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 mr1440 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
vg0816115289 sf0816112575 8 16115289 1.44E-07 1.44E-07
vg0223426765 sf0223420896 2 23426765 1.51E-07 1.51E-07
vg0805900956 sf0805899959 8 5900956 1.91E-07 1.91E-07
vg0805160234 sf0805159237 8 5160234 2.28E-07 2.28E-07
vg0223422221 sf0223416352 2 23422221 5.44E-07 5.44E-07
vg0416229064 sf0416057097 4 16229064 7.13E-07 7.13E-07
vg1214701815 sf1214699156 12 14701815 8.48E-07 8.49E-07
vg0403709681 sf0403705287 4 3709681 8.54E-07 8.54E-07
vg0112179197 sf0112178171 1 12179197 1.06E-06 1.06E-06
vg0335714781 sf0335707650 3 35714781 1.75E-06 1.76E-06
vg0102110353 sf0102109353 1 2110353 2.05E-06 2.05E-06
vg0817790397 sf0817787684 8 17790397 2.47E-06 2.47E-06
vg1221128182 sf1221094732 12 21128182 3.48E-06 3.48E-06
vg0805055129 sf0805054132 8 5055129 3.73E-06 3.73E-06
vg0223074046 sf0223068177 2 23074046 4.12E-06 4.12E-06
vg1214091707 sf1214089047 12 14091707 4.31E-06 4.31E-06
vg0509233251 sf0509233180 5 9233251 4.98E-06 4.98E-06
vg0112035600 sf0112034574 1 12035600 6.95E-06 6.95E-06