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 mr1168 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
vg0900044024 sf0900043024 9 44024 1.67E-10 3.10E-07
vg1000093464 sf1000092464 10 93464 7.26E-10 5.49E-07
vg0700053913 sf0700052913 7 53913 8.60E-10 3.77E-08
vg1001580134 sf1001579111 10 1580134 1.20E-08 7.64E-07
vg0700050082 sf0700049082 7 50082 1.89E-08 1.64E-08
vg0700260893 sf0700259893 7 260893 2.14E-08 5.82E-06
vg0700013379 sf0700012379 7 13379 2.15E-08 2.10E-08
vg1001586279 sf1001585256 10 1586279 5.36E-08 7.33E-07
vg0431473874 sf0431288772 4 31473874 6.95E-08 1.84E-06
vg0104860223 sf0104859223 1 4860223 1.70E-07 7.75E-08
vg0726196326 sf0726195332 7 26196326 5.89E-07 NA
vg0335164367 sf0335157236 3 35164367 3.60E-06 NA
vg1209153762 sf1209151171 12 9153762 NA 1.27E-06
vg1010010984 sf1009939805 10 10010984 NA 4.12E-06