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 mr1593 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
vg0507169486 sf0507169428 5 7169486 1.04E-94 1.48E-52
vg0507141002 sf0507140944 5 7141002 1.40E-93 6.70E-53
vg0619720091 sf0619719094 6 19720091 8.84E-19 NA
vg0507074482 sf0507074424 5 7074482 3.38E-17 1.05E-17
vg0506950500 sf0506950442 5 6950500 1.21E-15 4.69E-06
vg0508237720 sf0508237660 5 8237720 2.12E-15 7.16E-06
vg0506827010 sf0506826952 5 6827010 2.95E-14 1.05E-06
vg0508262368 sf0508262308 5 8262368 3.19E-13 3.40E-08
vg0506751886 sf0506751828 5 6751886 1.04E-10 2.54E-08
vg0506970510 sf0506970452 5 6970510 2.52E-09 1.51E-06
vg0510456115 sf0510459274 5 10456115 8.59E-09 1.13E-07
vg0506970223 sf0506970165 5 6970223 5.04E-08 2.57E-07
vg1220059475 sf1220030917 12 20059475 2.35E-07 NA
vg0121586545 sf0121585500 1 21586545 NA 5.53E-07
vg0512828870 sf0512771792 5 12828870 NA 1.08E-06
vg1127998183 sf1127526569 11 27998183 NA 2.27E-06
vg1017988748 sf1017917520 10 17988748 NA 2.84E-06
vg0130788466 sf0130787422 1 30788466 NA 3.26E-06