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Detailed information for vg0717726967:

Variant ID: vg0717726967 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17726967
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTAGCAGTCTACCAGTGTTTAATTTTGTAATACTTCTCCTTGTACATATATGTTTATGGCAGCCATGTAATGAAAAGGAAATGTTGAATAAAATATGAGT[T/C]
AGCCAGTTCCTCTCCTTTTATGGTTCATCTTGAGCATGCAGAAGCAATTTATTATGTGTATCTGTCGGTGCCACAAGAAACCAAGAGTTTCTCTTCTAAC

Reverse complement sequence

GTTAGAAGAGAAACTCTTGGTTTCTTGTGGCACCGACAGATACACATAATAAATTGCTTCTGCATGCTCAAGATGAACCATAAAAGGAGAGGAACTGGCT[A/G]
ACTCATATTTTATTCAACATTTCCTTTTCATTACATGGCTGCCATAAACATATATGTACAAGGAGAAGTATTACAAAATTAAACACTGGTAGACTGCTAC

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	95.00%	0.70%	3.39%	0.85%	NA
All Indica	2759	95.90%	0.90%	3.12%	0.00%	NA
All Japonica	1512	94.20%	0.50%	2.84%	2.51%	NA
Aus	269	87.40%	0.70%	11.52%	0.37%	NA
Indica I	595	89.70%	2.20%	8.07%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	97.90%	0.30%	1.75%	0.00%	NA
Indica Intermediate	786	96.30%	1.30%	2.42%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	87.50%	1.20%	8.13%	3.17%	NA
Japonica Intermediate	241	90.00%	0.40%	0.83%	8.71%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	0.00%	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
vg0717726967	T -> DEL	N	N	silent_mutation	Average:18.187; most accessible tissue: Callus, score: 44.457	N	N	N	N
vg0717726967	T -> C	LOC_Os07g30060.1	upstream_gene_variant ; 4373.0bp to feature; MODIFIER	silent_mutation	Average:18.187; most accessible tissue: Callus, score: 44.457	N	N	N	N
vg0717726967	T -> C	LOC_Os07g30050.1	downstream_gene_variant ; 301.0bp to feature; MODIFIER	silent_mutation	Average:18.187; most accessible tissue: Callus, score: 44.457	N	N	N	N
vg0717726967	T -> C	LOC_Os07g30050-LOC_Os07g30060	intergenic_region ; MODIFIER	silent_mutation	Average:18.187; most accessible tissue: Callus, score: 44.457	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717726967	NA	7.47E-07	mr1024_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
vg0717726967	3.40E-06	NA	mr1584_2	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
vg0717726967	5.72E-07	5.72E-07	mr1584_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