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 mr1052 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
vg0921454415 sf0921453934 9 21454415 2.55E-23 5.45E-17
vg0921456056 sf0921455575 9 21456056 3.78E-23 4.30E-18
vg0921374162 sf0921373681 9 21374162 9.47E-14 4.25E-09
vg1126773646 sf1126302033 11 26773646 3.06E-10 2.98E-06
vg0808270560 sf0808269564 8 8270560 6.98E-10 NA
vg0920981500 sf0920981019 9 20981500 9.72E-10 NA
vg0910063987 sf0910062986 9 10063987 1.85E-09 3.44E-06
vg1219410965 sf1219382435 12 19410965 2.13E-08 NA
vg0504038203 sf0504038180 5 4038203 9.84E-08 1.03E-07
vg0915096631 sf0915095630 9 15096631 1.57E-06 NA
vg0921250310 sf0921249829 9 21250310 1.60E-06 2.12E-06
vg0328906605 sf0328899657 3 28906605 2.35E-06 2.77E-06
vg0328872939 sf0328865992 3 28872939 4.67E-06 4.37E-06
vg0913080416 sf0913079415 9 13080416 NA 4.51E-07
vg0614703627 sf0614702628 6 14703627 NA 7.93E-07