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 mr1951 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
vg0106677498 sf0106676498 1 6677498 9.49E-41 2.95E-27
vg0106679257 sf0106678257 1 6679257 1.94E-40 2.54E-27
vg0106691928 sf0106690928 1 6691928 5.56E-40 1.02E-27
vg0317879120 sf0317877902 3 17879120 4.57E-22 1.59E-12
vg0112795017 sf0112793991 1 12795017 5.27E-18 3.42E-08
vg0229675574 sf0229669705 2 29675574 1.05E-14 NA
vg0105661905 sf0105660905 1 5661905 2.66E-14 6.52E-09
vg0105612155 sf0105611155 1 5612155 1.78E-13 4.62E-09
vg0104031438 sf0104030438 1 4031438 2.12E-13 1.23E-06
vg0224803179 sf0224797310 2 24803179 8.29E-13 1.74E-06
vg0105866541 sf0105865541 1 5866541 1.07E-12 2.79E-08
vg0205823956 sf0205823956 2 5823956 2.96E-11 3.99E-06
vg0402919496 sf0402915102 4 2919496 4.58E-11 8.26E-08
vg0106883091 sf0106882091 1 6883091 1.52E-10 1.15E-06
vg1221525771 sf1221492318 12 21525771 9.23E-09 6.39E-07
vg0105779349 sf0105778349 1 5779349 NA 1.58E-07
vg0106582661 sf0106581661 1 6582661 NA 8.71E-07
vg1016628494 sf1016557267 10 16628494 NA 1.37E-06