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 mr1188 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
vg0320733462 sf0320731972 3 20733462 5.56E-13 3.77E-10
vg0808212491 sf0808211495 8 8212491 8.20E-12 5.53E-08
vg1217301806 sf1217295761 12 17301806 7.53E-10 6.76E-07
vg0324683717 sf0324681796 3 24683717 8.80E-10 NA
vg0108993891 sf0108992891 1 8993891 9.38E-10 NA
vg0309108474 sf0309107410 3 9108474 3.72E-09 NA
vg1203173795 sf1203172798 12 3173795 9.92E-09 2.91E-06
vg1216421560 sf1216418853 12 16421560 2.10E-07 2.35E-07
vg0906772663 sf0906771663 9 6772663 3.88E-06 NA