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 mr1347 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
vg0430000535 sf0429815402 4 30000535 4.27E-32 6.87E-14
vg0429923292 sf0429738159 4 29923292 1.01E-25 3.51E-15
vg0429127324 sf0428942184 4 29127324 8.03E-17 4.28E-08
vg0102177582 sf0102176582 1 2177582 1.71E-15 NA
vg0131778131 sf0131777087 1 31778131 6.43E-15 NA
vg0527911628 sf0527848985 5 27911628 2.32E-14 NA
vg0430022461 sf0429837330 4 30022461 1.12E-13 7.67E-08
vg0429758012 sf0429572881 4 29758012 1.17E-09 1.57E-10
vg0304034292 sf0304033288 3 4034292 8.54E-09 9.78E-07
vg0921382154 sf0921381673 9 21382154 2.18E-08 1.23E-06
vg0727650948 sf0727649955 7 27650948 8.44E-08 2.31E-06
vg0804315269 sf0804314272 8 4315269 NA 5.94E-11
vg0804419898 sf0804418901 8 4419898 NA 2.36E-10
vg0804435056 sf0804434059 8 4435056 NA 3.34E-08
vg0804327523 sf0804326526 8 4327523 NA 3.94E-08
vg0620617222 sf0620616225 6 20617222 NA 3.21E-07
vg0107729775 sf0107728775 1 7729775 NA 9.67E-07
vg0429839310 sf0429654180 4 29839310 NA 1.24E-06
vg1215388040 sf1215385338 12 15388040 NA 2.00E-06
vg0527885330 sf0527822687 5 27885330 NA 3.53E-06