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 mr1858 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
vg0222730246 sf0222724377 2 22730246 3.11E-52 1.78E-21
vg0906971590 sf0906970590 9 6971590 1.98E-37 4.28E-06
vg0526113468 sf0526050888 5 26113468 2.62E-35 1.83E-06
vg0505989705 sf0505989644 5 5989705 6.32E-35 4.73E-06
vg1110107976 sf1110102553 11 10107976 1.79E-34 2.25E-06
vg0222693356 sf0222687487 2 22693356 6.63E-31 1.51E-11
vg0624490244 sf0624489247 6 24490244 1.47E-30 2.50E-06
vg0316104224 sf0316102871 3 16104224 1.03E-29 6.69E-08
vg0827431089 sf0827428375 8 27431089 1.24E-28 7.91E-07
vg1119961499 sf1119495422 11 19961499 1.88E-26 2.72E-07
vg0434765473 sf0434580364 4 34765473 1.01E-25 7.00E-07
vg0517791688 sf0517731174 5 17791688 1.37E-25 NA
vg0222725003 sf0222719134 2 22725003 NA 5.41E-10
vg0232357290 sf0232351421 2 32357290 NA 3.30E-08
vg1217928334 sf1217899768 12 17928334 NA 9.33E-07
vg1200546779 sf1200545779 12 546779 NA 1.28E-06
vg0434789415 sf0434604306 4 34789415 NA 2.40E-06
vg0819592476 sf0819589763 8 19592476 NA 2.94E-06
vg0711029957 sf0711028963 7 11029957 NA 3.24E-06
vg0224678499 sf0224672630 2 24678499 NA 3.90E-06
vg0819608857 sf0819606144 8 19608857 NA 4.46E-06
vg1217897242 sf1217868676 12 17897242 NA 4.55E-06
vg0232336916 sf0232331047 2 32336916 NA 4.67E-06
vg0301256734 sf0301255732 3 1256734 NA 4.75E-06
vg0129623631 sf0129622586 1 29623631 NA 4.83E-06