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 mr1446 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
vg1012357179 sf1012285994 10 12357179 3.62E-15 1.56E-07
vg1012245318 sf1012174133 10 12245318 3.83E-15 2.35E-08
vg0709322599 sf0709321605 7 9322599 8.42E-12 3.71E-06
vg0517221319 sf0517160960 5 17221319 1.69E-11 NA
vg1019373991 sf1019302546 10 19373991 3.21E-11 NA
vg1222488666 sf1222455105 12 22488666 4.14E-11 6.50E-06
vg0107647091 sf0107646091 1 7647091 1.04E-09 3.62E-09
vg1222487174 sf1222453613 12 22487174 1.06E-09 9.57E-07
vg0127410771 sf0127409727 1 27410771 6.12E-08 2.99E-06
vg0522454644 sf0522392086 5 22454644 6.70E-08 NA
vg0203416075 sf0203416073 2 3416075 3.52E-07 NA
vg1012424922 sf1012353737 10 12424922 NA 8.43E-09
vg1012833374 sf1012762189 10 12833374 NA 4.57E-08
vg0225323727 sf0225317858 2 25323727 NA 1.08E-06
vg0225225579 sf0225219710 2 25225579 NA 3.56E-06