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Detailed information for vg1203971725:

Variant ID: vg1203971725 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3971725
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAGTATTTACAAGATCACCAAAATGGTGAAAGAGAGAGAGAGGGGAGAGAAAGAAGCTACTACTAAAACAATGAAAATGTTCTAGGCAGATAATCTCG[T/C]
GATATTTGTTGTTCCACATATCTTCCATAGCTTGATTTCGTCCTGTATATTGTCTAGCAGCCGCGGCAGGGATTTTTCCTGATTCTGAAATGCTCATTTG

Reverse complement sequence

CAAATGAGCATTTCAGAATCAGGAAAAATCCCTGCCGCGGCTGCTAGACAATATACAGGACGAAATCAAGCTATGGAAGATATGTGGAACAACAAATATC[A/G]
CGAGATTATCTGCCTAGAACATTTTCATTGTTTTAGTAGTAGCTTCTTTCTCTCCCCTCTCTCTCTCTTTCACCATTTTGGTGATCTTGTAAATACTTTT

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	97.90%	1.60%	0.47%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.70%	5.00%	1.39%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	87.60%	9.80%	2.61%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg1203971725	T -> C	LOC_Os12g07840.1	downstream_gene_variant ; 313.0bp to feature; MODIFIER	silent_mutation	Average:39.066; most accessible tissue: Callus, score: 68.253	N	N	N	N
vg1203971725	T -> C	LOC_Os12g07850.1	downstream_gene_variant ; 2232.0bp to feature; MODIFIER	silent_mutation	Average:39.066; most accessible tissue: Callus, score: 68.253	N	N	N	N
vg1203971725	T -> C	LOC_Os12g07840-LOC_Os12g07850	intergenic_region ; MODIFIER	silent_mutation	Average:39.066; most accessible tissue: Callus, score: 68.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203971725	1.11E-06	NA	Heading_date	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652