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Detailed information for vg0714048670:

Variant ID: vg0714048670 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14048670
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCCCTAAATATCCCTTAGAACACCTTATATCAACCATGTTCTAGCATAGTAAGCCCTAACCGAAGCTCTGCGTCGAGTTTTACCTCGCCGCACCAAGC[T/C]
GAGCACCGCCGCCCCCGCGTTGCTCTGTTCTTCGCCGCCGCGAAGTTTTTCCGGCCGCAATCCGTCGTTTCAACCGATCTCGGTGAGTTCTTCCATTTCA

Reverse complement sequence

TGAAATGGAAGAACTCACCGAGATCGGTTGAAACGACGGATTGCGGCCGGAAAAACTTCGCGGCGGCGAAGAACAGAGCAACGCGGGGGCGGCGGTGCTC[A/G]
GCTTGGTGCGGCGAGGTAAAACTCGACGCAGAGCTTCGGTTAGGGCTTACTATGCTAGAACATGGTTGATATAAGGTGTTCTAAGGGATATTTAGGGCGG

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	46.60%	1.70%	9.82%	41.92%	NA
All Indica	2759	27.30%	2.50%	13.92%	56.29%	NA
All Japonica	1512	82.70%	0.30%	1.52%	15.41%	NA
Aus	269	24.90%	0.40%	19.33%	55.39%	NA
Indica I	595	49.90%	2.70%	10.92%	36.47%	NA
Indica II	465	28.40%	2.40%	13.12%	56.13%	NA
Indica III	913	6.50%	2.80%	16.98%	73.71%	NA
Indica Intermediate	786	33.70%	2.00%	13.10%	51.15%	NA
Temperate Japonica	767	83.80%	0.40%	1.30%	14.47%	NA
Tropical Japonica	504	92.50%	0.40%	0.99%	6.15%	NA
Japonica Intermediate	241	58.90%	0.00%	3.32%	37.76%	NA
VI/Aromatic	96	83.30%	0.00%	2.08%	14.58%	NA
Intermediate	90	57.80%	3.30%	3.33%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714048670	T -> DEL	N	N	silent_mutation	Average:10.731; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N
vg0714048670	T -> C	LOC_Os07g24700.1	upstream_gene_variant ; 3271.0bp to feature; MODIFIER	silent_mutation	Average:10.731; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N
vg0714048670	T -> C	LOC_Os07g24690.1	downstream_gene_variant ; 1909.0bp to feature; MODIFIER	silent_mutation	Average:10.731; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N
vg0714048670	T -> C	LOC_Os07g24690-LOC_Os07g24700	intergenic_region ; MODIFIER	silent_mutation	Average:10.731; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714048670	3.58E-06	3.83E-10	mr1850	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
vg0714048670	1.49E-06	1.48E-06	mr1850	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