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Detailed information for vg1004256106:

Variant ID: vg1004256106 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4256106
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTCCTTTTTTTTTTTTGGATCTGAATCGATCCACCATCCCAGCCCACAGATCGGCGACACACCATGCAGGAGGATGATGACACCGTGGCAGTTGATGG[C/T]
GGTGGCCTGGGCGGTTGAGGTGAAGGCACTACTTCGGCCTCACTGTCGGACGCTGGGCCGCACCTTAACCAGCAAGGAGGTGTTCACCTAGGCCAATAGC

Reverse complement sequence

GCTATTGGCCTAGGTGAACACCTCCTTGCTGGTTAAGGTGCGGCCCAGCGTCCGACAGTGAGGCCGAAGTAGTGCCTTCACCTCAACCGCCCAGGCCACC[G/A]
CCATCAACTGCCACGGTGTCATCATCCTCCTGCATGGTGTGTCGCCGATCTGTGGGCTGGGATGGTGGATCGATTCAGATCCAAAAAAAAAAAAGGAAAA

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	52.10%	47.70%	0.21%	0.00%	NA
All Indica	2759	26.20%	73.40%	0.33%	0.00%	NA
All Japonica	1512	88.30%	11.70%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	42.50%	56.80%	0.67%	0.00%	NA
Indica II	465	17.40%	81.90%	0.65%	0.00%	NA
Indica III	913	21.60%	78.40%	0.00%	0.00%	NA
Indica Intermediate	786	24.60%	75.20%	0.25%	0.00%	NA
Temperate Japonica	767	93.90%	6.10%	0.00%	0.00%	NA
Tropical Japonica	504	88.10%	11.90%	0.00%	0.00%	NA
Japonica Intermediate	241	71.00%	29.00%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	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
vg1004256106	C -> T	LOC_Os10g07970.1	downstream_gene_variant ; 3080.0bp to feature; MODIFIER	silent_mutation	Average:56.407; most accessible tissue: Minghui63 young leaf, score: 76.82	N	N	N	N
vg1004256106	C -> T	LOC_Os10g07974.1	downstream_gene_variant ; 3274.0bp to feature; MODIFIER	silent_mutation	Average:56.407; most accessible tissue: Minghui63 young leaf, score: 76.82	N	N	N	N
vg1004256106	C -> T	LOC_Os10g07970-LOC_Os10g07974	intergenic_region ; MODIFIER	silent_mutation	Average:56.407; most accessible tissue: Minghui63 young leaf, score: 76.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004256106	2.45E-07	NA	mr1853	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
vg1004256106	8.82E-07	8.82E-07	mr1853	Ind_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