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 mr1195 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
vg0507132804 sf0507132746 5 7132804 1.19E-19 3.27E-09
vg0800581691 sf0800580691 8 581691 9.38E-16 2.41E-06
vg0428960374 sf0428775232 4 28960374 1.24E-13 1.78E-06
vg0715293300 sf0715292307 7 15293300 1.65E-13 9.51E-06
vg0419249774 sf0419077812 4 19249774 7.57E-13 NA
vg0224822504 sf0224816635 2 24822504 9.44E-12 6.82E-06
vg0507139485 sf0507139427 5 7139485 2.50E-11 3.32E-06
vg0507128411 sf0507128353 5 7128411 2.09E-10 2.34E-09
vg0800648941 sf0800647941 8 648941 NA 5.25E-07
vg0800542016 sf0800541016 8 542016 NA 3.18E-06