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Detailed information for vg0827372513:

Variant ID: vg0827372513 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27372513
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCGTGGAGCCAGGACAAGCAGCGAAGCTCGTTTCGGCCGTTCCTCCTTAGCCTGCCTGCGAGGGAGTTTTTGCATCCGCTGGGCTTAGTTGTGGGACA[T/C]
GTACAGTCAACCAAACATCCTACAAGTTGCATCCGAGATGCGAGCCAAGTACGAGCCGGGCAACCAAACACGCCCCATGTAAACATCTTCGATCACGTTA

Reverse complement sequence

TAACGTGATCGAAGATGTTTACATGGGGCGTGTTTGGTTGCCCGGCTCGTACTTGGCTCGCATCTCGGATGCAACTTGTAGGATGTTTGGTTGACTGTAC[A/G]
TGTCCCACAACTAAGCCCAGCGGATGCAAAAACTCCCTCGCAGGCAGGCTAAGGAGGAACGGCCGAAACGAGCTTCGCTGCTTGTCCTGGCTCCACGCAT

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	36.10%	5.30%	1.95%	56.71%	NA
All Indica	2759	2.60%	7.10%	2.68%	87.68%	NA
All Japonica	1512	97.00%	0.30%	0.33%	2.38%	NA
Aus	269	15.20%	15.60%	4.46%	64.68%	NA
Indica I	595	2.50%	5.50%	3.19%	88.74%	NA
Indica II	465	1.70%	23.40%	1.94%	72.90%	NA
Indica III	913	2.10%	1.20%	1.75%	94.96%	NA
Indica Intermediate	786	3.70%	5.30%	3.82%	87.15%	NA
Temperate Japonica	767	96.70%	0.10%	0.52%	2.61%	NA
Tropical Japonica	504	97.60%	0.40%	0.20%	1.79%	NA
Japonica Intermediate	241	96.70%	0.40%	0.00%	2.90%	NA
VI/Aromatic	96	90.60%	2.10%	0.00%	7.29%	NA
Intermediate	90	42.20%	7.80%	1.11%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0827372513	T -> C	LOC_Os08g43300.1	upstream_gene_variant ; 1682.0bp to feature; MODIFIER	silent_mutation	Average:43.514; most accessible tissue: Callus, score: 97.645	N	N	N	N
vg0827372513	T -> C	LOC_Os08g43310.1	downstream_gene_variant ; 277.0bp to feature; MODIFIER	silent_mutation	Average:43.514; most accessible tissue: Callus, score: 97.645	N	N	N	N
vg0827372513	T -> C	LOC_Os08g43320.1	downstream_gene_variant ; 3502.0bp to feature; MODIFIER	silent_mutation	Average:43.514; most accessible tissue: Callus, score: 97.645	N	N	N	N
vg0827372513	T -> C	LOC_Os08g43300-LOC_Os08g43310	intergenic_region ; MODIFIER	silent_mutation	Average:43.514; most accessible tissue: Callus, score: 97.645	N	N	N	N
vg0827372513	T -> DEL	N	N	silent_mutation	Average:43.514; most accessible tissue: Callus, score: 97.645	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827372513	NA	9.45E-07	mr1887	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
vg0827372513	NA	1.45E-06	mr1887	Ind_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