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 mr1060 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
vg1215212934 sf1215210231 12 15212934 2.21E-09 5.15E-07
vg1218067233 sf1218038669 12 18067233 6.64E-09 8.82E-06
vg1217950270 sf1217921705 12 17950270 7.83E-09 NA
vg0607184594 sf0607183595 6 7184594 4.99E-08 NA
vg1218121777 sf1218093213 12 18121777 5.62E-08 1.35E-06
vg0136461943 sf0136460900 1 36461943 6.79E-08 NA