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 mr1350 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
vg1209327674 sf1209325083 12 9327674 6.25E-42 2.22E-06
vg1209191270 sf1209188679 12 9191270 1.71E-41 2.05E-07
vg0217539704 sf0217533834 2 17539704 1.96E-41 NA
vg0217208277 sf0217202407 2 17208277 2.51E-40 1.26E-09
vg0127815187 sf0127814143 1 27815187 2.80E-39 NA
vg0819999076 sf0819996363 8 19999076 8.65E-39 NA
vg0317523208 sf0317521990 3 17523208 7.56E-38 NA
vg0217023585 sf0217017715 2 17023585 NA 2.31E-07
vg0216876411 sf0216870541 2 16876411 NA 9.56E-07
vg1000092195 sf1000091195 10 92195 NA 1.24E-06
vg1208021026 sf1208018432 12 8021026 NA 2.14E-06
vg0216536586 sf0216530716 2 16536586 NA 2.31E-06