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 mr1113 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
vg0222679274 sf0222673405 2 22679274 3.46E-38 1.05E-17
vg1110425815 sf1110420360 11 10425815 1.18E-24 1.41E-08
vg0702584931 sf0702583932 7 2584931 1.53E-21 NA
vg0818156224 sf0818153511 8 18156224 2.24E-21 8.07E-07
vg0500664660 sf0500664660 5 664660 2.51E-21 1.75E-06
vg0818212763 sf0818210050 8 18212763 2.69E-21 4.56E-07
vg1117963441 sf1117497299 11 17963441 2.19E-20 1.62E-07
vg0434789415 sf0434604306 4 34789415 9.42E-20 8.89E-08
vg0525142447 sf0525079868 5 25142447 1.43E-16 NA
vg0222722554 sf0222716685 2 22722554 NA 1.21E-09
vg1008322169 sf1008251031 10 8322169 NA 4.08E-08
vg1006313286 sf1006328909 10 6313286 NA 9.06E-08
vg0915332745 sf0915331744 9 15332745 NA 9.80E-08
vg0915338714 sf0915337713 9 15338714 NA 1.12E-07
vg0432725690 sf0432540576 4 32725690 NA 1.34E-07
vg1016340773 sf1016269549 10 16340773 NA 2.79E-07
vg0222948971 sf0222943102 2 22948971 NA 3.59E-07
vg0133789224 sf0133788180 1 33789224 NA 4.69E-07
vg0913766899 sf0913765898 9 13766899 NA 5.61E-07
vg0421275808 sf0421103862 4 21275808 NA 5.71E-07
vg0209726556 sf0209726554 2 9726556 NA 1.01E-06
vg0224215547 sf0224209678 2 24215547 NA 1.06E-06
vg0506054042 sf0506053981 5 6054042 NA 1.07E-06
vg1016336897 sf1016265673 10 16336897 NA 1.32E-06
vg1204507349 sf1204506337 12 4507349 NA 1.33E-06
vg1005727273 sf1005743811 10 5727273 NA 1.52E-06
vg1200449391 sf1200448391 12 449391 NA 1.73E-06