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 mr1732 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
vg1016228567 sf1016157339 10 16228567 1.05E-21 5.45E-07
vg0519755571 sf0519693055 5 19755571 1.30E-19 NA
vg0132722496 sf0132721452 1 32722496 2.32E-19 NA
vg0129479532 sf0129478487 1 29479532 6.73E-19 NA
vg0414058287 sf0414049002 4 14058287 2.09E-18 NA
vg0806834963 sf0806833968 8 6834963 NA 6.35E-08
vg0321985645 sf0321984152 3 21985645 NA 3.73E-06
vg1002992765 sf1002991742 10 2992765 NA 3.80E-06