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 mr1457 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
vg1218514358 sf1218485794 12 18514358 1.81E-12 4.99E-08
vg1218595627 sf1218567063 12 18595627 1.62E-11 3.32E-08
vg1218931252 sf1218902687 12 18931252 2.02E-10 2.74E-06
vg1104406635 sf1104402537 11 4406635 1.18E-09 4.71E-06
vg1104411559 sf1104407461 11 4411559 1.20E-09 2.33E-06
vg1109870254 sf1109864831 11 9870254 2.30E-09 7.09E-07
vg0330512638 sf0330505527 3 30512638 3.89E-09 NA
vg0715323407 sf0715322414 7 15323407 9.00E-09 4.40E-06
vg1204159174 sf1204158162 12 4159174 9.43E-08 2.23E-06
vg1105076187 sf1105071998 11 5076187 6.64E-06 4.03E-06
vg1129016281 sf1128493060 11 29016281 NA 7.77E-06