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Detailed information for vg0715642858:

Variant ID: vg0715642858 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15642858
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TCATAGCATACCCAAAAACTACTTTTATAGCTACCCATTTACGGAGTAGCGTTTAGCAGTCCCTAAGTAAGCTACTACACATGTTGAGAACTATGATAAT[C/A]
TCAGGTCTAAGGATTCAACACCAGCACTAAATGAGATCACTGATGACACAACACATATGACTCTTGCAGTGTCTCATGTTGGGTCTATCCAACAACATGC

Reverse complement sequence

GCATGTTGTTGGATAGACCCAACATGAGACACTGCAAGAGTCATATGTGTTGTGTCATCAGTGATCTCATTTAGTGCTGGTGTTGAATCCTTAGACCTGA[G/T]
ATTATCATAGTTCTCAACATGTGTAGTAGCTTACTTAGGGACTGCTAAACGCTACTCCGTAAATGGGTAGCTATAAAAGTAGTTTTTGGGTATGCTATGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.60%	2.50%	0.87%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.11%	0.00%	NA
All Japonica	1512	90.10%	7.50%	2.45%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.50%	0.25%	0.00%	NA
Temperate Japonica	767	84.60%	10.70%	4.69%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	87.10%	12.40%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715642858	C -> A	LOC_Os07g27010.1	downstream_gene_variant ; 1924.0bp to feature; MODIFIER	silent_mutation	Average:34.226; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg0715642858	C -> A	LOC_Os07g27000-LOC_Os07g27010	intergenic_region ; MODIFIER	silent_mutation	Average:34.226; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715642858	3.35E-06	3.34E-06	mr1036_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