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 mr1412 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
vg0526873682 sf0526811040 5 26873682 1.30E-08 1.30E-08
vg0508292114 sf0508292054 5 8292114 1.00E-07 1.00E-07
vg0224267593 sf0224261724 2 24267593 1.13E-07 1.13E-07
vg1128667909 sf1128144688 11 28667909 1.47E-07 1.47E-07
vg0800263929 sf0800262929 8 263929 2.23E-07 2.23E-07
vg0111637418 sf0111636392 1 11637418 2.62E-07 2.62E-07
vg0727272382 sf0727271388 7 27272382 5.22E-07 5.22E-07
vg0232874306 sf0232868437 2 32874306 5.63E-07 5.63E-07
vg0619271869 sf0619270872 6 19271869 5.97E-07 5.97E-07
vg0228383216 sf0228377347 2 28383216 9.08E-07 9.08E-07
vg0315006009 sf0315004656 3 15006009 1.08E-06 1.08E-06
vg0133759034 sf0133757990 1 33759034 1.09E-06 1.09E-06
vg0529163752 sf0529101107 5 29163752 1.20E-06 1.20E-06
vg0201788461 sf0201788461 2 1788461 1.41E-06 1.41E-06
vg1209232946 sf1209230355 12 9232946 1.52E-06 1.52E-06
vg0331460056 sf0331452941 3 31460056 1.74E-06 1.74E-06
vg1217187746 sf1217181701 12 17187746 2.08E-06 2.08E-06
vg1001004126 sf1001003102 10 1004126 2.64E-06 2.64E-06
vg0105388283 sf0105387283 1 5388283 2.97E-06 2.97E-06
vg0229643363 sf0229637494 2 29643363 3.49E-06 3.49E-06