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 mr1066 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
vg0622823121 sf0622822124 6 22823121 1.14E-10 NA
vg1122514350 sf1122048221 11 22514350 1.67E-10 1.25E-07
vg1223934169 sf1223900622 12 23934169 1.75E-10 NA
vg0414057794 sf0414048509 4 14057794 6.32E-10 NA
vg1200200887 sf1200199887 12 200887 6.57E-10 NA
vg1218161842 sf1218133278 12 18161842 2.42E-08 4.55E-07
vg0818689829 sf0818687116 8 18689829 3.08E-07 3.40E-06
vg0625534713 sf0625533716 6 25534713 7.33E-06 NA
vg0622383384 sf0622382387 6 22383384 NA 6.68E-08
vg0402373904 sf0402369499 4 2373904 NA 5.73E-07
vg0820734484 sf0820731771 8 20734484 NA 7.49E-07