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 mr1742 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
vg0221812870 sf0221807001 2 21812870 1.04E-25 8.73E-16
vg0232210538 sf0232204669 2 32210538 1.63E-21 NA
vg0212332283 sf0212332279 2 12332283 2.33E-21 4.12E-10
vg1119579328 sf1119113016 11 19579328 2.78E-21 2.69E-10
vg0142015207 sf0142014164 1 42015207 5.98E-21 2.30E-06
vg1227454410 sf1227420810 12 27454410 1.21E-20 3.29E-07
vg0706728204 sf0706727209 7 6728204 4.80E-20 2.20E-07
vg0133325596 sf0133324552 1 33325596 5.68E-20 5.09E-06
vg0434357187 sf0434172081 4 34357187 9.96E-20 1.08E-06
vg1208277892 sf1208275298 12 8277892 3.43E-19 9.18E-07
vg0141996640 sf0141995597 1 41996640 8.45E-19 5.58E-07
vg1016092400 sf1016021172 10 16092400 9.13E-19 4.39E-07
vg0904344784 sf0904343784 9 4344784 9.86E-19 8.38E-07
vg1117949081 sf1117482939 11 17949081 5.70E-18 5.10E-07
vg0216188882 sf0216183012 2 16188882 1.30E-17 9.88E-09
vg0315238169 sf0315236816 3 15238169 2.76E-17 1.65E-07
vg0629150340 sf0629149342 6 29150340 1.38E-16 7.10E-08
vg0430557936 sf0430372811 4 30557936 5.97E-13 4.21E-08
vg0222465672 sf0222459803 2 22465672 9.45E-13 8.17E-07
vg0221907189 sf0221901320 2 21907189 NA 9.62E-09
vg0221866544 sf0221860675 2 21866544 NA 2.87E-08
vg0221875605 sf0221869736 2 21875605 NA 4.48E-08
vg0410109405 sf0410100103 4 10109405 NA 3.09E-07
vg0234351254 sf0234345385 2 34351254 NA 4.61E-07
vg0525746894 sf0525684315 5 25746894 NA 7.44E-07
vg0234495837 sf0234489968 2 34495837 NA 8.16E-07
vg1105403833 sf1105399584 11 5403833 NA 1.13E-06