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 mr1252 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
vg0400159440 sf0400158440 4 159440 4.78E-10 1.04E-06
vg0130697648 sf0130696604 1 30697648 5.27E-10 6.12E-07
vg0130670983 sf0130669939 1 30670983 5.28E-10 5.61E-07
vg0723551233 sf0723550240 7 23551233 5.20E-09 NA
vg0428761895 sf0428576746 4 28761895 6.26E-09 NA
vg0400613918 sf0400612918 4 613918 7.17E-09 NA
vg0810686573 sf0810685578 8 10686573 9.28E-09 NA
vg0601384228 sf0601383229 6 1384228 3.36E-08 3.10E-06
vg0432860646 sf0432675533 4 32860646 6.07E-08 2.44E-06
vg0432999456 sf0432814342 4 32999456 3.34E-07 1.63E-06
vg0431498426 sf0431313325 4 31498426 1.69E-06 NA