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
vg0128428246 sf0128427201 1 28428246 1.37E-08 1.37E-08
vg0402217448 sf0402213043 4 2217448 1.27E-07 1.27E-07
vg0223858890 sf0223853021 2 23858890 4.08E-07 4.08E-07
vg0130078302 sf0130077257 1 30078302 5.58E-07 5.58E-07
vg0403116859 sf0403112462 4 3116859 9.95E-07 9.95E-07
vg0408160817 sf0408156091 4 8160817 1.70E-06 1.70E-06
vg0419763927 sf0419591962 4 19763927 1.84E-06 1.84E-06
vg0102124242 sf0102123242 1 2124242 1.89E-06 1.89E-06
vg1208638605 sf1208636012 12 8638605 2.65E-06 2.66E-06
vg0906681211 sf0906680211 9 6681211 2.77E-06 2.77E-06
vg0800216569 sf0800215569 8 216569 3.42E-06 3.42E-06
vg0916049005 sf0916048004 9 16049005 3.93E-06 3.94E-06
vg0402172596 sf0402168191 4 2172596 3.98E-06 3.98E-06
vg0722219723 sf0722218730 7 22219723 4.55E-06 4.55E-06
vg0226725058 sf0226719189 2 26725058 4.56E-06 4.56E-06