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 mr1234 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
vg0610752378 sf0610751379 6 10752378 7.17E-11 7.17E-11
vg0626895745 sf0626894748 6 26895745 2.71E-08 2.71E-08
vg0627157824 sf0627156827 6 27157824 2.71E-08 2.71E-08
vg0809578434 sf0809577438 8 9578434 9.22E-08 9.23E-08
vg0611680365 sf0611679366 6 11680365 1.86E-07 1.86E-07
vg1216456173 sf1216453466 12 16456173 1.87E-07 1.87E-07
vg1217730651 sf1217724606 12 17730651 6.01E-07 6.01E-07
vg0204718853 sf0204718850 2 4718853 7.42E-07 7.42E-07
vg1215018131 sf1215015473 12 15018131 1.63E-06 1.63E-06
vg1203842140 sf1203841139 12 3842140 1.88E-06 1.88E-06
vg1014156474 sf1014085240 10 14156474 2.01E-06 2.01E-06
vg0823443665 sf0823440952 8 23443665 2.05E-06 2.05E-06
vg0207304262 sf0207304262 2 7304262 2.21E-06 2.21E-06
vg0610750309 sf0610749310 6 10750309 2.23E-06 2.23E-06
vg1104309736 sf1104305638 11 4309736 2.51E-06 2.51E-06
vg0817334525 sf0817331811 8 17334525 2.70E-06 2.70E-06
vg1122416969 sf1121950840 11 22416969 2.77E-06 2.77E-06
vg0724624705 sf0724623711 7 24624705 3.02E-06 3.02E-06
vg0805228024 sf0805227027 8 5228024 3.20E-06 3.21E-06
vg0507099666 sf0507099608 5 7099666 3.25E-06 3.25E-06
vg0805068769 sf0805067772 8 5068769 3.38E-06 3.38E-06
vg0902337033 sf0902336033 9 2337033 3.52E-06 3.52E-06