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 mr1806 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
vg1109467388 sf1109461965 11 9467388 4.61E-13 NA
vg0726458639 sf0726457645 7 26458639 1.24E-12 NA
vg0620493414 sf0620492417 6 20493414 5.91E-12 4.06E-06
vg0614490153 sf0614489154 6 14490153 9.42E-12 NA
vg0503973750 sf0503973727 5 3973750 1.41E-11 NA
vg1113313944 sf1112850265 11 13313944 3.98E-09 NA
vg0821385931 sf0821383218 8 21385931 5.42E-09 1.84E-06
vg1103943395 sf1103939297 11 3943395 9.54E-09 2.63E-06
vg0213593475 sf0213593471 2 13593475 2.40E-08 NA
vg0815795226 sf0815792512 8 15795226 NA 2.52E-06
vg0815798149 sf0815795435 8 15798149 NA 2.65E-06
vg0706453758 sf0706452763 7 6453758 NA 6.52E-06