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Detailed information for vg0427734968:

Variant ID: vg0427734968 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27734968
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GACATAAAACCACCGAATCTGGATATCTTTATTGGATAAATATGTACAAAGGAGCTTTTGACTCCAGGAAACTGTTGAATAGCAGCATTGGTTAATCAAT[G/T]
AGGATATGGGATGCATTGGCGTTTGGTGATAGATAGGTGATCTTTTAATGAGCCCTAGTCCTTTAGTTTCCATGAAGGGAACATTTGCGTTACTGAGCTA

Reverse complement sequence

TAGCTCAGTAACGCAAATGTTCCCTTCATGGAAACTAAAGGACTAGGGCTCATTAAAAGATCACCTATCTATCACCAAACGCCAATGCATCCCATATCCT[C/A]
ATTGATTAACCAATGCTGCTATTCAACAGTTTCCTGGAGTCAAAAGCTCCTTTGTACATATTTATCCAATAAAGATATCCAGATTCGGTGGTTTTATGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.30%	29.50%	0.95%	0.25%	NA
All Indica	2759	85.10%	14.10%	0.36%	0.36%	NA
All Japonica	1512	44.40%	53.40%	2.18%	0.00%	NA
Aus	269	74.00%	26.00%	0.00%	0.00%	NA
Indica I	595	83.50%	15.30%	0.84%	0.34%	NA
Indica II	465	92.70%	6.70%	0.22%	0.43%	NA
Indica III	913	83.80%	15.90%	0.11%	0.22%	NA
Indica Intermediate	786	83.50%	15.60%	0.38%	0.51%	NA
Temperate Japonica	767	62.80%	33.20%	3.91%	0.00%	NA
Tropical Japonica	504	11.50%	88.50%	0.00%	0.00%	NA
Japonica Intermediate	241	54.40%	44.40%	1.24%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	46.70%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427734968	G -> DEL	N	N	silent_mutation	Average:46.939; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427734968	G -> T	LOC_Os04g46800.1	upstream_gene_variant ; 3256.0bp to feature; MODIFIER	silent_mutation	Average:46.939; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427734968	G -> T	LOC_Os04g46770.1	downstream_gene_variant ; 3915.0bp to feature; MODIFIER	silent_mutation	Average:46.939; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427734968	G -> T	LOC_Os04g46790.1	downstream_gene_variant ; 1513.0bp to feature; MODIFIER	silent_mutation	Average:46.939; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427734968	G -> T	LOC_Os04g46780.1	intron_variant ; MODIFIER	silent_mutation	Average:46.939; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427734968	G -> T	LOC_Os04g46780.2	intron_variant ; MODIFIER	silent_mutation	Average:46.939; most accessible tissue: Callus, score: 87.686	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427734968	NA	5.92E-06	mr1657	Jap_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
vg0427734968	NA	1.45E-06	mr1993	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