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 mr1942 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
vg0140477113 sf0140476070 1 40477113 4.60E-10 NA
vg0424992689 sf0424807550 4 24992689 5.23E-10 NA
vg0427893228 sf0427708090 4 27893228 1.96E-09 NA
vg1122510926 sf1122044797 11 22510926 2.09E-09 NA
vg0143071013 sf0143069969 1 43071013 4.51E-09 NA
vg1116497154 sf1116032031 11 16497154 5.28E-07 6.57E-06
vg0809017868 sf0809016872 8 9017868 5.85E-07 NA
vg1124078478 sf1123612348 11 24078478 1.93E-06 2.42E-06
vg1106375766 sf1106371518 11 6375766 3.11E-06 1.22E-06
vg0431472905 sf0431287803 4 31472905 3.84E-06 5.65E-07
vg0826157104 sf0826154390 8 26157104 6.38E-06 1.08E-06
vg1008819475 sf1008748337 10 8819475 9.91E-06 NA
vg0514370755 sf0514313298 5 14370755 NA 1.86E-06
vg0707896183 sf0707895188 7 7896183 NA 3.43E-06