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 mr1671 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
vg0334633999 sf0334626869 3 34633999 8.86E-11 1.71E-09
vg0324945119 sf0324943199 3 24945119 1.88E-10 2.60E-06
vg0324808360 sf0324806439 3 24808360 2.78E-09 NA
vg0334422154 sf0334415024 3 34422154 5.92E-09 1.12E-09
vg0501018704 sf0501018688 5 1018704 1.80E-08 NA
vg0916428525 sf0916427524 9 16428525 2.19E-08 NA
vg0334712576 sf0334705446 3 34712576 7.08E-08 5.29E-07
vg0311147041 sf0311145759 3 11147041 1.43E-06 2.93E-06
vg1110994837 sf1110989154 11 10994837 5.08E-06 4.25E-07
vg0314985097 sf0314983744 3 14985097 9.95E-06 4.59E-06
vg0517753178 sf0517692819 5 17753178 NA 1.05E-06
vg1112283450 sf1112086685 11 12283450 NA 1.18E-06
vg0110090809 sf0110089785 1 10090809 NA 2.91E-06