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 mr1674 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
vg0321576069 sf0321574579 3 21576069 5.48E-08 5.48E-08
vg0805946030 sf0805945033 8 5946030 1.64E-07 1.64E-07
vg0804905723 sf0804904726 8 4905723 5.77E-07 5.77E-07
vg0329703696 sf0329696736 3 29703696 1.10E-06 1.10E-06
vg1127480350 sf1127008737 11 27480350 1.29E-06 1.29E-06
vg0807752750 sf0807751754 8 7752750 1.42E-06 1.42E-06
vg0107079035 sf0107078035 1 7079035 1.88E-06 1.88E-06
vg0605743908 sf0605742909 6 5743908 2.18E-06 2.18E-06
vg0206578247 sf0206578247 2 6578247 2.22E-06 2.22E-06
vg1020531763 sf1020460242 10 20531763 2.24E-06 2.24E-06
vg0222337580 sf0222331711 2 22337580 3.13E-06 3.13E-06
vg0124420479 sf0124419435 1 24420479 3.22E-06 3.22E-06
vg0901536604 sf0901535604 9 1536604 3.48E-06 3.48E-06
vg0826077942 sf0826075228 8 26077942 3.92E-06 3.92E-06
vg0308543438 sf0308542376 3 8543438 4.01E-06 4.02E-06
vg0610852582 sf0610851583 6 10852582 4.39E-06 4.39E-06