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 mr1196 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
vg1122514350 sf1122048221 11 22514350 8.74E-09 1.06E-06
vg1207774257 sf1207771663 12 7774257 4.34E-07 8.33E-07
vg1216072989 sf1216070285 12 16072989 1.36E-06 9.94E-06
vg1119511373 sf1119045061 11 19511373 1.51E-06 NA
vg1119340990 sf1118874678 11 19340990 NA 1.77E-06
vg1209676708 sf1209674117 12 9676708 NA 3.66E-06