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 mr1659 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
vg0623002089 sf0623001092 6 23002089 5.30E-14 5.50E-07
vg1102355785 sf1102351644 11 2355785 3.11E-13 NA
vg1219845187 sf1219816657 12 19845187 3.66E-12 NA
vg0130137856 sf0130136811 1 30137856 5.17E-12 NA
vg0800349379 sf0800348379 8 349379 5.21E-12 NA
vg0904007553 sf0904006553 9 4007553 6.06E-11 3.55E-06
vg1105542927 sf1105538679 11 5542927 1.02E-08 NA
vg0828205268 sf0828202554 8 28205268 1.79E-08 NA
vg0215095083 sf0215089213 2 15095083 5.00E-08 1.74E-07
vg0623056011 sf0623055014 6 23056011 NA 3.47E-07
vg1117402069 sf1116935922 11 17402069 NA 3.35E-06
vg0211188937 sf0211188934 2 11188937 NA 5.46E-06