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 mr1135 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
vg1227310775 sf1227277175 12 27310775 1.85E-09 4.77E-10
vg0813611459 sf0813608744 8 13611459 2.21E-09 8.95E-08
vg1011166207 sf1011095027 10 11166207 3.76E-09 6.83E-08
vg0138349324 sf0138348281 1 38349324 6.98E-09 1.24E-07
vg0118949515 sf0118948470 1 18949515 8.21E-08 9.90E-07
vg1227259456 sf1227225856 12 27259456 1.32E-07 5.79E-07
vg1109710245 sf1109704822 11 9710245 6.68E-07 4.09E-06
vg0207793650 sf0207793649 2 7793650 7.77E-07 1.81E-06
vg1124116182 sf1123650052 11 24116182 7.98E-07 4.86E-06
vg0116981684 sf0116980638 1 16981684 4.36E-06 NA