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 mr1834 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
vg0702586803 sf0702585804 7 2586803 4.05E-07 4.05E-07
vg0410180309 sf0410171006 4 10180309 1.41E-06 1.41E-06
vg0319079517 sf0319078277 3 19079517 1.57E-06 1.56E-06
vg0318738445 sf0318737205 3 18738445 1.70E-06 1.70E-06
vg0333586584 sf0333579454 3 33586584 2.46E-06 2.46E-06
vg0319832678 sf0319831189 3 19832678 2.53E-06 2.53E-06
vg0138783722 sf0138782679 1 38783722 4.52E-06 4.52E-06