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 mr1858 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
vg0628759426 sf0628758428 6 28759426 3.35E-10 9.98E-08
vg0222833455 sf0222827586 2 22833455 3.85E-09 6.77E-08
vg0627929341 sf0627928343 6 27929341 3.51E-08 1.22E-07
vg0420812162 sf0420640205 4 20812162 7.92E-08 NA
vg0609746842 sf0609745843 6 9746842 1.27E-07 2.09E-06
vg0714085405 sf0714084412 7 14085405 3.84E-07 4.73E-06
vg0727090466 sf0727089472 7 27090466 9.63E-07 4.28E-07
vg0425648422 sf0425463283 4 25648422 1.45E-06 NA
vg0432345183 sf0432160072 4 32345183 2.13E-06 2.57E-06
vg0221025908 sf0221020040 2 21025908 5.01E-06 4.84E-07
vg0814450879 sf0814448165 8 14450879 7.09E-06 NA
vg0224209424 sf0224203555 2 24209424 7.24E-06 4.13E-06
vg0400034044 sf0400033044 4 34044 NA 2.10E-06