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 mr1863 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
vg1214365340 sf1214362680 12 14365340 1.32E-07 1.32E-07
vg1100523028 sf1100522031 11 523028 4.08E-07 4.08E-07
vg0217031308 sf0217025438 2 17031308 4.18E-07 4.18E-07
vg1220236502 sf1220207944 12 20236502 1.03E-06 1.03E-06
vg0221740163 sf0221734294 2 21740163 1.31E-06 1.31E-06
vg1117095528 sf1116629380 11 17095528 1.96E-06 1.96E-06
vg0210071634 sf0210071632 2 10071634 2.82E-06 2.82E-06
vg1005360762 sf1005377299 10 5360762 6.66E-06 6.66E-06