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Detailed information for vg1100674728:

Variant ID: vg1100674728 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 674728
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.09, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GATGGTAACTGTAATATTTGCTATACAATGCTGGTGAACGACATTCCAGTAAAAGTTTTAAGTTTCGGTGTATATGGAGCAATGGAAATTTATATGGGCA[T/C]
AAATGAAAACAGTTCTGGAGACTCAGTTCTCACAGTAAGAGCTGAATTAATGGGCAAGAAGGTATATAAAATGACTGATCTTATAAATTATAATCTCCTT

Reverse complement sequence

AAGGAGATTATAATTTATAAGATCAGTCATTTTATATACCTTCTTGCCCATTAATTCAGCTCTTACTGTGAGAACTGAGTCTCCAGAACTGTTTTCATTT[A/G]
TGCCCATATAAATTTCCATTGCTCCATATACACCGAAACTTAAAACTTTTACTGGAATGTCGTTCACCAGCATTGTATAGCAAATATTACAGTTACCATC

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	72.50%	27.00%	0.38%	0.08%	NA
All Indica	2759	59.60%	39.70%	0.58%	0.14%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	39.80%	59.90%	0.37%	0.00%	NA
Indica I	595	64.50%	34.60%	0.84%	0.00%	NA
Indica II	465	76.60%	22.60%	0.65%	0.22%	NA
Indica III	913	48.00%	51.70%	0.11%	0.22%	NA
Indica Intermediate	786	59.30%	39.70%	0.89%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	1.11%	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
vg1100674728	T -> DEL	N	N	silent_mutation	Average:53.414; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg1100674728	T -> C	LOC_Os11g02310.1	3_prime_UTR_variant ; 1520.0bp to feature; MODIFIER	silent_mutation	Average:53.414; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg1100674728	T -> C	LOC_Os11g02320.1	upstream_gene_variant ; 3027.0bp to feature; MODIFIER	silent_mutation	Average:53.414; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg1100674728	T -> C	LOC_Os11g02320.2	upstream_gene_variant ; 3027.0bp to feature; MODIFIER	silent_mutation	Average:53.414; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg1100674728	T -> C	LOC_Os11g02320.3	upstream_gene_variant ; 3027.0bp to feature; MODIFIER	silent_mutation	Average:53.414; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N