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 mr1680 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
vg0221812870 sf0221807001 2 21812870 1.55E-10 1.06E-07
vg1118413569 sf1117947429 11 18413569 1.07E-09 NA
vg1117986945 sf1117520803 11 17986945 2.88E-09 NA
vg1023072667 sf1023001140 10 23072667 4.53E-09 NA
vg0403174609 sf0403170212 4 3174609 6.27E-09 NA
vg0418069807 sf0417897848 4 18069807 1.53E-08 9.35E-07
vg0901413043 sf0901412043 9 1413043 1.70E-08 2.24E-06
vg1001247771 sf1001246748 10 1247771 NA 1.55E-06