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 mr1364 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
vg0821334599 sf0821331886 8 21334599 3.71E-09 NA
vg1217491800 sf1217485755 12 17491800 3.89E-09 NA
vg1211062870 sf1211060236 12 11062870 4.06E-09 NA
vg0215631406 sf0215625536 2 15631406 1.03E-08 NA
vg0729442292 sf0729441300 7 29442292 1.16E-08 7.04E-06
vg1218111047 sf1218082483 12 18111047 4.37E-08 NA
vg1218659585 sf1218631020 12 18659585 1.48E-07 4.29E-06
vg1017321484 sf1017250257 10 17321484 2.89E-06 1.69E-06
vg1102804893 sf1102800797 11 2804893 NA 2.81E-06