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 mr1869 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
vg1214636770 sf1214634110 12 14636770 1.36E-09 5.90E-07
vg1214656787 sf1214654127 12 14656787 2.45E-09 2.98E-07
vg1004566535 sf1004583073 10 4566535 4.16E-09 4.54E-06
vg1217635489 sf1217629444 12 17635489 5.56E-08 NA
vg0800342787 sf0800341787 8 342787 8.12E-08 NA
vg1219631829 sf1219603299 12 19631829 9.36E-08 NA
vg1214822308 sf1214819649 12 14822308 NA 1.30E-06
vg0431515534 sf0431330433 4 31515534 NA 7.02E-06