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Detailed information for vg0815916978:

Variant ID: vg0815916978 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15916978
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACTTCAGGAATCACATAAGGATGAAAAACTTTTCTCCAAATATCATAATTCTCAGCCATAATGTAATATTGCATCCTACTACAACAATGAGAAAAATC[C/T]
GTTCCATCGAAAACATGAGGCTTAGTTGTAAACTTATTAGAAGTAGCCATGGCAAAAACTCAAGATCGGTAAAGATCGAAAAGAGCAAACGTGGCTCCGA

Reverse complement sequence

TCGGAGCCACGTTTGCTCTTTTCGATCTTTACCGATCTTGAGTTTTTGCCATGGCTACTTCTAATAAGTTTACAACTAAGCCTCATGTTTTCGATGGAAC[G/A]
GATTTTTCTCATTGTTGTAGTAGGATGCAATATTACATTATGGCTGAGAATTATGATATTTGGAGAAAAGTTTTTCATCCTTATGTGATTCCTGAAGTTA

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	96.00%	2.80%	1.12%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.14%	0.00%	NA
All Japonica	1512	88.70%	8.60%	2.71%	0.00%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	72.80%	20.20%	6.94%	0.00%	NA
Japonica Intermediate	241	90.90%	6.60%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	1.10%	3.33%	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
vg0815916978	C -> T	LOC_Os08g26160.1	downstream_gene_variant ; 973.0bp to feature; MODIFIER	silent_mutation	Average:32.188; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg0815916978	C -> T	LOC_Os08g26170.1	downstream_gene_variant ; 3649.0bp to feature; MODIFIER	silent_mutation	Average:32.188; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg0815916978	C -> T	LOC_Os08g26160-LOC_Os08g26170	intergenic_region ; MODIFIER	silent_mutation	Average:32.188; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815916978	6.74E-06	5.38E-07	mr1308_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
vg0815916978	6.44E-06	NA	mr1361_2	Jap_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