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
vg1212139228 sf1212136564 12 12139228 1.88E-10 2.92E-08
vg1214943582 sf1214940924 12 14943582 4.43E-09 7.21E-07
vg0408234717 sf0408229991 4 8234717 1.05E-08 3.49E-06
vg1217708909 sf1217702864 12 17708909 2.88E-08 4.13E-07
vg1113356571 sf1112892892 11 13356571 9.38E-08 NA
vg0910064812 sf0910063811 9 10064812 3.43E-07 1.32E-06
vg0714218412 sf0714217419 7 14218412 4.10E-07 2.73E-06
vg1106375766 sf1106371518 11 6375766 7.10E-06 4.51E-06