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 mr1964 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
vg0312535741 sf0312534459 3 12535741 4.49E-08 4.49E-08
vg1117569414 sf1117103271 11 17569414 1.88E-07 1.88E-07
vg0407000775 sf0406996046 4 7000775 4.08E-07 4.08E-07
vg0911098439 sf0911097438 9 11098439 9.65E-07 9.65E-07
vg1218084463 sf1218055899 12 18084463 1.04E-06 1.04E-06
vg0132416363 sf0132415319 1 32416363 1.13E-06 1.13E-06
vg1107376701 sf1107372446 11 7376701 2.27E-06 2.27E-06
vg0802780155 sf0802779158 8 2780155 4.15E-06 4.15E-06
vg1104315941 sf1104311843 11 4315941 4.22E-06 4.22E-06
vg0901019108 sf0901018108 9 1019108 6.25E-06 6.25E-06
vg0129100082 sf0129099037 1 29100082 7.71E-06 7.71E-06