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 mr1317 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
vg0216982985 sf0216977115 2 16982985 4.33E-15 4.32E-15
vg0507443101 sf0507443043 5 7443101 9.81E-09 9.81E-09
vg0210828426 sf0210828424 2 10828426 6.16E-08 6.16E-08
vg1004534495 sf1004551033 10 4534495 1.25E-07 1.25E-07
vg0400239462 sf0400238462 4 239462 3.00E-07 3.00E-07
vg0625912245 sf0625911248 6 25912245 5.07E-07 5.06E-07
vg0316596971 sf0316595616 3 16596971 6.72E-07 6.72E-07
vg0118822385 sf0118821340 1 18822385 1.10E-06 1.10E-06
vg0209641266 sf0209641264 2 9641266 1.13E-06 1.13E-06
vg0219293036 sf0219287168 2 19293036 1.86E-06 1.86E-06
vg1019961902 sf1019890402 10 19961902 2.91E-06 2.91E-06
vg0202831799 sf0202831797 2 2831799 4.06E-06 4.06E-06
vg0314814380 sf0314813067 3 14814380 4.06E-06 4.06E-06