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Detailed information for vg0315240706:

Variant ID: vg0315240706 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15240706
Reference Allele: C	Alternative Allele: T
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: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TATATTTCCTTGCGGTAATATCTTAATATAGAGTAGTATCGGAGTATTAGCCGATACATGCTAGATCTATCTTATCGGCTATGCTATGAACATATATAAT[C/T]
CCATTGTTAATACATGTTTCGATCTAAGTGATTTATACTGCCTCGGTATGGCGACTGATCTATCCCAATCACTTGGTTTAAGCATATACCGACATAAAGA

Reverse complement sequence

TCTTTATGTCGGTATATGCTTAAACCAAGTGATTGGGATAGATCAGTCGCCATACCGAGGCAGTATAAATCACTTAGATCGAAACATGTATTAACAATGG[G/A]
ATTATATATGTTCATAGCATAGCCGATAAGATAGATCTAGCATGTATCGGCTAATACTCCGATACTACTCTATATTAAGATATTACCGCAAGGAAATATA

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	53.40%	12.70%	9.82%	24.04%	NA
All Indica	2759	35.70%	14.60%	11.63%	38.09%	NA
All Japonica	1512	82.60%	10.90%	4.30%	2.18%	NA
Aus	269	51.70%	9.30%	24.16%	14.87%	NA
Indica I	595	54.80%	14.10%	5.71%	25.38%	NA
Indica II	465	37.20%	8.20%	5.81%	48.82%	NA
Indica III	913	20.30%	18.80%	19.39%	41.51%	NA
Indica Intermediate	786	38.20%	13.90%	10.56%	37.40%	NA
Temperate Japonica	767	96.50%	1.30%	0.26%	1.96%	NA
Tropical Japonica	504	64.10%	23.80%	11.11%	0.99%	NA
Japonica Intermediate	241	77.20%	14.50%	2.90%	5.39%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	65.60%	6.70%	14.44%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315240706	C -> T	LOC_Os03g26680.1	upstream_gene_variant ; 4636.0bp to feature; MODIFIER	silent_mutation	Average:11.852; most accessible tissue: Callus, score: 35.482	N	N	N	N
vg0315240706	C -> T	LOC_Os03g26704.1	downstream_gene_variant ; 2484.0bp to feature; MODIFIER	silent_mutation	Average:11.852; most accessible tissue: Callus, score: 35.482	N	N	N	N
vg0315240706	C -> T	LOC_Os03g26690.1	intron_variant ; MODIFIER	silent_mutation	Average:11.852; most accessible tissue: Callus, score: 35.482	N	N	N	N
vg0315240706	C -> DEL	N	N	silent_mutation	Average:11.852; most accessible tissue: Callus, score: 35.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315240706	4.90E-06	1.53E-07	mr1422_2	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
vg0315240706	NA	1.50E-07	mr1850_2	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