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 mr1977 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
vg0140815392 sf0140814349 1 40815392 7.93E-10 9.94E-07
vg0232298835 sf0232292966 2 32298835 1.25E-09 1.81E-07
vg0628725900 sf0628724902 6 28725900 1.96E-09 6.14E-08
vg0802147873 sf0802146876 8 2147873 2.75E-09 4.02E-08
vg0232433739 sf0232427870 2 32433739 5.12E-09 1.62E-07
vg0233185242 sf0233179373 2 33185242 6.75E-09 9.67E-08
vg0233270526 sf0233264657 2 33270526 1.24E-08 3.87E-08
vg0232485407 sf0232479538 2 32485407 2.37E-08 4.47E-07
vg0227537488 sf0227531619 2 27537488 2.45E-08 2.22E-07
vg0628396978 sf0628395980 6 28396978 5.21E-08 2.48E-08
vg0220098143 sf0220092275 2 20098143 8.95E-08 3.82E-06
vg0123522936 sf0123521892 1 23522936 1.30E-07 2.24E-06
vg0434586605 sf0434401497 4 34586605 2.14E-07 4.47E-06
vg1010454306 sf1010383127 10 10454306 4.65E-07 3.85E-06
vg0123634452 sf0123633408 1 23634452 2.46E-06 NA