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Detailed information for vg0607796859:

Variant ID: vg0607796859 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7796859
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GAGAGGGAGGAGGAAAAAGGATAGAAAGGGGATGACATTTGGGCCCCACATGATGAGGACATCACTTCATCGGATATACACATAACTTCACACATTCCAA[T/C]
GATAATTCTCAGTCTAAATCCAGTTCAGCCTCCGAAGACAGCACTGACTTTCAAACGGACCTAGCACCTTCATACCAACTCCGATTTGGGTGATCTTGCA

Reverse complement sequence

TGCAAGATCACCCAAATCGGAGTTGGTATGAAGGTGCTAGGTCCGTTTGAAAGTCAGTGCTGTCTTCGGAGGCTGAACTGGATTTAGACTGAGAATTATC[A/G]
TTGGAATGTGTGAAGTTATGTGTATATCCGATGAAGTGATGTCCTCATCATGTGGGGCCCAAATGTCATCCCCTTTCTATCCTTTTTCCTCCTCCCTCTC

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	59.10%	35.70%	0.32%	4.95%	NA
All Indica	2759	32.40%	60.20%	0.54%	6.89%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	84.00%	1.10%	0.00%	14.87%	NA
Indica I	595	13.90%	85.20%	0.17%	0.67%	NA
Indica II	465	73.10%	22.60%	0.43%	3.87%	NA
Indica III	913	20.00%	64.60%	1.10%	14.24%	NA
Indica Intermediate	786	36.60%	58.30%	0.25%	4.83%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	82.20%	15.60%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607796859	T -> C	LOC_Os06g14010.1	upstream_gene_variant ; 4178.0bp to feature; MODIFIER	silent_mutation	Average:62.899; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0607796859	T -> C	LOC_Os06g14020.1	downstream_gene_variant ; 312.0bp to feature; MODIFIER	silent_mutation	Average:62.899; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0607796859	T -> C	LOC_Os06g14030.1	downstream_gene_variant ; 2214.0bp to feature; MODIFIER	silent_mutation	Average:62.899; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0607796859	T -> C	LOC_Os06g14020-LOC_Os06g14030	intergenic_region ; MODIFIER	silent_mutation	Average:62.899; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0607796859	T -> DEL	N	N	silent_mutation	Average:62.899; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607796859	NA	5.90E-07	mr1458	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
vg0607796859	NA	5.43E-08	mr1860	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
vg0607796859	NA	1.69E-06	mr1272_2	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
vg0607796859	NA	4.90E-09	mr1457_2	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
vg0607796859	NA	9.97E-08	mr1458_2	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
vg0607796859	NA	4.57E-06	mr1677_2	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