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 mr1165 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
vg0727995401 sf0727994408 7 27995401 3.21E-12 3.65E-07
vg1217611967 sf1217605922 12 17611967 2.02E-08 NA
vg0726964336 sf0726963342 7 26964336 2.44E-08 NA
vg0613999068 sf0613998069 6 13999068 4.54E-08 NA
vg0138112582 sf0138111539 1 38112582 4.57E-08 NA
vg0518363321 sf0518302807 5 18363321 1.33E-07 4.31E-08
vg0502125341 sf0502125315 5 2125341 1.27E-06 4.73E-07
vg1002797270 sf1002796247 10 2797270 3.66E-06 NA
vg0525817711 sf0525755132 5 25817711 5.35E-06 NA
vg1121160624 sf1120694503 11 21160624 5.91E-06 NA
vg0610861074 sf0610860075 6 10861074 NA 1.07E-06