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 mr1683 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
vg0205310117 sf0205310116 2 5310117 7.91E-18 1.67E-07
vg1200800605 sf1200799605 12 800605 9.54E-16 NA
vg0215098426 sf0215092556 2 15098426 2.60E-15 NA
vg0805684701 sf0805683704 8 5684701 1.24E-14 NA
vg0909011341 sf0909010340 9 9011341 3.43E-14 NA
vg0818578468 sf0818575755 8 18578468 NA 1.11E-06
vg0809566293 sf0809565297 8 9566293 NA 1.16E-06
vg1023012141 sf1022940614 10 23012141 NA 1.47E-06