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 mr1295 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
vg1015690639 sf1015619409 10 15690639 3.85E-09 NA
vg0719446559 sf0719445566 7 19446559 6.05E-09 NA
vg0413858051 sf0413848769 4 13858051 1.12E-08 NA
vg1123404294 sf1122938164 11 23404294 2.81E-08 NA
vg0115087314 sf0115086288 1 15087314 2.83E-08 NA
vg0304482223 sf0304481225 3 4482223 3.62E-08 NA
vg0907966825 sf0907965825 9 7966825 NA 2.80E-06
vg1215952216 sf1215949512 12 15952216 NA 3.34E-06