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 mr1098 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
vg0108533994 sf0108532994 1 8533994 6.04E-10 6.04E-10
vg0627929341 sf0627928343 6 27929341 2.19E-09 2.19E-09
vg0628759426 sf0628758428 6 28759426 4.33E-08 4.33E-08
vg1002659326 sf1002658303 10 2659326 1.77E-07 1.77E-07
vg0421388196 sf0421216249 4 21388196 2.68E-07 2.68E-07
vg0221025908 sf0221020040 2 21025908 3.50E-07 3.50E-07
vg0906884682 sf0906883682 9 6884682 5.10E-07 5.10E-07
vg0222833455 sf0222827586 2 22833455 6.17E-07 6.17E-07
vg0402179876 sf0402175471 4 2179876 6.20E-07 6.20E-07
vg0621601441 sf0621600444 6 21601441 6.62E-07 6.62E-07
vg0625603773 sf0625602776 6 25603773 6.80E-07 6.80E-07
vg1103697850 sf1103693752 11 3697850 1.10E-06 1.10E-06
vg1106988724 sf1106984469 11 6988724 1.24E-06 1.24E-06
vg0709675216 sf0709674222 7 9675216 1.36E-06 1.36E-06
vg0420940131 sf0420768189 4 20940131 1.50E-06 1.50E-06
vg0107544024 sf0107543024 1 7544024 1.72E-06 1.72E-06
vg0727090466 sf0727089472 7 27090466 1.87E-06 1.87E-06
vg0819421680 sf0819418967 8 19421680 1.96E-06 1.96E-06
vg0910545581 sf0910544580 9 10545581 2.99E-06 2.99E-06
vg0121574351 sf0121573306 1 21574351 4.52E-06 4.52E-06