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 mr1754 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
vg0101992248 sf0101991248 1 1992248 5.61E-07 3.10E-06
vg0500820450 sf0500820432 5 820450 6.26E-07 3.29E-06
vg0105923602 sf0105922602 1 5923602 2.17E-06 1.40E-07
vg0221025908 sf0221020040 2 21025908 4.74E-06 1.23E-06
vg0624774901 sf0624773904 6 24774901 NA 2.38E-07
vg0113723567 sf0113722541 1 13723567 NA 2.40E-07
vg0226215115 sf0226209246 2 26215115 NA 2.43E-07
vg0805936415 sf0805935418 8 5936415 NA 4.68E-07
vg0506413525 sf0506413464 5 6413525 NA 9.50E-07
vg1000929697 sf1000928673 10 929697 NA 1.04E-06
vg1126957950 sf1126486337 11 26957950 NA 1.13E-06
vg1000561568 sf1000560544 10 561568 NA 1.27E-06
vg0913198487 sf0913197486 9 13198487 NA 1.79E-06
vg0424454435 sf0424269296 4 24454435 NA 2.15E-06
vg0206920077 sf0206920077 2 6920077 NA 2.48E-06
vg1216316780 sf1216314076 12 16316780 NA 4.89E-06