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 mr1327 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
vg0131964524 sf0131963480 1 31964524 3.64E-08 7.23E-07
vg0504429178 sf0504429155 5 4429178 3.33E-06 6.22E-06
vg1217896822 sf1217868256 12 17896822 6.25E-06 NA
vg0134059270 sf0134058226 1 34059270 9.34E-06 NA
vg0103416308 sf0103415308 1 3416308 NA 4.09E-08
vg1002941120 sf1002940097 10 2941120 NA 9.74E-07
vg1002941211 sf1002940188 10 2941211 NA 1.20E-06
vg0712096394 sf0712095400 7 12096394 NA 3.48E-06
vg0726257978 sf0726256984 7 26257978 NA 4.19E-06