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 mr1011 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
vg0134092893 sf0134091849 1 34092893 1.01E-08 9.95E-07
vg0421062242 sf0420890297 4 21062242 1.95E-08 1.30E-06
vg0130089725 sf0130088680 1 30089725 5.28E-08 NA
vg0713442761 sf0713441768 7 13442761 5.69E-08 3.75E-06
vg0421030366 sf0420858419 4 21030366 7.03E-08 9.27E-07
vg1217386152 sf1217380107 12 17386152 3.36E-07 1.07E-06
vg0725369051 sf0725368057 7 25369051 1.30E-06 2.17E-06
vg0431094486 sf0430909375 4 31094486 3.92E-06 NA
vg1001814606 sf1001813583 10 1814606 NA 3.84E-06
vg0520828244 sf0520765685 5 20828244 NA 6.57E-06