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 mr1549 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
vg0705477376	sf0705476377	7	5477376	1.58E-17	2.02E-15
vg0729061858	sf0729060866	7	29061858	3.71E-13	3.37E-10
vg0907387974	sf0907386974	9	7387974	3.65E-12	1.02E-07
vg1020589936	sf1020518415	10	20589936	5.99E-12	1.74E-07
vg0602753568	sf0602752569	6	2753568	6.93E-12	2.60E-09
vg0105586222	sf0105585222	1	5586222	9.62E-12	4.19E-07
vg0129128700	sf0129127655	1	29128700	3.12E-11	3.56E-07
vg0608132926	sf0608131927	6	8132926	3.61E-11	3.76E-08
vg1127976664	sf1127505050	11	27976664	1.62E-10	8.39E-07
vg0601369122	sf0601368123	6	1369122	1.89E-10	1.21E-06
vg0308843941	sf0308842879	3	8843941	1.94E-10	2.70E-07
vg0419005856	sf0418833898	4	19005856	2.96E-10	2.56E-07
vg0909518112	sf0909517111	9	9518112	4.98E-10	6.03E-06
vg1000480049	sf1000479025	10	480049	6.97E-10	6.32E-07
vg0402346536	sf0402342131	4	2346536	1.14E-09	1.44E-07
vg0423691960	sf0423506817	4	23691960	1.22E-09	2.73E-07
vg1011837474	sf1011766289	10	11837474	6.46E-09	8.25E-07
vg0412960952	sf0412951663	4	12960952	9.82E-09	1.04E-07
vg0406137915	sf0406133355	4	6137915	3.06E-08	1.05E-06
vg0500777407	sf0500777389	5	777407	5.58E-07	NA
vg0100966110	sf0100965110	1	966110	1.25E-06	1.39E-06
vg0404559892	sf0404555495	4	4559892	1.45E-06	1.09E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0705477376

sf0705476377

5477376

1.58E-17

2.02E-15

vg0729061858