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Detailed information for vg0713275159:

Variant ID: vg0713275159 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13275159
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: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCCACTATATGAAAGACTGTTGGTTGGCTCACTAGGAGCAGGATTGGGGTGAACGCATGCGTAAGGAGGTTGGGGGCATGGTTCACAACGGTGGAACC[C/T]
GTGAAAGCAGCGACCATGTAGCCTTGCCTAGGCCTGGCAAGTGCCCGACTGCTAGGACGGATCAATATCCCACTCGTGCAGTAACTAGTAGTAAGTGGGA

Reverse complement sequence

TCCCACTTACTACTAGTTACTGCACGAGTGGGATATTGATCCGTCCTAGCAGTCGGGCACTTGCCAGGCCTAGGCAAGGCTACATGGTCGCTGCTTTCAC[G/A]
GGTTCCACCGTTGTGAACCATGCCCCCAACCTCCTTACGCATGCGTTCACCCCAATCCTGCTCCTAGTGAGCCAACCAACAGTCTTTCATATAGTGGGAC

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	42.50%	14.40%	24.42%	18.68%	NA
All Indica	2759	23.60%	23.80%	35.88%	16.71%	NA
All Japonica	1512	73.00%	0.40%	3.77%	22.82%	NA
Aus	269	58.70%	3.70%	21.19%	16.36%	NA
Indica I	595	7.70%	24.50%	52.44%	15.29%	NA
Indica II	465	15.70%	28.00%	40.86%	15.48%	NA
Indica III	913	41.80%	19.20%	22.02%	16.98%	NA
Indica Intermediate	786	19.00%	26.30%	36.51%	18.19%	NA
Temperate Japonica	767	67.30%	0.40%	2.09%	30.25%	NA
Tropical Japonica	504	91.70%	0.40%	3.97%	3.97%	NA
Japonica Intermediate	241	52.30%	0.40%	8.71%	38.59%	NA
VI/Aromatic	96	47.90%	3.10%	32.29%	16.67%	NA
Intermediate	90	55.60%	4.40%	21.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713275159	C -> DEL	N	N	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0713275159	C -> T	LOC_Os07g23485.1	3_prime_UTR_variant ; 1987.0bp to feature; MODIFIER	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0713275159	C -> T	LOC_Os07g23480.1	upstream_gene_variant ; 3657.0bp to feature; MODIFIER	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0713275159	C -> T	LOC_Os07g23494.1	downstream_gene_variant ; 1055.0bp to feature; MODIFIER	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713275159	NA	5.68E-10	mr1623_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