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 mr1044 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
vg0327912257 sf0327905311 3 27912257 4.80E-09 NA
vg1210415341 sf1210412754 12 10415341 5.37E-09 NA
vg0516758193 sf0516697835 5 16758193 9.15E-09 NA
vg1210372103 sf1210369516 12 10372103 1.16E-08 NA
vg0603117706 sf0603116707 6 3117706 1.34E-08 NA
vg0526371956 sf0526309319 5 26371956 1.44E-08 NA
vg1111530123 sf1111524440 11 11530123 7.34E-08 4.05E-06
vg0221905933 sf0221900064 2 21905933 5.42E-07 NA
vg0335309577 sf0335302446 3 35309577 5.66E-06 NA
vg0232442595 sf0232436726 2 32442595 NA 3.96E-06