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Detailed information for vg0204058910:

Variant ID: vg0204058910 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4058910
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GATAGGCTTTCTCCAGGATGGACTGCATGTACTTCCCCTGCGCTTCGATCCTCATCTGCAGATGCTTCTGCACCTGCATGTCACCAATTAGAATTCATGC[C/G]
CAATTTTAATTTGTTGGACAATTCAAATTGTCCATATATATGCATGATGATGAGCTTTGCTAATTAGGGCATAATTATTAGCCTAATTAACTAATCTTGT

Reverse complement sequence

ACAAGATTAGTTAATTAGGCTAATAATTATGCCCTAATTAGCAAAGCTCATCATCATGCATATATATGGACAATTTGAATTGTCCAACAAATTAAAATTG[G/C]
GCATGAATTCTAATTGGTGACATGCAGGTGCAGAAGCATCTGCAGATGAGGATCGAAGCGCAGGGGAAGTACATGCAGTCCATCCTGGAGAAAGCCTATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.20%	1.80%	0.00%	0.00%	NA
All Indica	2759	97.00%	3.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	92.30%	7.70%	0.00%	0.00%	NA
Indica III	913	96.10%	3.90%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.40%	0.00%	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	98.90%	1.10%	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
vg0204058910	C -> G	LOC_Os02g07770.1	intron_variant ; MODIFIER	silent_mutation	Average:56.488; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N