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Detailed information for vg0610070964:

Variant ID: vg0610070964 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10070964
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGAACGATTCAAGTAGATTGTATTCGGGGGTTTTACAATGAACCGGCCTTGTCCCTTAAATAGGGGTTGGTCTTGCCCTCTACAGGCCCTTCTCCATG[C/T]
CCAACTCGGGATAGAAACCAAAGGAAACACGGAACATGCCTTCCCGAGCAAGGAAACCCGAGACCCGACGTAAACAGACTCGGACTCGGACCCTGCCGGT

Reverse complement sequence

ACCGGCAGGGTCCGAGTCCGAGTCTGTTTACGTCGGGTCTCGGGTTTCCTTGCTCGGGAAGGCATGTTCCGTGTTTCCTTTGGTTTCTATCCCGAGTTGG[G/A]
CATGGAGAAGGGCCTGTAGAGGGCAAGACCAACCCCTATTTAAGGGACAAGGCCGGTTCATTGTAAAACCCCCGAATACAATCTACTTGAATCGTTCTTT

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	76.30%	23.70%	0.04%	0.00%	NA
All Indica	2759	98.40%	1.60%	0.00%	0.00%	NA
All Japonica	1512	49.90%	50.10%	0.07%	0.00%	NA
Aus	269	19.30%	80.70%	0.00%	0.00%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.90%	0.00%	0.00%	NA
Temperate Japonica	767	64.30%	35.70%	0.00%	0.00%	NA
Tropical Japonica	504	38.70%	61.10%	0.20%	0.00%	NA
Japonica Intermediate	241	27.40%	72.60%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	76.70%	22.20%	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
vg0610070964	C -> T	LOC_Os06g17370.1	upstream_gene_variant ; 1010.0bp to feature; MODIFIER	silent_mutation	Average:43.438; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0610070964	C -> T	LOC_Os06g17380.1	upstream_gene_variant ; 1274.0bp to feature; MODIFIER	silent_mutation	Average:43.438; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0610070964	C -> T	LOC_Os06g17370-LOC_Os06g17380	intergenic_region ; MODIFIER	silent_mutation	Average:43.438; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610070964	NA	2.53E-07	mr1057	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
vg0610070964	NA	1.83E-08	mr1465	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
vg0610070964	6.35E-08	NA	mr1679	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