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 mr1566 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
vg0819934549 sf0819931836 8 19934549 3.11E-09 NA
vg0808447137 sf0808446141 8 8447137 8.57E-08 6.84E-07
vg0322532678 sf0322531167 3 22532678 2.86E-07 NA
vg1207456492 sf1207453898 12 7456492 4.20E-06 NA
vg1124304377 sf1123838247 11 24304377 6.80E-06 NA
vg0802888568 sf0802887571 8 2888568 7.36E-06 3.29E-06
vg0808861923 sf0808860927 8 8861923 NA 6.81E-07
vg1213091376 sf1213088715 12 13091376 NA 3.64E-06
vg1126298252 sf1125826665 11 26298252 NA 4.16E-06
vg0609106483 sf0609105484 6 9106483 NA 5.02E-06