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 mr1837 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
vg0431614537 sf0431429432 4 31614537 2.53E-09 NA
vg0414540932 sf0414531646 4 14540932 2.57E-09 NA
vg1109209726 sf1109204305 11 9209726 6.25E-09 NA
vg1011510153 sf1011438972 10 11510153 9.54E-09 NA
vg0123658680 sf0123657636 1 23658680 1.68E-08 NA
vg0728769587 sf0728768595 7 28769587 2.09E-07 8.07E-06
vg1000454303 sf1000453279 10 454303 1.35E-06 NA
vg1122341383 sf1121875254 11 22341383 2.47E-06 NA
vg0216120585 sf0216114715 2 16120585 5.77E-06 NA
vg1119326733 sf1118860421 11 19326733 NA 3.28E-06