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Detailed information for vg1203872985:

Variant ID: vg1203872985 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3872985
Reference Allele: A	Alternative Allele: G,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATAATCTTGAGAGGTCATAATCAGGAAAAAAACCGTCACCCACACATTGACAACACCAAAACACATACCCGAGAGAAGGCTAACACCAAACCGACTATC[A/G,C]
CTAGACCAACAAAGTACCTACAACCGAGATCGCTCAAAACCTATCCCTAACACTGACACCAAATCTCACCGGAAGATGTTTTTGGTATAATGGTTCTTTT

Reverse complement sequence

AAAAGAACCATTATACCAAAAACATCTTCCGGTGAGATTTGGTGTCAGTGTTAGGGATAGGTTTTGAGCGATCTCGGTTGTAGGTACTTTGTTGGTCTAG[T/C,G]
GATAGTCGGTTTGGTGTTAGCCTTCTCTCGGGTATGTGTTTTGGTGTTGTCAATGTGTGGGTGACGGTTTTTTTCCTGATTATGACCTCTCAAGATTATA

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	18.60%	12.10%	10.73%	58.59%	NA
All Indica	2759	1.90%	0.30%	6.92%	90.87%	NA
All Japonica	1512	46.40%	36.20%	12.43%	4.96%	NA
Aus	269	6.70%	0.40%	39.78%	53.16%	NA
Indica I	595	0.70%	0.20%	5.55%	93.61%	NA
Indica II	465	1.50%	0.40%	9.68%	88.39%	NA
Indica III	913	1.50%	0.40%	5.59%	92.44%	NA
Indica Intermediate	786	3.40%	0.30%	7.89%	88.42%	NA
Temperate Japonica	767	28.40%	60.50%	9.65%	1.43%	NA
Tropical Japonica	504	71.20%	4.00%	16.27%	8.53%	NA
Japonica Intermediate	241	51.50%	26.60%	13.28%	8.71%	NA
VI/Aromatic	96	77.10%	0.00%	8.33%	14.58%	NA
Intermediate	90	35.60%	16.70%	14.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1203872985	A -> C	LOC_Os12g07710.1	upstream_gene_variant ; 1426.0bp to feature; MODIFIER	N	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> C	LOC_Os12g07720.1	upstream_gene_variant ; 365.0bp to feature; MODIFIER	N	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> C	LOC_Os12g07700.1	downstream_gene_variant ; 3129.0bp to feature; MODIFIER	N	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> C	LOC_Os12g07710-LOC_Os12g07720	intergenic_region ; MODIFIER	N	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> DEL	N	N	silent_mutation	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> G	LOC_Os12g07710.1	upstream_gene_variant ; 1426.0bp to feature; MODIFIER	silent_mutation	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> G	LOC_Os12g07720.1	upstream_gene_variant ; 365.0bp to feature; MODIFIER	silent_mutation	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> G	LOC_Os12g07700.1	downstream_gene_variant ; 3129.0bp to feature; MODIFIER	silent_mutation	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N
vg1203872985	A -> G	LOC_Os12g07710-LOC_Os12g07720	intergenic_region ; MODIFIER	silent_mutation	Average:59.423; most accessible tissue: Callus, score: 92.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203872985	NA	1.11E-09	mr1575	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
vg1203872985	4.83E-06	NA	mr1974	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