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 mr1489 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 1.40E-50 6.62E-23
vg1215955191 sf1215952487 12 15955191 1.18E-49 7.16E-26
vg1215967035 sf1215964331 12 15967035 1.03E-39 4.27E-20
vg1211103816 sf1211101182 12 11103816 1.74E-18 NA
vg1212877317 sf1212874656 12 12877317 4.07E-17 3.29E-06
vg0228430651 sf0228424782 2 28430651 2.33E-16 NA
vg1202865605 sf1202864607 12 2865605 1.85E-15 3.37E-06
vg1014467198 sf1014395964 10 14467198 3.78E-15 NA
vg1216138955 sf1216136251 12 16138955 NA 1.58E-10
vg1215970005 sf1215967301 12 15970005 NA 3.83E-08
vg1218663003 sf1218634438 12 18663003 NA 1.41E-07
vg1006587700 sf1006603323 10 6587700 NA 3.12E-07
vg1216087745 sf1216085041 12 16087745 NA 3.42E-07
vg0408293903 sf0408289177 4 8293903 NA 1.54E-06
vg1216463200 sf1216460493 12 16463200 NA 1.58E-06
vg1022588644 sf1022517118 10 22588644 NA 1.67E-06
vg1214779245 sf1214776586 12 14779245 NA 2.14E-06
vg1215896444 sf1215893740 12 15896444 NA 3.10E-06