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 mr1763 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
vg0519242289 sf0519179773 5 19242289 5.30E-10 NA
vg0402401496 sf0402397091 4 2401496 6.93E-10 NA
vg0431615949 sf0431430844 4 31615949 9.77E-10 NA
vg1203113723 sf1203112726 12 3113723 1.11E-09 NA
vg1011380412 sf1011309231 10 11380412 1.85E-09 NA
vg0431840206 sf0431655100 4 31840206 2.76E-09 6.14E-06
vg0402290555 sf0402286150 4 2290555 9.26E-09 7.87E-06
vg0707896183 sf0707895188 7 7896183 5.65E-06 NA
vg1208638766 sf1208636173 12 8638766 6.21E-06 NA