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 mr1201 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
vg0605269202 sf0605268203 6 5269202 1.42E-47 1.54E-27
vg0605306584 sf0605305585 6 5306584 1.06E-19 4.09E-21
vg0605739124 sf0605738125 6 5739124 3.99E-16 3.37E-07
vg0605311849 sf0605310850 6 5311849 1.83E-15 1.84E-22
vg0600826406 sf0600825407 6 826406 4.87E-15 NA
vg0605917767 sf0605916768 6 5917767 8.73E-15 1.51E-07
vg0605205203 sf0605204204 6 5205203 4.58E-14 8.81E-08
vg0604786256 sf0604785257 6 4786256 3.67E-13 4.14E-07
vg0234516971 sf0234511102 2 34516971 1.16E-06 2.06E-06
vg0605330241 sf0605329242 6 5330241 1.45E-06 6.92E-09
vg0605443272 sf0605442273 6 5443272 8.68E-06 1.51E-06
vg0605259601 sf0605258602 6 5259601 NA 3.14E-09
vg1218161219 sf1218132655 12 18161219 NA 4.69E-07
vg0122255774 sf0122254729 1 22255774 NA 1.81E-06
vg0127364959 sf0127363915 1 27364959 NA 2.00E-06
vg1219787869 sf1219759339 12 19787869 NA 2.48E-06
vg0605674708 sf0605673709 6 5674708 NA 2.59E-06
vg0713012318 sf0713011325 7 13012318 NA 2.92E-06
vg0604840256 sf0604839257 6 4840256 NA 3.01E-06
vg0106766299 sf0106765299 1 6766299 NA 4.44E-06
vg1219906683 sf1219878153 12 19906683 NA 4.78E-06