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Detailed information for vg1223326871:

Variant ID: vg1223326871 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23326871
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTGCATACCAGTTGCAGGTCCTCCTGCTCTGTCCATGGCCCTTTGCGTATCTCTTCTCTCACTGTCACCATATTGATTACCCTAGTATATGATGACAG[T/C]
GTTGCACTAACGCTGCTCGCTCCTACCTTGTATCGGCTCGGAGCCGGTCTTCTTGCTCTTCTTCCACCTCTGTGTGCTTGTTGGCTCCAGCTTCAGGATG

Reverse complement sequence

CATCCTGAAGCTGGAGCCAACAAGCACACAGAGGTGGAAGAAGAGCAAGAAGACCGGCTCCGAGCCGATACAAGGTAGGAGCGAGCAGCGTTAGTGCAAC[A/G]
CTGTCATCATATACTAGGGTAATCAATATGGTGACAGTGAGAGAAGAGATACGCAAAGGGCCATGGACAGAGCAGGAGGACCTGCAACTGGTATGCACTG

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	99.80%	0.10%	0.08%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.30%	0.50%	0.26%	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	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	2.50%	1.24%	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
vg1223326871	T -> C	LOC_Os12g37970.1	5_prime_UTR_variant ; 28.0bp to feature; MODIFIER	silent_mutation	Average:80.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N
vg1223326871	T -> C	LOC_Os12g37970.2	5_prime_UTR_variant ; 351.0bp to feature; MODIFIER	silent_mutation	Average:80.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N
vg1223326871	T -> C	LOC_Os12g37970.3	5_prime_UTR_variant ; 351.0bp to feature; MODIFIER	silent_mutation	Average:80.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N
vg1223326871	T -> C	LOC_Os12g37960.1	downstream_gene_variant ; 3118.0bp to feature; MODIFIER	silent_mutation	Average:80.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N
vg1223326871	T -> C	LOC_Os12g37960.2	downstream_gene_variant ; 3118.0bp to feature; MODIFIER	silent_mutation	Average:80.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N