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Detailed information for vg0625104002:

Variant ID: vg0625104002 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25104002
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, A: 0.36, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGTTGGTCAAAGTAGCATCTCAAAGACTGTGACGAGGTCCAAAAATGCTTATATTTCAGGACGGAGGAAGTAGTTATTTTTTTCGTTTATATTTAATA[C/A]
TCCATGCATGTGTCTAAATATTCGATGTGACAGGATGTAAAAATTTGTTAGGGGATTTAAACATGCTCTTTATCTCTCTGTAGCCTACTTCCTCCGTCCC

Reverse complement sequence

GGGACGGAGGAAGTAGGCTACAGAGAGATAAAGAGCATGTTTAAATCCCCTAACAAATTTTTACATCCTGTCACATCGAATATTTAGACACATGCATGGA[G/T]
TATTAAATATAAACGAAAAAAATAACTACTTCCTCCGTCCTGAAATATAAGCATTTTTGGACCTCGTCACAGTCTTTGAGATGCTACTTTGACCAACAAT

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	80.70%	19.10%	0.21%	0.00%	NA
All Indica	2759	97.20%	2.70%	0.07%	0.00%	NA
All Japonica	1512	53.40%	46.30%	0.26%	0.00%	NA
Aus	269	91.40%	7.80%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	6.00%	0.25%	0.00%	NA
Temperate Japonica	767	81.40%	18.60%	0.00%	0.00%	NA
Tropical Japonica	504	21.20%	78.40%	0.40%	0.00%	NA
Japonica Intermediate	241	32.00%	67.20%	0.83%	0.00%	NA
VI/Aromatic	96	19.80%	80.20%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	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
vg0625104002	C -> A	LOC_Os06g41860.1	downstream_gene_variant ; 4849.0bp to feature; MODIFIER	silent_mutation	Average:31.271; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0625104002	C -> A	LOC_Os06g41870.1	downstream_gene_variant ; 4482.0bp to feature; MODIFIER	silent_mutation	Average:31.271; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0625104002	C -> A	LOC_Os06g41860-LOC_Os06g41870	intergenic_region ; MODIFIER	silent_mutation	Average:31.271; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625104002	NA	4.50E-11	mr1084	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
vg0625104002	2.34E-06	NA	mr1697	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
vg0625104002	NA	4.70E-07	mr1582_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