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Detailed information for vg1004716113:

Variant ID: vg1004716113 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4716113
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.81, C: 0.20, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TTTATGCAAATGAAACCCTACTATGCCATCCTTTGTTATCCTGTGCACTTGCATATTTGCTGCGTGGCTTGCTGAGTATGTCATATACTCACCTTGCAAT[T/C]
ATTTATCAGAGGAGGAGTTCTACAGTGATGCTGATGGTGTGGATGATTAGGCGTAGCCCTGGTCAAACTGCCTGTGGAGAGGAGTCGCCTGCGCTGTTTC

Reverse complement sequence

GAAACAGCGCAGGCGACTCCTCTCCACAGGCAGTTTGACCAGGGCTACGCCTAATCATCCACACCATCAGCATCACTGTAGAACTCCTCCTCTGATAAAT[A/G]
ATTGCAAGGTGAGTATATGACATACTCAGCAAGCCACGCAGCAAATATGCAAGTGCACAGGATAACAAAGGATGGCATAGTAGGGTTTCATTTGCATAAA

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	16.50%	1.40%	22.24%	59.84%	NA
All Indica	2759	1.70%	1.90%	12.36%	84.02%	NA
All Japonica	1512	45.80%	0.90%	40.74%	12.50%	NA
Aus	269	1.90%	0.00%	2.97%	95.17%	NA
Indica I	595	1.70%	0.80%	2.86%	94.62%	NA
Indica II	465	1.10%	3.20%	17.20%	78.49%	NA
Indica III	913	1.30%	1.80%	17.96%	78.97%	NA
Indica Intermediate	786	2.70%	2.00%	10.18%	85.11%	NA
Temperate Japonica	767	82.00%	0.50%	9.78%	7.69%	NA
Tropical Japonica	504	3.40%	1.60%	84.13%	10.91%	NA
Japonica Intermediate	241	19.50%	0.80%	48.55%	31.12%	NA
VI/Aromatic	96	19.80%	0.00%	60.42%	19.79%	NA
Intermediate	90	15.60%	2.20%	31.11%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004716113	T -> C	LOC_Os10g08690.1	upstream_gene_variant ; 1190.0bp to feature; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg1004716113	T -> C	LOC_Os10g08702.1	upstream_gene_variant ; 1860.0bp to feature; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg1004716113	T -> C	LOC_Os10g08680.1	downstream_gene_variant ; 2132.0bp to feature; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg1004716113	T -> C	LOC_Os10g08696.1	intron_variant ; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg1004716113	T -> DEL	N	N	silent_mutation	Average:18.775; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004716113	4.50E-06	7.68E-06	mr1207	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
vg1004716113	7.23E-06	NA	mr1622	Ind_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