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Detailed information for vg0718471109:

Variant ID: vg0718471109 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 18471109
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, G: 0.02, T: 0.01, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTGGGAGGATCCAACACTTCGTATAAGCCGTTGGATGAATATATCTAAGGATAAAAAAATATATATAGGTGTTTGATGAAGTCGTACTTTTTGTGTGA[C/T]
ACCTTGAAAACCTCAAATTTGTAAAAATCAAGTCTAATTTGATATATATTAACAAATAGGTAGAACCGAGTCTAATTTGATCAATTAGCATAGGATTTAG

Reverse complement sequence

CTAAATCCTATGCTAATTGATCAAATTAGACTCGGTTCTACCTATTTGTTAATATATATCAAATTAGACTTGATTTTTACAAATTTGAGGTTTTCAAGGT[G/A]
TCACACAAAAAGTACGACTTCATCAAACACCTATATATATTTTTTTATCCTTAGATATATTCATCCAACGGCTTATACGAAGTGTTGGATCCTCCCAGCA

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	48.20%	37.00%	0.78%	14.09%	NA
All Indica	2759	38.00%	58.90%	0.47%	2.61%	NA
All Japonica	1512	71.70%	0.70%	0.20%	27.38%	NA
Aus	269	1.10%	32.70%	7.43%	58.74%	NA
Indica I	595	19.50%	80.30%	0.17%	0.00%	NA
Indica II	465	12.30%	82.60%	0.22%	4.95%	NA
Indica III	913	52.70%	45.60%	0.44%	1.31%	NA
Indica Intermediate	786	50.30%	44.10%	0.89%	4.71%	NA
Temperate Japonica	767	90.10%	0.50%	0.00%	9.39%	NA
Tropical Japonica	504	47.40%	1.00%	0.00%	51.59%	NA
Japonica Intermediate	241	63.90%	0.80%	1.24%	34.02%	NA
VI/Aromatic	96	91.70%	1.00%	0.00%	7.29%	NA
Intermediate	90	57.80%	24.40%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0718471109	C -> DEL	N	N	silent_mutation	Average:74.695; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N
vg0718471109	C -> T	LOC_Os07g31200.1	upstream_gene_variant ; 3927.0bp to feature; MODIFIER	silent_mutation	Average:74.695; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N
vg0718471109	C -> T	LOC_Os07g31194.1	downstream_gene_variant ; 4669.0bp to feature; MODIFIER	silent_mutation	Average:74.695; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N
vg0718471109	C -> T	LOC_Os07g31194-LOC_Os07g31200	intergenic_region ; MODIFIER	silent_mutation	Average:74.695; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0718471109	NA	2.09E-08	mr1257	Jap_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