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 mr1574 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
vg0916968554 sf0916967553 9 16968554 5.57E-11 NA
vg0307917185 sf0307916123 3 7917185 8.95E-11 NA
vg0105207598 sf0105206598 1 5207598 1.93E-10 NA
vg0113767498 sf0113766472 1 13767498 2.24E-10 NA
vg1010535541 sf1010464362 10 10535541 2.80E-10 NA
vg1214204170 sf1214201510 12 14204170 4.19E-07 NA
vg0140618344 sf0140617301 1 40618344 1.48E-06 5.00E-06
vg1224524026 sf1224490480 12 24524026 3.02E-06 4.37E-06
vg0205235092 sf0205235089 2 5235092 4.33E-06 NA
vg1218543377 sf1218514813 12 18543377 NA 4.21E-06
vg1018173239 sf1018101798 10 18173239 NA 7.97E-06