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Detailed information for vg1213201263:

Variant ID: vg1213201263 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13201263
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.21, others allele: 0.00, population size: 136. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGAATCAACTCCACAAAGCTCAGCAAACAATCCTTTCAGCCAAACTGATTCTTTACATGTTTCAGCAATAGCCATGTATTCTGATTCAGTGGTAGACT[A/G]
GGCAACAACAGGCTGCAATGTTGCCTTCCAACTCACAGCACAACTACCAATGGTAAACACATAACCTGTGAGTGACCTTCTCTTATCCAAATCTGCAGCA

Reverse complement sequence

TGCTGCAGATTTGGATAAGAGAAGGTCACTCACAGGTTATGTGTTTACCATTGGTAGTTGTGCTGTGAGTTGGAAGGCAACATTGCAGCCTGTTGTTGCC[T/C]
AGTCTACCACTGAATCAGAATACATGGCTATTGCTGAAACATGTAAAGAATCAGTTTGGCTGAAAGGATTGTTTGCTGAGCTTTGTGGAGTTGATTCTTG

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	37.10%	0.50%	33.14%	29.28%	NA
All Indica	2759	17.90%	0.80%	49.29%	32.00%	NA
All Japonica	1512	60.70%	0.00%	7.87%	31.42%	NA
Aus	269	92.20%	0.00%	4.83%	2.97%	NA
Indica I	595	10.60%	0.50%	44.37%	44.54%	NA
Indica II	465	18.70%	0.20%	45.59%	35.48%	NA
Indica III	913	17.30%	1.10%	57.39%	24.21%	NA
Indica Intermediate	786	23.70%	1.00%	45.80%	29.52%	NA
Temperate Japonica	767	81.70%	0.00%	2.35%	15.91%	NA
Tropical Japonica	504	32.90%	0.00%	15.48%	51.59%	NA
Japonica Intermediate	241	51.90%	0.00%	9.54%	38.59%	NA
VI/Aromatic	96	46.90%	2.10%	47.92%	3.12%	NA
Intermediate	90	52.20%	0.00%	31.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213201263	A -> DEL	N	N	silent_mutation	Average:14.359; most accessible tissue: Callus, score: 26.559	N	N	N	N
vg1213201263	A -> G	LOC_Os12g23300.1	upstream_gene_variant ; 4078.0bp to feature; MODIFIER	silent_mutation	Average:14.359; most accessible tissue: Callus, score: 26.559	N	N	N	N
vg1213201263	A -> G	LOC_Os12g23310.1	downstream_gene_variant ; 1076.0bp to feature; MODIFIER	silent_mutation	Average:14.359; most accessible tissue: Callus, score: 26.559	N	N	N	N
vg1213201263	A -> G	LOC_Os12g23320.1	intron_variant ; MODIFIER	silent_mutation	Average:14.359; most accessible tissue: Callus, score: 26.559	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213201263	NA	2.79E-08	mr1030	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
vg1213201263	NA	7.15E-06	mr1037	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
vg1213201263	NA	6.94E-06	mr1155	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