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 mr1023 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
vg1215869969 sf1215867265 12 15869969 1.90E-53 1.84E-24
vg1215955191 sf1215952487 12 15955191 3.31E-53 3.66E-26
vg1215967035 sf1215964331 12 15967035 4.65E-39 1.10E-20
vg1214606134 sf1214603474 12 14606134 5.58E-28 1.43E-07
vg1211103816 sf1211101182 12 11103816 9.73E-20 NA
vg1014467198 sf1014395964 10 14467198 2.31E-17 NA
vg1212877317 sf1212874656 12 12877317 6.35E-17 2.57E-06
vg0228430651 sf0228424782 2 28430651 1.68E-16 NA
vg1204108880 sf1204107868 12 4108880 2.40E-16 NA
vg1215870946 sf1215868242 12 15870946 NA 4.92E-11
vg1215970005 sf1215967301 12 15970005 NA 1.78E-08
vg1216017848 sf1216015144 12 16017848 NA 1.88E-08
vg1218663003 sf1218634438 12 18663003 NA 6.10E-08
vg1022588644 sf1022517118 10 22588644 NA 9.00E-08
vg0408293903 sf0408289177 4 8293903 NA 1.24E-07
vg1006587700 sf1006603323 10 6587700 NA 1.78E-07
vg0901555680 sf0901554680 9 1555680 NA 6.29E-07
vg1213186520 sf1213183858 12 13186520 NA 1.49E-06
vg1215896444 sf1215893740 12 15896444 NA 1.55E-06
vg0101661898 sf0101660898 1 1661898 NA 1.79E-06
vg0715496749 sf0715495756 7 15496749 NA 2.03E-06
vg1202736323 sf1202735325 12 2736323 NA 2.41E-06
vg0123658384 sf0123657340 1 23658384 NA 2.81E-06
vg0610620315 sf0610619316 6 10620315 NA 2.86E-06
vg1214779245 sf1214776586 12 14779245 NA 3.66E-06
vg0315357505 sf0315356152 3 15357505 NA 4.20E-06
vg0316037703 sf0316036350 3 16037703 NA 4.39E-06
vg0225153266 sf0225147397 2 25153266 NA 4.47E-06