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 mr1803 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
vg1216986995 sf1216980949 12 16986995 2.19E-09 1.42E-06
vg1215975950 sf1215973246 12 15975950 3.55E-09 1.67E-08
vg1209388214 sf1209385623 12 9388214 1.73E-08 1.93E-07
vg1216003198 sf1216000494 12 16003198 3.50E-08 2.69E-07
vg1210919096 sf1210916462 12 10919096 4.76E-08 7.09E-08
vg1127555232 sf1127083619 11 27555232 2.09E-07 1.36E-06
vg0916218134 sf0916217133 9 16218134 8.83E-07 2.14E-06
vg1205810555 sf1205809537 12 5810555 8.98E-07 3.61E-07
vg1205811130 sf1205810112 12 5811130 NA 1.21E-06