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 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 ID	Variation ID V6	Chromosome	Position	LR P-value	LMM P-value
vg0605262883	sf0605261884	6	5262883	5.73E-43	3.32E-25
vg0605269202	sf0605268203	6	5269202	1.04E-42	2.20E-25
vg0600826406	sf0600825407	6	826406	4.62E-17	NA
vg0605306584	sf0605305585	6	5306584	4.02E-15	6.10E-15
vg0607699285	sf0607698286	6	7699285	7.74E-15	4.26E-07
vg0607614170	sf0607613171	6	7614170	9.04E-15	2.43E-07
vg0203428380	sf0203428378	2	3428380	3.95E-14	7.49E-06
vg0605311849	sf0605310850	6	5311849	3.42E-13	1.22E-20
vg0209219211	sf0209219209	2	9219211	7.37E-13	3.25E-07
vg0605739124	sf0605738125	6	5739124	1.04E-12	6.20E-07
vg0605173997	sf0605172998	6	5173997	1.44E-10	3.17E-07
vg0803676578	sf0803675581	8	3676578	6.53E-08	7.67E-07
vg0605330241	sf0605329242	6	5330241	1.75E-07	1.15E-08
vg0519823381	sf0519760857	5	19823381	1.98E-07	8.66E-06
vg0605312569	sf0605311570	6	5312569	2.48E-07	5.40E-09
vg1123438684	sf1122972554	11	23438684	4.34E-06	NA
vg0605259601	sf0605258602	6	5259601	NA	2.52E-09
vg0200067614	sf0200067614	2	67614	NA	9.61E-07
vg0605682284	sf0605681285	6	5682284	NA	1.27E-06
vg0604840256	sf0604839257	6	4840256	NA	1.47E-06
vg0127396120	sf0127395076	1	27396120	NA	1.79E-06
vg1008013432	sf1008030805	10	8013432	NA	3.39E-06
vg0621097248	sf0621096251	6	21097248	NA	4.98E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0605262883

sf0605261884

5262883

5.73E-43

3.32E-25

vg0605269202