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 mr1187 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
vg0314683577 sf0314682264 3 14683577 9.84E-08 NA
vg0604517236 sf0604516237 6 4517236 2.59E-07 2.01E-06
vg0434528001 sf0434342894 4 34528001 NA 1.06E-06
vg0518708516 sf0518645999 5 18708516 NA 1.66E-06
vg1221736592 sf1221703139 12 21736592 NA 3.13E-06
vg0604316445 sf0604315446 6 4316445 NA 4.07E-06
vg0712460832 sf0712459839 7 12460832 NA 4.62E-06
vg1119346406 sf1118880094 11 19346406 NA 6.96E-06