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
vg0142322025 sf0142320981 1 42322025 6.97E-08 NA
vg0818736737 sf0818734024 8 18736737 8.87E-08 NA
vg0918827520 sf0918826520 9 18827520 1.18E-06 2.84E-06
vg0905341973 sf0905340973 9 5341973 2.10E-06 3.09E-06
vg1218107451 sf1218078887 12 18107451 3.66E-06 1.93E-06
vg0709159938 sf0709158944 7 9159938 4.41E-06 NA
vg1108100448 sf1108096193 11 8100448 5.37E-06 4.43E-06
vg0121827646 sf0121826601 1 21827646 NA 7.17E-07
vg1208174078 sf1208171484 12 8174078 NA 2.79E-06
vg0104007398 sf0104006398 1 4007398 NA 3.51E-06
vg0104000364 sf0103999364 1 4000364 NA 4.85E-06