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 mr1332 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
vg0300353676 sf0300352674 3 353676 9.49E-11 NA
vg0907448324 sf0907447324 9 7448324 1.23E-09 NA
vg0319113443 sf0319112203 3 19113443 1.31E-09 3.09E-07
vg1000628143 sf1000627119 10 628143 2.01E-09 NA
vg0527902831 sf0527840188 5 27902831 7.05E-09 NA
vg1000702985 sf1000701961 10 702985 2.01E-08 3.08E-06
vg0219483986 sf0219478118 2 19483986 4.26E-08 1.45E-07
vg0141090615 sf0141089572 1 41090615 1.53E-07 3.23E-06
vg1122092252 sf1121626123 11 22092252 2.90E-06 4.17E-06
vg0628827535 sf0628826537 6 28827535 3.01E-06 2.67E-06
vg0221240541 sf0221234673 2 21240541 NA 3.93E-06