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
vg1215976937 sf1215974233 12 15976937 2.05E-68 1.27E-32
vg1215854444 sf1215851740 12 15854444 2.70E-68 1.33E-32
vg1209571445 sf1209568854 12 9571445 1.67E-53 5.01E-21
vg1223872806 sf1223839259 12 23872806 8.16E-38 3.15E-07
vg1223827289 sf1223793742 12 23827289 1.61E-33 2.53E-07
vg1212726422 sf1212723761 12 12726422 2.23E-25 5.12E-08
vg0410423427 sf0410414126 4 10423427 2.50E-20 NA
vg1219373193 sf1219344662 12 19373193 6.60E-19 2.41E-06
vg1207827697 sf1207825103 12 7827697 4.03E-16 1.02E-10
vg1216192507 sf1216189803 12 16192507 5.83E-16 7.59E-12
vg0219058637 sf0219052769 2 19058637 1.85E-15 5.73E-07
vg0217462843 sf0217456973 2 17462843 4.14E-15 1.17E-06
vg0315452372 sf0315451019 3 15452372 8.04E-15 8.25E-07
vg1215916353 sf1215913649 12 15916353 1.69E-14 3.80E-07
vg1214847524 sf1214844865 12 14847524 3.03E-13 8.85E-12
vg1215974646 sf1215971942 12 15974646 2.28E-11 1.10E-06
vg1215803442 sf1215800739 12 15803442 3.33E-11 3.17E-08
vg1216279541 sf1216276837 12 16279541 9.99E-11 1.06E-08
vg0232825688 sf0232819819 2 32825688 NA 8.67E-07
vg1216542145 sf1216539438 12 16542145 NA 9.73E-07
vg0807809853 sf0807808857 8 7809853 NA 1.02E-06
vg1205718847 sf1205716942 12 5718847 NA 1.19E-06
vg1214779581 sf1214776922 12 14779581 NA 3.39E-06