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Detailed information for vg0331481556:

Variant ID: vg0331481556 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31481556
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGCCAACCGGACTGTGATACTTACACCATGATGATAAAAATGTTCTGTGAGAATGACAAGGTAGAGATGGCACTCAAGGTATGGAAGTATATGAGGTT[G/A]
AAGCAGTTTCTCCCAAGCATGCACACGTTCTCTGTACTGATCAATGGGTTGTGTGACAAGCGTGAGGTTAGTCAAGCTTGTGTTTTGCTTGAAGATATGA

Reverse complement sequence

TCATATCTTCAAGCAAAACACAAGCTTGACTAACCTCACGCTTGTCACACAACCCATTGATCAGTACAGAGAACGTGTGCATGCTTGGGAGAAACTGCTT[C/T]
AACCTCATATACTTCCATACCTTGAGTGCCATCTCTACCTTGTCATTCTCACAGAACATTTTTATCATCATGGTGTAAGTATCACAGTCCGGTTGGCAAC

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	92.80%	7.20%	0.00%	0.00%	NA
All Indica	2759	97.80%	2.20%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	94.90%	5.10%	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	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0331481556	G -> A	LOC_Os03g55340.1	synonymous_variant ; p.Leu406Leu; LOW	synonymous_codon	Average:64.388; most accessible tissue: Callus, score: 87.437	N	N	N	N