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Detailed information for vg0406982385:

Variant ID: vg0406982385 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6982385
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGCTAATAATCACTGTGTAGATGTATATACTACTTCTAGTTTTACTCCTATACAATATGCTTATAATGCTATGGGGGGTCAATGAGTGTTTATACGGC[T/C]
GATTACACAGGAATCGGCTATATGCAAAACCTAGATAACGGTATGACTGGTCATGACACCGGTCTAACCGCATCCTATGCCGGTTAGACCGTGCCCACCA

Reverse complement sequence

TGGTGGGCACGGTCTAACCGGCATAGGATGCGGTTAGACCGGTGTCATGACCAGTCATACCGTTATCTAGGTTTTGCATATAGCCGATTCCTGTGTAATC[A/G]
GCCGTATAAACACTCATTGACCCCCCATAGCATTATAAGCATATTGTATAGGAGTAAAACTAGAAGTAGTATATACATCTACACAGTGATTATTAGCAAA

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	63.40%	14.90%	2.92%	18.71%	NA
All Indica	2759	92.50%	0.50%	2.28%	4.71%	NA
All Japonica	1512	5.60%	41.90%	4.43%	48.08%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.17%	0.17%	NA
Indica II	465	95.90%	1.10%	1.08%	1.94%	NA
Indica III	913	83.20%	0.20%	5.26%	11.28%	NA
Indica Intermediate	786	96.10%	0.60%	1.15%	2.16%	NA
Temperate Japonica	767	2.00%	56.10%	1.04%	40.94%	NA
Tropical Japonica	504	11.30%	9.70%	10.91%	68.06%	NA
Japonica Intermediate	241	5.00%	64.30%	1.66%	29.05%	NA
VI/Aromatic	96	45.80%	38.50%	2.08%	13.54%	NA
Intermediate	90	54.40%	23.30%	6.67%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406982385	T -> C	LOC_Os04g12600.1	upstream_gene_variant ; 3136.0bp to feature; MODIFIER	silent_mutation	Average:65.214; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N
vg0406982385	T -> C	LOC_Os04g12610.1	upstream_gene_variant ; 100.0bp to feature; MODIFIER	silent_mutation	Average:65.214; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N
vg0406982385	T -> C	LOC_Os04g12600-LOC_Os04g12610	intergenic_region ; MODIFIER	silent_mutation	Average:65.214; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N
vg0406982385	T -> DEL	N	N	silent_mutation	Average:65.214; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406982385	8.17E-06	NA	mr1765	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
vg0406982385	1.51E-06	NA	mr1765	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