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 mr1746 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
vg0800182659 sf0800181659 8 182659 1.16E-13 NA
vg0800328264 sf0800327264 8 328264 3.06E-13 2.43E-06
vg0815566806 sf0815564092 8 15566806 4.66E-12 NA
vg0812694622 sf0812692447 8 12694622 2.19E-11 NA
vg0819922574 sf0819919861 8 19922574 7.27E-11 NA
vg0420546726 sf0420374770 4 20546726 1.33E-10 NA
vg1002771978 sf1002770955 10 2771978 8.20E-10 3.70E-06
vg1011760237 sf1011689052 10 11760237 NA 1.06E-06
vg1217045327 sf1217039281 12 17045327 NA 2.70E-06