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Detailed information for vg0708083717:

Variant ID: vg0708083717 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8083717
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTAAATAATAAAATAGCATATATTTTATTTTATTTTTTCTAGAAAAAAGTCCGTGTGTTGCTACGGGTGACTATTTTAATCTTATTTTGCTACGATC[C/T]
AGGTCGCCGAGTTTTTTCCGGCTGATCTGGTAGTTTTTGTCCGGGTCGCTAGTTTACGGTTTTTTTTGTTCGATCTAGGCTTTTGGTTGGGTTGCCAGTT

Reverse complement sequence

AACTGGCAACCCAACCAAAAGCCTAGATCGAACAAAAAAAACCGTAAACTAGCGACCCGGACAAAAACTACCAGATCAGCCGGAAAAAACTCGGCGACCT[G/A]
GATCGTAGCAAAATAAGATTAAAATAGTCACCCGTAGCAACACACGGACTTTTTTCTAGAAAAAATAAAATAAAATATATGCTATTTTATTATTTAAAAA

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	91.90%	0.40%	2.90%	4.78%	NA
All Indica	2759	96.60%	0.00%	0.07%	3.30%	NA
All Japonica	1512	82.40%	1.20%	8.73%	7.67%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.00%	0.50%	NA
Indica II	465	97.80%	0.00%	0.43%	1.72%	NA
Indica III	913	99.10%	0.00%	0.00%	0.88%	NA
Indica Intermediate	786	90.80%	0.00%	0.00%	9.16%	NA
Temperate Japonica	767	67.30%	2.20%	16.17%	14.34%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	95.00%	0.40%	2.07%	2.49%	NA
VI/Aromatic	96	81.20%	0.00%	0.00%	18.75%	NA
Intermediate	90	95.60%	0.00%	3.33%	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
vg0708083717	C -> DEL	N	N	silent_mutation	Average:40.252; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0708083717	C -> T	LOC_Os07g14160.1	upstream_gene_variant ; 917.0bp to feature; MODIFIER	silent_mutation	Average:40.252; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0708083717	C -> T	LOC_Os07g14160.3	upstream_gene_variant ; 917.0bp to feature; MODIFIER	silent_mutation	Average:40.252; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0708083717	C -> T	LOC_Os07g14160.4	upstream_gene_variant ; 917.0bp to feature; MODIFIER	silent_mutation	Average:40.252; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0708083717	C -> T	LOC_Os07g14160.2	upstream_gene_variant ; 910.0bp to feature; MODIFIER	silent_mutation	Average:40.252; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0708083717	C -> T	LOC_Os07g14160-LOC_Os07g14170	intergenic_region ; MODIFIER	silent_mutation	Average:40.252; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708083717	1.23E-06	1.45E-08	mr1588_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