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 mr1253 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
vg0217105844 sf0217099974 2 17105844 5.07E-55 2.16E-22
vg0216804396 sf0216798526 2 16804396 1.25E-54 1.62E-23
vg0526229307 sf0526166671 5 26229307 1.01E-30 NA
vg0719968935 sf0719967942 7 19968935 6.59E-29 NA
vg0205731162 sf0205731162 2 5731162 4.20E-27 NA
vg0317475146 sf0317473928 3 17475146 4.44E-27 NA
vg0213525745 sf0213525741 2 13525745 1.22E-25 6.93E-09
vg0216631728 sf0216625858 2 16631728 4.61E-23 4.26E-09
vg0812023942 sf0812022947 8 12023942 6.49E-22 9.62E-07
vg0900336799 sf0900335799 9 336799 5.10E-21 2.28E-06
vg0217214807 sf0217208937 2 17214807 NA 5.83E-15
vg0216381408 sf0216375538 2 16381408 NA 9.23E-10
vg0217266536 sf0217260666 2 17266536 NA 1.65E-08
vg0615635376 sf0615634378 6 15635376 NA 1.25E-06
vg0217027146 sf0217021276 2 17027146 NA 1.41E-06
vg0719512715 sf0719511722 7 19512715 NA 1.53E-06
vg0215683252 sf0215677382 2 15683252 NA 1.96E-06
vg0212875961 sf0212875957 2 12875961 NA 2.06E-06
vg0525029650 sf0524967065 5 25029650 NA 2.36E-06
vg0427400029 sf0427214893 4 27400029 NA 3.64E-06
vg0524832921 sf0524770336 5 24832921 NA 3.81E-06
vg0908960274 sf0908959273 9 8960274 NA 3.83E-06
vg0719520013 sf0719519020 7 19520013 NA 3.87E-06