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 mr1728 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
vg0918158744 sf0918157743 9 18158744 1.30E-36 3.46E-17
vg0918447666 sf0918446665 9 18447666 2.25E-34 2.25E-17
vg0916213257 sf0916212256 9 16213257 2.38E-31 1.47E-15
vg0916105872 sf0916104871 9 16105872 5.45E-26 1.45E-11
vg0916036241 sf0916035240 9 16036241 2.35E-25 1.04E-09
vg0918185651 sf0918184650 9 18185651 5.64E-20 1.49E-08
vg0916986888 sf0916985887 9 16986888 8.19E-16 4.47E-07
vg0919214450 sf0919214040 9 19214450 4.61E-15 9.34E-08
vg1203687735 sf1203686734 12 3687735 4.04E-14 NA
vg0119842659 sf0119841614 1 19842659 5.35E-12 3.49E-06
vg0101339236 sf0101338236 1 1339236 1.02E-11 1.42E-06
vg0116932562 sf0116931516 1 16932562 1.22E-11 1.58E-06
vg0600544648 sf0600543649 6 544648 1.27E-11 2.10E-06
vg0917926619 sf0917925618 9 17926619 6.44E-11 3.30E-08
vg0714473083 sf0714472090 7 14473083 1.84E-10 7.80E-07
vg0403292001 sf0403287604 4 3292001 5.95E-08 3.62E-06
vg0402204023 sf0402199618 4 2204023 2.25E-07 4.37E-06
vg0725964478 sf0725963484 7 25964478 5.44E-07 NA
vg0800131056 sf0800130056 8 131056 7.11E-07 NA
vg0916777400 sf0916776399 9 16777400 NA 1.59E-09
vg0916259464 sf0916258463 9 16259464 NA 2.83E-09
vg0704618174 sf0704617175 7 4618174 NA 3.31E-07
vg0302505659 sf0302504655 3 2505659 NA 1.26E-06
vg0522020155 sf0521957597 5 22020155 NA 2.26E-06
vg0806410047 sf0806409052 8 6410047 NA 2.72E-06
vg0611539236 sf0611538237 6 11539236 NA 3.67E-06
vg1114939039 sf1114475353 11 14939039 NA 4.54E-06
vg0800670300 sf0800669300 8 670300 NA 4.59E-06