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 mr1236 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
vg0106771714 sf0106770714 1 6771714 4.29E-17 1.76E-11
vg0106686481 sf0106685481 1 6686481 9.02E-17 2.21E-12
vg0216755793 sf0216749923 2 16755793 1.35E-15 9.64E-10
vg0217023273 sf0217017403 2 17023273 9.31E-15 8.63E-11
vg0900337342 sf0900336342 9 337342 1.29E-12 7.51E-08
vg0216764474 sf0216758604 2 16764474 2.43E-12 1.33E-06
vg0142706258 sf0142705214 1 42706258 3.38E-12 1.21E-06
vg1202070344 sf1202069342 12 2070344 3.65E-11 3.02E-07
vg0217023879 sf0217018009 2 17023879 4.08E-11 1.16E-06
vg0217155630 sf0217149760 2 17155630 2.13E-08 4.16E-06
vg0106684586 sf0106683586 1 6684586 3.36E-08 1.89E-07
vg0106669651 sf0106668651 1 6669651 5.09E-08 4.33E-06
vg0118245978 sf0118244932 1 18245978 1.20E-07 2.46E-06
vg0132411125 sf0132410081 1 32411125 1.61E-06 NA
vg1207087743 sf1207086633 12 7087743 NA 4.72E-07
vg1207088249 sf1207087139 12 7088249 NA 1.09E-06
vg0208546299 sf0208546298 2 8546299 NA 2.09E-06