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 mr1646 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
vg0915815139 sf0915814138 9 15815139 8.59E-17 5.18E-08
vg0528836237 sf0528773592 5 28836237 7.17E-15 1.92E-07
vg0140420361 sf0140419318 1 40420361 1.74E-14 NA
vg1219760769 sf1219732239 12 19760769 6.95E-14 NA
vg0724945438 sf0724944444 7 24945438 9.84E-14 NA
vg0914831651 sf0914830650 9 14831651 4.04E-13 1.47E-06
vg1219631829 sf1219603299 12 19631829 6.49E-13 2.57E-06
vg1219837830 sf1219809300 12 19837830 1.85E-10 2.22E-06
vg0431515534 sf0431330433 4 31515534 NA 1.05E-06
vg1215167085 sf1215164421 12 15167085 NA 3.22E-06
vg0432591580 sf0432406471 4 32591580 NA 3.28E-06
vg0906798732 sf0906797732 9 6798732 NA 3.78E-06