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 mr1277 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
vg0800302779 sf0800301779 8 302779 6.30E-17 2.89E-13
vg0435408492 sf0435223372 4 35408492 1.63E-10 NA
vg0135647035 sf0135645992 1 35647035 2.00E-10 NA
vg0133381779 sf0133380735 1 33381779 5.98E-10 NA
vg0500169773 sf0500169773 5 169773 2.03E-09 NA
vg0500026688 sf0500026688 5 26688 9.20E-09 NA
vg0800452763 sf0800451763 8 452763 2.00E-08 6.84E-09
vg0800300760 sf0800299760 8 300760 9.06E-08 7.76E-11
vg0801307168 sf0801306170 8 1307168 7.10E-06 3.64E-06