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 mr1842 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
vg0331307645	sf0331300530	3	31307645	3.63E-33	3.48E-12
vg0331281109	sf0331273994	3	31281109	1.40E-32	1.62E-12
vg0724515913	sf0724514919	7	24515913	2.46E-27	5.07E-15
vg0723120973	sf0723119980	7	23120973	1.06E-25	1.95E-10
vg0517963882	sf0517903368	5	17963882	1.50E-24	4.48E-09
vg0725312603	sf0725311609	7	25312603	8.56E-22	2.18E-13
vg0235445101	sf0235439232	2	35445101	1.06E-20	3.18E-08
vg0404658487	sf0404653926	4	4658487	1.60E-19	5.86E-10
vg0808276376	sf0808275380	8	8276376	4.31E-18	3.22E-09
vg0400999452	sf0400995004	4	999452	1.30E-17	1.21E-07
vg1005832870	sf1005849408	10	5832870	3.56E-17	1.25E-09
vg0423394772	sf0423209627	4	23394772	4.81E-17	6.19E-08
vg0724502952	sf0724501958	7	24502952	NA	2.14E-11
vg0724642132	sf0724641138	7	24642132	NA	4.16E-10
vg0621137518	sf0621136521	6	21137518	NA	8.88E-10
vg0725325993	sf0725324999	7	25325993	NA	1.14E-09
vg0234359485	sf0234353616	2	34359485	NA	4.58E-08
vg0710962546	sf0710961552	7	10962546	NA	9.63E-08
vg0525416226	sf0525353647	5	25416226	NA	1.04E-07
vg0313459666	sf0313458384	3	13459666	NA	1.46E-07
vg1201219940	sf1201218940	12	1219940	NA	2.06E-07
vg0331256576	sf0331249461	3	31256576	NA	2.32E-07
vg0914828139	sf0914827138	9	14828139	NA	2.40E-07

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0331307645

sf0331300530

31307645

3.63E-33

3.48E-12

vg0331281109