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Detailed information for vg0818709501:

Variant ID: vg0818709501 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18709501
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, A: 0.14, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCTATTATGCAGCTATTGTTGGGCGTCTACCTCTTCACCGACTGGCCGCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTATACGGTTGGCCTATTATG[A/C]
AGCCGTTGTTGGGCGTCTACCTCTTCACTGACTGACCGCCTCGTCCGCTGCCGGCTGGTATTTCCGCCTGCACTGTTGGCCTATTATGCCGCCGTTGTTG

Reverse complement sequence

CAACAACGGCGGCATAATAGGCCAACAGTGCAGGCGGAAATACCAGCCGGCAGCGGACGAGGCGGTCAGTCAGTGAAGAGGTAGACGCCCAACAACGGCT[T/G]
CATAATAGGCCAACCGTATAGGCGGAAACACCAGTCGGCGGCGGACGAGGCGGCCAGTCGGTGAAGAGGTAGACGCCCAACAATAGCTGCATAATAGGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.10%	5.20%	4.59%	46.11%	NA
All Indica	2759	19.00%	1.90%	7.32%	71.84%	NA
All Japonica	1512	87.00%	3.00%	0.73%	9.26%	NA
Aus	269	37.90%	50.60%	0.74%	10.78%	NA
Indica I	595	22.00%	0.00%	2.18%	75.80%	NA
Indica II	465	14.20%	0.60%	4.95%	80.22%	NA
Indica III	913	14.20%	1.90%	11.83%	72.07%	NA
Indica Intermediate	786	24.90%	4.10%	7.38%	63.61%	NA
Temperate Japonica	767	98.70%	0.30%	0.13%	0.91%	NA
Tropical Japonica	504	69.40%	4.60%	1.98%	24.01%	NA
Japonica Intermediate	241	86.30%	8.70%	0.00%	4.98%	NA
VI/Aromatic	96	89.60%	8.30%	0.00%	2.08%	NA
Intermediate	90	63.30%	5.60%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818709501	A -> C	LOC_Os08g30410.1	downstream_gene_variant ; 1903.0bp to feature; MODIFIER	silent_mutation	Average:52.319; most accessible tissue: Zhenshan97 flag leaf, score: 76.925	N	N	N	N
vg0818709501	A -> C	LOC_Os08g30410-LOC_Os08g30420	intergenic_region ; MODIFIER	silent_mutation	Average:52.319; most accessible tissue: Zhenshan97 flag leaf, score: 76.925	N	N	N	N
vg0818709501	A -> DEL	N	N	silent_mutation	Average:52.319; most accessible tissue: Zhenshan97 flag leaf, score: 76.925	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818709501	3.42E-06	NA	mr1113_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0818709501	3.80E-08	5.08E-09	mr1113_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