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Detailed information for vg1215094362:

Variant ID: vg1215094362 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15094362
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

ATCGACCCAAGCCAACGATCCCTCTACTTCAAGCTTGGATCAAGGTGAAGAAGGCGAGCAAGTGCCACCCTCTCCGATAAATCTAGCTCACCCAAGAATC[T/C]
ACCAAAGTATCTAACGAGATCACCCCACCGACAACATCTTAGGAGACATCAACAAGGGAGTATCCACTCGTTCTCGTATTGCAAATTTTTGTGAGCATTA

Reverse complement sequence

TAATGCTCACAAAAATTTGCAATACGAGAACGAGTGGATACTCCCTTGTTGATGTCTCCTAAGATGTTGTCGGTGGGGTGATCTCGTTAGATACTTTGGT[A/G]
GATTCTTGGGTGAGCTAGATTTATCGGAGAGGGTGGCACTTGCTCGCCTTCTTCACCTTGATCCAAGCTTGAAGTAGAGGGATCGTTGGCTTGGGTCGAT

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	12.10%	11.20%	7.45%	69.21%	NA
All Indica	2759	1.20%	1.60%	10.62%	86.55%	NA
All Japonica	1512	33.90%	31.30%	2.91%	31.88%	NA
Aus	269	4.50%	0.00%	1.86%	93.68%	NA
Indica I	595	0.30%	1.70%	25.04%	72.94%	NA
Indica II	465	1.90%	1.90%	4.30%	91.83%	NA
Indica III	913	1.10%	0.40%	2.96%	95.51%	NA
Indica Intermediate	786	1.70%	2.70%	12.34%	83.33%	NA
Temperate Japonica	767	31.70%	54.00%	3.00%	11.34%	NA
Tropical Japonica	504	36.90%	1.60%	2.98%	58.53%	NA
Japonica Intermediate	241	34.40%	21.60%	2.49%	41.49%	NA
VI/Aromatic	96	0.00%	0.00%	2.08%	97.92%	NA
Intermediate	90	16.70%	13.30%	8.89%	61.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215094362	T -> C	LOC_Os12g26000.1	downstream_gene_variant ; 4296.0bp to feature; MODIFIER	silent_mutation	Average:6.748; most accessible tissue: Callus, score: 18.566	N	N	N	N
vg1215094362	T -> C	LOC_Os12g25990.1	intron_variant ; MODIFIER	silent_mutation	Average:6.748; most accessible tissue: Callus, score: 18.566	N	N	N	N
vg1215094362	T -> DEL	N	N	silent_mutation	Average:6.748; most accessible tissue: Callus, score: 18.566	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215094362	NA	7.84E-06	mr1050_2	Ind_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
vg1215094362	1.84E-06	NA	mr1195_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