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 mr1354 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
vg0724513327 sf0724512333 7 24513327 2.90E-35 2.49E-27
vg0724524521 sf0724523527 7 24524521 8.86E-35 4.19E-27
vg0800238957 sf0800237957 8 238957 1.39E-11 NA
vg0232872507 sf0232866638 2 32872507 1.69E-11 NA
vg1122418019 sf1121951890 11 22418019 1.80E-11 4.97E-06
vg0724427664 sf0724426670 7 24427664 2.26E-11 1.01E-14
vg1011931840 sf1011860655 10 11931840 2.39E-11 2.63E-06
vg0725312091 sf0725311097 7 25312091 1.07E-09 3.44E-06
vg0724487049 sf0724486055 7 24487049 3.41E-09 6.56E-16
vg0618906581 sf0618905584 6 18906581 1.14E-08 4.27E-06
vg0724557637 sf0724556643 7 24557637 NA 3.29E-08
vg1205142686 sf1205141672 12 5142686 NA 1.18E-06