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 mr1668 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
vg0413157681 sf0413148391 4 13157681 2.01E-10 2.27E-06
vg1016847285 sf1016776057 10 16847285 4.99E-10 NA
vg0915258271 sf0915257270 9 15258271 5.25E-10 NA
vg1011870467 sf1011799282 10 11870467 8.20E-10 NA
vg0809915175 sf0809914179 8 9915175 1.11E-09 NA
vg0915238376 sf0915237375 9 15238376 1.29E-08 NA
vg0303295477 sf0303294473 3 3295477 8.03E-08 NA
vg0501482241 sf0501482225 5 1482241 1.42E-07 NA
vg0526058922 sf0525996342 5 26058922 2.36E-07 NA
vg0700326410 sf0700325410 7 326410 3.03E-07 3.16E-07
vg0401225551 sf0401221101 4 1225551 1.08E-06 NA
vg0700362980 sf0700361980 7 362980 2.71E-06 2.89E-07
vg0424939205 sf0424754066 4 24939205 NA 1.30E-06
vg1012875705 sf1012804520 10 12875705 NA 2.45E-06