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 mr1585 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
vg0325696417	sf0325694435	3	25696417	2.66E-42	1.16E-33
vg1121970827	sf1121504698	11	21970827	6.19E-18	5.70E-10
vg1004789770	sf1004806307	10	4789770	5.18E-16	3.93E-11
vg0400345487	sf0400344487	4	345487	1.48E-14	5.97E-08
vg1207091088	sf1207089978	12	7091088	7.92E-14	2.47E-07
vg0315495912	sf0315494559	3	15495912	8.68E-14	4.04E-09
vg1012888857	sf1012817672	10	12888857	1.14E-13	3.94E-12
vg1002067295	sf1002066272	10	2067295	2.63E-13	1.94E-08
vg0609841754	sf0609840755	6	9841754	4.77E-13	1.55E-08
vg1005598877	sf1005615415	10	5598877	1.09E-12	7.70E-08
vg0317037478	sf0317036352	3	17037478	2.44E-12	1.99E-08
vg1010626225	sf1010555046	10	10626225	2.65E-12	1.39E-08
vg0416712669	sf0416540713	4	16712669	3.86E-12	4.36E-08
vg0219605813	sf0219599945	2	19605813	4.24E-12	2.75E-08
vg0304415129	sf0304414131	3	4415129	1.88E-11	9.35E-08
vg0322820996	sf0322819485	3	22820996	2.06E-11	1.06E-09
vg0327423375	sf0327416428	3	27423375	4.18E-11	2.47E-08
vg1202269648	sf1202268648	12	2269648	8.57E-11	1.20E-07
vg1015794218	sf1015722988	10	15794218	2.79E-10	5.86E-08
vg1022604309	sf1022532783	10	22604309	3.58E-08	1.73E-07
vg0907841289	sf0907840289	9	7841289	NA	4.12E-08
vg0907836758	sf0907835758	9	7836758	NA	6.08E-08

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0325696417

sf0325694435

25696417

2.66E-42

1.16E-33

vg1121970827