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 mr1611 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
vg0604234049 sf0604233050 6 4234049 4.22E-32 3.46E-10
vg0604336470 sf0604335471 6 4336470 4.66E-30 1.85E-10
vg0805137142 sf0805136145 8 5137142 6.23E-29 NA
vg0811152944 sf0811151949 8 11152944 9.50E-29 4.59E-06
vg1117907120 sf1117440978 11 17907120 1.85E-27 NA
vg0140038034 sf0140036991 1 40038034 2.38E-27 NA
vg0604233778 sf0604232779 6 4233778 NA 1.27E-07
vg1004059501 sf1004058477 10 4059501 NA 1.63E-07
vg0402111447 sf0402107041 4 2111447 NA 3.56E-07
vg1116933718 sf1116468597 11 16933718 NA 3.43E-06
vg0826363216 sf0826360502 8 26363216 NA 4.11E-06
vg0433044174 sf0432859061 4 33044174 NA 4.37E-06
vg0518984986 sf0518922470 5 18984986 NA 4.52E-06