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 mr1071 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
vg0406465683 sf0406461126 4 6465683 1.47E-28 4.10E-21
vg0817327521 sf0817324807 8 17327521 1.27E-11 5.97E-08
vg1016565386 sf1016494159 10 16565386 4.30E-11 NA
vg0912864929 sf0912863928 9 12864929 3.72E-10 4.06E-07
vg1016503494 sf1016432267 10 16503494 4.85E-10 NA
vg0912877788 sf0912876787 9 12877788 4.91E-10 2.42E-07
vg1017940079 sf1017868851 10 17940079 5.33E-10 2.34E-06
vg0503312521 sf0503312497 5 3312521 8.31E-10 2.40E-06
vg0807357132 sf0807356137 8 7357132 9.41E-10 3.11E-07
vg0622629240 sf0622628243 6 22629240 5.56E-09 8.80E-08
vg0912152486 sf0912151485 9 12152486 1.55E-08 1.39E-06
vg0406060650 sf0406056089 4 6060650 4.07E-08 4.86E-07
vg0900339005 sf0900338005 9 339005 2.66E-07 2.10E-06
vg1216561117 sf1216558410 12 16561117 2.79E-07 4.74E-07
vg1209797289 sf1209794699 12 9797289 2.84E-07 8.99E-07
vg1216438393 sf1216435686 12 16438393 3.35E-07 2.89E-06
vg1116610872 sf1116145750 11 16610872 7.46E-07 9.23E-07
vg0417549349 sf0417377391 4 17549349 4.56E-06 3.59E-06
vg0819433740 sf0819431027 8 19433740 5.30E-06 4.33E-06
vg0128388692 sf0128387648 1 28388692 6.13E-06 3.68E-06
vg0406345590 sf0406341030 4 6345590 NA 1.53E-08