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 mr1484 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
vg1125118463 sf1124652303 11 25118463 2.59E-30 2.59E-30
vg1124875808 sf1124409648 11 24875808 2.94E-11 2.94E-11
vg1124897169 sf1124431009 11 24897169 1.73E-09 1.73E-09
vg1124959837 sf1124493677 11 24959837 2.59E-09 2.59E-09
vg0328637867 sf0328630920 3 28637867 3.26E-07 3.26E-07
vg1128437977 sf1127914756 11 28437977 7.87E-07 7.87E-07
vg0106089280 sf0106088280 1 6089280 8.54E-07 8.54E-07
vg1125103237 sf1124637077 11 25103237 9.36E-07 9.36E-07
vg0224273930 sf0224268061 2 24273930 1.01E-06 1.01E-06
vg0814644208 sf0814641494 8 14644208 1.69E-06 1.69E-06