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 mr1518 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
vg0919848647 sf0919848166 9 19848647 8.60E-29 2.91E-09
vg0920166366 sf0920165885 9 20166366 5.58E-26 3.34E-10
vg0920428177 sf0920427696 9 20428177 8.21E-26 5.15E-10
vg0917485210 sf0917484209 9 17485210 9.78E-26 2.69E-06
vg0106963119 sf0106962119 1 6963119 4.55E-24 1.79E-10
vg0305233552 sf0305232552 3 5233552 1.46E-23 3.80E-07
vg0143167776 sf0143166732 1 43167776 2.27E-22 5.92E-06
vg0719250996 sf0719250003 7 19250996 2.87E-22 NA
vg0608680831 sf0608679832 6 8680831 4.76E-21 2.51E-06
vg0617709303 sf0617708306 6 17709303 5.21E-21 3.77E-07
vg0107015621 sf0107014621 1 7015621 NA 1.04E-10
vg0920461569 sf0920461088 9 20461569 NA 2.33E-07
vg0107066469 sf0107065469 1 7066469 NA 9.35E-07
vg0910780392 sf0910779391 9 10780392 NA 1.49E-06
vg1221475948 sf1221442495 12 21475948 NA 2.12E-06
vg1021824431 sf1021752907 10 21824431 NA 2.60E-06