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 mr1735 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
vg0131768366 sf0131767322 1 31768366 9.29E-09 NA
vg1117584893 sf1117118750 11 17584893 1.72E-08 NA
vg0132947824 sf0132946780 1 32947824 2.59E-08 NA
vg0521749407 sf0521686849 5 21749407 4.89E-08 NA
vg0724948333 sf0724947339 7 24948333 4.93E-08 NA
vg0123683673 sf0123682629 1 23683673 5.01E-08 NA
vg0800635903 sf0800634903 8 635903 2.06E-07 6.97E-07
vg0811006885 sf0811005890 8 11006885 5.90E-07 3.89E-07
vg0423651585 sf0423466442 4 23651585 1.61E-06 2.88E-07
vg0120798282 sf0120797237 1 20798282 NA 3.79E-07