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 mr1655 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
vg1119227478 sf1118761166 11 19227478 4.43E-09 4.43E-09
vg0221233305 sf0221227437 2 21233305 4.14E-07 4.14E-07
vg1107147822 sf1107143567 11 7147822 6.84E-07 6.85E-07
vg0529570513 sf0529507868 5 29570513 2.13E-06 2.13E-06
vg1101287366 sf1101286367 11 1287366 3.72E-06 3.72E-06
vg0307395283 sf0307394281 3 7395283 4.80E-06 4.80E-06