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 mr1327 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
vg0139588846 sf0139587803 1 39588846 3.22E-24 2.99E-09
vg0139032129 sf0139031086 1 39032129 4.99E-23 1.25E-09
vg0139257498 sf0139256455 1 39257498 6.44E-23 1.50E-09
vg0134974043 sf0134973000 1 34974043 5.98E-19 4.49E-06
vg0134815001 sf0134813958 1 34815001 6.80E-19 1.71E-06
vg0141771079 sf0141770036 1 41771079 1.53E-18 7.21E-07
vg0132243424 sf0132242380 1 32243424 8.93E-17 NA
vg0142014185 sf0142013142 1 42014185 3.42E-16 NA
vg0131986813 sf0131985769 1 31986813 2.17E-15 NA
vg0300483843 sf0300482841 3 483843 4.91E-10 3.42E-06
vg0801822513 sf0801821516 8 1822513 7.65E-10 NA
vg1004625809 sf1004642347 10 4625809 NA 2.60E-08
vg1108503240 sf1108497850 11 8503240 NA 1.01E-06
vg1004654643 sf1004671180 10 4654643 NA 2.05E-06