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 mr1960 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
vg0726964336 sf0726963342 7 26964336 3.84E-09 NA
vg1104966222 sf1104962033 11 4966222 1.64E-08 NA
vg0131504952 sf0131503908 1 31504952 5.96E-08 NA
vg1110305257 sf1110299834 11 10305257 7.42E-08 NA
vg0821751104 sf0821748391 8 21751104 1.57E-07 NA
vg1106375766 sf1106371518 11 6375766 8.79E-07 9.78E-07
vg0710610393 sf0710609399 7 10610393 2.56E-06 1.71E-06
vg0125460372 sf0125459328 1 25460372 2.57E-06 NA
vg1204560575 sf1204559563 12 4560575 3.21E-06 1.36E-06
vg0412436211 sf0412426925 4 12436211 NA 4.76E-06