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 mr1043 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
vg1105925054 sf1105920806 11 5925054 1.19E-11 1.06E-06
vg1219173044 sf1219144514 12 19173044 1.19E-10 NA
vg0618104196 sf0618103199 6 18104196 2.87E-09 NA
vg0116413548 sf0116412522 1 16413548 8.73E-09 1.70E-06
vg0613092710 sf0613091711 6 13092710 1.96E-08 NA
vg0413435949 sf0413426663 4 13435949 2.67E-06 2.35E-06
vg0321065461 sf0321063971 3 21065461 5.37E-06 NA
vg0520358656 sf0520296129 5 20358656 NA 5.44E-07
vg1000843357 sf1000842333 10 843357 NA 6.09E-07
vg0520332453 sf0520269926 5 20332453 NA 8.88E-07
vg0715317227 sf0715316234 7 15317227 NA 3.27E-06
vg0314017083 sf0314015800 3 14017083 NA 3.94E-06
vg0221875581 sf0221869712 2 21875581 NA 4.47E-06
vg0310177475 sf0310176391 3 10177475 NA 4.99E-06