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 mr1935 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
vg0524494561 sf0524431982 5 24494561 1.96E-99 1.23E-26
vg1207595087 sf1207592492 12 7595087 2.13E-58 NA
vg0330889700 sf0330882587 3 30889700 2.79E-58 3.34E-06
vg0330839138 sf0330832025 3 30839138 4.04E-58 4.26E-07
vg0807152208 sf0807151213 8 7152208 4.73E-58 NA
vg0317818639 sf0317817421 3 17818639 5.71E-57 NA
vg0524738001 sf0524675422 5 24738001 NA 6.25E-17
vg1205231921 sf1205230907 12 5231921 NA 4.36E-08
vg0323982616 sf0323980790 3 23982616 NA 2.32E-07
vg1100512559 sf1100511562 11 512559 NA 1.19E-06
vg0412757195 sf0412747905 4 12757195 NA 1.43E-06
vg0132120323 sf0132119279 1 32120323 NA 1.59E-06
vg0525443073 sf0525380494 5 25443073 NA 1.86E-06
vg0815172680 sf0815169966 8 15172680 NA 2.41E-06
vg0312620511 sf0312619229 3 12620511 NA 3.92E-06
vg0524582362 sf0524519783 5 24582362 NA 3.94E-06
vg1118868501 sf1118402310 11 18868501 NA 4.89E-06