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Detailed information for vg1006613053:

Variant ID: vg1006613053 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6613053
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, C: 0.14, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AACAAGCCGTCACATGCGACTAGGAAAGCTGTGAGATAGCCCAAACCCGCGAGATCATGATCGCCCGAGAAGATATCCGATTGGCTGCAACCACGGCAAG[T/C]
GAAGGAGAAGTGCCTGCAACCAAGATCCCAAAGAGTGGAGAAAGCGAAGCCAAGACCAAGAAAATTCCTCTAGATCCCTCTAATCCTACTAAGACTGCTG

Reverse complement sequence

CAGCAGTCTTAGTAGGATTAGAGGGATCTAGAGGAATTTTCTTGGTCTTGGCTTCGCTTTCTCCACTCTTTGGGATCTTGGTTGCAGGCACTTCTCCTTC[A/G]
CTTGCCGTGGTTGCAGCCAATCGGATATCTTCTCGGGCGATCATGATCTCGCGGGTTTGGGCTATCTCACAGCTTTCCTAGTCGCATGTGACGGCTTGTT

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	24.20%	19.30%	3.87%	52.54%	NA
All Indica	2759	38.90%	1.30%	4.42%	55.45%	NA
All Japonica	1512	1.20%	56.50%	0.40%	41.87%	NA
Aus	269	5.90%	0.40%	16.36%	77.32%	NA
Indica I	595	13.10%	2.20%	4.87%	79.83%	NA
Indica II	465	61.10%	0.90%	2.15%	35.91%	NA
Indica III	913	40.40%	0.90%	5.04%	53.67%	NA
Indica Intermediate	786	43.40%	1.30%	4.71%	50.64%	NA
Temperate Japonica	767	0.40%	88.70%	0.00%	10.95%	NA
Tropical Japonica	504	1.00%	8.70%	0.79%	89.48%	NA
Japonica Intermediate	241	4.10%	54.40%	0.83%	40.66%	NA
VI/Aromatic	96	15.60%	5.20%	6.25%	72.92%	NA
Intermediate	90	27.80%	20.00%	5.56%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006613053	T -> C	LOC_Os10g11910.1	downstream_gene_variant ; 4346.0bp to feature; MODIFIER	silent_mutation	Average:9.844; most accessible tissue: Callus, score: 38.526	N	N	N	N
vg1006613053	T -> C	LOC_Os10g11930.1	downstream_gene_variant ; 3691.0bp to feature; MODIFIER	silent_mutation	Average:9.844; most accessible tissue: Callus, score: 38.526	N	N	N	N
vg1006613053	T -> C	LOC_Os10g11920.1	intron_variant ; MODIFIER	silent_mutation	Average:9.844; most accessible tissue: Callus, score: 38.526	N	N	N	N
vg1006613053	T -> DEL	N	N	silent_mutation	Average:9.844; most accessible tissue: Callus, score: 38.526	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006613053	2.75E-06	2.75E-06	mr1266	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