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 mr1521 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
vg0722226606 sf0722225613 7 22226606 7.50E-13 3.82E-07
vg0431599291 sf0431414186 4 31599291 3.19E-12 NA
vg0419265062 sf0419093100 4 19265062 3.61E-12 NA
vg0810151808 sf0810150812 8 10151808 5.40E-12 NA
vg0402720584 sf0402716189 4 2720584 8.90E-12 NA
vg0400264186 sf0400263186 4 264186 8.16E-11 NA
vg0809692778 sf0809691782 8 9692778 6.59E-09 NA
vg0914463142 sf0914462141 9 14463142 3.06E-08 1.65E-06
vg0721363546 sf0721362553 7 21363546 7.52E-08 1.95E-06
vg0415115564 sf0415106279 4 15115564 5.35E-07 NA