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Detailed information for vg0618463864:

Variant ID: vg0618463864 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18463864
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.55, C: 0.45, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

ATAACCCGGTCTGACCGGCCAATGGCCCAGTCTGACCGGTGGTCAATGATGCGGTCAGACCGGCCACAGGAGGCACGATCTGGCCAAGATAAGGTACGGT[T/C]
TGACCAGCTATGGTTGGCGCGGTCTGACCGGCAAAGATTGCTATCTGACCAGCGTGATGCGCGGTCTAACTGTTGGCTAAGCTTTTCGTATAACCGATTC

Reverse complement sequence

GAATCGGTTATACGAAAAGCTTAGCCAACAGTTAGACCGCGCATCACGCTGGTCAGATAGCAATCTTTGCCGGTCAGACCGCGCCAACCATAGCTGGTCA[A/G]
ACCGTACCTTATCTTGGCCAGATCGTGCCTCCTGTGGCCGGTCTGACCGCATCATTGACCACCGGTCAGACTGGGCCATTGGCCGGTCAGACCGGGTTAT

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	43.30%	6.50%	0.78%	49.37%	NA
All Indica	2759	23.10%	3.70%	0.94%	72.31%	NA
All Japonica	1512	86.10%	6.60%	0.40%	6.88%	NA
Aus	269	22.70%	0.40%	1.49%	75.46%	NA
Indica I	595	42.40%	4.50%	0.50%	52.61%	NA
Indica II	465	26.00%	1.50%	1.51%	70.97%	NA
Indica III	913	6.80%	1.60%	0.77%	90.80%	NA
Indica Intermediate	786	25.60%	6.70%	1.15%	66.54%	NA
Temperate Japonica	767	85.90%	8.00%	0.26%	5.87%	NA
Tropical Japonica	504	87.90%	3.40%	0.79%	7.94%	NA
Japonica Intermediate	241	83.00%	9.10%	0.00%	7.88%	NA
VI/Aromatic	96	3.10%	93.80%	0.00%	3.12%	NA
Intermediate	90	50.00%	17.80%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618463864	T -> C	LOC_Os06g31790.1	upstream_gene_variant ; 847.0bp to feature; MODIFIER	silent_mutation	Average:7.835; most accessible tissue: Callus, score: 36.64	N	N	N	N
vg0618463864	T -> C	LOC_Os06g31800.1	downstream_gene_variant ; 3110.0bp to feature; MODIFIER	silent_mutation	Average:7.835; most accessible tissue: Callus, score: 36.64	N	N	N	N
vg0618463864	T -> C	LOC_Os06g31790-LOC_Os06g31800	intergenic_region ; MODIFIER	silent_mutation	Average:7.835; most accessible tissue: Callus, score: 36.64	N	N	N	N
vg0618463864	T -> DEL	N	N	silent_mutation	Average:7.835; most accessible tissue: Callus, score: 36.64	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618463864	NA	1.33E-06	mr1036_2	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
vg0618463864	4.49E-06	1.38E-08	mr1169_2	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