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 mr1166 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
vg0325710457 sf0325708475 3 25710457 2.72E-13 2.72E-13
vg1121711093 sf1121244970 11 21711093 2.33E-08 2.33E-08
vg1017190380 sf1017119153 10 17190380 1.44E-07 1.44E-07
vg1002824620 sf1002823597 10 2824620 1.59E-07 1.59E-07
vg0900240275 sf0900239275 9 240275 1.72E-07 1.72E-07
vg1105209650 sf1105205461 11 5209650 3.32E-07 3.32E-07
vg0222035625 sf0222029756 2 22035625 6.35E-07 6.35E-07
vg0525124226 sf0525061641 5 25124226 7.01E-07 7.01E-07
vg0907844471 sf0907843471 9 7844471 7.82E-07 7.81E-07
vg1003304680 sf1003303657 10 3304680 8.09E-07 8.09E-07
vg0202817095 sf0202817093 2 2817095 8.54E-07 8.54E-07
vg1006011150 sf1006027688 10 6011150 8.92E-07 8.92E-07
vg0400362758 sf0400361756 4 362758 9.94E-07 9.94E-07
vg0627929341 sf0627928343 6 27929341 1.31E-06 1.31E-06
vg0103658465 sf0103657465 1 3658465 2.20E-06 2.20E-06
vg0229389860 sf0229383991 2 29389860 2.80E-06 2.80E-06
vg0711956562 sf0711955568 7 11956562 3.08E-06 3.08E-06
vg0222594490 sf0222588621 2 22594490 3.48E-06 3.48E-06
vg1009009289 sf1008938150 10 9009289 3.55E-06 3.55E-06
vg0220048340 sf0220042472 2 20048340 3.56E-06 3.56E-06