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 mr1172 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
vg0827553670	sf0827550956	8	27553670	1.04E-09	8.81E-10
vg0810398690	sf0810397694	8	10398690	1.99E-09	3.75E-08
vg0208995135	sf0208995133	2	8995135	3.91E-09	4.11E-08
vg1219072772	sf1219044208	12	19072772	6.79E-09	1.67E-07
vg0907342967	sf0907341967	9	7342967	1.15E-08	9.82E-09
vg0305905056	sf0305904056	3	5905056	1.34E-08	1.29E-07
vg0222817936	sf0222812067	2	22817936	2.99E-08	1.05E-07
vg1215041722	sf1215039064	12	15041722	3.29E-08	1.47E-07
vg0320596106	sf0320594616	3	20596106	9.57E-08	1.38E-07
vg0433300288	sf0433115176	4	33300288	1.04E-07	9.35E-07
vg0141145804	sf0141144761	1	41145804	1.70E-07	7.88E-10
vg0909046504	sf0909045503	9	9046504	1.71E-07	4.88E-07
vg1211632465	sf1211629801	12	11632465	1.95E-07	1.76E-07
vg0223694286	sf0223688417	2	23694286	1.95E-07	3.99E-07
vg1201002233	sf1201001233	12	1002233	2.17E-07	2.64E-07
vg0204550038	sf0204550035	2	4550038	4.55E-07	4.37E-07
vg0912513638	sf0912512637	9	12513638	6.63E-07	9.18E-07
vg0300232324	sf0300231324	3	232324	1.09E-06	NA
vg1127763517	sf1127291903	11	27763517	1.70E-06	3.22E-07
vg0819068739	sf0819066026	8	19068739	2.54E-06	2.77E-07
vg0500017915	sf0500017915	5	17915	3.17E-06	7.37E-07
vg0907333374	sf0907332374	9	7333374	4.53E-06	3.76E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0827553670

sf0827550956

27553670

1.04E-09

8.81E-10

vg0810398690