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Detailed information for vg0505530545:

Variant ID: vg0505530545 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5530545
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGTAAAATAAATAATTGCATAAATTTTTTGATTAATTAAGACGAATGGTCAAAACATATATCAATGTCAACAATGTTATGCATTAAAAACCGGAGGGAG[C/T]
ACTTATTATCCTAAAATCATTCGTTACAAAGGACGATATGGGACCTAGGGGTCATTGTCTTGATACCAGTAAATATGAATGCATCCCTACATGGTCGTCT

Reverse complement sequence

AGACGACCATGTAGGGATGCATTCATATTTACTGGTATCAAGACAATGACCCCTAGGTCCCATATCGTCCTTTGTAACGAATGATTTTAGGATAATAAGT[G/A]
CTCCCTCCGGTTTTTAATGCATAACATTGTTGACATTGATATATGTTTTGACCATTCGTCTTAATTAATCAAAAAATTTATGCAATTATTTATTTTACTA

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	88.70%	8.10%	3.22%	0.00%	NA
All Indica	2759	97.00%	0.80%	2.28%	0.00%	NA
All Japonica	1512	71.90%	22.70%	5.42%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	91.10%	1.80%	7.06%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.70%	0.10%	0.22%	0.00%	NA
Indica Intermediate	786	96.70%	1.10%	2.16%	0.00%	NA
Temperate Japonica	767	53.70%	38.20%	8.08%	0.00%	NA
Tropical Japonica	504	96.40%	3.60%	0.00%	0.00%	NA
Japonica Intermediate	241	78.40%	13.30%	8.30%	0.00%	NA
VI/Aromatic	96	93.80%	5.20%	1.04%	0.00%	NA
Intermediate	90	81.10%	12.20%	6.67%	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
vg0505530545	C -> T	LOC_Os05g09736.1	upstream_gene_variant ; 4195.0bp to feature; MODIFIER	silent_mutation	Average:46.703; most accessible tissue: Zhenshan97 flower, score: 66.02	N	N	N	N
vg0505530545	C -> T	LOC_Os05g09740.1	downstream_gene_variant ; 3983.0bp to feature; MODIFIER	silent_mutation	Average:46.703; most accessible tissue: Zhenshan97 flower, score: 66.02	N	N	N	N
vg0505530545	C -> T	LOC_Os05g09736-LOC_Os05g09740	intergenic_region ; MODIFIER	silent_mutation	Average:46.703; most accessible tissue: Zhenshan97 flower, score: 66.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505530545	NA	1.04E-10	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
vg0505530545	NA	6.80E-07	mr1791	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
vg0505530545	NA	5.14E-09	mr1002_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
vg0505530545	NA	1.26E-06	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
vg0505530545	2.11E-06	NA	mr1588_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
vg0505530545	1.54E-06	2.89E-10	mr1588_2	Jap_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
vg0505530545	NA	2.16E-10	mr1829_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
vg0505530545	NA	7.45E-06	mr1829_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