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 mr1809 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
vg0713417596 sf0713416603 7 13417596 1.09E-06 4.50E-06
vg0910447508 sf0910446507 9 10447508 6.08E-06 2.19E-06
vg1110517362 sf1110511907 11 10517362 6.98E-06 NA
vg1214045971 sf1214043311 12 14045971 NA 4.40E-07
vg1210649825 sf1210647238 12 10649825 NA 1.20E-06
vg1218126488 sf1218097924 12 18126488 NA 2.93E-06
vg0103143509 sf0103142509 1 3143509 NA 3.03E-06
vg0204866147 sf0204866144 2 4866147 NA 3.06E-06
vg1213935504 sf1213932842 12 13935504 NA 3.53E-06