Search for Variation information by Variation ID:

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

Detailed information for vg0205346587:

Variant ID: vg0205346587 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5346587
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGAAGCCGCAGTTATTGATGCAAAGGATTGGGCCCTCGGGCTGCTGGCAGCCAGCCTCCTTGTGTTCCATCGCAACTGTGATCTGTTCATCAAACAAA[C/T]
AATGCAAAACTCAATACCGAAATGCGTATAAGAAACAAATTTAAAATTTAACATACGGATAAATCAACTAGTGTCCAATTAAATCGGGCGGTAAGATAAT

Reverse complement sequence

ATTATCTTACCGCCCGATTTAATTGGACACTAGTTGATTTATCCGTATGTTAAATTTTAAATTTGTTTCTTATACGCATTTCGGTATTGAGTTTTGCATT[G/A]
TTTGTTTGATGAACAGATCACAGTTGCGATGGAACACAAGGAGGCTGGCTGCCAGCAGCCCGAGGGCCCAATCCTTTGCATCAATAACTGCGGCTTCTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.10%	0.11%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.40%	0.30%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.80%	0.50%	0.65%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0205346587	C -> T	LOC_Os02g10210.1	upstream_gene_variant ; 2133.0bp to feature; MODIFIER	N	Average:73.418; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0205346587	C -> T	LOC_Os02g10220.1	upstream_gene_variant ; 4880.0bp to feature; MODIFIER	N	Average:73.418; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0205346587	C -> T	LOC_Os02g10190.1	downstream_gene_variant ; 2069.0bp to feature; MODIFIER	N	Average:73.418; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0205346587	C -> T	LOC_Os02g10200.1	intron_variant ; MODIFIER	N	Average:73.418; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0205346587	C -> T	LOC_Os02g10200.2	intron_variant ; MODIFIER	N	Average:73.418; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N