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Detailed information for vg1101998891:

Variant ID: vg1101998891 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1998891
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCGGGTGAAGAACCATGGTCAAGCGAGGCCTCCGACGATGTCCCCGACACATCGCACATGTCGGACGAACAATTTCAACAGTTCATCGACCAGTACTG[G/A]
GCAGAGCAAGGATTCAACATTTGGAGTTGGATTCGTGCTTCCAGGACGTCGTCAAGCTCCACGCCGGGGCCAACCAGGCGGACGGCGGCGTCATGGCAGG

Reverse complement sequence

CCTGCCATGACGCCGCCGTCCGCCTGGTTGGCCCCGGCGTGGAGCTTGACGACGTCCTGGAAGCACGAATCCAACTCCAAATGTTGAATCCTTGCTCTGC[C/T]
CAGTACTGGTCGATGAACTGTTGAAATTGTTCGTCCGACATGTGCGATGTGTCGGGGACATCGTCGGAGGCCTCGCTTGACCATGGTTCTTCACCCGCCA

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	99.20%	0.80%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	88.10%	11.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1101998891	G -> A	LOC_Os11g04690.1	stop_gained ; p.Trp34*; HIGH	stop_gained	Average:64.34; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N