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 mr1961 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
vg1007457578 sf1007473201 10 7457578 1.02E-09 7.17E-06
vg1006376447 sf1006392070 10 6376447 1.27E-08 1.29E-06
vg1007941662 sf1007957272 10 7941662 4.19E-08 1.63E-06
vg0709174478 sf0709173484 7 9174478 6.78E-08 NA
vg1202110385 sf1202109383 12 2110385 8.36E-08 NA
vg1007689790 sf1007705399 10 7689790 1.44E-07 NA
vg1118218762 sf1117752620 11 18218762 4.93E-06 NA
vg0224323881 sf0224318012 2 24323881 5.69E-06 4.38E-07
vg0202989092 sf0202989090 2 2989092 9.39E-06 1.07E-07
vg0222735055 sf0222729186 2 22735055 NA 1.36E-06
vg0514034074 sf0513976618 5 14034074 NA 1.97E-06