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 mr1125 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
vg0523879200 sf0523816621 5 23879200 8.98E-57 NA
vg0622416625 sf0622415628 6 22416625 1.36E-55 NA
vg0434660067 sf0434474957 4 34660067 4.98E-55 NA
vg0434271661 sf0434086555 4 34271661 7.69E-55 NA
vg0204270525 sf0204270522 2 4270525 8.22E-55 NA
vg0127041283 sf0127040239 1 27041283 2.63E-54 NA
vg0211839911 sf0211839907 2 11839911 5.44E-52 2.50E-06
vg0523880474 sf0523817895 5 23880474 NA 3.51E-08
vg1114018010 sf1113554331 11 14018010 NA 1.96E-07
vg0602769653 sf0602768654 6 2769653 NA 3.31E-07
vg0918682395 sf0918681394 9 18682395 NA 4.64E-07
vg0815679964 sf0815677250 8 15679964 NA 4.83E-07
vg0630510502 sf0630509504 6 30510502 NA 6.79E-07
vg0602813024 sf0602812025 6 2813024 NA 7.75E-07
vg0235323589 sf0235317720 2 35323589 NA 9.02E-07
vg0315367742 sf0315366389 3 15367742 NA 1.30E-06