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 mr1907 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
vg0524494561 sf0524431982 5 24494561 2.16E-139 1.56E-31
vg0524593054 sf0524530474 5 24593054 6.80E-138 4.41E-33
vg0412536062 sf0412526772 4 12536062 9.49E-84 NA
vg0807294325 sf0807293330 8 7294325 2.36E-83 NA
vg1208970617 sf1208968025 12 8970617 1.29E-82 NA
vg0528998640 sf0528935995 5 28998640 1.35E-82 NA
vg0917059579 sf0917058578 9 17059579 3.10E-81 3.42E-06
vg0524738001 sf0524675422 5 24738001 NA 3.63E-19
vg1205231921 sf1205230907 12 5231921 NA 4.16E-08
vg1100512559 sf1100511562 11 512559 NA 7.50E-07
vg1223867548 sf1223834001 12 23867548 NA 8.00E-07
vg1108799422 sf1108794032 11 8799422 NA 1.49E-06
vg1122476819 sf1122010690 11 22476819 NA 2.39E-06
vg1223859563 sf1223826016 12 23859563 NA 4.50E-06