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 mr1764 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
vg0332499847 sf0332492720 3 32499847 5.37E-11 NA
vg0233865573 sf0233859704 2 33865573 1.10E-10 1.31E-06
vg1218087170 sf1218058606 12 18087170 1.25E-10 9.13E-07
vg0602215438 sf0602214439 6 2215438 3.58E-10 NA
vg0623156256 sf0623155259 6 23156256 6.03E-10 7.08E-06
vg0914766283 sf0914765282 9 14766283 8.90E-09 1.20E-06