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Detailed information for vg0705161092:

Variant ID: vg0705161092 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 5161092
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.09, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGTCAAATTAATCTATTTTTTTAAAAAATAACTAATACTTAATTAATCACGCATTAATAAACTGCTCAGTTTTCCGTACGGAGGGGATGGGTTCCCAA[T/C]
CCATCCTATGGAACACAACCTTAAGGCTGTGTTTGGAACTCCAAGTTCCCAACCCCTCTCCCTCGTTTTCCGCGCGCACGCTTTTCAAACTGCTAAACGG

Reverse complement sequence

CCGTTTAGCAGTTTGAAAAGCGTGCGCGCGGAAAACGAGGGAGAGGGGTTGGGAACTTGGAGTTCCAAACACAGCCTTAAGGTTGTGTTCCATAGGATGG[A/G]
TTGGGAACCCATCCCCTCCGTACGGAAAACTGAGCAGTTTATTAATGCGTGATTAATTAAGTATTAGTTATTTTTTAAAAAAATAGATTAATTTGACTTT

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	77.30%	10.30%	3.07%	9.35%	NA
All Indica	2759	71.40%	11.30%	3.70%	13.59%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.07%	NA
Aus	269	3.30%	58.00%	15.61%	23.05%	NA
Indica I	595	81.70%	6.90%	3.36%	8.07%	NA
Indica II	465	85.20%	7.10%	2.15%	5.59%	NA
Indica III	913	60.40%	15.60%	3.18%	20.92%	NA
Indica Intermediate	786	68.20%	12.30%	5.47%	13.99%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	13.30%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0705161092	T -> DEL	N	N	silent_mutation	Average:50.75; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0705161092	T -> C	LOC_Os07g09700.1	upstream_gene_variant ; 1185.0bp to feature; MODIFIER	silent_mutation	Average:50.75; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0705161092	T -> C	LOC_Os07g09710.1	downstream_gene_variant ; 3779.0bp to feature; MODIFIER	silent_mutation	Average:50.75; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0705161092	T -> C	LOC_Os07g09690-LOC_Os07g09700	intergenic_region ; MODIFIER	silent_mutation	Average:50.75; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0705161092	NA	8.53E-06	mr1063	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
vg0705161092	NA	1.24E-06	mr1177	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
vg0705161092	NA	3.27E-07	mr1177	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
vg0705161092	1.10E-06	1.10E-06	mr1260	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
vg0705161092	NA	1.26E-06	mr1261	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
vg0705161092	NA	6.26E-10	mr1730	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
vg0705161092	NA	1.23E-06	mr1803	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
vg0705161092	NA	4.26E-07	mr1063_2	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
vg0705161092	NA	4.86E-06	mr1511_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