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 mr1859 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 3.87E-52 1.77E-21
vg0906971590 sf0906970590 9 6971590 1.75E-37 4.25E-06
vg0526113468 sf0526050888 5 26113468 2.37E-35 1.76E-06
vg0505989705 sf0505989644 5 5989705 5.61E-35 4.49E-06
vg1110107976 sf1110102553 11 10107976 1.63E-34 2.20E-06
vg0222693356 sf0222687487 2 22693356 5.94E-31 1.46E-11
vg0624490244 sf0624489247 6 24490244 1.34E-30 2.41E-06
vg0316104224 sf0316102871 3 16104224 9.35E-30 6.26E-08
vg0827431089 sf0827428375 8 27431089 1.14E-28 7.31E-07
vg1119961499 sf1119495422 11 19961499 1.72E-26 2.58E-07
vg0434765473 sf0434580364 4 34765473 9.48E-26 6.85E-07
vg0517791688 sf0517731174 5 17791688 1.28E-25 NA
vg0222725003 sf0222719134 2 22725003 NA 5.34E-10
vg0232357290 sf0232351421 2 32357290 NA 3.25E-08
vg1217928334 sf1217899768 12 17928334 NA 9.45E-07
vg1200546779 sf1200545779 12 546779 NA 1.24E-06
vg0434789415 sf0434604306 4 34789415 NA 2.36E-06
vg0819592476 sf0819589763 8 19592476 NA 2.88E-06
vg0711029957 sf0711028963 7 11029957 NA 3.11E-06
vg0224678499 sf0224672630 2 24678499 NA 3.78E-06
vg0819608857 sf0819606144 8 19608857 NA 4.37E-06
vg0301256734 sf0301255732 3 1256734 NA 4.59E-06
vg1217897242 sf1217868676 12 17897242 NA 4.72E-06
vg0129623631 sf0129622586 1 29623631 NA 4.74E-06