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 mr1053 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
vg1004296464 sf1004313002 10 4296464 4.36E-11 2.47E-07
vg1006943122 sf1006958745 10 6943122 1.11E-10 4.15E-07
vg1010479547 sf1010408368 10 10479547 4.62E-10 1.07E-06
vg1009413787 sf1009342608 10 9413787 4.44E-09 3.53E-08
vg1009320431 sf1009249252 10 9320431 5.32E-09 1.37E-08
vg0726847020 sf0726846026 7 26847020 7.20E-09 NA
vg1009450763 sf1009379584 10 9450763 1.23E-08 1.40E-08
vg0207335149 sf0207335149 2 7335149 2.74E-08 2.16E-06
vg0412457639 sf0412448354 4 12457639 2.80E-08 7.26E-08
vg0204345674 sf0204345671 2 4345674 2.60E-07 3.15E-06
vg1005176953 sf1005193490 10 5176953 2.78E-07 3.78E-06
vg1102158811 sf1102154669 11 2158811 1.59E-06 NA
vg0819603039 sf0819600326 8 19603039 3.42E-06 NA
vg1207329016 sf1207326423 12 7329016 7.70E-06 NA
vg1019397969 sf1019326524 10 19397969 NA 3.21E-06