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 mr1015 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
vg0133489903 sf0133488859 1 33489903 3.24E-104 6.25E-21
vg0130140335 sf0130139290 1 30140335 2.93E-83 NA
vg0137837960 sf0137836917 1 37837960 2.28E-81 NA
vg0903208447 sf0903207447 9 3208447 2.70E-80 NA
vg0212168370 sf0212168366 2 12168370 5.22E-80 NA
vg0130732205 sf0130731161 1 30732205 8.96E-78 3.11E-06
vg0133689947 sf0133688903 1 33689947 NA 4.57E-07
vg1020760386 sf1020688865 10 20760386 NA 1.06E-06
vg0118219073 sf0118218027 1 18219073 NA 2.06E-06
vg0133259170 sf0133258126 1 33259170 NA 2.17E-06
vg0221380162 sf0221374294 2 21380162 NA 2.20E-06