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 mr1974 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
vg0142688928 sf0142687884 1 42688928 5.98E-18 7.64E-13
vg0142633231 sf0142632187 1 42633231 2.26E-16 1.08E-12
vg0142727279 sf0142726235 1 42727279 8.77E-13 3.18E-08
vg0142706516 sf0142705472 1 42706516 9.90E-13 1.21E-08
vg0303448503 sf0303447499 3 3448503 3.55E-10 3.68E-06
vg0142434413 sf0142433369 1 42434413 3.56E-10 2.84E-09
vg0918931136 sf0918930136 9 18931136 1.14E-09 NA
vg1105945195 sf1105940947 11 5945195 1.37E-09 3.80E-06
vg0628658970 sf0628657972 6 28658970 3.83E-08 2.67E-06
vg0313853015 sf0313851732 3 13853015 5.96E-08 2.73E-08
vg0624941329 sf0624940332 6 24941329 1.57E-07 2.07E-06
vg0517977616 sf0517917102 5 17977616 4.31E-07 2.10E-06
vg1222634771 sf1222601210 12 22634771 1.88E-06 4.14E-06
vg0235663840 sf0235657971 2 35663840 2.28E-06 4.47E-06
vg0142638768 sf0142637724 1 42638768 3.05E-06 9.99E-09
vg0628585506 sf0628584508 6 28585506 5.79E-06 NA
vg0141519930 sf0141518887 1 41519930 6.04E-06 1.84E-06
vg1122327512 sf1121861383 11 22327512 NA 2.69E-06
vg0235581681 sf0235575812 2 35581681 NA 3.29E-06
vg0143089279 sf0143088235 1 43089279 NA 3.56E-06