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 mr1399 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
vg0919811754 sf0919811273 9 19811754 3.55E-13 9.28E-06
vg0223718136 sf0223712267 2 23718136 2.23E-11 NA
vg0140816254 sf0140815211 1 40816254 2.94E-11 NA
vg0329591755 sf0329584795 3 29591755 7.81E-10 NA
vg1221513306 sf1221479853 12 21513306 8.74E-10 4.40E-06
vg1221477991 sf1221444538 12 21477991 2.00E-09 3.42E-06
vg1221584421 sf1221550968 12 21584421 2.88E-09 5.32E-06
vg0919872267 sf0919871786 9 19872267 3.72E-08 4.85E-06
vg0143247814 sf0143246770 1 43247814 7.53E-07 NA
vg0208782569 sf0208782567 2 8782569 NA 1.72E-06
vg0614629248 sf0614628249 6 14629248 NA 2.42E-06