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 mr1536 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
vg0921462199 sf0921461718 9 21462199 2.65E-14 6.25E-08
vg0921471036 sf0921470555 9 21471036 3.41E-13 8.08E-10
vg0626324304 sf0626323307 6 26324304 3.89E-10 NA
vg0335583124 sf0335575993 3 35583124 7.62E-09 NA
vg0701295150 sf0701294150 7 1295150 1.17E-08 NA
vg0328911258 sf0328904310 3 28911258 1.58E-08 8.82E-07
vg0825340502 sf0825337788 8 25340502 6.25E-08 NA
vg0328920994 sf0328914046 3 28920994 1.02E-07 1.40E-06
vg0113770672 sf0113769646 1 13770672 5.33E-06 2.63E-06
vg0707252342 sf0707251347 7 7252342 8.55E-06 9.80E-08
vg0132159113 sf0132158069 1 32159113 NA 2.24E-07
vg0132025232 sf0132024188 1 32025232 NA 1.65E-06
vg1010575676 sf1010504497 10 10575676 NA 4.68E-06