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 mr1889 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
vg0524494561 sf0524431982 5 24494561 2.48E-103 1.63E-20
vg0524593054 sf0524530474 5 24593054 5.62E-101 4.84E-21
vg1209153210 sf1209150619 12 9153210 3.50E-74 NA
vg0411668128 sf0411658834 4 11668128 1.77E-73 NA
vg0229905485 sf0229899616 2 29905485 2.45E-71 NA
vg0917689463 sf0917688462 9 17689463 3.52E-71 NA
vg0524427660 sf0524365081 5 24427660 3.22E-69 3.63E-07
vg0915088136 sf0915087135 9 15088136 1.26E-66 NA
vg0524793384 sf0524730799 5 24793384 NA 1.44E-09
vg0141203398 sf0141202355 1 41203398 NA 1.38E-08
vg0141183119 sf0141182076 1 41183119 NA 2.10E-08
vg0102113150 sf0102112150 1 2113150 NA 1.20E-07
vg1100087658 sf1100086658 11 87658 NA 2.56E-07
vg0101328049 sf0101327049 1 1328049 NA 2.72E-07
vg1012107605 sf1012036420 10 12107605 NA 5.62E-07
vg0524300922 sf0524238341 5 24300922 NA 8.17E-07
vg0141212324 sf0141211281 1 41212324 NA 1.12E-06
vg0433421279 sf0433236168 4 33421279 NA 1.14E-06
vg1100407637 sf1100406640 11 407637 NA 1.22E-06
vg0433416660 sf0433231549 4 33416660 NA 1.25E-06
vg0901583779 sf0901582779 9 1583779 NA 1.59E-06
vg0301847279 sf0301846275 3 1847279 NA 2.55E-06
vg0327064329 sf0327057382 3 27064329 NA 3.36E-06