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Detailed information for vg0816931318:

Variant ID: vg0816931318 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16931318
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGGCCGCAAGACTTGTGTGATCGTGTAAGGTCCTTCCCATTTTGGTGAGAGTTTGTTTCGCCCTGCTTGGGTTTGAACTCGTTGGAGGACATAGTCGC[T/C]
GATCGAAAGTATGCGTGCTCGGATGCGCTTCTCGTGATAACGGCGGAGGGACTGTTGATAGCTGGATGCTCAGACGGCAACTCGCTCACGATGCTCCTCG

Reverse complement sequence

CGAGGAGCATCGTGAGCGAGTTGCCGTCTGAGCATCCAGCTATCAACAGTCCCTCCGCCGTTATCACGAGAAGCGCATCCGAGCACGCATACTTTCGATC[A/G]
GCGACTATGTCCTCCAACGAGTTCAAACCCAAGCAGGGCGAAACAAACTCTCACCAAAATGGGAAGGACCTTACACGATCACACAAGTCTTGCGGCCAGG

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	35.80%	28.70%	23.83%	11.70%	NA
All Indica	2759	24.50%	37.00%	23.74%	14.75%	NA
All Japonica	1512	62.40%	6.30%	22.35%	8.99%	NA
Aus	269	8.60%	77.00%	13.75%	0.74%	NA
Indica I	595	15.10%	60.50%	13.78%	10.59%	NA
Indica II	465	20.60%	12.90%	38.06%	28.39%	NA
Indica III	913	30.30%	36.50%	23.22%	9.97%	NA
Indica Intermediate	786	27.00%	34.20%	23.41%	15.39%	NA
Temperate Japonica	767	79.90%	0.40%	8.47%	11.21%	NA
Tropical Japonica	504	32.10%	17.10%	46.83%	3.97%	NA
Japonica Intermediate	241	69.70%	2.50%	15.35%	12.45%	NA
VI/Aromatic	96	19.80%	8.30%	69.79%	2.08%	NA
Intermediate	90	36.70%	24.40%	32.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816931318	T -> C	LOC_Os08g27790.1	downstream_gene_variant ; 795.0bp to feature; MODIFIER	silent_mutation	Average:30.126; most accessible tissue: Zhenshan97 flag leaf, score: 69.147	N	N	N	N
vg0816931318	T -> C	LOC_Os08g27800.1	downstream_gene_variant ; 304.0bp to feature; MODIFIER	silent_mutation	Average:30.126; most accessible tissue: Zhenshan97 flag leaf, score: 69.147	N	N	N	N
vg0816931318	T -> C	LOC_Os08g27790-LOC_Os08g27800	intergenic_region ; MODIFIER	silent_mutation	Average:30.126; most accessible tissue: Zhenshan97 flag leaf, score: 69.147	N	N	N	N
vg0816931318	T -> DEL	N	N	silent_mutation	Average:30.126; most accessible tissue: Zhenshan97 flag leaf, score: 69.147	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816931318	NA	6.29E-06	mr1159_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
vg0816931318	NA	7.84E-06	mr1373_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
vg0816931318	4.29E-06	4.29E-06	mr1412_2	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
vg0816931318	9.22E-06	4.94E-07	mr1747_2	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
vg0816931318	2.80E-06	NA	mr1764_2	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
vg0816931318	9.30E-06	NA	mr1812_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
vg0816931318	2.87E-06	NA	mr1816_2	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
vg0816931318	NA	9.20E-07	mr1831_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
vg0816931318	4.25E-06	NA	mr1833_2	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
vg0816931318	6.78E-06	2.07E-08	mr1840_2	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
vg0816931318	7.18E-06	7.22E-06	mr1847_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
vg0816931318	5.19E-06	3.11E-08	mr1856_2	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