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Detailed information for vg1023166459:

Variant ID: vg1023166459 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 23166459
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTTTCAGGGTCGGAATATCTTTAATGTAACCCATCAAGGAGTAGCCACCTGAGATAATCATGTATTGTGAGAACAAAATTAACATTAAAATTATTATG[T/A]
ATTAAGTCTACATCACCGTTGGGCAGAAAATAGACATAACACATAAAGCCATAACTATAACATTGCAATTATCAACGTTGGTCAGAAAAATTACAACATC

Reverse complement sequence

GATGTTGTAATTTTTCTGACCAACGTTGATAATTGCAATGTTATAGTTATGGCTTTATGTGTTATGTCTATTTTCTGCCCAACGGTGATGTAGACTTAAT[A/T]
CATAATAATTTTAATGTTAATTTTGTTCTCACAATACATGATTATCTCAGGTGGCTACTCCTTGATGGGTTACATTAAAGATATTCCGACCCTGAAAGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.20%	0.10%	24.06%	24.69%	NA
All Indica	2759	63.40%	0.10%	13.74%	22.76%	NA
All Japonica	1512	26.90%	0.00%	42.20%	30.95%	NA
Aus	269	77.30%	0.00%	13.75%	8.92%	NA
Indica I	595	43.00%	0.00%	15.97%	41.01%	NA
Indica II	465	58.50%	0.00%	9.68%	31.83%	NA
Indica III	913	81.30%	0.30%	13.03%	5.37%	NA
Indica Intermediate	786	60.80%	0.10%	15.27%	23.79%	NA
Temperate Japonica	767	34.60%	0.00%	21.51%	43.94%	NA
Tropical Japonica	504	18.50%	0.00%	67.66%	13.89%	NA
Japonica Intermediate	241	19.90%	0.00%	54.77%	25.31%	NA
VI/Aromatic	96	20.80%	0.00%	52.08%	27.08%	NA
Intermediate	90	40.00%	0.00%	36.67%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1023166459	T -> A	LOC_Os10g42970.1	upstream_gene_variant ; 4044.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023166459	T -> A	LOC_Os10g42999.1	upstream_gene_variant ; 2994.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023166459	T -> A	LOC_Os10g42970.2	upstream_gene_variant ; 4044.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023166459	T -> A	LOC_Os10g42980.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023166459	T -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N