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 mr1134 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 7.30E-12 7.18E-11
vg0138349324 sf0138348281 1 38349324 1.38E-11 1.34E-09
vg0810755455 sf0810754460 8 10755455 4.20E-10 1.02E-06
vg0814668918 sf0814666204 8 14668918 1.48E-09 8.05E-06
vg0813611459 sf0813608744 8 13611459 1.82E-09 1.94E-06
vg0630841543 sf0630840545 6 30841543 9.32E-09 NA
vg1124116182 sf1123650052 11 24116182 2.35E-08 1.35E-06
vg1011166207 sf1011095027 10 11166207 2.01E-07 2.07E-06
vg1227259456 sf1227225856 12 27259456 9.73E-07 1.45E-06
vg0127823831 sf0127822787 1 27823831 2.79E-06 1.65E-06
vg0423923614 sf0423738474 4 23923614 5.51E-06 NA