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 mr1936 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
vg0222726563 sf0222720694 2 22726563 1.96E-16 5.71E-13
vg0122405293 sf0122404248 1 22405293 2.98E-09 NA
vg1009170616 sf1009099437 10 9170616 6.36E-09 5.46E-06
vg1005841803 sf1005858341 10 5841803 1.52E-08 NA
vg0223976143 sf0223970274 2 23976143 1.60E-08 1.02E-06
vg0223973381 sf0223967512 2 23973381 2.10E-08 9.35E-07
vg0222765370 sf0222759501 2 22765370 2.65E-08 3.79E-06
vg0224819438 sf0224813569 2 24819438 5.41E-07 3.49E-06
vg0223723973 sf0223718104 2 23723973 2.27E-06 4.92E-06
vg0820834591 sf0820831878 8 20834591 3.09E-06 1.80E-07
vg1008031463 sf1008012774 10 8031463 6.33E-06 NA
vg0413845447 sf0413836165 4 13845447 NA 2.78E-06
vg0614073107 sf0614072108 6 14073107 NA 4.39E-06