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 mr1992 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
vg0724945438 sf0724944444 7 24945438 1.15E-10 2.33E-07
vg1219850678 sf1219822148 12 19850678 1.40E-09 5.57E-06
vg1219794221 sf1219765691 12 19794221 1.69E-09 NA
vg0724648364 sf0724647370 7 24648364 6.49E-09 NA
vg1103184231 sf1103180134 11 3184231 8.35E-09 NA
vg1109865508 sf1109860085 11 9865508 1.02E-07 NA
vg0302112470 sf0302111466 3 2112470 NA 7.31E-07