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Detailed information for vg0425395594:

Variant ID: vg0425395594 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 25395594
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.10, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GAATAAATTTCATAAACCAAAATTTAAATACAAATTTATTGAGTTTGCCGACAAGTTCTCGAAAACCGGTTGGTTTTGGTGAAATTCCGATCGAAATCAT[C/T]
GAAATTTCGACCAGTAATTTGTAATAGAGGTAATTTGCTGAAATTCTTTTTTTTCTTATGTAAGTTTCAGTAAATACATACAATACTTTTTTAAAAAAAT

Reverse complement sequence

ATTTTTTTAAAAAAGTATTGTATGTATTTACTGAAACTTACATAAGAAAAAAAAGAATTTCAGCAAATTACCTCTATTACAAATTACTGGTCGAAATTTC[G/A]
ATGATTTCGATCGGAATTTCACCAAAACCAACCGGTTTTCGAGAACTTGTCGGCAAACTCAATAAATTTGTATTTAAATTTTGGTTTATGAAATTTATTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.70%	42.70%	0.21%	0.34%	NA
All Indica	2759	84.80%	14.50%	0.22%	0.43%	NA
All Japonica	1512	4.80%	94.80%	0.13%	0.20%	NA
Aus	269	52.40%	47.60%	0.00%	0.00%	NA
Indica I	595	83.70%	15.30%	0.50%	0.50%	NA
Indica II	465	95.30%	3.40%	0.22%	1.08%	NA
Indica III	913	85.00%	14.90%	0.11%	0.00%	NA
Indica Intermediate	786	79.40%	20.00%	0.13%	0.51%	NA
Temperate Japonica	767	1.80%	98.00%	0.00%	0.13%	NA
Tropical Japonica	504	7.50%	92.10%	0.20%	0.20%	NA
Japonica Intermediate	241	8.70%	90.50%	0.41%	0.41%	NA
VI/Aromatic	96	86.50%	12.50%	1.04%	0.00%	NA
Intermediate	90	47.80%	50.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0425395594	C -> DEL	N	N	silent_mutation	Average:41.118; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0425395594	C -> T	LOC_Os04g42930.1	upstream_gene_variant ; 1345.0bp to feature; MODIFIER	silent_mutation	Average:41.118; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0425395594	C -> T	LOC_Os04g42930.2	upstream_gene_variant ; 1345.0bp to feature; MODIFIER	silent_mutation	Average:41.118; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0425395594	C -> T	LOC_Os04g42920.1	downstream_gene_variant ; 49.0bp to feature; MODIFIER	silent_mutation	Average:41.118; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0425395594	C -> T	LOC_Os04g42940.1	downstream_gene_variant ; 4662.0bp to feature; MODIFIER	silent_mutation	Average:41.118; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0425395594	C -> T	LOC_Os04g42920-LOC_Os04g42930	intergenic_region ; MODIFIER	silent_mutation	Average:41.118; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0425395594	NA	2.65E-06	mr1561_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