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 mr1288 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
vg0623833223 sf0623832226 6 23833223 1.76E-10 1.76E-10
vg0614627605 sf0614626606 6 14627605 2.06E-07 2.06E-07
vg0216867976 sf0216862106 2 16867976 1.08E-06 1.08E-06
vg0729692653 sf0729691661 7 29692653 1.48E-06 1.48E-06
vg0109929600 sf0109928576 1 9929600 1.97E-06 1.97E-06
vg0606072382 sf0606071383 6 6072382 2.45E-06 2.45E-06
vg1016075640 sf1016004412 10 16075640 3.16E-06 3.16E-06
vg0910546070 sf0910545069 9 10546070 3.19E-06 3.20E-06
vg0826159919 sf0826157205 8 26159919 3.81E-06 3.81E-06
vg1016324780 sf1016253556 10 16324780 3.85E-06 3.86E-06
vg0608550861 sf0608549862 6 8550861 4.28E-06 4.28E-06