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 mr1840 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
vg0801629578 sf0801628580 8 1629578 6.73E-10 4.63E-06
vg0223518528 sf0223512659 2 23518528 2.56E-09 NA
vg0517975909 sf0517915395 5 17975909 2.75E-09 NA
vg0105644298 sf0105643298 1 5644298 6.39E-09 NA
vg0300761827 sf0300760825 3 761827 1.64E-08 NA
vg0816931318 sf0816928604 8 16931318 2.07E-08 6.78E-06
vg1118337629 sf1117871486 11 18337629 7.96E-08 NA
vg0115887270 sf0115886244 1 15887270 2.90E-07 NA
vg1010572055 sf1010500876 10 10572055 NA 2.46E-06
vg0916030541 sf0916029540 9 16030541 NA 3.20E-06
vg0801628860 sf0801627862 8 1628860 NA 4.55E-06