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 mr1545 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
vg0502159367 sf0502159342 5 2159367 1.10E-08 1.10E-08
vg0316680679 sf0316679324 3 16680679 1.13E-08 1.13E-08
vg0828200030 sf0828197316 8 28200030 4.68E-07 4.68E-07
vg0105512728 sf0105511728 1 5512728 9.00E-07 9.01E-07
vg1220367571 sf1220339013 12 20367571 9.96E-07 9.96E-07
vg1218047368 sf1218018804 12 18047368 1.41E-06 1.41E-06
vg0140479397 sf0140478354 1 40479397 1.83E-06 1.83E-06
vg0105068923 sf0105067923 1 5068923 1.90E-06 1.90E-06
vg1200750451 sf1200749451 12 750451 2.18E-06 2.18E-06
vg0407000775 sf0406996046 4 7000775 2.60E-06 2.61E-06
vg1121555599 sf1121089476 11 21555599 2.76E-06 2.76E-06
vg1207844031 sf1207841437 12 7844031 4.87E-06 4.87E-06
vg1216994216 sf1216988170 12 16994216 9.10E-06 9.10E-06