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 mr1572 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
vg0429705737 sf0429520605 4 29705737 2.04E-08 2.04E-08
vg1116933705 sf1116468584 11 16933705 4.47E-07 4.47E-07
vg0701065951 sf0701064951 7 1065951 1.18E-06 1.18E-06
vg0715859839 sf0715858846 7 15859839 1.48E-06 1.48E-06
vg1214799098 sf1214796439 12 14799098 2.17E-06 2.17E-06
vg1127258370 sf1126786757 11 27258370 2.78E-06 2.78E-06
vg0504924350 sf0504924328 5 4924350 3.12E-06 3.12E-06
vg1104596397 sf1104592299 11 4596397 3.16E-06 3.16E-06
vg0315044254 sf0315042901 3 15044254 4.49E-06 4.49E-06
vg1116817015 sf1116351893 11 16817015 4.64E-06 4.64E-06