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 mr1692 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
vg0205305322 sf0205305321 2 5305322 1.49E-59 5.79E-12
vg0628556574 sf0628555576 6 28556574 3.21E-58 NA
vg0140789733 sf0140788690 1 40789733 5.82E-58 NA
vg0221211819 sf0221205951 2 21211819 1.83E-57 NA
vg0628752358 sf0628751360 6 28752358 3.75E-57 5.55E-07
vg0822031104 sf0822028391 8 22031104 4.85E-57 NA
vg0230028319 sf0230022450 2 30028319 4.43E-55 1.01E-06
vg0909162329 sf0909161328 9 9162329 1.57E-50 6.15E-07
vg0629626076 sf0629625078 6 29626076 5.75E-50 NA
vg0718117891 sf0718116898 7 18117891 NA 2.09E-08
vg0718112109 sf0718111116 7 18112109 NA 1.27E-07
vg0207175630 sf0207175630 2 7175630 NA 1.55E-06
vg0701128221 sf0701127221 7 1128221 NA 2.17E-06
vg1124031127 sf1123564997 11 24031127 NA 2.45E-06
vg0234326223 sf0234320354 2 34326223 NA 4.99E-06
vg0909165763 sf0909164762 9 9165763 NA 5.60E-06