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 mr1201 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
vg0605262883 sf0605261884 6 5262883 4.61E-44 1.18E-23
vg0605374097 sf0605373098 6 5374097 3.66E-43 3.99E-23
vg0605311849 sf0605310850 6 5311849 4.09E-42 1.04E-25
vg0605276737 sf0605275738 6 5276737 8.12E-35 6.39E-18
vg0605332135 sf0605331136 6 5332135 8.36E-33 4.17E-14
vg0605415117 sf0605414118 6 5415117 1.73E-29 1.14E-13
vg0605412605 sf0605411606 6 5412605 1.36E-17 1.48E-08
vg0600826406 sf0600825407 6 826406 7.37E-17 NA
vg0605162589 sf0605161590 6 5162589 1.05E-16 2.69E-09
vg0203428380 sf0203428378 2 3428380 3.38E-15 3.30E-06
vg0605440935 sf0605439936 6 5440935 1.61E-14 2.61E-08
vg0604988139 sf0604987140 6 4988139 2.36E-14 4.70E-08
vg0502963065 sf0502963041 5 2963065 5.11E-14 NA
vg0607699285 sf0607698286 6 7699285 6.37E-14 7.90E-07
vg0209219211 sf0209219209 2 9219211 3.17E-13 9.26E-08
vg0500532294 sf0500532294 5 532294 2.02E-11 3.30E-06
vg0612526873 sf0612525874 6 12526873 NA 1.61E-06
vg0604839039 sf0604838040 6 4839039 NA 2.04E-06