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 mr1353 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
vg1123190871 sf1122724742 11 23190871 2.61E-09 8.87E-06
vg0422558702 sf0422373587 4 22558702 5.59E-08 NA
vg0216320543 sf0216314673 2 16320543 6.05E-08 9.84E-06
vg0122798728 sf0122797684 1 22798728 8.21E-08 NA
vg1117535965 sf1117069820 11 17535965 4.83E-07 NA
vg1001246161 sf1001245138 10 1246161 6.21E-07 1.01E-06
vg0406854976 sf0406850421 4 6854976 NA 4.98E-07
vg1218127441 sf1218098877 12 18127441 NA 1.90E-06
vg1215235888 sf1218062462 12 15235888 NA 6.32E-06