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Detailed information for vg0620602332:

Variant ID: vg0620602332 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20602332
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CCAACCGTCATACCTACCGCTATATAAAGACATCACTCCCTCACTTCACTTACACACTTCCAAGCTTGAGCTGAATTATAAGAGGCTCTATTGTACTATA[T/C]
TGTATACTAGAATAGGAAGAGAGTAGAGTAGAAGAAGTCGGAAGAATTCCGGAGTTGTCAGTAATCTTCTCCTATTTCTTTTATTCTGTTTATTACTCTG

Reverse complement sequence

CAGAGTAATAAACAGAATAAAAGAAATAGGAGAAGATTACTGACAACTCCGGAATTCTTCCGACTTCTTCTACTCTACTCTCTTCCTATTCTAGTATACA[A/G]
TATAGTACAATAGAGCCTCTTATAATTCAGCTCAAGCTTGGAAGTGTGTAAGTGAAGTGAGGGAGTGATGTCTTTATATAGCGGTAGGTATGACGGTTGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.80%	23.90%	0.13%	1.25%	NA
All Indica	2759	72.10%	27.60%	0.18%	0.07%	NA
All Japonica	1512	93.70%	2.60%	0.07%	3.64%	NA
Aus	269	1.10%	98.90%	0.00%	0.00%	NA
Indica I	595	95.50%	4.50%	0.00%	0.00%	NA
Indica II	465	68.60%	31.40%	0.00%	0.00%	NA
Indica III	913	56.80%	42.70%	0.33%	0.11%	NA
Indica Intermediate	786	74.30%	25.30%	0.25%	0.13%	NA
Temperate Japonica	767	97.90%	1.20%	0.13%	0.78%	NA
Tropical Japonica	504	92.90%	5.80%	0.00%	1.39%	NA
Japonica Intermediate	241	81.70%	0.80%	0.00%	17.43%	NA
VI/Aromatic	96	58.30%	41.70%	0.00%	0.00%	NA
Intermediate	90	75.60%	22.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620602332	T -> C	LOC_Os06g35340.1	intron_variant ; MODIFIER	silent_mutation	Average:8.1; most accessible tissue: Minghui63 root, score: 10.708	N	N	N	N
vg0620602332	T -> DEL	N	N	silent_mutation	Average:8.1; most accessible tissue: Minghui63 root, score: 10.708	N	N	N	N