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 mr1203 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 7.15E-21 4.38E-13
vg0406944478 sf0406939746 4 6944478 5.69E-20 1.87E-14
vg0406620026 sf0406615470 4 6620026 2.16E-17 1.65E-10
vg1000524606 sf1000523582 10 524606 2.24E-12 1.68E-07
vg0420577297 sf0420405341 4 20577297 6.35E-12 2.08E-07
vg0618618072 sf0618617075 6 18618072 1.54E-11 1.82E-09
vg1107318404 sf1107314149 11 7318404 1.28E-10 3.94E-08
vg0406524319 sf0406519762 4 6524319 1.49E-10 2.30E-09
vg0412144728 sf0412135439 4 12144728 1.81E-10 1.81E-09
vg0507926447 sf0507926388 5 7926447 3.11E-10 1.37E-07
vg0424423524 sf0424238385 4 24423524 5.82E-10 7.26E-08
vg1216282887 sf1216280183 12 16282887 2.95E-09 1.30E-07
vg0919977401 sf0919976920 9 19977401 3.51E-09 1.27E-08
vg0616244147 sf0616243149 6 16244147 4.67E-09 1.57E-09
vg0411431095 sf0411421797 4 11431095 4.80E-09 5.85E-08
vg0412431746 sf0412422460 4 12431746 4.82E-09 3.62E-09
vg0406877319 sf0406872764 4 6877319 1.02E-08 4.94E-08
vg0806502338 sf0806501343 8 6502338 1.25E-08 2.62E-08
vg1216930362 sf1216924316 12 16930362 3.36E-08 1.31E-08
vg0407872167 sf0407867435 4 7872167 NA 9.96E-10
vg0412292000 sf0412282715 4 12292000 NA 3.37E-09
vg1215976459 sf1215973755 12 15976459 NA 1.40E-08
vg0412455940 sf0412446655 4 12455940 NA 9.90E-08
vg0412484073 sf0412474788 4 12484073 NA 1.34E-07