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 mr1701 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
vg1001022580 sf1001021556 10 1022580 2.94E-17 NA
vg0208726203 sf0208726202 2 8726203 5.33E-17 NA
vg0313617458 sf0313616175 3 13617458 9.90E-17 NA
vg1113617489 sf1113153811 11 13617489 1.93E-16 NA
vg0317301896 sf0317300706 3 17301896 3.24E-16 6.62E-07
vg0222236600 sf0222230731 2 22236600 NA 5.29E-07
vg0323648273 sf0323646447 3 23648273 NA 1.36E-06
vg0403922755 sf0403918361 4 3922755 NA 2.77E-06
vg1122246415 sf1121780286 11 22246415 NA 3.75E-06
vg1223038204 sf1223004664 12 23038204 NA 4.05E-06