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 mr1448 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
vg0202216666 sf0202216666 2 2216666 2.49E-07 2.49E-07
vg0235365192 sf0235359323 2 35365192 2.91E-07 2.91E-07
vg0202218781 sf0202218781 2 2218781 3.58E-07 3.58E-07
vg0523792337 sf0523729758 5 23792337 4.33E-07 4.33E-07
vg0418975362 sf0418803405 4 18975362 5.82E-07 5.82E-07
vg0320861467 sf0320859977 3 20861467 6.65E-07 6.65E-07
vg0802960649 sf0802959652 8 2960649 7.99E-07 8.00E-07
vg0823617230 sf0823614516 8 23617230 8.41E-07 8.41E-07
vg1204256697 sf1204255685 12 4256697 1.31E-06 1.31E-06
vg0317873017 sf0317871799 3 17873017 1.32E-06 1.32E-06
vg0921335551 sf0921335070 9 21335551 1.56E-06 1.56E-06
vg0322728335 sf0322726824 3 22728335 2.51E-06 2.51E-06
vg1208116243 sf1208113649 12 8116243 4.13E-06 4.14E-06
vg1110300227 sf1110294804 11 10300227 4.27E-06 4.27E-06
vg1220307862 sf1220279304 12 20307862 4.43E-06 4.43E-06
vg1203938514 sf1203937513 12 3938514 4.73E-06 4.73E-06
vg0811997358 sf0811996363 8 11997358 4.76E-06 4.76E-06