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 mr1097 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
vg0132932503 sf0132931459 1 32932503 3.40E-19 NA
vg0129917132 sf0129916087 1 29917132 4.33E-19 4.22E-06
vg0900665681 sf0900664681 9 665681 9.89E-19 NA
vg0122013723 sf0122012678 1 22013723 3.81E-18 9.76E-07
vg0304256703 sf0304255705 3 4256703 7.65E-18 NA
vg1109729286 sf1109723863 11 9729286 9.96E-18 3.08E-08
vg1115480914 sf1115017227 11 15480914 3.26E-17 1.69E-09
vg0406998246 sf0406993517 4 6998246 4.56E-14 NA
vg0815688098 sf0815685384 8 15688098 4.85E-13 8.71E-07
vg1115509243 sf1115045556 11 15509243 7.91E-13 1.19E-10
vg0131033386 sf0131032342 1 31033386 1.96E-12 3.65E-06
vg0130736176 sf0130735132 1 30736176 NA 4.59E-14
vg0130670983 sf0130669939 1 30670983 NA 6.56E-14
vg1115499343 sf1115035656 11 15499343 NA 1.53E-08
vg1110447272 sf1110441817 11 10447272 NA 2.95E-08
vg1115379165 sf1114915477 11 15379165 NA 1.14E-06
vg1115517044 sf1115053357 11 15517044 NA 1.34E-06
vg0905354568 sf0905353568 9 5354568 NA 1.63E-06
vg1109793060 sf1109787637 11 9793060 NA 1.81E-06
vg0434326797 sf0434141691 4 34326797 NA 3.92E-06
vg0808527211 sf0808526215 8 8527211 NA 9.19E-06