Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0809615964:

Variant ID: vg0809615964 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9615964
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.05, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTGCCTCCAAAACTTTTAGATTTGTGTCAATCGGATTGCCTCGATATTTGTGCATGAATGGAAAAAAATTGCTAGAAAGAAATTTTCATACATGTCA[T/C]
GCGTAAGATCCTGGTGCTATCCAACCAAATTATAGTTGAATACAAGTTTCATATAAGTTATATTAAGTTATATCGTAGTTATAATACAGTTATAGTGCAG

Reverse complement sequence

CTGCACTATAACTGTATTATAACTACGATATAACTTAATATAACTTATATGAAACTTGTATTCAACTATAATTTGGTTGGATAGCACCAGGATCTTACGC[A/G]
TGACATGTATGAAAATTTCTTTCTAGCAATTTTTTTCCATTCATGCACAAATATCGAGGCAATCCGATTGACACAAATCTAAAAGTTTTGGAGGCAAAAA

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	46.10%	37.00%	4.66%	12.29%	NA
All Indica	2759	55.60%	23.30%	6.74%	14.43%	NA
All Japonica	1512	39.00%	55.50%	0.93%	4.56%	NA
Aus	269	2.60%	49.80%	6.69%	40.89%	NA
Indica I	595	59.50%	9.40%	5.21%	25.88%	NA
Indica II	465	58.10%	23.40%	5.81%	12.69%	NA
Indica III	913	49.30%	32.10%	7.67%	10.95%	NA
Indica Intermediate	786	58.40%	23.40%	7.38%	10.81%	NA
Temperate Japonica	767	67.30%	24.30%	0.78%	7.69%	NA
Tropical Japonica	504	2.20%	95.60%	0.99%	1.19%	NA
Japonica Intermediate	241	26.10%	71.00%	1.24%	1.66%	NA
VI/Aromatic	96	5.20%	93.80%	0.00%	1.04%	NA
Intermediate	90	47.80%	46.70%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809615964	T -> C	LOC_Os08g15830.1	intron_variant ; MODIFIER	silent_mutation	Average:47.1; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0809615964	T -> DEL	N	N	silent_mutation	Average:47.1; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809615964	NA	1.20E-09	Heading_date	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652