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 mr1970 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
vg0607282803 sf0607281804 6 7282803 1.73E-101 7.21E-18
vg0428552129 sf0428366981 4 28552129 4.33E-80 NA
vg0717275313 sf0717274320 7 17275313 1.86E-78 6.43E-06
vg0717362404 sf0717361411 7 17362404 3.64E-77 1.10E-09
vg0612897677 sf0612896678 6 12897677 1.80E-75 NA
vg0501552425 sf0501552409 5 1552425 4.79E-75 3.06E-06
vg0107527372 sf0107526372 1 7527372 1.15E-67 5.09E-07
vg0607242219 sf0607241220 6 7242219 NA 5.44E-12
vg0607252722 sf0607251723 6 7252722 NA 7.15E-12
vg0606988364 sf0606987365 6 6988364 NA 1.32E-09
vg1017284750 sf1017213523 10 17284750 NA 2.81E-07
vg0721221414 sf0721220421 7 21221414 NA 1.15E-06
vg0702261563 sf0702260564 7 2261563 NA 1.38E-06
vg0606974113 sf0606973114 6 6974113 NA 2.95E-06
vg1105862690 sf1105858442 11 5862690 NA 4.04E-06