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 mr1592 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
vg0222721389 sf0222715520 2 22721389 1.07E-29 7.23E-14
vg0222739748 sf0222733879 2 22739748 6.62E-29 4.96E-16
vg0529227658 sf0529165013 5 29227658 1.48E-17 NA
vg0204877627 sf0204877624 2 4877627 3.60E-17 NA
vg0728786301 sf0728785309 7 28786301 5.18E-17 6.74E-06
vg0708379053 sf0708378058 7 8379053 5.76E-17 NA
vg0908759965 sf0908758964 9 8759965 2.52E-16 2.66E-06
vg0222725003 sf0222719134 2 22725003 NA 1.37E-07
vg0421077205 sf0420905258 4 21077205 NA 3.14E-06