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 mr1322 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
vg0519281720 sf0519219204 5 19281720 3.39E-12 4.80E-06
vg0601266215 sf0601265216 6 1266215 1.41E-10 NA
vg1108676355 sf1108670965 11 8676355 2.67E-10 NA
vg0501832883 sf0501832866 5 1832883 1.95E-09 NA
vg0136579184 sf0136578141 1 36579184 2.14E-09 NA
vg0415965987 sf0415794020 4 15965987 2.28E-09 7.69E-06
vg0519079761 sf0519017245 5 19079761 3.19E-09 3.06E-06
vg0101289411 sf0101288411 1 1289411 1.97E-08 5.26E-06
vg0907408814 sf0907407814 9 7408814 1.24E-07 NA
vg0519193960 sf0519131444 5 19193960 NA 4.44E-06
vg0434701142 sf0434516031 4 34701142 NA 6.18E-06