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 mr1877 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
vg0610567310 sf0610566311 6 10567310 3.68E-57 2.30E-17
vg0610661343 sf0610660344 6 10661343 8.52E-52 6.56E-21
vg0610608095 sf0610607096 6 10608095 6.15E-49 1.26E-16
vg0617223679 sf0617222682 6 17223679 7.21E-39 5.69E-09
vg0614029605 sf0614028606 6 14029605 9.19E-35 9.17E-07
vg0222628680 sf0222622811 2 22628680 1.08E-33 4.37E-13
vg0222573327 sf0222567458 2 22573327 1.18E-33 9.38E-15
vg1108308382 sf1108302992 11 8308382 4.52E-30 NA
vg0421627867 sf0421455917 4 21627867 2.29E-29 6.78E-09
vg0222743329 sf0222737460 2 22743329 NA 1.80E-14
vg0222725103 sf0222719234 2 22725103 NA 4.60E-14
vg0610787522 sf0610786523 6 10787522 NA 2.86E-10
vg0610584087 sf0610583088 6 10584087 NA 4.76E-09
vg1008319187 sf1008248049 10 8319187 NA 1.49E-08
vg0609865675 sf0609864676 6 9865675 NA 1.14E-07
vg0610014443 sf0610013444 6 10014443 NA 1.29E-07
vg0220366353 sf0220360485 2 20366353 NA 1.42E-07
vg0610089141 sf0610088142 6 10089141 NA 1.67E-07
vg0610086748 sf0610085749 6 10086748 NA 3.66E-07
vg0610323245 sf0610322246 6 10323245 NA 1.86E-06
vg0221656001 sf0221650132 2 21656001 NA 1.87E-06
vg0609678694 sf0609677695 6 9678694 NA 2.57E-06
vg0610467785 sf0610466786 6 10467785 NA 2.61E-06
vg0611735326 sf0611734327 6 11735326 NA 2.73E-06
vg0609873887 sf0609872888 6 9873887 NA 2.83E-06
vg0712641466 sf0712640473 7 12641466 NA 2.86E-06
vg0317944391 sf0317943173 3 17944391 NA 3.38E-06
vg0224723753 sf0224717884 2 24723753 NA 3.75E-06
vg0224787962 sf0224782093 2 24787962 NA 3.78E-06
vg0414782841 sf0414773555 4 14782841 NA 3.98E-06