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 mr1227 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
vg0816447256	sf0816444542	8	16447256	9.72E-12	1.97E-08
vg0419327742	sf0419155780	4	19327742	1.28E-11	3.23E-09
vg0704902745	sf0704901746	7	4902745	1.08E-10	1.48E-07
vg0128344213	sf0128343169	1	28344213	1.52E-09	2.28E-07
vg0800964801	sf0800963803	8	964801	1.83E-09	7.20E-08
vg0809442889	sf0809441893	8	9442889	2.49E-09	8.25E-07
vg0805104035	sf0805103038	8	5104035	5.41E-09	6.37E-07
vg0521749530	sf0521686972	5	21749530	8.43E-09	2.34E-06
vg0610494475	sf0610493476	6	10494475	1.51E-08	3.05E-06
vg0124676757	sf0124675713	1	24676757	1.55E-08	4.76E-08
vg0228803071	sf0228797202	2	28803071	2.05E-08	1.50E-06
vg0224317158	sf0224311289	2	24317158	2.56E-08	2.18E-07
vg0517761858	sf0517701499	5	17761858	5.35E-08	2.09E-06
vg0403670419	sf0403666025	4	3670419	5.78E-08	3.27E-07
vg1219077433	sf1219048869	12	19077433	7.01E-08	1.93E-06
vg0217023868	sf0217017998	2	17023868	9.88E-08	1.18E-06
vg0819104807	sf0819102094	8	19104807	6.30E-07	2.02E-06
vg0719041786	sf0719040793	7	19041786	9.39E-07	4.40E-07
vg0428739520	sf0428554372	4	28739520	1.23E-06	2.27E-06
vg0405200386	sf0405195827	4	5200386	2.65E-06	NA
vg0527282068	sf0527219424	5	27282068	2.67E-06	1.08E-06
vg1017100634	sf1017029406	10	17100634	NA	5.07E-07

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0816447256

sf0816444542

16447256

9.72E-12

1.97E-08

vg0419327742