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 mr1780 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
vg0506262292 sf0506262231 5 6262292 6.97E-10 NA
vg0618214950 sf0618213953 6 18214950 8.25E-10 NA
vg0400068159 sf0400067159 4 68159 1.57E-09 NA
vg0218948347 sf0218942478 2 18948347 2.42E-09 NA
vg0316518526 sf0316517171 3 16518526 1.01E-08 3.90E-06
vg0519854040 sf0519791516 5 19854040 5.09E-07 NA
vg1000628000 sf1000626976 10 628000 1.40E-06 NA