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 mr1154 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
vg1111006799 sf1111001116 11 11006799 3.14E-08 NA
vg0627174899 sf0627173902 6 27174899 6.33E-08 NA
vg0208607058 sf0208607057 2 8607058 7.02E-08 NA
vg1009253419 sf1009182240 10 9253419 1.16E-07 3.05E-06
vg1115413712 sf1114950024 11 15413712 1.33E-06 3.53E-07
vg1110370746 sf1110365291 11 10370746 1.90E-06 2.01E-06
vg1111145602 sf1111139919 11 11145602 2.10E-06 NA
vg1110437041 sf1110431586 11 10437041 3.23E-06 3.65E-07
vg1109845531 sf1109840108 11 9845531 NA 2.30E-06