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Detailed information for vg0128477203:

Variant ID: vg0128477203 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28477203
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GAATGTATCTGGCCGGGGCTGACGTGCCAACTCCAGGAGTTCCCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGATG[G/A]
GGCGAGGCGTGTGTCAGGCCGCCTGTTGCCCCCTAACCCGCGATCTGACCGGTCTGTGACCGGTCACACACTGCGACCGATCACGGACCGGATAAGCATG

Reverse complement sequence

CATGCTTATCCGGTCCGTGATCGGTCGCAGTGTGTGACCGGTCACAGACCGGTCAGATCGCGGGTTAGGGGGCAACAGGCGGCCTGACACACGCCTCGCC[C/T]
CATCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGGGAACTCCTGGAGTTGGCACGTCAGCCCCGGCCAGATACATTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.50%	0.70%	1.95%	66.84%	NA
All Indica	2759	2.20%	0.00%	2.43%	95.32%	NA
All Japonica	1512	87.60%	2.10%	0.26%	10.05%	NA
Aus	269	1.10%	0.00%	4.09%	94.80%	NA
Indica I	595	2.70%	0.00%	5.88%	91.43%	NA
Indica II	465	3.90%	0.20%	0.22%	95.70%	NA
Indica III	913	0.70%	0.00%	1.10%	98.25%	NA
Indica Intermediate	786	2.70%	0.00%	2.67%	94.66%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	66.90%	6.20%	0.40%	26.59%	NA
Japonica Intermediate	241	92.90%	0.40%	0.83%	5.81%	NA
VI/Aromatic	96	14.60%	0.00%	5.21%	80.21%	NA
Intermediate	90	42.20%	2.20%	5.56%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0128477203	G -> A	LOC_Os01g49500.1	stop_gained ; p.Trp97*; HIGH	stop_gained	Average:5.724; most accessible tissue: Callus, score: 15.328	N	N	N	N
vg0128477203	G -> DEL	LOC_Os01g49500.1	N	frameshift_variant	Average:5.724; most accessible tissue: Callus, score: 15.328	N	N	N	N