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 mr1671 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
vg0311534838 sf0311533556 3 11534838 2.29E-09 NA
vg0132898168 sf0132897124 1 32898168 2.79E-09 NA
vg0414275568 sf0414266281 4 14275568 3.22E-09 NA
vg0304417215 sf0304416217 3 4417215 4.52E-09 NA
vg0223394543 sf0223388674 2 23394543 5.66E-09 NA
vg1016390830 sf1016319606 10 16390830 3.34E-07 NA
vg0127445588 sf0127444544 1 27445588 9.16E-07 NA
vg1222234300 sf1222200847 12 22234300 NA 3.96E-06
vg1123394499 sf1122928369 11 23394499 NA 5.79E-06