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Detailed information for vg1206348060:

Variant ID: vg1206348060 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6348060
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.36, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGCGGCAGTCCCGGTTGGTCACTATTTTTTTTCTTTTTTTATTGTTTCTTTGCTCACTACATTTTGCTTTTCCAAATCGAGTTGCTCCCTACATATCC[C/T]
TAAATCATCCACAAATCAAAGTAGCATCACAGATCATAGATTCACATCACAAATTCTCAAAAAAAAATACAACACAAATCAAATACATCACACATTATAT

Reverse complement sequence

ATATAATGTGTGATGTATTTGATTTGTGTTGTATTTTTTTTTGAGAATTTGTGATGTGAATCTATGATCTGTGATGCTACTTTGATTTGTGGATGATTTA[G/A]
GGATATGTAGGGAGCAACTCGATTTGGAAAAGCAAAATGTAGTGAGCAAAGAAACAATAAAAAAAGAAAAAAAATAGTGACCAACCGGGACTGCCGCTAT

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	24.50%	15.10%	0.25%	60.22%	NA
All Indica	2759	35.20%	3.30%	0.11%	61.40%	NA
All Japonica	1512	5.40%	37.30%	0.60%	56.68%	NA
Aus	269	2.60%	15.60%	0.00%	81.78%	NA
Indica I	595	85.40%	6.10%	0.00%	8.57%	NA
Indica II	465	18.70%	1.30%	0.00%	80.00%	NA
Indica III	913	10.80%	2.40%	0.22%	86.53%	NA
Indica Intermediate	786	35.40%	3.30%	0.13%	61.20%	NA
Temperate Japonica	767	9.40%	43.40%	0.65%	46.54%	NA
Tropical Japonica	504	1.00%	22.20%	0.40%	76.39%	NA
Japonica Intermediate	241	2.10%	49.40%	0.83%	47.72%	NA
VI/Aromatic	96	68.80%	1.00%	0.00%	30.21%	NA
Intermediate	90	32.20%	16.70%	0.00%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206348060	C -> DEL	N	N	silent_mutation	Average:55.168; most accessible tissue: Callus, score: 75.486	N	N	N	N
vg1206348060	C -> T	LOC_Os12g11690.1	upstream_gene_variant ; 941.0bp to feature; MODIFIER	silent_mutation	Average:55.168; most accessible tissue: Callus, score: 75.486	N	N	N	N
vg1206348060	C -> T	LOC_Os12g11700.1	upstream_gene_variant ; 680.0bp to feature; MODIFIER	silent_mutation	Average:55.168; most accessible tissue: Callus, score: 75.486	N	N	N	N
vg1206348060	C -> T	LOC_Os12g11680.1	downstream_gene_variant ; 3971.0bp to feature; MODIFIER	silent_mutation	Average:55.168; most accessible tissue: Callus, score: 75.486	N	N	N	N
vg1206348060	C -> T	LOC_Os12g11690-LOC_Os12g11700	intergenic_region ; MODIFIER	silent_mutation	Average:55.168; most accessible tissue: Callus, score: 75.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206348060	5.93E-06	5.97E-06	mr1381	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
vg1206348060	3.25E-06	3.23E-06	mr1954	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