RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0222673217:

Variant ID: vg0222673217 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22673217
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGTCACAATATTAGGGGTGAAAACGGATCGGATAATATCTAATCCGATCCGCTCCGAATCTGTCCGAAACGAGGATATGGTATGGGCTTCTAGAAATCC[G/A]
GCGGATGCGGATGCGGATAGTATGAGACGGACGCGGAAATGGTATCTCTAAAATCCGGCGGATGCGGATTATCCGATATTTTTGTCGGATAATCCAAAAT

Reverse complement sequence

ATTTTGGATTATCCGACAAAAATATCGGATAATCCGCATCCGCCGGATTTTAGAGATACCATTTCCGCGTCCGTCTCATACTATCCGCATCCGCATCCGC[C/T]
GGATTTCTAGAAGCCCATACCATATCCTCGTTTCGGACAGATTCGGAGCGGATCGGATTAGATATTATCCGATCCGTTTTCACCCCTAATATTGTGACAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.20%	4.50%	0.00%	1.29%	NA
All Indica	2759	95.60%	2.20%	0.00%	2.17%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	48.30%	51.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	93.00%	1.90%	0.00%	5.15%	NA
Indica Intermediate	786	94.50%	3.80%	0.00%	1.65%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	0.00%	1.11%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222673217	G -> A	LOC_Os02g37580.1	upstream_gene_variant ; 1738.0bp to feature; MODIFIER	silent_mutation	Average:62.896; most accessible tissue: Zhenshan97 panicle, score: 85.254	N	N	N	N
vg0222673217	G -> A	LOC_Os02g37580-LOC_Os02g37590	intergenic_region ; MODIFIER	silent_mutation	Average:62.896; most accessible tissue: Zhenshan97 panicle, score: 85.254	N	N	N	N
vg0222673217	G -> DEL	N	N	silent_mutation	Average:62.896; most accessible tissue: Zhenshan97 panicle, score: 85.254	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222673217	1.38E-07	1.43E-22	mr1095	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	2.38E-11	3.62E-36	mr1098	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	1.17E-09	1.50E-30	mr1099	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	7.51E-12	8.37E-35	mr1101	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	3.01E-17	1.38E-36	mr1113	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	7.73E-22	1.59E-46	mr1114	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	1.03E-21	6.22E-39	mr1116	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	5.97E-19	3.12E-46	mr1117	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	5.54E-19	4.00E-27	mr1118	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0222673217	4.29E-18	1.05E-41	mr1119	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251

Showing 1 to 10 of 46 entries

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Search for Variation information by Variation ID:

Detailed information for vg0222673217:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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