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 mr1308 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
vg0310396466 sf0310395382 3 10396466 4.14E-26 NA
vg1018673969 sf1018602527 10 18673969 2.43E-25 NA
vg0315146805 sf0315145452 3 15146805 7.88E-25 NA
vg0805968808 sf0805967811 8 5968808 9.34E-25 NA
vg0800333217 sf0800332217 8 333217 1.51E-24 NA
vg1212822297 sf1212819636 12 12822297 1.89E-24 9.12E-09
vg1212139228 sf1212136564 12 12139228 NA 7.24E-08
vg1217708909 sf1217702864 12 17708909 NA 7.48E-07
vg1208634025 sf1208631432 12 8634025 NA 1.42E-06
vg1214217183 sf1214214523 12 14217183 NA 1.68E-06
vg0714218412 sf0714217419 7 14218412 NA 1.94E-06
vg0213591886 sf0213591882 2 13591886 NA 2.50E-06
vg1214943582 sf1214940924 12 14943582 NA 4.01E-06