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 mr1758 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
vg1116259036 sf1115793906 11 16259036 1.15E-168 2.79E-16
vg1113080694 sf1112617015 11 13080694 2.99E-168 8.73E-14
vg1112284007 sf1112087242 11 12284007 1.24E-162 5.89E-15
vg1114456393 sf1113992710 11 14456393 2.27E-162 6.91E-15
vg1115788579 sf1115324887 11 15788579 5.21E-154 1.30E-17
vg0903435730 sf0903434730 9 3435730 2.26E-137 NA
vg1119348627 sf1118882315 11 19348627 4.27E-137 NA
vg1109790194 sf1109784771 11 9790194 9.96E-137 NA
vg0111860182 sf0111859156 1 11860182 4.76E-135 6.72E-07
vg0109355984 sf0109354960 1 9355984 NA 1.55E-09
vg1002259298 sf1002258275 10 2259298 NA 7.59E-09
vg0216734558 sf0216728688 2 16734558 NA 8.92E-09
vg0301117237 sf0301116235 3 1117237 NA 1.67E-08
vg0316164526 sf0316163173 3 16164526 NA 3.12E-08
vg0103116049 sf0103115049 1 3116049 NA 3.59E-08
vg0410309978 sf0410300676 4 10309978 NA 3.71E-08
vg0621032172 sf0621031175 6 21032172 NA 3.90E-08
vg1116298980 sf1115833853 11 16298980 NA 4.13E-08
vg0315359978 sf0315358625 3 15359978 NA 6.30E-08
vg0722741441 sf0722740448 7 22741441 NA 7.27E-08
vg0826147631 sf0826144917 8 26147631 NA 7.31E-08
vg1124647866 sf1124181706 11 24647866 NA 9.57E-08
vg1116611084 sf1116145962 11 16611084 NA 1.13E-07
vg0900590846 sf0900589846 9 590846 NA 1.82E-07
vg0518095913 sf0518035399 5 18095913 NA 1.83E-07
vg0111823078 sf0111822052 1 11823078 NA 2.91E-07
vg1116298623 sf1115833496 11 16298623 NA 3.44E-07
vg0518096322 sf0518035808 5 18096322 NA 3.45E-07
vg0316219278 sf0316217926 3 16219278 NA 8.28E-06