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Detailed information for vg0128355011:

Variant ID: vg0128355011 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28355011
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTCATTACAGACAGTTTAGATGCAATTTGGACATAGTTCATTACAGACATAGACACATAGTTTAAATGCAACTTGCAAAATTAAATCAACAAGGTCCGGT[C/G]
GGTGTACATTCTATCCCTACCGGAGGGAGGCCGGAGCACGGAAAACATCCATAAAACTATTTAAAAAGGCTATGCTTATTTCAAACGCCTGTGAATATGA

Reverse complement sequence

TCATATTCACAGGCGTTTGAAATAAGCATAGCCTTTTTAAATAGTTTTATGGATGTTTTCCGTGCTCCGGCCTCCCTCCGGTAGGGATAGAATGTACACC[G/C]
ACCGGACCTTGTTGATTTAATTTTGCAAGTTGCATTTAAACTATGTGTCTATGTCTGTAATGAACTATGTCCAAATTGCATCTAAACTGTCTGTAATGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.90%	0.10%	0.00%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	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	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0128355011	C -> G	LOC_Os01g49320.1	3_prime_UTR_variant ; 129.0bp to feature; MODIFIER	N	Average:66.505; most accessible tissue: Callus, score: 94.082	N	N	N	N
vg0128355011	C -> G	LOC_Os01g49310.1	downstream_gene_variant ; 3961.0bp to feature; MODIFIER	N	Average:66.505; most accessible tissue: Callus, score: 94.082	N	N	N	N
vg0128355011	C -> G	LOC_Os01g49310.2	downstream_gene_variant ; 3977.0bp to feature; MODIFIER	N	Average:66.505; most accessible tissue: Callus, score: 94.082	N	N	N	N