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 mr1588 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
vg0204738000	sf0204737997	2	4738000	9.69E-12	2.90E-09
vg1221437756	sf1221404303	12	21437756	1.83E-11	1.23E-10
vg1102558247	sf1102554151	11	2558247	2.41E-10	7.75E-09
vg0920389319	sf0920388838	9	20389319	2.47E-10	2.01E-06
vg0505530545	sf0505530483	5	5530545	2.89E-10	1.54E-06
vg0502492380	sf0502492356	5	2492380	3.50E-10	9.70E-08
vg0515288716	sf0515231257	5	15288716	4.15E-10	7.36E-08
vg0507601642	sf0507601583	5	7601642	5.80E-10	3.54E-08
vg0512306429	sf0512306359	5	12306429	6.47E-10	8.05E-09
vg0920353731	sf0920353250	9	20353731	6.62E-10	1.70E-06
vg0228010095	sf0228004226	2	28010095	9.65E-10	1.19E-07
vg0705191402	sf0705190403	7	5191402	1.61E-09	1.36E-08
vg0220330169	sf0220324301	2	20330169	4.04E-09	2.82E-07
vg0802388554	sf0802387557	8	2388554	6.74E-09	1.03E-07
vg0201291485	sf0201291485	2	1291485	1.34E-08	3.94E-07
vg0708083717	sf0708082722	7	8083717	1.45E-08	1.23E-06
vg0419029854	sf0418857893	4	19029854	1.54E-08	1.33E-06
vg0705275989	sf0705274990	7	5275989	1.94E-08	4.53E-07
vg0418137389	sf0417965432	4	18137389	4.50E-08	7.00E-07
vg0526981407	sf0526918763	5	26981407	8.96E-08	6.06E-07
vg0917716816	sf0917715815	9	17716816	4.14E-06	NA
vg0233556355	sf0233550486	2	33556355	NA	9.86E-07

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg0204738000

sf0204737997

4738000

9.69E-12

2.90E-09

vg1221437756