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 mr1726 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
vg0405709009 sf0405704448 4 5709009 1.41E-13 NA
vg0101399336 sf0101398336 1 1399336 1.11E-12 NA
vg0707026664 sf0707025669 7 7026664 4.96E-12 2.03E-06
vg0412701005 sf0412691716 4 12701005 1.33E-11 NA
vg0408653397 sf0408648673 4 8653397 2.21E-11 NA
vg0112714249 sf0112713223 1 12714249 2.23E-09 NA
vg0604919053 sf0604918054 6 4919053 3.23E-09 NA
vg0431647376 sf0431462269 4 31647376 1.07E-07 NA
vg0507602235 sf0507602176 5 7602235 NA 3.09E-06
vg1214823299 sf1214820640 12 14823299 NA 3.59E-06
vg0408431062 sf0408426336 4 8431062 NA 4.21E-06
vg0336059373 sf0336052242 3 36059373 NA 5.08E-06