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 mr1741 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
vg0502519195 sf0502519171 5 2519195 9.29E-17 4.62E-06
vg0431882216 sf0431697111 4 31882216 4.50E-16 9.88E-06
vg0431907845 sf0431722740 4 31907845 1.90E-15 3.82E-06
vg0207161968 sf0207161968 2 7161968 2.07E-15 NA
vg0219188568 sf0219182700 2 19188568 2.84E-15 NA
vg0107736682 sf0107735682 1 7736682 3.07E-15 3.76E-06
vg0801522955 sf0801521957 8 1522955 6.62E-13 NA
vg1002959463 sf1002949517 10 2959463 1.89E-12 NA
vg1100795910 sf1100794911 11 795910 NA 8.14E-10
vg0824393669 sf0824390955 8 24393669 NA 1.11E-06
vg0228620949 sf0228615080 2 28620949 NA 2.08E-06
vg0910742193 sf0910741192 9 10742193 NA 2.65E-06
vg1217121743 sf1217115698 12 17121743 NA 2.70E-06
vg0314811183 sf0314809870 3 14811183 NA 3.19E-06
vg0431684545 sf0431499438 4 31684545 NA 3.89E-06
vg0401293960 sf0401289510 4 1293960 NA 4.83E-06