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 mr1624 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
vg0107178303 sf0107177303 1 7178303 1.24E-14 1.39E-06
vg0131413071 sf0131412027 1 31413071 3.65E-14 NA
vg0917466490 sf0917465489 9 17466490 4.41E-14 NA
vg1118331453 sf1117865311 11 18331453 6.31E-14 NA
vg0710971660 sf0710970666 7 10971660 7.91E-14 NA
vg0803657241 sf0803656244 8 3657241 1.76E-11 2.53E-07
vg1105257664 sf1105253415 11 5257664 2.70E-09 1.02E-06
vg1105407599 sf1105403350 11 5407599 NA 5.47E-07
vg0433403124 sf0433218013 4 33403124 NA 6.80E-07
vg0709678550 sf0709677556 7 9678550 NA 1.27E-06
vg1105281315 sf1105277066 11 5281315 NA 3.22E-06