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Detailed information for vg1202830380:

Variant ID: vg1202830380 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2830380
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

TGGATTAGCCATTCATTTTGGGCTGGTAACTGATACTGTCACATGCAATATTCTCATCAACTTGTACACAAAATGTGGCCAGAATGATTGTGCTCGTCGC[G/A]
TTTTTGATGCAATGTCTGTCAGAAGCATAATCTCTTGGAATACCATGATTGCTGGATATACTCATAATAGAGAGGATGTAGAAGCACTGAAGCTTTTTTC

Reverse complement sequence

GAAAAAAGCTTCAGTGCTTCTACATCCTCTCTATTATGAGTATATCCAGCAATCATGGTATTCCAAGAGATTATGCTTCTGACAGACATTGCATCAAAAA[C/T]
GCGACGAGCACAATCATTCTGGCCACATTTTGTGTACAAGTTGATGAGAATATTGCATGTGACAGTATCAGTTACCAGCCCAAAATGAATGGCTAATCCA

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	99.80%	0.10%	0.04%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	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	100.00%	0.00%	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
vg1202830380	G -> A	LOC_Os12g06070.1	missense_variant ; p.Val113Ile; MODERATE	N	Average:53.027; most accessible tissue: Zhenshan97 young leaf, score: 74.675	N	N	N	N