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 mr1284 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
vg0220342715 sf0220336847 2 20342715 3.99E-09 4.05E-07
vg0102103204 sf0102102204 1 2103204 1.05E-08 3.87E-07
vg1020531763 sf1020460242 10 20531763 4.17E-08 8.75E-07
vg0142427760 sf0142426716 1 42427760 6.95E-08 2.38E-06
vg0726559146 sf0726558152 7 26559146 1.41E-07 4.77E-06
vg0516885177 sf0516824818 5 16885177 1.42E-06 6.72E-07
vg0420718113 sf0420546156 4 20718113 4.34E-06 3.99E-06
vg0232480149 sf0232474280 2 32480149 NA 4.04E-06