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 mr1529 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
vg1207510234 sf1207507640 12 7510234 7.55E-20 NA
vg0107647091 sf0107646091 1 7647091 4.23E-18 1.22E-06
vg1207539985 sf1207537391 12 7539985 8.63E-18 6.94E-06
vg0800304464 sf0800303464 8 304464 4.46E-17 5.02E-06
vg0140889895 sf0140888852 1 40889895 7.73E-17 NA
vg0805968808 sf0805967811 8 5968808 1.28E-16 NA
vg1221634437 sf1221600984 12 21634437 7.73E-16 1.13E-06
vg1214484150 sf1214481491 12 14484150 8.76E-16 1.89E-06
vg1222349529 sf1222315968 12 22349529 NA 4.00E-08
vg0510071302 sf0510071231 5 10071302 NA 8.26E-07
vg0308881162 sf0308880100 3 8881162 NA 3.39E-06
vg0101356395 sf0101355395 1 1356395 NA 4.41E-06