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 mr1243 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
vg0216768561 sf0216762691 2 16768561 4.24E-43 5.27E-10
vg0216757703 sf0216751833 2 16757703 7.75E-41 1.35E-09
vg0216800422 sf0216794552 2 16800422 8.08E-38 1.64E-13
vg1100991046 sf1100990047 11 991046 1.13E-37 4.65E-06
vg0800290426 sf0800289426 8 290426 9.66E-37 NA
vg0823140129 sf0823137416 8 23140129 2.58E-36 NA
vg0220342684 sf0220336816 2 20342684 1.40E-33 1.20E-06
vg0717217950 sf0717216957 7 17217950 1.46E-33 4.32E-07
vg0217137734 sf0217131864 2 17137734 NA 3.44E-08
vg1114473442 sf1114009759 11 14473442 NA 6.30E-08
vg0412040642 sf0412031353 4 12040642 NA 4.47E-07
vg1121397365 sf1120931242 11 21397365 NA 7.00E-07
vg1121397261 sf1120931138 11 21397261 NA 1.09E-06
vg0715724667 sf0715723674 7 15724667 NA 4.64E-06