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Detailed information for vg0709199737:

Variant ID: vg0709199737 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9199737
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: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAACTAGCTAATACCCTTTTTCCGATGCCCTCTTAGTACTACGAGAAGTTACTCCTGACTGTCGAGTTCCTTACGACATCTCGTCTTACCATACAACC[G/A]
GGGCTAAATACGGAGGAGTACCCTCCCCAGGGAATTAACTTAGGACTATATACACGCGCGGAGGAATACCCATACTGAGCTGTCACCATCAGCGGACCAC

Reverse complement sequence

GTGGTCCGCTGATGGTGACAGCTCAGTATGGGTATTCCTCCGCGCGTGTATATAGTCCTAAGTTAATTCCCTGGGGAGGGTACTCCTCCGTATTTAGCCC[C/T]
GGTTGTATGGTAAGACGAGATGTCGTAAGGAACTCGACAGTCAGGAGTAACTTCTCGTAGTACTAAGAGGGCATCGGAAAAAGGGTATTAGCTAGTTAAT

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	85.50%	12.80%	1.71%	0.00%	NA
All Indica	2759	78.60%	18.80%	2.61%	0.00%	NA
All Japonica	1512	95.00%	4.60%	0.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	33.90%	58.70%	7.39%	0.00%	NA
Indica II	465	92.70%	6.50%	0.86%	0.00%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	80.50%	16.40%	3.05%	0.00%	NA
Temperate Japonica	767	97.90%	1.30%	0.78%	0.00%	NA
Tropical Japonica	504	89.10%	10.90%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.70%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg0709199737	G -> A	LOC_Os07g15830.1	upstream_gene_variant ; 3226.0bp to feature; MODIFIER	silent_mutation	Average:50.92; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N
vg0709199737	G -> A	LOC_Os07g15840.1	downstream_gene_variant ; 2612.0bp to feature; MODIFIER	silent_mutation	Average:50.92; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N
vg0709199737	G -> A	LOC_Os07g15830-LOC_Os07g15840	intergenic_region ; MODIFIER	silent_mutation	Average:50.92; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709199737	NA	8.38E-10	Heading_date	Ind_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
vg0709199737	NA	2.34E-06	mr1170	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
vg0709199737	NA	7.53E-06	mr1219	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
vg0709199737	NA	1.08E-06	mr1274	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
vg0709199737	NA	3.35E-06	mr1274_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
vg0709199737	NA	5.23E-06	mr1520_2	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
vg0709199737	8.55E-06	NA	mr1657_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