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 mr1112 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
vg0610559165	sf0610558166	6	10559165	2.51E-60	4.09E-36
vg0610412338	sf0610411339	6	10412338	1.02E-29	2.33E-20
vg0610683293	sf0610682294	6	10683293	3.54E-27	1.66E-23
vg0617319066	sf0617318069	6	17319066	2.92E-18	4.99E-06
vg0611292337	sf0611291338	6	11292337	3.13E-17	8.29E-12
vg0610147528	sf0610146529	6	10147528	2.89E-16	1.15E-10
vg0610846322	sf0610845323	6	10846322	9.59E-15	6.50E-10
vg0610154955	sf0610153956	6	10154955	1.39E-14	1.92E-09
vg0611139955	sf0611138956	6	11139955	1.45E-14	1.15E-09
vg0610442142	sf0610441143	6	10442142	2.99E-12	2.06E-12
vg0617595576	sf0617594579	6	17595576	5.43E-12	4.34E-07
vg0611643367	sf0611642368	6	11643367	2.34E-11	7.99E-12
vg0613012821	sf0613011822	6	13012821	2.78E-11	3.03E-07
vg0610488879	sf0610487880	6	10488879	5.71E-11	3.92E-07
vg0610211069	sf0610210070	6	10211069	9.07E-10	9.84E-09
vg0611651819	sf0611650820	6	11651819	9.16E-10	1.09E-08
vg0613809145	sf0613808146	6	13809145	1.16E-09	3.91E-07
vg0610752419	sf0610751420	6	10752419	2.87E-09	6.58E-07
vg0610611540	sf0610610541	6	10611540	2.67E-08	1.79E-07
vg0610127588	sf0610126589	6	10127588	NA	2.09E-12
vg0618988041	sf0618987044	6	18988041	NA	1.77E-07
vg0610957761	sf0610956762	6	10957761	NA	4.45E-07

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0610559165

sf0610558166

10559165

2.51E-60

4.09E-36

vg0610412338