Search for Variation information by Variation ID:

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

Detailed information for vg0141809107:

Variant ID: vg0141809107 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41809107
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCTGGTGAGTCCTCATACAGTCCTCGGACCCGGTGTACTCCCAGGCACCCCGGGCGCGCCGCTGGAGTGGCGCGATCCGGCGACGAAGATAGTCGCC[G/A]
TACACCATGGCCCCTGTGAGCCCCAGGGATCGCAGGCCCGCCAGGCGGTCGAGGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCCGCCAGCTGG

Reverse complement sequence

CCAGCTGGCGGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCCTCGACCGCCTGGCGGGCCTGCGATCCCTGGGGCTCACAGGGGCCATGGTGTA[C/T]
GGCGACTATCTTCGTCGCCGGATCGCGCCACTCCAGCGGCGCGCCCGGGGTGCCTGGGAGTACACCGGGTCCGAGGACTGTATGAGGACTCACCAGGGAG

Allele Frequencies:

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	5.10%	2.70%	10.54%	81.61%	NA
All Indica	2759	0.40%	0.30%	0.69%	98.55%	NA
All Japonica	1512	14.60%	7.20%	24.54%	53.70%	NA
Aus	269	0.70%	3.00%	31.23%	65.06%	NA
Indica I	595	0.30%	1.20%	1.01%	97.48%	NA
Indica II	465	0.60%	0.00%	0.00%	99.35%	NA
Indica III	913	0.10%	0.00%	0.11%	99.78%	NA
Indica Intermediate	786	0.80%	0.30%	1.53%	97.46%	NA
Temperate Japonica	767	25.40%	13.00%	39.77%	21.77%	NA
Tropical Japonica	504	3.20%	0.60%	5.36%	90.87%	NA
Japonica Intermediate	241	3.70%	2.50%	16.18%	77.59%	NA
VI/Aromatic	96	1.00%	1.00%	12.50%	85.42%	NA
Intermediate	90	8.90%	1.10%	13.33%	76.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141809107	G -> A	LOC_Os01g72070.1	synonymous_variant ; p.Tyr155Tyr; LOW	synonymous_codon	Average:5.016; most accessible tissue: Callus, score: 10.504	N	N	N	N
vg0141809107	G -> DEL	LOC_Os01g72070.1	N	frameshift_variant	Average:5.016; most accessible tissue: Callus, score: 10.504	N	N	N	N