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 mr1897 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
vg0217109099 sf0217103229 2 17109099 6.61E-25 1.06E-11
vg0217155660 sf0217149790 2 17155660 1.59E-24 2.93E-12
vg0500526354 sf0500526354 5 526354 9.89E-17 NA
vg1220336402 sf1220307844 12 20336402 4.41E-16 NA
vg0103605322 sf0103604322 1 3605322 4.56E-16 NA
vg0135335946 sf0135334903 1 35335946 6.36E-16 NA
vg1210007164 sf1210004575 12 10007164 1.51E-14 NA
vg0205155355 sf0205155352 2 5155355 6.37E-14 1.78E-07
vg0217112842 sf0217106972 2 17112842 NA 1.06E-09
vg0218499482 sf0218493613 2 18499482 NA 1.06E-07
vg0217125730 sf0217119860 2 17125730 NA 1.09E-07
vg0317014991 sf0317013865 3 17014991 NA 1.21E-06
vg0427120618 sf0426935488 4 27120618 NA 2.93E-06
vg0214881617 sf0214875747 2 14881617 NA 3.10E-06
vg0217345159 sf0217339289 2 17345159 NA 4.29E-06
vg0203404863 sf0203404861 2 3404863 NA 7.43E-06
vg0511189064 sf0511188993 5 11189064 NA 7.62E-06