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 mr1605 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
vg1214111586 sf1214108926 12 14111586 1.22E-08 1.22E-08
vg1122514350 sf1122048221 11 22514350 2.95E-07 2.95E-07
vg0434860506 sf0434675397 4 34860506 5.02E-07 5.03E-07
vg0315321037 sf0315319684 3 15321037 5.87E-07 5.87E-07
vg1217604890 sf1217598845 12 17604890 7.96E-07 7.97E-07
vg1013275525 sf1013204295 10 13275525 1.09E-06 1.09E-06
vg0206178879 sf0206178879 2 6178879 2.49E-06 2.50E-06
vg0320864432 sf0320862942 3 20864432 2.64E-06 2.64E-06
vg1128595453 sf1128072232 11 28595453 3.78E-06 3.78E-06
vg0727801024 sf0727800031 7 27801024 3.93E-06 3.93E-06
vg0316985667 sf0316984541 3 16985667 4.02E-06 4.02E-06
vg1211450881 sf1211448217 12 11450881 4.41E-06 4.41E-06