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 mr1808 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
vg1118461807 sf1117995666 11 18461807 2.36E-13 2.44E-06
vg0804856202 sf0804855205 8 4856202 2.89E-13 NA
vg0124380181 sf0124379137 1 24380181 2.80E-12 NA
vg0904296667 sf0904295667 9 4296667 4.46E-12 NA
vg0228468795 sf0228462926 2 28468795 1.85E-11 NA
vg0103390736 sf0103389736 1 3390736 2.45E-11 2.47E-06
vg0909829640 sf0909828639 9 9829640 3.69E-11 4.73E-06
vg0323497027 sf0323495201 3 23497027 9.64E-11 5.07E-06
vg0726450998 sf0726450004 7 26450998 9.03E-10 4.10E-06
vg1209890482 sf1209887892 12 9890482 3.46E-09 2.83E-06
vg0302227248 sf0302226244 3 2227248 3.58E-07 NA
vg0133325596 sf0133324552 1 33325596 4.33E-07 9.65E-08
vg0421016929 sf0420844982 4 21016929 NA 7.17E-07
vg0800342787 sf0800341787 8 342787 NA 2.90E-06
vg0904245458 sf0904244458 9 4245458 NA 4.71E-06