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Detailed information for vg0709235829:

Variant ID: vg0709235829 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9235829
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GATATCTCTCCATAGGAGGGGCAAATCCCATCTTGATTATTCATATCCCACTACATGTTTCATAGCATACCCAAAAACTACTTTTATAGCTACCCATTTA[C/T]
GGAGTAGCATTTAGCAGTCCCTAAGTAAGCTACTACATATGTTGAGAACCATGATAATCTCAGGTCTAAGGATTCAACACCAACACTAAATGAGATCACT

Reverse complement sequence

AGTGATCTCATTTAGTGTTGGTGTTGAATCCTTAGACCTGAGATTATCATGGTTCTCAACATATGTAGTAGCTTACTTAGGGACTGCTAAATGCTACTCC[G/A]
TAAATGGGTAGCTATAAAAGTAGTTTTTGGGTATGCTATGAAACATGTAGTGGGATATGAATAATCAAGATGGGATTTGCCCCTCCTATGGAGAGATATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.80%	9.10%	4.06%	0.00%	NA
All Indica	2759	80.10%	13.00%	6.92%	0.00%	NA
All Japonica	1512	96.20%	3.80%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	36.30%	40.80%	22.86%	0.00%	NA
Indica II	465	93.80%	3.40%	2.80%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	82.40%	12.20%	5.34%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	89.30%	10.70%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	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
vg0709235829	C -> T	LOC_Os07g15890.1	upstream_gene_variant ; 143.0bp to feature; MODIFIER	silent_mutation	Average:30.004; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N
vg0709235829	C -> T	LOC_Os07g15890-LOC_Os07g15910	intergenic_region ; MODIFIER	silent_mutation	Average:30.004; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709235829	6.46E-06	NA	mr1682_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
vg0709235829	NA	6.14E-06	mr1682_2	Ind_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