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 mr1110 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
vg0610559165 sf0610558166 6 10559165 1.02E-42 3.33E-26
vg0610566237 sf0610565238 6 10566237 1.07E-39 5.91E-27
vg0610071156 sf0610070157 6 10071156 2.06E-24 6.01E-17
vg0610412033 sf0610411034 6 10412033 6.34E-21 1.97E-15
vg0610556004 sf0610555005 6 10556004 1.19E-20 9.83E-14
vg0610683043 sf0610682044 6 10683043 3.51E-20 2.02E-14
vg0609696057 sf0609695058 6 9696057 1.54E-17 8.34E-10
vg0609643429 sf0609642430 6 9643429 5.27E-16 1.65E-12
vg0609697276 sf0609696277 6 9697276 1.88E-15 4.36E-10
vg0611929029 sf0611928030 6 11929029 5.97E-15 8.40E-09
vg0610447618 sf0610446619 6 10447618 8.84E-15 5.38E-12
vg0610676484 sf0610675485 6 10676484 2.26E-13 1.25E-10
vg0629122924 sf0629121926 6 29122924 1.27E-12 1.33E-06
vg0610819871 sf0610818872 6 10819871 2.92E-12 6.07E-11
vg0920308003 sf0920307522 9 20308003 9.59E-12 1.10E-06
vg0610127588 sf0610126589 6 10127588 3.64E-11 4.24E-10
vg0610435285 sf0610434286 6 10435285 8.53E-11 2.64E-09
vg0610757993 sf0610756994 6 10757993 4.79E-10 1.25E-07
vg0611590484 sf0611589485 6 11590484 1.24E-08 3.36E-06
vg0617876285 sf0617875288 6 17876285 6.68E-07 2.23E-07
vg0612056790 sf0612055791 6 12056790 9.47E-07 3.63E-06
vg0611643367 sf0611642368 6 11643367 1.63E-06 8.27E-07
vg1006522902 sf1006538525 10 6522902 NA 1.33E-06
vg1008504224 sf1008433086 10 8504224 NA 2.00E-06
vg0105753465 sf0105752465 1 5753465 NA 3.21E-06
vg0223038233 sf0223032364 2 23038233 NA 3.53E-06