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Detailed information for vg0809666825:

Variant ID: vg0809666825 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9666825
Reference Allele: C	Alternative Allele: G,A
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, G: 0.19, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTACAGATGATGAAGCTAAGTTTGCCAGGTGGTCCTTGAATAAATAAAGAAGTTGAAACCTACCTGGAGGTTTTTTTTTTCTTTGAAACGATAGACGG[C/G,A]
AGGAAGGCTGCCGGTTATATTAGAAGGAATAAAAATGAGGGAAAAACAAAGATGGTCTTTACAGAGTAAGCATAAGACAAGAGGGTAGGGAAATTAGCTA

Reverse complement sequence

TAGCTAATTTCCCTACCCTCTTGTCTTATGCTTACTCTGTAAAGACCATCTTTGTTTTTCCCTCATTTTTATTCCTTCTAATATAACCGGCAGCCTTCCT[G/C,T]
CCGTCTATCGTTTCAAAGAAAAAAAAAACCTCCAGGTAGGTTTCAACTTCTTTATTTATTCAAGGACCACCTGGCAAACTTAGCTTCATCATCTGTAAGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.90%	28.50%	0.85%	10.79%	A: 0.02%
All Indica	2759	47.40%	46.40%	0.87%	5.36%	NA
All Japonica	1512	78.80%	2.10%	0.66%	18.39%	NA
Aus	269	97.00%	0.70%	0.00%	1.86%	A: 0.37%
Indica I	595	53.10%	46.60%	0.17%	0.17%	NA
Indica II	465	44.30%	41.30%	1.08%	13.33%	NA
Indica III	913	47.80%	44.90%	0.99%	6.35%	NA
Indica Intermediate	786	44.40%	51.00%	1.15%	3.44%	NA
Temperate Japonica	767	88.90%	2.00%	0.26%	8.87%	NA
Tropical Japonica	504	62.70%	1.60%	1.59%	34.13%	NA
Japonica Intermediate	241	80.50%	3.70%	0.00%	15.77%	NA
VI/Aromatic	96	16.70%	7.30%	6.25%	69.79%	NA
Intermediate	90	60.00%	26.70%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809666825	C -> G	LOC_Os08g15880.1	intron_variant ; MODIFIER	silent_mutation	Average:47.788; most accessible tissue: Callus, score: 76.111	N	N	N	N
vg0809666825	C -> A	LOC_Os08g15880.1	intron_variant ; MODIFIER	silent_mutation	Average:47.788; most accessible tissue: Callus, score: 76.111	N	N	N	N
vg0809666825	C -> DEL	N	N	silent_mutation	Average:47.788; most accessible tissue: Callus, score: 76.111	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809666825	1.13E-06	NA	mr1107_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251