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Detailed information for vg0141809446:

Variant ID: vg0141809446 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41809446
Reference Allele: T	Alternative Allele: C
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: 81. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGGAAGTAGCAGCCACCAACCACCGACGGCGGCGACACCGACTGTACGGTGAAGAACCACCGGAACAGCCGAAGGGATGGGCGCACCCCGATGAACAT[T/C]
TCGCACAGGTGCGCGAAGATGGCCAATGTCATTACCGCGTTGGGGGTGAGGTGCGCCATCTGGAGATCGTAAAACTCCAGAACATCCATGAAGAAAGAAG

Reverse complement sequence

CTTCTTTCTTCATGGATGTTCTGGAGTTTTACGATCTCCAGATGGCGCACCTCACCCCCAACGCGGTAATGACATTGGCCATCTTCGCGCACCTGTGCGA[A/G]
ATGTTCATCGGGGTGCGCCCATCCCTTCGGCTGTTCCGGTGGTTCTTCACCGTACAGTCGGTGTCGCCGCCGTCGGTGGTTGGTGGCTGCTACTTCCAAC

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	12.70%	4.70%	0.19%	82.33%	NA
All Indica	2759	1.10%	0.40%	0.18%	98.33%	NA
All Japonica	1512	30.00%	13.40%	0.20%	56.35%	NA
Aus	269	34.20%	0.70%	0.00%	65.06%	NA
Indica I	595	2.20%	0.30%	0.34%	97.14%	NA
Indica II	465	0.20%	0.40%	0.00%	99.35%	NA
Indica III	913	0.10%	0.00%	0.11%	99.78%	NA
Indica Intermediate	786	1.90%	0.90%	0.25%	96.95%	NA
Temperate Japonica	767	51.40%	25.30%	0.13%	23.21%	NA
Tropical Japonica	504	3.60%	0.60%	0.00%	95.83%	NA
Japonica Intermediate	241	17.40%	2.50%	0.83%	79.25%	NA
VI/Aromatic	96	13.50%	0.00%	0.00%	86.46%	NA
Intermediate	90	14.40%	8.90%	1.11%	75.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141809446	T -> DEL	LOC_Os01g72070.1	N	frameshift_variant	Average:5.092; most accessible tissue: Callus, score: 11.339	N	N	N	N
vg0141809446	T -> C	LOC_Os01g72070.1	synonymous_variant ; p.Glu42Glu; LOW	synonymous_codon	Average:5.092; most accessible tissue: Callus, score: 11.339	N	N	N	N