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 mr1919 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
vg0142382043 sf0142380999 1 42382043 1.15E-09 9.25E-06
vg1104729857 sf1104725759 11 4729857 1.83E-09 NA
vg0142590577 sf0142589533 1 42590577 8.62E-09 4.20E-06
vg0142909216 sf0142908172 1 42909216 1.21E-08 NA
vg1105905203 sf1105900955 11 5905203 1.78E-08 NA
vg0133089010 sf0133087966 1 33089010 2.06E-08 NA
vg1113127725 sf1112664046 11 13127725 2.75E-08 NA
vg0809346327 sf0809345331 8 9346327 3.25E-06 NA
vg0401777097 sf0401772693 4 1777097 7.22E-06 NA