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 mr1943 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
vg0106352079 sf0106351079 1 6352079 1.95E-13 1.96E-08
vg0106330759 sf0106329759 1 6330759 2.01E-13 4.09E-09
vg0709984451 sf0709983457 7 9984451 1.26E-09 3.38E-06
vg0200529411 sf0200529411 2 529411 3.55E-09 NA
vg0821970212 sf0821967499 8 21970212 5.19E-09 NA
vg0404447044 sf0404442648 4 4447044 1.04E-08 NA
vg0710610393 sf0710609399 7 10610393 2.59E-08 5.00E-07
vg0525550165 sf0525487586 5 25550165 1.11E-07 4.41E-06
vg1107375253 sf1107370998 11 7375253 1.13E-07 3.82E-07
vg0518984986 sf0518922470 5 18984986 1.20E-07 3.32E-07
vg0106463385 sf0106462385 1 6463385 4.69E-07 2.76E-06
vg1106375766 sf1106371518 11 6375766 4.97E-07 8.01E-07
vg0718838390 sf0718837397 7 18838390 9.43E-06 NA