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 mr1963 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
vg0405832157 sf0405827596 4 5832157 9.62E-10 1.88E-06
vg0405832151 sf0405827590 4 5832151 1.03E-09 4.20E-07
vg0819078104 sf0819075391 8 19078104 6.33E-09 3.45E-06
vg1114648304 sf1114184622 11 14648304 5.50E-08 NA
vg0714252145 sf0714251152 7 14252145 4.16E-06 NA
vg0712977464 sf0712976471 7 12977464 7.19E-06 5.16E-06
vg0119654822 sf0119653777 1 19654822 7.92E-06 NA
vg0817490978 sf0817488264 8 17490978 NA 2.12E-06