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Detailed information for vg1105342974:

Variant ID: vg1105342974 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5342974
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.28, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTTACCATCCTTTAGGTCTCAACCTTCTGAATAATCAAAATGGTGGTGCATCAAGCATCTTCATTGTCATCCTCATTTCCCTCTTCGTAAGAGTCTTC[G/A]
TCTTCATCTTCATCATCATCGTCTTCGTAAGAGTCTTCATCTTCATCTTTATCATCATCGTCTTCGTAAGAGTCTTCATCATCATCTCCATCTCTATCTT

Reverse complement sequence

AAGATAGAGATGGAGATGATGATGAAGACTCTTACGAAGACGATGATGATAAAGATGAAGATGAAGACTCTTACGAAGACGATGATGATGAAGATGAAGA[C/T]
GAAGACTCTTACGAAGAGGGAAATGAGGATGACAATGAAGATGCTTGATGCACCACCATTTTGATTATTCAGAAGGTTGAGACCTAAAGGATGGTAACAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.20%	16.80%	0.04%	0.00%	NA
All Indica	2759	93.80%	6.10%	0.07%	0.00%	NA
All Japonica	1512	66.40%	33.60%	0.00%	0.00%	NA
Aus	269	90.70%	9.30%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	95.10%	4.70%	0.22%	0.00%	NA
Indica III	913	92.60%	7.40%	0.00%	0.00%	NA
Indica Intermediate	786	91.20%	8.80%	0.00%	0.00%	NA
Temperate Japonica	767	63.00%	37.00%	0.00%	0.00%	NA
Tropical Japonica	504	81.00%	19.00%	0.00%	0.00%	NA
Japonica Intermediate	241	46.90%	53.10%	0.00%	0.00%	NA
VI/Aromatic	96	21.90%	78.10%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg1105342974	G -> A	LOC_Os11g09970.1	synonymous_variant ; p.Asp477Asp; LOW	synonymous_codon	Average:52.958; most accessible tissue: Callus, score: 80.414	N	N	N	N