596120 1.78E-08 8.32E-07
vg0709984421 sf0709983427 7 9984421 5.28E-08 NA
vg1013689775 sf1013618544 10 13689775 9.29E-07 8.84E-09
vg0131880868 sf0131879824 1 31880868 NA 4.33E-06