RiceVarMap2

Phenotype and GWAS Information:

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 mr1868 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 ID	Variation ID V6	Chromosome	Position	LR P-value	LMM P-value
vg0222724011	sf0222718142	2	22724011	3.17E-59	9.82E-37
vg0525141137	sf0525078558	5	25141137	1.08E-34	NA
vg0906971590	sf0906970590	9	6971590	5.43E-34	NA
vg0500664660	sf0500664660	5	664660	7.97E-33	NA
vg0702447377	sf0702446378	7	2447377	9.64E-33	NA
vg0222693356	sf0222687487	2	22693356	2.53E-26	2.39E-07
vg0222741692	sf0222735823	2	22741692	1.06E-25	4.98E-17
vg0222567385	sf0222561516	2	22567385	NA	5.40E-15
vg0224832469	sf0224826600	2	24832469	NA	9.91E-09
vg0222729853	sf0222723984	2	22729853	NA	1.87E-08
vg0224019660	sf0224013791	2	24019660	NA	2.04E-07
vg0222847562	sf0222841693	2	22847562	NA	2.39E-07
vg0610463015	sf0610462016	6	10463015	NA	3.37E-07
vg0223638265	sf0223632396	2	23638265	NA	4.48E-07
vg0222799084	sf0222793215	2	22799084	NA	1.84E-06
vg0525239875	sf0525177296	5	25239875	NA	2.15E-06
vg0224293593	sf0224287724	2	24293593	NA	2.16E-06
vg0222730936	sf0222725067	2	22730936	NA	2.26E-06
vg0220759001	sf0220753133	2	20759001	NA	2.38E-06
vg0224821353	sf0224815484	2	24821353	NA	3.10E-06
vg0224856480	sf0224850611	2	24856480	NA	3.77E-06
vg0724693961	sf0724692967	7	24693961	NA	3.89E-06
vg1012841072	sf1012769887	10	12841072	NA	4.37E-06
vg0224820512	sf0224814643	2	24820512	NA	4.45E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0222724011

sf0222718142

22724011

3.17E-59

9.82E-37

vg0525141137