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 mr1035 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
vg0405636478 sf0405631919 4 5636478 1.86E-15 4.12E-12
vg0405883865 sf0405879305 4 5883865 1.72E-08 1.81E-06
vg0805321568 sf0805320571 8 5321568 7.42E-08 NA
vg0314931433 sf0314930080 3 14931433 2.80E-07 4.36E-06
vg0405188317 sf0405183759 4 5188317 4.67E-07 2.11E-06
vg1213717963 sf1213715301 12 13717963 6.44E-06 4.30E-06
vg0921699962 sf0921699481 9 21699962 6.85E-06 3.13E-06