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 mr1217 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
vg0819249760 sf0819247047 8 19249760 3.67E-26 4.79E-06
vg0212556837 sf0212556833 2 12556837 5.11E-26 NA
vg0819114272 sf0819111559 8 19114272 3.07E-25 4.42E-06
vg0317761505 sf0317760287 3 17761505 1.90E-24 NA
vg0816275999 sf0816273285 8 16275999 2.12E-24 NA
vg1119464462 sf1118998150 11 19464462 6.40E-24 6.16E-06
vg0329663008 sf0329656048 3 29663008 9.75E-24 NA
vg1218873031 sf1218844466 12 18873031 NA 1.36E-07
vg0818666272 sf0818663559 8 18666272 NA 5.92E-07
vg1216058251 sf1216055547 12 16058251 NA 1.03E-06
vg1001392877 sf1001391854 10 1392877 NA 1.21E-06
vg1001404304 sf1001403281 10 1404304 NA 1.83E-06
vg1218119528 sf1218090964 12 18119528 NA 4.72E-06
vg1119511373 sf1119045061 11 19511373 NA 4.77E-06