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 mr1419 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
vg0316217499 sf0316216147 3 16217499 2.31E-07 2.31E-07
vg0327981236 sf0327974290 3 27981236 2.57E-07 2.57E-07
vg1106690644 sf1106686397 11 6690644 4.30E-07 4.30E-07
vg1117584893 sf1117118750 11 17584893 6.87E-07 6.87E-07
vg0522014819 sf0521952261 5 22014819 1.49E-06 1.49E-06
vg1105850139 sf1105845891 11 5850139 1.56E-06 1.56E-06
vg0402100710 sf0402096304 4 2100710 2.32E-06 2.32E-06
vg0327950422 sf0327943476 3 27950422 2.44E-06 2.44E-06
vg0140491195 sf0140490152 1 40491195 3.34E-06 3.35E-06
vg1105849420 sf1105845172 11 5849420 4.47E-06 4.47E-06
vg0319641267 sf0319639778 3 19641267 4.63E-06 4.63E-06