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 mr1687 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
vg0433083637 sf0432898526 4 33083637 7.11E-07 7.12E-07
vg0817401463 sf0817398749 8 17401463 1.19E-06 1.19E-06
vg1221694446 sf1221660993 12 21694446 1.40E-06 1.40E-06
vg1120403301 sf1119937226 11 20403301 2.35E-06 2.35E-06
vg0525124226 sf0525061641 5 25124226 2.46E-06 2.46E-06
vg1002823088 sf1002822065 10 2823088 2.61E-06 2.61E-06
vg0627796033 sf0627795035 6 27796033 4.46E-06 4.46E-06