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 mr1043 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
vg1105906134 sf1105901886 11 5906134 4.10E-08 1.23E-06
vg1105900588 sf1105896340 11 5900588 4.42E-08 8.95E-07
vg0320879541 sf0320878051 3 20879541 7.18E-08 1.30E-06
vg0416027738 sf0415855771 4 16027738 3.37E-07 1.23E-06
vg0630585467 sf0630584469 6 30585467 3.74E-07 3.07E-06
vg0416101905 sf0415929938 4 16101905 1.39E-06 4.92E-06
vg0415621401 sf0415612088 4 15621401 1.44E-06 2.09E-06
vg1109243978 sf1109238555 11 9243978 1.97E-06 2.54E-06