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 mr1048 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
vg1117625330 sf1117159186 11 17625330 1.12E-07 NA
vg0433298009 sf0433112897 4 33298009 4.23E-06 NA
vg0825484750 sf0825482036 8 25484750 5.62E-06 2.60E-06
vg1216060120 sf1216057416 12 16060120 7.01E-06 NA
vg1218210959 sf1218182395 12 18210959 7.85E-06 2.50E-06
vg1218062102 sf1218033538 12 18062102 NA 1.73E-06
vg1017085147 sf1017013919 10 17085147 NA 7.82E-06