Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0208199705:

Variant ID: vg0208199705 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8199705
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.03, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

GCTATAAAGGAGAATATTTTTGTTGGTTGCTGCCTATTAATTTCTGTATTCTCATGTTATGTTTAAACGTGGTGAAACACTGTTATTTGCACTATTTGAA[T/C]
GTCAGACATACATATCTCTTTATGGCCATCTGTTACTTAAAATATATGTTTTAGCTTCTGCTGTTTTGCTGTTGTGAAATGTGCTTGTCTTGAAAGTTCA

Reverse complement sequence

TGAACTTTCAAGACAAGCACATTTCACAACAGCAAAACAGCAGAAGCTAAAACATATATTTTAAGTAACAGATGGCCATAAAGAGATATGTATGTCTGAC[A/G]
TTCAAATAGTGCAAATAACAGTGTTTCACCACGTTTAAACATAACATGAGAATACAGAAATTAATAGGCAGCAACCAACAAAAATATTCTCCTTTATAGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.10%	26.50%	0.06%	0.28%	NA
All Indica	2759	72.70%	26.90%	0.07%	0.36%	NA
All Japonica	1512	69.80%	30.10%	0.00%	0.13%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	68.10%	31.60%	0.00%	0.34%	NA
Indica II	465	86.70%	13.10%	0.00%	0.22%	NA
Indica III	913	67.70%	32.00%	0.00%	0.33%	NA
Indica Intermediate	786	73.80%	25.40%	0.25%	0.51%	NA
Temperate Japonica	767	96.10%	3.90%	0.00%	0.00%	NA
Tropical Japonica	504	28.80%	71.00%	0.00%	0.20%	NA
Japonica Intermediate	241	71.80%	27.80%	0.00%	0.41%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	80.00%	17.80%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208199705	T -> DEL	N	N	silent_mutation	Average:57.439; most accessible tissue: Callus, score: 85.441	N	N	N	N
vg0208199705	T -> C	LOC_Os02g14780.1	3_prime_UTR_variant ; 154.0bp to feature; MODIFIER	silent_mutation	Average:57.439; most accessible tissue: Callus, score: 85.441	N	N	N	N
vg0208199705	T -> C	LOC_Os02g14780.2	intron_variant ; MODIFIER	silent_mutation	Average:57.439; most accessible tissue: Callus, score: 85.441	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208199705	NA	1.55E-07	mr1531	Jap_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
vg0208199705	NA	8.63E-06	mr1701	Ind_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
vg0208199705	8.96E-06	8.95E-06	mr1703	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
vg0208199705	NA	2.41E-07	mr1880	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
vg0208199705	NA	5.88E-08	mr1350_2	Jap_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
vg0208199705	NA	1.22E-06	mr1363_2	Jap_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