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 mr1730 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
vg0329805919 sf0329798959 3 29805919 5.65E-15 NA
vg0332501464 sf0332494337 3 32501464 3.38E-14 NA
vg1224029750 sf1223996203 12 24029750 4.38E-14 NA
vg0307834076 sf0307833014 3 7834076 4.66E-14 NA
vg0529106995 sf0529044350 5 29106995 1.71E-13 NA
vg0313123547 sf0313122265 3 13123547 1.89E-11 9.56E-06
vg0333248231 sf0333241101 3 33248231 2.46E-11 4.49E-06
vg0721165888 sf0721164895 7 21165888 NA 5.45E-07
vg0413770148 sf0413760862 4 13770148 NA 5.86E-07
vg1119288479 sf1118822167 11 19288479 NA 5.99E-07
vg0413770697 sf0413761411 4 13770697 NA 1.77E-06
vg0502444924 sf0502444900 5 2444924 NA 2.83E-06
vg0413771259 sf0413761973 4 13771259 NA 4.58E-06