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 mr1661 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
vg1013275525 sf1013204295 10 13275525 1.13E-08 1.54E-07
vg0320733462 sf0320731972 3 20733462 1.45E-08 7.97E-08
vg0818230180 sf0818227467 8 18230180 3.05E-07 6.55E-07
vg0406854032 sf0406849477 4 6854032 4.48E-07 6.77E-07
vg0818605378 sf0818602665 8 18605378 1.19E-06 3.75E-06
vg0319121263 sf0319120023 3 19121263 2.67E-06 3.20E-06
vg0406853685 sf0406849130 4 6853685 NA 3.03E-06
vg0529433705 sf0529371060 5 29433705 NA 4.27E-06