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 mr1071 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
vg0406519287 sf0406514730 4 6519287 5.61E-21 2.90E-15
vg0406464503 sf0406459946 4 6464503 5.06E-20 4.34E-14
vg1016565386 sf1016494159 10 16565386 1.90E-09 8.29E-06
vg0722687147 sf0722686154 7 22687147 2.33E-09 1.77E-06
vg0722626782 sf0722625789 7 22626782 5.97E-09 3.49E-07
vg0823019901 sf0823017188 8 23019901 9.23E-09 2.14E-06
vg1122614316 sf1122148187 11 22614316 2.14E-08 NA