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 mr1078 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
vg0610752378 sf0610751379 6 10752378 1.58E-20 1.37E-17
vg0910025779 sf0910024778 9 10025779 1.16E-09 1.35E-06
vg1010198226 sf1010127047 10 10198226 5.91E-09 NA
vg0403922278 sf0403917884 4 3922278 7.77E-09 1.78E-06
vg1008740483 sf1008669345 10 8740483 2.91E-08 5.90E-06
vg0610779574 sf0610778575 6 10779574 3.31E-07 3.64E-06
vg0622627470 sf0622626473 6 22627470 1.30E-06 2.78E-06
vg0428010105 sf0427824969 4 28010105 4.78E-06 NA
vg1225527437 sf1225493832 12 25527437 5.17E-06 NA