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 mr1125 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
vg0428353570 sf0428168429 4 28353570 9.98E-11 NA
vg0428358065 sf0428172924 4 28358065 2.87E-10 2.05E-06
vg0113491943 sf0113490917 1 13491943 9.52E-10 9.96E-06
vg0627447078 sf0627446081 6 27447078 4.55E-09 NA
vg0210098817 sf0210098815 2 10098817 8.07E-09 NA
vg0420836689 sf0420664732 4 20836689 8.37E-09 5.20E-06
vg0608669135 sf0608668136 6 8669135 1.34E-06 2.88E-07
vg0214609392 sf0214603522 2 14609392 1.42E-06 1.08E-06
vg1222391001 sf1222357440 12 22391001 6.95E-06 NA
vg0302095273 sf0302094269 3 2095273 8.10E-06 NA
vg0110745222 sf0110744198 1 10745222 NA 3.11E-06
vg1109851321 sf1109845898 11 9851321 NA 3.41E-06