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 mr1220 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
vg0719471192 sf0719470199 7 19471192 3.63E-18 2.33E-06
vg0228211032 sf0228205163 2 28211032 6.76E-17 NA
vg0610410251 sf0610409252 6 10410251 1.04E-15 NA
vg1218842150 sf1218813585 12 18842150 9.29E-15 NA
vg0719395586 sf0719394593 7 19395586 1.23E-14 4.22E-07
vg0725367049 sf0725366055 7 25367049 3.84E-14 NA
vg0316474025 sf0316472670 3 16474025 5.97E-10 NA
vg0806428787 sf0806427792 8 6428787 1.83E-09 NA
vg0607445929 sf0607444930 6 7445929 3.84E-09 1.90E-06
vg1214822308 sf1214819649 12 14822308 NA 3.79E-07
vg0727650948 sf0727649955 7 27650948 NA 4.83E-06
vg1004557426 sf1004573964 10 4557426 NA 8.74E-06