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 2.18E-26 6.96E-14
vg0916213257 sf0916212256 9 16213257 4.37E-22 9.93E-13
vg0916119204 sf0916118203 9 16119204 1.29E-17 2.65E-09
vg0919157155 sf0919156744 9 19157155 1.30E-10 NA
vg0919214450 sf0919214040 9 19214450 5.58E-10 1.40E-06
vg0131798662 sf0131797618 1 31798662 1.14E-09 NA
vg0704618174 sf0704617175 7 4618174 1.41E-08 9.77E-07
vg0101338524 sf0101337524 1 1338524 1.79E-07 2.64E-07
vg1210333331 sf1210330744 12 10333331 1.74E-06 9.43E-07
vg0332229065 sf0332221943 3 32229065 3.80E-06 NA
vg0102177568 sf0102176568 1 2177568 NA 7.85E-07
vg0810204965 sf0810203969 8 10204965 NA 3.48E-06