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 mr1911 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
vg0222739831 sf0222733962 2 22739831 9.96E-36 1.18E-34
vg0223053830 sf0223047961 2 23053830 1.80E-10 NA
vg0222879623 sf0222873754 2 22879623 3.66E-09 2.33E-10
vg0223641214 sf0223635345 2 23641214 9.45E-09 3.83E-08
vg0222730109 sf0222724240 2 22730109 1.41E-08 3.36E-06
vg0224788519 sf0224782650 2 24788519 3.99E-08 2.02E-06
vg0224678258 sf0224672389 2 24678258 2.77E-07 4.18E-06
vg0713058371 sf0713057378 7 13058371 1.94E-06 9.21E-07
vg0224263783 sf0224257914 2 24263783 2.30E-06 4.59E-06
vg0224775330 sf0224769461 2 24775330 4.41E-06 1.52E-06
vg0717054690 sf0717053697 7 17054690 8.93E-06 3.26E-06
vg0222163084 sf0222157215 2 22163084 NA 9.93E-08
vg0318691018 sf0318689778 3 18691018 NA 2.28E-06
vg0119929841 sf0119928796 1 19929841 NA 4.01E-06