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 mr1580 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
vg1015671866 sf1015600636 10 15671866 5.56E-14 NA
vg0410543813 sf0410534512 4 10543813 3.40E-13 NA
vg1002758363 sf1002757340 10 2758363 4.48E-13 NA
vg1125116621 sf1124650461 11 25116621 8.95E-13 NA
vg1011049314 sf1010978134 10 11049314 1.60E-12 NA
vg1000645768 sf1000644744 10 645768 1.08E-11 NA
vg0411642803 sf0411633509 4 11642803 6.68E-10 NA
vg1123670478 sf1123204348 11 23670478 9.83E-10 NA
vg1227219456 sf1227185856 12 27219456 NA 1.06E-06
vg0205237949 sf0205237946 2 5237949 NA 4.37E-06