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 mr1293 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
vg0328006168 sf0327999222 3 28006168 4.86E-07 NA
vg1200964236 sf1200963236 12 964236 3.51E-06 NA
vg0208593323 sf0208593322 2 8593323 7.30E-06 NA
vg1214031439 sf1214028779 12 14031439 NA 6.47E-07
vg1213935504 sf1213932842 12 13935504 NA 2.49E-06
vg0400103190 sf0400102190 4 103190 NA 2.60E-06
vg1210995463 sf1210992829 12 10995463 NA 2.67E-06