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 mr1425 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
vg1208480617 sf1208478024 12 8480617 1.49E-12 8.34E-09
vg1216690134 sf1216684088 12 16690134 2.44E-11 NA
vg1213458686 sf1213456024 12 13458686 2.62E-11 6.78E-06
vg0912185687 sf0912184686 9 12185687 4.79E-11 1.30E-06
vg1213459800 sf1213457138 12 13459800 8.18E-11 4.71E-06
vg0910516438 sf0910515437 9 10516438 1.14E-10 NA
vg1209677354 sf1209674763 12 9677354 4.68E-10 4.20E-07
vg0600809385 sf0600808386 6 809385 3.95E-08 1.06E-06
vg1218169210 sf1218140646 12 18169210 4.54E-07 NA
vg1203906173 sf1203905172 12 3906173 9.11E-07 9.23E-07
vg0726050168 sf0726049174 7 26050168 1.43E-06 1.95E-06
vg1200312356 sf1200311356 12 312356 NA 5.89E-07