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Detailed information for vg1126903582:

Variant ID: vg1126903582 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26903582
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, C: 0.13, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGGTGAAGACGCGGCGGGCGAGCTGCTCGCACTCCTTCTTGTTCTGCTGAGCCGTCATCGC[T/C]
GCCTGCATGATCATGGTGATGAGGCCGCCGATGTCCGCCCCGACCAGCTGCGCCACCGTTGCCGCTTGCCCCAGCCCGCCCCACAGCGCCATGCTACTCG

Reverse complement sequence

CGAGTAGCATGGCGCTGTGGGGCGGGCTGGGGCAAGCGGCAACGGTGGCGCAGCTGGTCGGGGCGGACATCGGCGGCCTCATCACCATGATCATGCAGGC[A/G]
GCGATGACGGCTCAGCAGAACAAGAAGGAGTGCGAGCAGCTCGCCCGCCGCGTCTTCACCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGA

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	17.20%	1.10%	0.19%	81.55%	NA
All Indica	2759	8.20%	0.90%	0.18%	90.65%	NA
All Japonica	1512	37.00%	0.10%	0.20%	62.70%	NA
Aus	269	4.80%	7.80%	0.00%	87.36%	NA
Indica I	595	13.80%	0.00%	0.17%	86.05%	NA
Indica II	465	3.70%	0.60%	0.22%	95.48%	NA
Indica III	913	2.60%	0.80%	0.11%	96.50%	NA
Indica Intermediate	786	13.20%	2.00%	0.25%	84.48%	NA
Temperate Japonica	767	64.50%	0.10%	0.26%	35.07%	NA
Tropical Japonica	504	3.00%	0.00%	0.00%	97.02%	NA
Japonica Intermediate	241	20.70%	0.00%	0.41%	78.84%	NA
VI/Aromatic	96	0.00%	0.00%	0.00%	100.00%	NA
Intermediate	90	14.40%	2.20%	1.11%	82.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126903582	T -> DEL	LOC_Os11g44460.1	N	frameshift_variant	Average:12.252; most accessible tissue: Callus, score: 33.952	N	N	N	N
vg1126903582	T -> C	LOC_Os11g44460.1	synonymous_variant ; p.Ala31Ala; LOW	synonymous_codon	Average:12.252; most accessible tissue: Callus, score: 33.952	N	N	N	N