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Detailed information for vg0101920426:

Variant ID: vg0101920426 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1920426
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

CCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCA[T/C]
GACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCATCTCCATCCGTGTACTTTTGT

Reverse complement sequence

ACAAAAGTACACGGATGGAGATGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTC[A/G]
TGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGG

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	88.80%	0.70%	2.24%	8.19%	NA
All Indica	2759	91.40%	1.10%	3.48%	4.06%	NA
All Japonica	1512	81.50%	0.00%	0.53%	17.99%	NA
Aus	269	97.40%	2.20%	0.00%	0.37%	NA
Indica I	595	84.00%	0.20%	3.70%	12.10%	NA
Indica II	465	89.70%	1.50%	6.02%	2.80%	NA
Indica III	913	96.30%	1.00%	2.63%	0.11%	NA
Indica Intermediate	786	92.40%	1.50%	2.80%	3.31%	NA
Temperate Japonica	767	88.80%	0.00%	0.65%	10.56%	NA
Tropical Japonica	504	78.60%	0.00%	0.40%	21.03%	NA
Japonica Intermediate	241	64.30%	0.00%	0.41%	35.27%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	2.22%	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
vg0101920426	T -> DEL	LOC_Os01g04310.1	N	frameshift_variant	Average:7.607; most accessible tissue: Callus, score: 11.73	N	N	N	N
vg0101920426	T -> C	LOC_Os01g04310.1	synonymous_variant ; p.Ser2Ser; LOW	synonymous_codon	Average:7.607; most accessible tissue: Callus, score: 11.73	N	N	N	N