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 mr1647 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
vg0319113443 sf0319112203 3 19113443 1.40E-08 2.79E-07
vg1010774180 sf1010703001 10 10774180 6.09E-08 7.80E-07
vg0514820986 sf0514763529 5 14820986 7.42E-08 4.27E-06
vg0516841556 sf0516781197 5 16841556 7.70E-08 6.30E-07
vg0232481318 sf0232475449 2 32481318 4.11E-07 1.89E-06
vg1118378850 sf1117912710 11 18378850 1.56E-06 NA
vg0819150140 sf0819147427 8 19150140 NA 1.29E-07
vg1010728828 sf1010657649 10 10728828 NA 2.93E-07
vg0718397736 sf0718396743 7 18397736 NA 1.46E-06
vg0608550861 sf0608549862 6 8550861 NA 2.09E-06