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Detailed information for vg0210667883:

Variant ID: vg0210667883 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10667883
Reference Allele: C	Alternative Allele: T
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCATGCATGCTACCATGTTGACACATATTGAATATATCAGCTATAACTCTTTAATTTGTTTAAATTAATGGCATTTCTTATTGTTCTTCATTTTGTCG[C/T]
GGATAAGAGATTGATGTAGTATATATGCCATTTTATGGTGCGTGGTCAATATTAATTGGAGCCAGGAATAAGATCTTAACCAAGGCAGGTGATAGAGAAG

Reverse complement sequence

CTTCTCTATCACCTGCCTTGGTTAAGATCTTATTCCTGGCTCCAATTAATATTGACCACGCACCATAAAATGGCATATATACTACATCAATCTCTTATCC[G/A]
CGACAAAATGAAGAACAATAAGAAATGCCATTAATTTAAACAAATTAAAGAGTTATAGCTGATATATTCAATATGTGTCAACATGGTAGCATGCATGCAT

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	88.00%	8.00%	3.91%	0.00%	NA
All Indica	2759	96.80%	1.60%	1.59%	0.00%	NA
All Japonica	1512	69.90%	21.60%	8.53%	0.00%	NA
Aus	269	97.00%	0.70%	2.23%	0.00%	NA
Indica I	595	91.10%	4.70%	4.20%	0.00%	NA
Indica II	465	97.20%	0.60%	2.15%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.60%	1.30%	1.15%	0.00%	NA
Temperate Japonica	767	52.80%	36.50%	10.69%	0.00%	NA
Tropical Japonica	504	91.90%	2.80%	5.36%	0.00%	NA
Japonica Intermediate	241	78.40%	13.30%	8.30%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	86.70%	7.80%	5.56%	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
vg0210667883	C -> T	LOC_Os02g18340.1	downstream_gene_variant ; 4812.0bp to feature; MODIFIER	silent_mutation	Average:46.031; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg0210667883	C -> T	LOC_Os02g18340-LOC_Os02g18350	intergenic_region ; MODIFIER	silent_mutation	Average:46.031; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210667883	NA	3.29E-14	Heading_date	All	Not	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
vg0210667883	NA	1.79E-12	Heading_date	Jap_All	Not	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
vg0210667883	NA	1.45E-08	mr1163	Jap_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
vg0210667883	NA	1.61E-09	mr1757	Jap_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
vg0210667883	NA	4.23E-12	mr1011_2	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
vg0210667883	NA	2.73E-08	mr1011_2	Jap_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
vg0210667883	5.81E-08	NA	mr1549_2	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
vg0210667883	NA	5.03E-09	mr1549_2	Jap_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
vg0210667883	NA	2.35E-06	mr1757_2	Jap_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