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 mr1670 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
vg0400407662 sf0400406660 4 407662 2.53E-08 2.53E-08
vg0138144207 sf0138143164 1 38144207 7.25E-08 7.24E-08
vg1005691241 sf1005707779 10 5691241 3.59E-07 3.59E-07
vg0401346827 sf0401342377 4 1346827 2.91E-06 2.91E-06
vg0314830047 sf0314828694 3 14830047 3.00E-06 3.00E-06
vg0138075905 sf0138074862 1 38075905 6.18E-06 6.18E-06