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 mr1362 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
vg0817612440 sf0817609727 8 17612440 1.93E-27 2.89E-10
vg0922141578 sf0922141097 9 22141578 2.22E-24 3.36E-06
vg0115643577 sf0115642551 1 15643577 2.90E-23 NA
vg0628353577 sf0628352579 6 28353577 4.25E-23 NA
vg0812793667 sf0812791492 8 12793667 6.30E-23 2.17E-06
vg0433018887 sf0432833773 4 33018887 1.14E-20 6.59E-06
vg0908734371 sf0908733370 9 8734371 2.67E-20 4.59E-06
vg0817660759 sf0817658046 8 17660759 NA 2.11E-08
vg0817611509 sf0817608796 8 17611509 NA 4.42E-08
vg1204697591 sf1204696579 12 4697591 NA 6.65E-07
vg1214779250 sf1214776591 12 14779250 NA 1.05E-06
vg0817682484 sf0817679771 8 17682484 NA 2.85E-06
vg1010547694 sf1010476515 10 10547694 NA 3.06E-06
vg0818143094 sf0818140381 8 18143094 NA 3.96E-06
vg0601634959 sf0601633960 6 1634959 NA 4.59E-06
vg0630863586 sf0630862588 6 30863586 NA 4.72E-06
vg1206419905 sf1206418795 12 6419905 NA 6.85E-06