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 mr1133 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
vg1125494245	sf1125028084	11	25494245	8.13E-41	7.96E-20
vg1125501745	sf1125035584	11	25501745	4.41E-40	2.52E-20
vg0713261979	sf0713260986	7	13261979	3.14E-30	5.29E-10
vg0514949605	sf0514892148	5	14949605	6.70E-30	1.08E-06
vg0713262120	sf0713261127	7	13262120	5.99E-28	4.66E-11
vg1123627766	sf1123161636	11	23627766	1.64E-24	3.73E-08
vg0809299619	sf0809298623	8	9299619	1.68E-23	NA
vg1125145452	sf1124679292	11	25145452	3.78E-21	1.70E-08
vg0612544928	sf0612543929	6	12544928	7.60E-21	3.43E-09
vg0809374950	sf0809373954	8	9374950	9.25E-19	NA
vg1125312631	sf1124846471	11	25312631	1.08E-17	9.41E-07
vg1127762582	sf1127290968	11	27762582	NA	2.23E-09
vg1125146479	sf1124680319	11	25146479	NA	2.11E-08
vg1127582186	sf1127110573	11	27582186	NA	6.63E-08
vg1125628490	sf1125162329	11	25628490	NA	2.24E-07
vg1126328140	sf1125856553	11	26328140	NA	5.74E-07
vg1125555062	sf1125088901	11	25555062	NA	6.18E-07
vg1125264481	sf1124798321	11	25264481	NA	8.12E-07
vg1125162869	sf1124696709	11	25162869	NA	1.19E-06
vg1124305955	sf1123839825	11	24305955	NA	1.97E-06
vg1125935268	sf1125463682	11	25935268	NA	2.26E-06
vg1000703179	sf1000702155	10	703179	NA	2.74E-06
vg1124078708	sf1123612578	11	24078708	NA	4.59E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg1125494245

sf1125028084

25494245

8.13E-41

7.96E-20

vg1125501745