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 mr1703 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
vg1121146057 sf1120679936 11 21146057 2.34E-09 2.34E-09
vg0410821067 sf0410811769 4 10821067 5.07E-08 5.08E-08
vg0715801688 sf0715800695 7 15801688 1.24E-07 1.25E-07
vg0314998474 sf0314997121 3 14998474 1.36E-07 1.36E-07
vg0208200175 sf0208200174 2 8200175 1.68E-07 1.69E-07
vg0125860145 sf0125859101 1 25860145 2.56E-07 2.56E-07
vg1020537939 sf1020466418 10 20537939 4.15E-07 4.17E-07
vg1008749397 sf1008678259 10 8749397 4.34E-07 4.36E-07
vg0713891677 sf0713890684 7 13891677 4.46E-07 4.48E-07
vg0724265249 sf0724264255 7 24265249 6.53E-07 6.54E-07
vg0216482818 sf0216476948 2 16482818 7.54E-07 7.56E-07
vg1125849043 sf1125382962 11 25849043 8.61E-07 8.65E-07
vg0324949842 sf0324947922 3 24949842 1.07E-06 1.07E-06
vg0311333429 sf0311332147 3 11333429 1.11E-06 1.11E-06
vg1212666777 sf1212664116 12 12666777 1.28E-06 1.28E-06
vg0719028476 sf0719027483 7 19028476 1.46E-06 1.46E-06
vg0202387673 sf0202387671 2 2387673 1.48E-06 1.48E-06
vg0417243569 sf0417071610 4 17243569 1.52E-06 1.53E-06
vg0414190832 sf0414181548 4 14190832 1.95E-06 1.96E-06
vg0211686764 sf0211686760 2 11686764 2.14E-06 2.15E-06