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 mr1642 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
vg0322721883 sf0322720372 3 22721883 4.12E-09 1.15E-06
vg1219106260 sf1219077696 12 19106260 7.25E-09 3.40E-06
vg0142061158 sf0142060115 1 42061158 2.79E-08 NA
vg0816220261 sf0816217547 8 16220261 4.88E-08 4.35E-07
vg0200604919 sf0200604919 2 604919 1.22E-06 NA
vg0431806376 sf0431621269 4 31806376 2.15E-06 7.07E-07
vg0114839906 sf0114838880 1 14839906 3.27E-06 3.38E-06
vg0526987574 sf0526924930 5 26987574 NA 1.92E-06
vg0431810267 sf0431625160 4 31810267 NA 2.99E-06