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 mr1553 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
vg1126878566 sf1126406953 11 26878566 4.93E-09 4.05E-06
vg0809212456 sf0809211460 8 9212456 2.29E-08 NA
vg0721461360 sf0721460367 7 21461360 3.90E-08 NA
vg1126568779 sf1126097194 11 26568779 6.40E-08 NA
vg1203289460 sf1203288463 12 3289460 7.82E-08 NA
vg0808435872 sf0808434876 8 8435872 8.02E-07 NA
vg0714953061 sf0714952068 7 14953061 1.40E-06 1.35E-06
vg0717067453 sf0717066460 7 17067453 2.02E-06 1.24E-06
vg0219830859 sf0219824991 2 19830859 6.35E-06 NA