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Detailed information for vg1100674823:

Variant ID: vg1100674823 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 674823
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.05, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCATAAATGAAAACAGTTCTGGAGACTCAGTTCTCACAGTAAGAGCTGAATTAATGGGCAAGAAGGTATATAAAATGACTGATCTTATAAATTATAAT[C/A]
TCCTTTGTCATTGGCATATCTAATCTTATCTCCTTAATTCCATATAAATTAATTAGTACCCCCTATCATTTTCTTATTTCAGGCATGCAGTTGGTTGGTG

Reverse complement sequence

CACCAACCAACTGCATGCCTGAAATAAGAAAATGATAGGGGGTACTAATTAATTTATATGGAATTAAGGAGATAAGATTAGATATGCCAATGACAAAGGA[G/T]
ATTATAATTTATAAGATCAGTCATTTTATATACCTTCTTGCCCATTAATTCAGCTCTTACTGTGAGAACTGAGTCTCCAGAACTGTTTTCATTTATGCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.90%	26.70%	0.17%	0.23%	NA
All Indica	2759	60.20%	39.20%	0.25%	0.36%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	39.80%	59.50%	0.37%	0.37%	NA
Indica I	595	66.40%	32.90%	0.67%	0.00%	NA
Indica II	465	76.60%	22.80%	0.22%	0.43%	NA
Indica III	913	47.80%	51.80%	0.00%	0.44%	NA
Indica Intermediate	786	60.20%	39.10%	0.25%	0.51%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1100674823	C -> A	LOC_Os11g02320.1	upstream_gene_variant ; 3122.0bp to feature; MODIFIER	silent_mutation	Average:59.463; most accessible tissue: Minghui63 panicle, score: 88.893	N	N	N	N
vg1100674823	C -> A	LOC_Os11g02320.2	upstream_gene_variant ; 3122.0bp to feature; MODIFIER	silent_mutation	Average:59.463; most accessible tissue: Minghui63 panicle, score: 88.893	N	N	N	N
vg1100674823	C -> A	LOC_Os11g02320.3	upstream_gene_variant ; 3122.0bp to feature; MODIFIER	silent_mutation	Average:59.463; most accessible tissue: Minghui63 panicle, score: 88.893	N	N	N	N
vg1100674823	C -> A	LOC_Os11g02310.1	intron_variant ; MODIFIER	silent_mutation	Average:59.463; most accessible tissue: Minghui63 panicle, score: 88.893	N	N	N	N
vg1100674823	C -> DEL	N	N	silent_mutation	Average:59.463; most accessible tissue: Minghui63 panicle, score: 88.893	N	N	N	N