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Detailed information for vg1223326911:

Variant ID: vg1223326911 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23326911
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTTTGCGTATCTCTTCTCTCACTGTCACCATATTGATTACCCTAGTATATGATGACAGTGTTGCACTAACGCTGCTCGCTCCTACCTTGTATCGGCTC[G/A,C]
GAGCCGGTCTTCTTGCTCTTCTTCCACCTCTGTGTGCTTGTTGGCTCCAGCTTCAGGATGTGATCCTTGATGAACTCCAGCCTGTTCAGCAGCAGAGGAA

Reverse complement sequence

TTCCTCTGCTGCTGAACAGGCTGGAGTTCATCAAGGATCACATCCTGAAGCTGGAGCCAACAAGCACACAGAGGTGGAAGAAGAGCAAGAAGACCGGCTC[C/T,G]
GAGCCGATACAAGGTAGGAGCGAGCAGCGTTAGTGCAACACTGTCATCATATACTAGGGTAATCAATATGGTGACAGTGAGAGAAGAGATACGCAAAGGG

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	99.50%	0.50%	0.00%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	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	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	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	98.90%	1.10%	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
vg1223326911	G -> C	LOC_Os12g37970.1	5_prime_UTR_variant ; 68.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> C	LOC_Os12g37970.2	5_prime_UTR_variant ; 391.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> C	LOC_Os12g37970.3	5_prime_UTR_variant ; 391.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> C	LOC_Os12g37960.1	downstream_gene_variant ; 3158.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> C	LOC_Os12g37960.2	downstream_gene_variant ; 3158.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37970.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37970.2	5_prime_UTR_premature_start_codon_gain_variant ; LOW	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37970.3	5_prime_UTR_premature_start_codon_gain_variant ; LOW	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37970.1	5_prime_UTR_variant ; 68.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37970.2	5_prime_UTR_variant ; 391.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37970.3	5_prime_UTR_variant ; 391.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37960.1	downstream_gene_variant ; 3158.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N
vg1223326911	G -> A	LOC_Os12g37960.2	downstream_gene_variant ; 3158.0bp to feature; MODIFIER	N	Average:81.676; most accessible tissue: Minghui63 root, score: 88.381	N	N	N	N