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Detailed information for vg0614114557:

Variant ID: vg0614114557 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14114557
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: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAATCCGCAAGCGCACGGATATACCGATGTAGCACTTCCCCTAAGGAGTATTCCAAGGGTATCGAATCCAAGGAAACGTGTGTGATCAGAGTTTCCTC[C/T]
GGTTCATCCAAGGACACCAAGCAAATGATAGGCCAGGATAGAGAGGATTCACTAGTGAGAAACAGTGTCTAGGGAAAGCTTAATTTTAATCCTAACGCAA

Reverse complement sequence

TTGCGTTAGGATTAAAATTAAGCTTTCCCTAGACACTGTTTCTCACTAGTGAATCCTCTCTATCCTGGCCTATCATTTGCTTGGTGTCCTTGGATGAACC[G/A]
GAGGAAACTCTGATCACACACGTTTCCTTGGATTCGATACCCTTGGAATACTCCTTAGGGGAAGTGCTACATCGGTATATCCGTGCGCTTGCGGATTTTT

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	94.80%	2.00%	3.24%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.22%	0.00%	NA
All Japonica	1512	88.40%	6.20%	5.42%	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	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.50%	0.00%	0.51%	0.00%	NA
Temperate Japonica	767	78.70%	11.90%	9.39%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	96.70%	0.80%	2.49%	0.00%	NA
VI/Aromatic	96	36.50%	0.00%	63.54%	0.00%	NA
Intermediate	90	94.40%	1.10%	4.44%	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
vg0614114557	C -> T	LOC_Os06g24110.1	upstream_gene_variant ; 2330.0bp to feature; MODIFIER	silent_mutation	Average:44.116; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0614114557	C -> T	LOC_Os06g24120.1	upstream_gene_variant ; 1418.0bp to feature; MODIFIER	silent_mutation	Average:44.116; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0614114557	C -> T	LOC_Os06g24130.1	downstream_gene_variant ; 2039.0bp to feature; MODIFIER	silent_mutation	Average:44.116; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0614114557	C -> T	LOC_Os06g24120-LOC_Os06g24130	intergenic_region ; MODIFIER	silent_mutation	Average:44.116; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614114557	8.23E-07	8.23E-07	mr1945_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