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 mr1257 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
vg0217047369 sf0217041499 2 17047369 1.80E-58 1.76E-30
vg0213525745 sf0213525741 2 13525745 2.15E-25 1.16E-09
vg0213047786 sf0213047782 2 13047786 1.27E-23 4.21E-10
vg0900337327 sf0900336327 9 337327 5.43E-22 4.59E-08
vg0900336799 sf0900335799 9 336799 2.22E-20 4.44E-08
vg0812023942 sf0812022947 8 12023942 5.13E-18 NA
vg0216372724 sf0216366854 2 16372724 6.66E-18 2.41E-08
vg0216357484 sf0216351614 2 16357484 2.66E-17 5.42E-09
vg0217737734 sf0217731864 2 17737734 1.51E-15 1.35E-08
vg0216278300 sf0216272430 2 16278300 2.90E-15 1.82E-06
vg0217809768 sf0217803899 2 17809768 2.13E-12 2.83E-06
vg1005364262 sf1005380799 10 5364262 6.69E-11 7.23E-07
vg0216876069 sf0216870199 2 16876069 1.81E-10 3.87E-09
vg0218858392 sf0218852523 2 18858392 3.75E-10 1.79E-06
vg0215670936 sf0215665066 2 15670936 7.83E-08 NA
vg0217296517 sf0217290647 2 17296517 NA 4.55E-07