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 mr1986 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
vg0921456056 sf0921455575 9 21456056 2.81E-20 3.80E-14
vg0135939815 sf0135938772 1 35939815 1.09E-14 NA
vg0223630786 sf0223624917 2 23630786 2.23E-14 NA
vg0523014690 sf0522952131 5 23014690 2.25E-14 NA
vg0800333217 sf0800332217 8 333217 5.12E-14 NA
vg0711642430 sf0711641436 7 11642430 6.73E-12 NA
vg1108670109 sf1108664719 11 8670109 4.84E-11 NA
vg0614036522 sf0614035523 6 14036522 5.08E-11 NA
vg0921533165 sf0921532684 9 21533165 NA 2.70E-07
vg0706567686 sf0706566691 7 6567686 NA 1.32E-06
vg1214822308 sf1214819649 12 14822308 NA 1.57E-06