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Detailed information for vg0805516079:

Variant ID: vg0805516079 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5516079
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.11, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTCTCTGTGTTTACAAAGTGCACCAACAGCACTCCTTACAAAAATTTCGACTAAACTCGAAACCCTAACTCAAAACTCAACTCAATTGCTCTCTAAAG[T/C]
GATACCGGGAAGCCTCACGGTCCCTCTCTATTTATACATGAGGTAGGCAGCCTAAAGCCACGAACCAAACTCATACTAGGAGTCCTAAACACCTTAGGAA

Reverse complement sequence

TTCCTAAGGTGTTTAGGACTCCTAGTATGAGTTTGGTTCGTGGCTTTAGGCTGCCTACCTCATGTATAAATAGAGAGGGACCGTGAGGCTTCCCGGTATC[A/G]
CTTTAGAGAGCAATTGAGTTGAGTTTTGAGTTAGGGTTTCGAGTTTAGTCGAAATTTTTGTAAGGAGTGCTGTTGGTGCACTTTGTAAACACAGAGAGAA

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	72.20%	0.10%	17.39%	10.24%	NA
All Indica	2759	64.70%	0.20%	24.14%	10.98%	NA
All Japonica	1512	91.90%	0.00%	1.52%	6.55%	NA
Aus	269	53.50%	0.40%	35.69%	10.41%	NA
Indica I	595	53.30%	0.30%	28.07%	18.32%	NA
Indica II	465	67.50%	0.20%	18.06%	14.19%	NA
Indica III	913	69.60%	0.10%	24.64%	5.70%	NA
Indica Intermediate	786	66.00%	0.10%	24.17%	9.67%	NA
Temperate Japonica	767	97.90%	0.00%	0.39%	1.69%	NA
Tropical Japonica	504	85.30%	0.00%	2.78%	11.90%	NA
Japonica Intermediate	241	86.70%	0.00%	2.49%	10.79%	NA
VI/Aromatic	96	30.20%	0.00%	25.00%	44.79%	NA
Intermediate	90	73.30%	0.00%	14.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805516079	T -> C	LOC_Os08g09510.1	upstream_gene_variant ; 499.0bp to feature; MODIFIER	silent_mutation	Average:23.234; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0805516079	T -> C	LOC_Os08g09520.1	downstream_gene_variant ; 3800.0bp to feature; MODIFIER	silent_mutation	Average:23.234; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0805516079	T -> C	LOC_Os08g09510-LOC_Os08g09520	intergenic_region ; MODIFIER	silent_mutation	Average:23.234; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0805516079	T -> DEL	N	N	silent_mutation	Average:23.234; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805516079	2.03E-06	4.39E-06	mr1268	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
vg0805516079	1.12E-06	9.68E-07	mr1268	Ind_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