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 mr1494 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
vg0819439794 sf0819437081 8 19439794 1.90E-08 NA
vg0105521069 sf0105520069 1 5521069 3.47E-08 NA
vg1217711180 sf1217705135 12 17711180 7.89E-08 NA
vg0603318281 sf0603317282 6 3318281 8.74E-08 NA
vg1126312813 sf1125841226 11 26312813 9.22E-08 NA
vg1125669886 sf1125203725 11 25669886 1.98E-07 1.65E-06
vg1013275525 sf1013204295 10 13275525 2.27E-07 2.22E-06
vg0434768134 sf0434583025 4 34768134 3.17E-07 1.61E-07
vg0232481318 sf0232475449 2 32481318 3.23E-07 1.76E-07
vg1104987392 sf1104983203 11 4987392 7.22E-06 NA
vg0232480149 sf0232474280 2 32480149 NA 1.75E-06
vg1207943829 sf1207941235 12 7943829 NA 3.67E-06