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 mr1942 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
vg0142061158 sf0142060115 1 42061158 1.90E-16 NA
vg0134230502 sf0134229459 1 34230502 5.49E-15 NA
vg0726519355 sf0726518361 7 26519355 1.54E-14 NA
vg0129901522 sf0129900477 1 29901522 3.43E-14 NA
vg0805076219 sf0805075222 8 5076219 3.39E-13 NA
vg1128664243 sf1128141022 11 28664243 2.57E-09 1.57E-06
vg0727217188 sf0727216194 7 27217188 1.44E-08 5.18E-06
vg0713647333 sf0713646340 7 13647333 6.86E-08 NA
vg1003478452 sf1003477429 10 3478452 NA 2.78E-06
vg0319343182 sf0319341693 3 19343182 NA 7.83E-06