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 mr1439 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
vg0101289411 sf0101288411 1 1289411 1.20E-09 4.43E-07
vg0132376950 sf0132375906 1 32376950 4.51E-09 NA
vg0139575130 sf0139574087 1 39575130 1.17E-08 NA
vg0233999998 sf0233994129 2 33999998 2.04E-08 NA
vg0630306971 sf0630305973 6 30306971 2.54E-08 6.97E-06
vg0804887405 sf0804886408 8 4887405 3.40E-08 1.31E-06
vg0318566007 sf0318564789 3 18566007 6.37E-08 2.43E-07
vg0412733978 sf0412724688 4 12733978 1.17E-06 NA
vg0622857113 sf0622856116 6 22857113 5.55E-06 NA
vg0107647091 sf0107646091 1 7647091 NA 9.28E-10
vg0319113443 sf0319112203 3 19113443 NA 1.73E-06
vg0404710590 sf0404706029 4 4710590 NA 2.84E-06
vg0307765595 sf0307764533 3 7765595 NA 4.10E-06