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 mr1910 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
vg0232077620 sf0232071751 2 32077620 3.78E-09 2.01E-07
vg0403452712 sf0403448315 4 3452712 1.19E-08 NA
vg0907519938 sf0907518938 9 7519938 2.95E-08 NA
vg0232030438 sf0232024569 2 32030438 3.85E-08 1.69E-06
vg1208281275 sf1208278681 12 8281275 7.63E-08 1.62E-07
vg0423923614 sf0423738474 4 23923614 7.73E-08 NA
vg0519405460 sf0519342944 5 19405460 2.28E-07 2.51E-07
vg0614105710 sf0614104711 6 14105710 1.67E-06 1.39E-06
vg0335289111 sf0335281980 3 35289111 4.48E-06 NA
vg0504904086 sf0504904064 5 4904086 5.97E-06 4.69E-06