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 mr1113 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
vg1009632737 sf1009561558 10 9632737 2.74E-14 2.47E-09
vg1009640089 sf1009568910 10 9640089 3.76E-14 3.85E-11
vg1006938226 sf1006953849 10 6938226 2.34E-13 3.91E-09
vg0407822984 sf0407818252 4 7822984 1.83E-12 2.61E-07
vg0407826743 sf0407822011 4 7826743 2.48E-12 1.12E-07
vg1216843191 sf1216837145 12 16843191 1.29E-11 1.51E-07
vg0716828374 sf0716827381 7 16828374 8.02E-11 9.57E-07
vg0403205910 sf0403201513 4 3205910 5.38E-10 1.29E-06
vg1006725677 sf1006741300 10 6725677 6.73E-10 1.94E-07
vg0210471651 sf0210471649 2 10471651 1.68E-09 3.02E-09
vg1009709662 sf1009638483 10 9709662 5.96E-09 3.22E-06
vg0314497973 sf0314496661 3 14497973 1.96E-08 1.27E-06
vg0501612224 sf0501612208 5 1612224 5.45E-08 6.25E-07
vg0332006580 sf0331999457 3 32006580 1.26E-07 NA
vg0911953487 sf0911952486 9 11953487 1.67E-07 6.37E-07
vg0316605932 sf0316604577 3 16605932 2.52E-07 7.00E-07
vg1128168473 sf1127645252 11 28168473 5.67E-07 6.54E-06
vg0618223778 sf0618222781 6 18223778 9.59E-07 4.45E-06
vg0617480222 sf0617479225 6 17480222 1.86E-06 1.92E-06
vg0905694212 sf0905693212 9 5694212 2.73E-06 NA
vg0505304774 sf0505304752 5 5304774 8.81E-06 2.03E-06
vg0120765747 sf0120764702 1 20765747 9.75E-06 4.60E-06
vg0905540776 sf0905539776 9 5540776 NA 4.37E-07
vg0407109406 sf0407104676 4 7109406 NA 8.40E-07
vg0627350084 sf0627349087 6 27350084 NA 4.34E-06