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 mr1423 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
vg0217071444 sf0217065574 2 17071444 5.28E-29 3.31E-23
vg0217088291 sf0217082421 2 17088291 2.14E-28 2.73E-23
vg0216662827 sf0216656957 2 16662827 8.57E-15 1.12E-10
vg0812023942 sf0812022947 8 12023942 3.55E-13 1.92E-08
vg1005364262 sf1005380799 10 5364262 3.79E-13 1.02E-10
vg0217737368 sf0217731498 2 17737368 1.80E-12 1.02E-07
vg0216771267 sf0216765397 2 16771267 4.13E-11 4.19E-06
vg0900337327 sf0900336327 9 337327 4.66E-11 7.46E-07
vg0217677256 sf0217671386 2 17677256 1.47E-10 1.32E-06
vg0217612660 sf0217606790 2 17612660 3.37E-10 3.92E-08
vg0212179963 sf0212179959 2 12179963 3.66E-10 7.61E-07
vg1114473442 sf1114009759 11 14473442 4.91E-10 3.76E-07
vg0216243264 sf0216237394 2 16243264 6.21E-10 7.12E-07
vg0804838042 sf0804837045 8 4838042 1.45E-09 3.54E-06
vg1105770829 sf1105766581 11 5770829 3.63E-09 8.14E-08
vg0216773376 sf0216767506 2 16773376 8.93E-09 7.55E-07
vg1209798487 sf1209795897 12 9798487 1.03E-08 3.66E-06
vg0115588521 sf0115587495 1 15588521 1.45E-08 2.27E-06
vg0217845537 sf0217839668 2 17845537 2.95E-08 5.95E-07
vg0217520188 sf0217514318 2 17520188 3.82E-08 1.82E-07
vg0216616335 sf0216610465 2 16616335 6.29E-07 1.13E-06
vg0124673365 sf0124672321 1 24673365 7.62E-07 7.58E-07