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 mr1713 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
vg1104930000 sf1104925811 11 4930000 8.87E-09 NA
vg0433624149 sf0433439032 4 33624149 3.96E-08 NA
vg1215165691 sf1215163027 12 15165691 4.16E-08 NA
vg0821751104 sf0821748391 8 21751104 6.55E-08 7.55E-06
vg0103429839 sf0103428839 1 3429839 6.77E-08 2.36E-06
vg0103396097 sf0103395097 1 3396097 2.00E-07 1.62E-06
vg0709254491 sf0709253497 7 9254491 3.65E-07 3.10E-06
vg1107375253 sf1107370998 11 7375253 5.66E-07 8.78E-07