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 mr1547 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
vg0125628571 sf0125627527 1 25628571 1.65E-07 1.65E-07
vg0316504158 sf0316502803 3 16504158 2.97E-07 2.97E-07
vg1005164238 sf1005180775 10 5164238 4.94E-07 4.95E-07
vg0920369641 sf0920369160 9 20369641 5.75E-07 5.75E-07
vg0207729665 sf0207729664 2 7729665 2.43E-06 2.43E-06
vg1122954720 sf1122488591 11 22954720 2.70E-06 2.70E-06
vg0308205423 sf0308204361 3 8205423 3.18E-06 3.18E-06
vg1213717963 sf1213715301 12 13717963 3.50E-06 3.50E-06
vg0312872747 sf0312871465 3 12872747 3.50E-06 3.50E-06