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 mr1768 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
vg1005357425 sf1005373962 10 5357425 8.06E-14 1.58E-07
vg1010151674 sf1010080495 10 10151674 3.69E-13 5.04E-06
vg1005371251 sf1005387788 10 5371251 8.99E-13 3.49E-09
vg1006613497 sf1006629120 10 6613497 2.08E-11 3.70E-07
vg1007541835 sf1007557447 10 7541835 2.53E-11 2.41E-07
vg1010488113 sf1010416934 10 10488113 2.88E-11 1.11E-06
vg0231638633 sf0231632764 2 31638633 7.87E-10 2.01E-07
vg0235282248 sf0235276379 2 35282248 3.32E-09 NA
vg1009180380 sf1009109201 10 9180380 8.87E-09 NA
vg1004375218 sf1004391756 10 4375218 1.40E-07 3.13E-06
vg1005377616 sf1005394153 10 5377616 2.24E-06 1.69E-06
vg0626222999 sf0626222002 6 26222999 2.57E-06 7.72E-06
vg1115719147 sf1115255456 11 15719147 NA 9.90E-07