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 mr1913 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
vg0406238909 sf0406234349 4 6238909 2.08E-25 1.83E-08
vg0406399511 sf0406394951 4 6399511 3.22E-25 1.30E-12
vg1122484031 sf1122017902 11 22484031 3.08E-24 NA
vg0406420651 sf0406416091 4 6420651 1.10E-23 1.73E-13
vg0520620647 sf0520558088 5 20620647 3.69E-22 NA
vg0123462204 sf0123461160 1 23462204 7.84E-22 NA
vg1005798322 sf1005814860 10 5798322 1.61E-21 NA
vg0406838033 sf0406833478 4 6838033 6.12E-21 3.07E-06
vg1006687337 sf1006702960 10 6687337 6.95E-18 3.67E-07
vg1009344337 sf1009273158 10 9344337 3.87E-17 NA
vg0222717596 sf0222711727 2 22717596 NA 3.53E-17
vg0406521772 sf0406517215 4 6521772 NA 1.53E-07
vg0406513963 sf0406509406 4 6513963 NA 1.90E-07
vg0406404953 sf0406400393 4 6404953 NA 6.79E-07
vg0116882132 sf0116881106 1 16882132 NA 8.32E-07
vg0229030086 sf0229024217 2 29030086 NA 1.24E-06
vg0431707471 sf0431522364 4 31707471 NA 2.29E-06
vg0406139947 sf0406135387 4 6139947 NA 3.58E-06
vg0710267058 sf0710266064 7 10267058 NA 4.37E-06
vg0222557148 sf0222551279 2 22557148 NA 4.58E-06