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 mr1657 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
vg0228243369 sf0228237500 2 28243369 1.24E-09 NA
vg0104429723 sf0104428723 1 4429723 1.50E-09 NA
vg0129289299 sf0129288254 1 29289299 3.81E-09 1.30E-06
vg0721382199 sf0721381206 7 21382199 5.95E-09 NA
vg0805348696 sf0805347699 8 5348696 7.11E-09 NA
vg0432213299 sf0432028191 4 32213299 1.40E-08 3.75E-06
vg0139227377 sf0139226334 1 39227377 1.66E-08 6.60E-07
vg1217884983 sf1217856417 12 17884983 1.13E-07 3.66E-06
vg1116554195 sf1116089073 11 16554195 1.64E-07 NA
vg0217766680 sf0217760811 2 17766680 1.94E-06 2.12E-06
vg0902028402 sf0902027402 9 2028402 3.47E-06 NA