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 mr1261 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
vg1215988583 sf1215985879 12 15988583 2.01E-24 2.90E-16
vg1212877317 sf1212874656 12 12877317 1.12E-13 8.47E-07
vg1203243070 sf1203242073 12 3243070 7.72E-13 7.14E-06
vg0228500377 sf0228494508 2 28500377 3.50E-11 NA
vg1116068177 sf1115603049 11 16068177 6.77E-11 3.84E-06
vg1018571610 sf1018500167 10 18571610 1.52E-10 2.88E-06
vg1218663003 sf1218634438 12 18663003 5.60E-10 5.44E-07
vg1006587700 sf1006603323 10 6587700 7.10E-09 4.64E-06
vg1022588644 sf1022517118 10 22588644 1.01E-07 1.84E-06
vg1216138955 sf1216136251 12 16138955 NA 1.09E-07
vg0408294799 sf0408290073 4 8294799 NA 4.35E-06