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 mr1158 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
vg1201028561 sf1201027561 12 1028561 1.86E-20 NA
vg0702662015 sf0702661016 7 2662015 3.36E-20 NA
vg0529415546 sf0529352901 5 29415546 4.44E-20 NA
vg0700118813 sf0700117813 7 118813 5.80E-20 NA
vg1110109078 sf1110103655 11 10109078 5.96E-20 NA
vg0434891799 sf0434706689 4 34891799 2.51E-17 1.79E-07
vg1204312140 sf1204311128 12 4312140 7.30E-17 4.98E-08
vg1211114784 sf1211112148 12 11114784 5.29E-16 NA
vg0700407866 sf0700406866 7 407866 1.26E-15 NA
vg0700013444 sf0700012444 7 13444 NA 2.11E-10
vg0814573882 sf0814571168 8 14573882 NA 1.59E-06
vg0904682424 sf0904681424 9 4682424 NA 1.97E-06
vg0206503587 sf0206503587 2 6503587 NA 2.32E-06
vg0107884262 sf0107883262 1 7884262 NA 3.18E-06
vg0318764531 sf0318763291 3 18764531 NA 7.75E-06