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 mr1045 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
vg0420823688 sf0420651731 4 20823688 6.72E-13 NA
vg0315369587 sf0315368234 3 15369587 5.20E-12 NA
vg0122917286 sf0122916242 1 22917286 7.15E-12 NA
vg0728388990 sf0728387998 7 28388990 1.18E-11 NA
vg0501839750 sf0501839733 5 1839750 1.72E-11 NA
vg0409772222 sf0409762920 4 9772222 4.17E-09 NA
vg0514921243 sf0514863786 5 14921243 9.73E-09 NA
vg0615113512 sf0615112513 6 15113512 9.77E-08 NA
vg0922468532 sf0922468051 9 22468532 1.13E-07 NA
vg1122514350 sf1122048221 11 22514350 NA 4.36E-06
vg0103143509 sf0103142509 1 3143509 NA 6.62E-06