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 mr1498 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
vg0106730666 sf0106729666 1 6730666 7.51E-60 8.99E-43
vg0106693749 sf0106692749 1 6693749 3.28E-59 9.22E-47
vg0106715029 sf0106714029 1 6715029 1.82E-27 3.25E-17
vg0106732224 sf0106731224 1 6732224 5.22E-27 7.55E-24
vg0106607583 sf0106606583 1 6607583 1.68E-22 2.11E-07
vg0106260213 sf0106259213 1 6260213 2.23E-21 1.53E-09
vg0105640821 sf0105639821 1 5640821 9.40E-19 9.46E-08
vg0105650370 sf0105649370 1 5650370 5.29E-18 3.66E-08
vg0107145126 sf0107144126 1 7145126 2.09E-16 1.78E-07
vg0105379062 sf0105378062 1 5379062 4.99E-14 1.20E-07
vg0106959659 sf0106958659 1 6959659 1.63E-12 7.77E-21
vg0106703618 sf0106702618 1 6703618 6.09E-11 1.80E-07
vg0107157245 sf0107156245 1 7157245 1.94E-09 1.25E-10
vg0910097490 sf0910096489 9 10097490 7.43E-09 NA
vg0106686584 sf0106685584 1 6686584 5.33E-08 8.51E-09
vg0624535916 sf0624534919 6 24535916 5.61E-08 7.22E-09
vg1016932373 sf1016861145 10 16932373 1.08E-07 NA
vg0106725146 sf0106724146 1 6725146 1.84E-07 3.02E-09
vg0107070642 sf0107069642 1 7070642 3.21E-07 3.12E-08
vg0432633924 sf0432448813 4 32633924 5.22E-07 NA
vg0106470262 sf0106469262 1 6470262 NA 2.87E-12
vg0106463385 sf0106462385 1 6463385 NA 2.10E-10
vg0110290364 sf0110289340 1 10290364 NA 1.75E-08
vg0428528974 sf0428343827 4 28528974 NA 3.03E-08
vg0105635044 sf0105634044 1 5635044 NA 6.53E-08
vg0429103995 sf0428918855 4 29103995 NA 1.10E-07
vg0215664387 sf0215658517 2 15664387 NA 5.33E-07