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Detailed information for vg1200761690:

Variant ID: vg1200761690 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 761690
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTATAATTGAATAATTTTTCATAATATACTTGTCTTGGGTTAAAAATGTTACTACTTTTTTTCTACAAAATCAGTCAAACTTATAATAGTTCGACTTT[G/A]
ACTAAAGTCAAAACGTCTTATAACCTGAAACGGAGTAATAGTTAATAAAAACTTTTACAAGTTAAAATAGATTATCATATGTGAGATATATCTCACTTCA

Reverse complement sequence

TGAAGTGAGATATATCTCACATATGATAATCTATTTTAACTTGTAAAAGTTTTTATTAACTATTACTCCGTTTCAGGTTATAAGACGTTTTGACTTTAGT[C/T]
AAAGTCGAACTATTATAAGTTTGACTGATTTTGTAGAAAAAAAGTAGTAACATTTTTAACCCAAGACAAGTATATTATGAAAAATTATTCAATTATAGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.00%	2.90%	0.11%	0.00%	NA
All Indica	2759	95.00%	4.90%	0.14%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	86.40%	13.40%	0.17%	0.00%	NA
Indica II	465	96.10%	3.90%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	4.70%	0.25%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1200761690	G -> A	LOC_Os12g02350.1	upstream_gene_variant ; 2101.0bp to feature; MODIFIER	silent_mutation	Average:32.129; most accessible tissue: Zhenshan97 flower, score: 75.428	N	N	N	N
vg1200761690	G -> A	LOC_Os12g02370.2	downstream_gene_variant ; 4744.0bp to feature; MODIFIER	silent_mutation	Average:32.129; most accessible tissue: Zhenshan97 flower, score: 75.428	N	N	N	N
vg1200761690	G -> A	LOC_Os12g02370.4	downstream_gene_variant ; 4744.0bp to feature; MODIFIER	silent_mutation	Average:32.129; most accessible tissue: Zhenshan97 flower, score: 75.428	N	N	N	N
vg1200761690	G -> A	LOC_Os12g02340.1	intron_variant ; MODIFIER	silent_mutation	Average:32.129; most accessible tissue: Zhenshan97 flower, score: 75.428	N	N	N	N
vg1200761690	G -> A	LOC_Os12g02340.2	intron_variant ; MODIFIER	silent_mutation	Average:32.129; most accessible tissue: Zhenshan97 flower, score: 75.428	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200761690	NA	7.47E-07	mr1216	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