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 mr1855 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
vg0217093461	sf0217087591	2	17093461	1.49E-146	2.21E-58
vg0217102196	sf0217096326	2	17102196	2.51E-140	4.07E-62
vg1015182556	sf1015111324	10	15182556	3.25E-57	6.82E-09
vg1220336324	sf1220307766	12	20336324	9.48E-55	3.06E-10
vg1226816492	sf1226782891	12	26816492	7.06E-47	2.98E-08
vg0107836036	sf0107835036	1	7836036	6.36E-41	2.50E-07
vg1103133067	sf1103128970	11	3133067	1.40E-31	1.98E-07
vg1216728800	sf1216722754	12	16728800	4.84E-31	1.04E-09
vg0217344818	sf0217338948	2	17344818	4.40E-25	1.51E-15
vg1005364284	sf1005380821	10	5364284	6.44E-25	1.23E-07
vg0216163461	sf0216157591	2	16163461	7.50E-25	2.08E-11
vg0216754099	sf0216748229	2	16754099	2.38E-23	4.27E-08
vg0217937456	sf0217931587	2	17937456	5.09E-23	3.53E-12
vg0217144860	sf0217138990	2	17144860	1.09E-22	2.00E-33
vg0217474288	sf0217468418	2	17474288	1.86E-19	1.40E-09
vg0213253468	sf0213253464	2	13253468	3.68E-19	6.01E-10
vg0512377294	sf0512377224	5	12377294	8.43E-19	3.47E-07
vg0215779498	sf0215773628	2	15779498	1.48E-18	2.26E-08
vg0217345118	sf0217339248	2	17345118	NA	1.58E-11
vg0217919982	sf0217914113	2	17919982	NA	1.02E-08
vg0417133455	sf0416961496	4	17133455	NA	4.02E-07
vg0432620685	sf0432435575	4	32620685	NA	6.21E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0217093461

sf0217087591

17093461

1.49E-146

2.21E-58

vg0217102196