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 mr1161 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
vg1006540721 sf1006556344 10 6540721 1.38E-52 1.45E-10
vg1010570787 sf1010499608 10 10570787 3.26E-50 3.47E-07
vg0407826844 sf0407822112 4 7826844 1.72E-45 NA
vg1201368299 sf1201367299 12 1368299 1.50E-44 2.31E-06
vg0407824609 sf0407819877 4 7824609 1.10E-43 3.30E-08
vg1008775084 sf1008703946 10 8775084 4.23E-43 1.23E-12
vg0719086317 sf0719085324 7 19086317 6.49E-42 NA
vg1202107188 sf1202106186 12 2107188 1.69E-40 1.13E-06
vg1007528865 sf1007544487 10 7528865 2.77E-39 1.62E-08
vg1006028591 sf1006045129 10 6028591 7.46E-39 9.82E-09
vg0403206873 sf0403202476 4 3206873 6.31E-37 2.31E-07
vg0528707739 sf0528645094 5 28707739 3.18E-34 9.13E-08
vg1006522696 sf1006538319 10 6522696 NA 5.74E-09
vg1007581489 sf1007597101 10 7581489 NA 9.36E-08
vg1010564258 sf1010493079 10 10564258 NA 1.38E-07
vg1006494648 sf1006510271 10 6494648 NA 1.44E-07
vg0142683989 sf0142682945 1 42683989 NA 4.87E-07
vg0110929029 sf0110928005 1 10929029 NA 5.57E-07
vg1009530878 sf1009459699 10 9530878 NA 1.10E-06
vg0407826743 sf0407822011 4 7826743 NA 2.01E-06
vg0529371054 sf0529308409 5 29371054 NA 2.02E-06
vg1007555829 sf1007571441 10 7555829 NA 2.09E-06
vg0403515281 sf0403510884 4 3515281 NA 2.75E-06
vg0222725881 sf0222720012 2 22725881 NA 4.82E-06