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 mr1324 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
vg0920030283 sf0920029802 9 20030283 1.98E-20 6.34E-06
vg0122690936 sf0122689891 1 22690936 9.45E-20 3.23E-07
vg0914717208 sf0914716207 9 14717208 1.70E-19 NA
vg0725046371 sf0725045377 7 25046371 1.87E-19 8.34E-06
vg0504766271 sf0504766248 5 4766271 4.36E-19 NA
vg0504742919 sf0504742896 5 4742919 5.90E-19 4.80E-06
vg1002992765 sf1002991742 10 2992765 1.15E-18 1.33E-06
vg1013444607 sf1013373377 10 13444607 5.37E-17 1.27E-07
vg0332518144 sf0332511017 3 32518144 NA 4.22E-07
vg0822936315 sf0822933602 8 22936315 NA 7.71E-07
vg0522004462 sf0521941904 5 22004462 NA 1.43E-06
vg0520708958 sf0520646399 5 20708958 NA 3.15E-06
vg1214644530 sf1214641870 12 14644530 NA 6.86E-06
vg1218022381 sf1217993817 12 18022381 NA 7.16E-06
vg0520223717 sf0520161190 5 20223717 NA 8.44E-06