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 mr1081 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
vg0607687919 sf0607686920 6 7687919 2.75E-07 2.75E-07
vg0906637914 sf0906636914 9 6637914 6.15E-07 6.15E-07
vg0800219292 sf0800218292 8 219292 7.89E-07 7.89E-07
vg0622522792 sf0622521795 6 22522792 8.89E-07 8.89E-07
vg0709265984 sf0709264990 7 9265984 9.50E-07 9.50E-07
vg1211771710 sf1211769046 12 11771710 1.06E-06 1.07E-06
vg0722488401 sf0722487408 7 22488401 1.09E-06 1.09E-06
vg1204614277 sf1204613265 12 4614277 1.14E-06 1.14E-06
vg0416668164 sf0416496204 4 16668164 1.43E-06 1.43E-06
vg0728305875 sf0728304883 7 28305875 1.55E-06 1.55E-06
vg0138784720 sf0138783677 1 38784720 1.71E-06 1.71E-06
vg1215874878 sf1215872174 12 15874878 1.74E-06 1.74E-06
vg0101263892 sf0101262892 1 1263892 2.83E-06 2.83E-06
vg0712875165 sf0712874172 7 12875165 3.15E-06 3.15E-06
vg0818939785 sf0818937072 8 18939785 3.25E-06 3.25E-06
vg0505168151 sf0505168129 5 5168151 3.27E-06 3.27E-06
vg0113327952 sf0113326926 1 13327952 3.31E-06 3.31E-06
vg0311641017 sf0311639735 3 11641017 4.05E-06 4.05E-06
vg1209244804 sf1209242213 12 9244804 4.54E-06 4.54E-06