Search for Variation information by Variation ID:

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

Detailed information for vg1100674535:

Variant ID: vg1100674535 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 674535
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

AACTCTGTCCTCTGCCTAGAAGTGATGAACTAAATTTCAATGTGGACGCTTCGCTAGATCAGTAGCCCATGAAAGGTGGAATATTCAGCAAGTACCAAAG[C/A]
AAGTACCATGGTGAGGAGCTCGAGAAGCTGATCCAGATGGGCAAACACAAATAGGATTGCAGAATGCATTCTTTCTTGGCTTCATATTGCCAGATGGTAA

Reverse complement sequence

TTACCATCTGGCAATATGAAGCCAAGAAAGAATGCATTCTGCAATCCTATTTGTGTTTGCCCATCTGGATCAGCTTCTCGAGCTCCTCACCATGGTACTT[G/T]
CTTTGGTACTTGCTGAATATTCCACCTTTCATGGGCTACTGATCTAGCGAAGCGTCCACATTGAAATTTAGTTCATCACTTCTAGGCAGAGGACAGAGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	22.20%	0.23%	0.04%	NA
All Indica	2759	62.50%	37.00%	0.40%	0.07%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	66.60%	33.10%	0.34%	0.00%	NA
Indica II	465	77.40%	21.90%	0.65%	0.00%	NA
Indica III	913	50.70%	48.80%	0.22%	0.22%	NA
Indica Intermediate	786	64.20%	35.20%	0.51%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	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	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg1100674535	C -> A	LOC_Os11g02310.1	3_prime_UTR_variant ; 1327.0bp to feature; MODIFIER	silent_mutation	Average:55.34; most accessible tissue: Callus, score: 71.15	N	N	N	N
vg1100674535	C -> A	LOC_Os11g02320.1	upstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:55.34; most accessible tissue: Callus, score: 71.15	N	N	N	N
vg1100674535	C -> A	LOC_Os11g02320.2	upstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:55.34; most accessible tissue: Callus, score: 71.15	N	N	N	N
vg1100674535	C -> A	LOC_Os11g02320.3	upstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:55.34; most accessible tissue: Callus, score: 71.15	N	N	N	N
vg1100674535	C -> DEL	N	N	silent_mutation	Average:55.34; most accessible tissue: Callus, score: 71.15	N	N	N	N