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Detailed information for vg0629061927:

Variant ID: vg0629061927 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29061927
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTCCATTTAAGCCCCTTGGTCTAGAAGAACTCTCTCCGTCAAATGCCCTGTTTCTCATAACCTCAGCCCTCTTATTATGAATAGAATTAGCTGAAGAA[C/T]
AGCCAGAAGGCAAAACATCAGATATTGATGTGCAGCCAAGGTTTTTTAGAGTACGTCTCTGTACCCCAGGGCCAGCAGCATTTGATGATTTCACACCATT

Reverse complement sequence

AATGGTGTGAAATCATCAAATGCTGCTGGCCCTGGGGTACAGAGACGTACTCTAAAAAACCTTGGCTGCACATCAATATCTGATGTTTTGCCTTCTGGCT[G/A]
TTCTTCAGCTAATTCTATTCATAATAAGAGGGCTGAGGTTATGAGAAACAGGGCATTTGACGGAGAGAGTTCTTCTAGACCAAGGGGCTTAAATGGACAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.20%	0.00%	0.00%	NA
All Indica	2759	99.70%	0.30%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	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	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
vg0629061927	C -> T	LOC_Os06g48040.1	missense_variant ; p.Cys239Tyr; MODERATE	N	Average:75.666; most accessible tissue: Minghui63 flower, score: 85.386	N	N	N	N