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Detailed information for vg0702845695:

Variant ID: vg0702845695 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2845695
Reference Allele: A	Alternative Allele: G,T
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

GTAAAAAAACATACGGGATTATTCTTCCGTTGCCTTGTATCTGTCATCGCTGGATTGGAGTGTTTCGATTTGTCCATTGTGTGTAATATTCAGATATATA[A/G,T]
CTAATATATTTAAATTTTATATGAAACAATCAAGCTGAATGGAAACCAAATACCTACAGCAAGAAACATCTATGGAACGTGATGCACAAGCGCCGGTGGT

Reverse complement sequence

ACCACCGGCGCTTGTGCATCACGTTCCATAGATGTTTCTTGCTGTAGGTATTTGGTTTCCATTCAGCTTGATTGTTTCATATAAAATTTAAATATATTAG[T/C,A]
TATATATCTGAATATTACACACAATGGACAAATCGAAACACTCCAATCCAGCGATGACAGATACAAGGCAACGGAAGAATAATCCCGTATGTTTTTTTAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.20%	23.20%	0.53%	0.00%	T: 0.02%
All Indica	2759	60.40%	38.80%	0.83%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	T: 0.07%
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	71.10%	28.10%	0.84%	0.00%	NA
Indica II	465	41.70%	57.40%	0.86%	0.00%	NA
Indica III	913	59.90%	39.40%	0.66%	0.00%	NA
Indica Intermediate	786	63.90%	35.10%	1.02%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.00%	T: 0.20%
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702845695	A -> G	LOC_Os07g05910.1	upstream_gene_variant ; 2752.0bp to feature; MODIFIER	silent_mutation	Average:37.972; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0702845695	A -> G	LOC_Os07g05900-LOC_Os07g05910	intergenic_region ; MODIFIER	silent_mutation	Average:37.972; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0702845695	A -> T	LOC_Os07g05910.1	upstream_gene_variant ; 2752.0bp to feature; MODIFIER	silent_mutation	Average:37.972; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0702845695	A -> T	LOC_Os07g05900-LOC_Os07g05910	intergenic_region ; MODIFIER	silent_mutation	Average:37.972; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702845695	NA	9.15E-08	mr1060_2	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
vg0702845695	NA	2.92E-07	mr1158_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
vg0702845695	NA	3.46E-06	mr1359_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
vg0702845695	NA	1.14E-06	mr1576_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
vg0702845695	NA	9.28E-06	mr1971_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