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 3.49E-16 1.11E-11
vg0142699503 sf0142698459 1 42699503 4.91E-16 1.39E-11
vg0143095495 sf0143094451 1 43095495 6.32E-10 5.81E-07
vg0142120136 sf0142119093 1 42120136 1.18E-09 NA
vg0143143412 sf0143142368 1 43143412 1.37E-09 3.29E-07
vg0628633192 sf0628632194 6 28633192 2.56E-08 8.03E-06
vg0143171338 sf0143170294 1 43171338 3.70E-08 3.36E-06
vg0141519930 sf0141518887 1 41519930 4.22E-08 1.87E-06
vg0141249435 sf0141248392 1 41249435 9.26E-08 4.51E-06
vg0628658970 sf0628657972 6 28658970 2.78E-07 1.33E-06
vg1016432531 sf1016361305 10 16432531 1.33E-06 2.88E-06
vg1122327512 sf1121861383 11 22327512 3.19E-06 5.29E-06
vg0512739819 sf0512682741 5 12739819 3.64E-06 4.57E-06
vg0313853015 sf0313851732 3 13853015 NA 5.12E-07