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 mr1004 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
vg0921524668 sf0921524187 9 21524668 8.15E-18 2.26E-12
vg0726064673 sf0726063679 7 26064673 1.38E-13 2.05E-07
vg0726065533 sf0726064539 7 26065533 1.91E-13 5.03E-08
vg0725253822 sf0725252828 7 25253822 2.35E-13 NA
vg0206284604 sf0206284604 2 6284604 2.92E-13 NA
vg0205034600 sf0205034597 2 5034600 6.33E-12 NA
vg0206400695 sf0206400695 2 6400695 1.69E-11 2.80E-06
vg0133492949 sf0133491905 1 33492949 3.62E-11 7.50E-07
vg0205950133 sf0205950133 2 5950133 8.77E-11 8.93E-06
vg0724979429 sf0724978435 7 24979429 3.36E-09 2.90E-07
vg1217386152 sf1217380107 12 17386152 3.47E-09 1.40E-06
vg0303778438 sf0303777434 3 3778438 6.65E-08 NA
vg0921522197 sf0921521716 9 21522197 NA 3.90E-09
vg1215306171 sf1215303469 12 15306171 NA 7.48E-07
vg0300976326 sf0300975324 3 976326 NA 3.38E-06
vg0906442847 sf0906441847 9 6442847 NA 3.81E-06
vg0725957540 sf0725956546 7 25957540 NA 4.16E-06
vg0230079962 sf0230074093 2 30079962 NA 4.82E-06