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 mr1761 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
vg0626092352 sf0626091355 6 26092352 4.00E-09 1.56E-08
vg0412733978 sf0412724688 4 12733978 3.24E-08 4.56E-06
vg0306314152 sf0306313152 3 6314152 5.15E-08 NA
vg0614104937 sf0614103938 6 14104937 9.28E-08 3.14E-06
vg0529437664 sf0529375019 5 29437664 1.43E-07 1.07E-06
vg0920459138 sf0920458657 9 20459138 9.75E-07 3.02E-07
vg1012820139 sf1012748954 10 12820139 1.68E-06 2.88E-07
vg0515364844 sf0515307385 5 15364844 1.93E-06 4.70E-06
vg0221675215 sf0221669346 2 21675215 2.60E-06 3.91E-06
vg1121646803 sf1121180680 11 21646803 4.15E-06 7.13E-06
vg0319793532 sf0319792043 3 19793532 7.58E-06 4.51E-06