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 mr1017 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
vg1215967035 sf1215964331 12 15967035 4.43E-42 2.69E-23
vg1212873997 sf1212871336 12 12873997 2.72E-17 2.19E-06
vg1110282765 sf1110277342 11 10282765 1.04E-16 1.09E-06
vg1011511779 sf1011440598 10 11511779 1.55E-16 2.07E-06
vg1006590352 sf1006605975 10 6590352 8.08E-16 NA
vg1212877317 sf1212874656 12 12877317 1.37E-15 1.19E-06
vg0521485463 sf0521422904 5 21485463 1.41E-15 4.42E-07
vg1218663003 sf1218634438 12 18663003 5.74E-14 1.80E-09
vg1006587700 sf1006603323 10 6587700 1.11E-13 1.24E-09
vg1022588644 sf1022517118 10 22588644 2.36E-12 1.36E-12
vg1208048502 sf1208045908 12 8048502 5.86E-12 9.38E-09
vg1011512046 sf1011440865 10 11512046 5.23E-11 3.81E-08
vg1215876237 sf1215873533 12 15876237 3.66E-10 4.22E-06
vg1215852700 sf1215849996 12 15852700 NA 7.78E-12
vg0612563711 sf0612562712 6 12563711 NA 4.66E-07
vg0408293903 sf0408289177 4 8293903 NA 8.94E-07
vg1213186520 sf1213183858 12 13186520 NA 1.08E-06
vg0432161866 sf0431976759 4 32161866 NA 1.13E-06
vg1215211990 sf1215209287 12 15211990 NA 1.86E-06
vg1117387081 sf1116920934 11 17387081 NA 2.39E-06
vg0816293722 sf0816291008 8 16293722 NA 3.05E-06
vg0224510095 sf0224504226 2 24510095 NA 3.90E-06
vg0602179233 sf0602178234 6 2179233 NA 4.83E-06
vg0824114764 sf0824112050 8 24114764 NA 4.94E-06