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 mr1326 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
vg0315486151 sf0315484798 3 15486151 1.01E-18 6.11E-08
vg0706513088 sf0706512093 7 6513088 1.18E-17 5.89E-06
vg0207900353 sf0207900352 2 7900353 2.19E-17 NA
vg0708681067 sf0708680072 7 8681067 3.37E-17 9.76E-06
vg1000967617 sf1000966593 10 967617 1.32E-16 NA
vg0504757155 sf0504757132 5 4757155 3.90E-16 NA
vg0107647091 sf0107646091 1 7647091 NA 1.35E-07
vg0205031937 sf0205031934 2 5031937 NA 1.56E-06
vg0519159149 sf0519096633 5 19159149 NA 3.24E-06
vg0518984986 sf0518922470 5 18984986 NA 4.42E-06