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Detailed information for vg0701295150:

Variant ID: vg0701295150 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1295150
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, A: 0.08, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTACTTGTACTCGCTGAATGCCCGTACTTTGCATCAGAATTAAAAAAAAAAGAGAACCACCATATACTCTAAAGCCCCAAAAATCATAATAAAAAA[T/A]
ATTCCATTGCAATCAATATTTCATCATTTTGTTTTACATATATATCAAGCTACATGTTGTTTTTTTACATGTAATATGTATCTGTACATGTCTATGTCTA

Reverse complement sequence

TAGACATAGACATGTACAGATACATATTACATGTAAAAAAACAACATGTAGCTTGATATATATGTAAAACAAAATGATGAAATATTGATTGCAATGGAAT[A/T]
TTTTTTATTATGATTTTTGGGGCTTTAGAGTATATGGTGGTTCTCTTTTTTTTTTAATTCTGATGCAAAGTACGGGCATTCAGCGAGTACAAGTAAATTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.60%	8.80%	0.61%	0.00%	NA
All Indica	2759	86.30%	12.60%	1.05%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	77.30%	22.70%	0.00%	0.00%	NA
Indica I	595	69.20%	27.40%	3.36%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	88.00%	11.80%	0.22%	0.00%	NA
Indica Intermediate	786	91.20%	7.90%	0.89%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0701295150	T -> A	LOC_Os07g03250.1	upstream_gene_variant ; 4448.0bp to feature; MODIFIER	silent_mutation	Average:38.006; most accessible tissue: Zhenshan97 flower, score: 61.872	N	N	N	N
vg0701295150	T -> A	LOC_Os07g03240-LOC_Os07g03250	intergenic_region ; MODIFIER	silent_mutation	Average:38.006; most accessible tissue: Zhenshan97 flower, score: 61.872	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701295150	NA	1.17E-08	mr1536	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
vg0701295150	NA	2.46E-07	mr1728	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
vg0701295150	NA	6.96E-07	mr1536_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