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 mr1164 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
vg1214485336 sf1214482677 12 14485336 1.35E-08 9.15E-06
vg0300483843 sf0300482841 3 483843 1.45E-08 NA
vg1220271730 sf1220243172 12 20271730 1.57E-08 NA
vg0131768610 sf0131767566 1 31768610 3.80E-08 NA
vg1210713193 sf1210710606 12 10713193 5.69E-08 NA
vg0819371692 sf0819368979 8 19371692 7.09E-08 3.54E-06
vg0301371771 sf0301370769 3 1371771 6.49E-06 2.58E-06