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Detailed information for vg1223326890:

Variant ID: vg1223326890 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23326890
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCTCCTGCTCTGTCCATGGCCCTTTGCGTATCTCTTCTCTCACTGTCACCATATTGATTACCCTAGTATATGATGACAGTGTTGCACTAACGCTGCTC[G/A]
CTCCTACCTTGTATCGGCTCGGAGCCGGTCTTCTTGCTCTTCTTCCACCTCTGTGTGCTTGTTGGCTCCAGCTTCAGGATGTGATCCTTGATGAACTCCA

Reverse complement sequence

TGGAGTTCATCAAGGATCACATCCTGAAGCTGGAGCCAACAAGCACACAGAGGTGGAAGAAGAGCAAGAAGACCGGCTCCGAGCCGATACAAGGTAGGAG[C/T]
GAGCAGCGTTAGTGCAACACTGTCATCATATACTAGGGTAATCAATATGGTGACAGTGAGAGAAGAGATACGCAAAGGGCCATGGACAGAGCAGGAGGAC

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	99.40%	0.50%	0.04%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	98.20%	1.70%	0.13%	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	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	94.80%	4.80%	0.40%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	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
vg1223326890	G -> A	LOC_Os12g37970.1	5_prime_UTR_variant ; 47.0bp to feature; MODIFIER	silent_mutation	Average:80.66; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg1223326890	G -> A	LOC_Os12g37970.2	5_prime_UTR_variant ; 370.0bp to feature; MODIFIER	silent_mutation	Average:80.66; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg1223326890	G -> A	LOC_Os12g37970.3	5_prime_UTR_variant ; 370.0bp to feature; MODIFIER	silent_mutation	Average:80.66; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg1223326890	G -> A	LOC_Os12g37960.1	downstream_gene_variant ; 3137.0bp to feature; MODIFIER	silent_mutation	Average:80.66; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N
vg1223326890	G -> A	LOC_Os12g37960.2	downstream_gene_variant ; 3137.0bp to feature; MODIFIER	silent_mutation	Average:80.66; most accessible tissue: Minghui63 root, score: 87.595	N	N	N	N