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 mr1378 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
vg1117597661 sf1117131518 11 17597661 4.49E-09 3.68E-06
vg0208721621 sf0208721620 2 8721621 2.46E-08 6.98E-08
vg0208731146 sf0208731145 2 8731146 5.54E-08 6.52E-08
vg0626294443 sf0626293446 6 26294443 6.83E-08 NA
vg1016500010 sf1016428783 10 16500010 7.70E-08 NA
vg0411129111 sf0411119812 4 11129111 1.56E-07 3.91E-06
vg0103426681 sf0103425681 1 3426681 NA 1.37E-06
vg1122800334 sf1122334205 11 22800334 NA 1.61E-06
vg0200620734 sf0200620734 2 620734 NA 8.22E-06