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 mr1071 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
vg0406948359 sf0406943627 4 6948359 3.44E-21 1.27E-12
vg0406944478 sf0406939746 4 6944478 1.86E-19 2.62E-13
vg0406620026 sf0406615470 4 6620026 3.90E-17 1.46E-09
vg0406524319 sf0406519762 4 6524319 1.65E-13 9.62E-10
vg1216282260 sf1216279556 12 16282260 1.04E-12 2.44E-07
vg0424423524 sf0424238385 4 24423524 2.61E-12 9.18E-08
vg0618618072 sf0618617075 6 18618072 4.29E-11 1.24E-08
vg0412144728 sf0412135439 4 12144728 3.78E-10 2.05E-08
vg1216282445 sf1216279741 12 16282445 4.02E-10 1.91E-08
vg0412484073 sf0412474788 4 12484073 4.35E-10 5.81E-09
vg0407872167 sf0407867435 4 7872167 1.21E-09 1.04E-10
vg0222746228 sf0222740359 2 22746228 1.29E-09 NA
vg0616244147 sf0616243149 6 16244147 2.19E-09 4.83E-09
vg0411431095 sf0411421797 4 11431095 6.27E-09 9.71E-08
vg0412292000 sf0412282715 4 12292000 NA 8.17E-10
vg1215976459 sf1215973755 12 15976459 NA 1.05E-09
vg0406869782 sf0406865227 4 6869782 NA 5.01E-09
vg0415345317 sf0415336033 4 15345317 NA 3.97E-08
vg1005181911 sf1005198448 10 5181911 NA 7.19E-08
vg0412477593 sf0412468308 4 12477593 NA 7.43E-08
vg1210397897 sf1210395310 12 10397897 NA 9.79E-08
vg0400257725 sf0400256725 4 257725 NA 1.04E-07
vg0412431746 sf0412422460 4 12431746 NA 1.19E-07
vg0806502338 sf0806501343 8 6502338 NA 1.65E-07