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Detailed information for vg0808821817:

Variant ID: vg0808821817 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8821817
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGAAGTACATCACCTACTACTAAAGAATAATTTGCCGTAAACACTGCTGGAGAAACCATCTTTCGTTGGTCGGCCGATTTCCATAATAGTCCCGGATG[C/T]
AATAAAAACCGGGGCTAAAGATGATCTTTAGTCCCGGTTCAAAAGGGTAACGGGCATATTTGATCTTTAGTCCCGGTTGGTAACACCAACCGGGACTAAT

Reverse complement sequence

ATTAGTCCCGGTTGGTGTTACCAACCGGGACTAAAGATCAAATATGCCCGTTACCCTTTTGAACCGGGACTAAAGATCATCTTTAGCCCCGGTTTTTATT[G/A]
CATCCGGGACTATTATGGAAATCGGCCGACCAACGAAAGATGGTTTCTCCAGCAGTGTTTACGGCAAATTATTCTTTAGTAGTAGGTGATGTACTTCACA

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	41.70%	1.20%	45.07%	12.08%	NA
All Indica	2759	18.50%	1.90%	68.97%	10.62%	NA
All Japonica	1512	86.30%	0.00%	1.65%	12.04%	NA
Aus	269	39.80%	0.40%	45.35%	14.50%	NA
Indica I	595	24.90%	1.00%	54.12%	20.00%	NA
Indica II	465	4.10%	3.00%	82.80%	10.11%	NA
Indica III	913	26.10%	1.40%	68.46%	4.05%	NA
Indica Intermediate	786	13.40%	2.50%	72.65%	11.45%	NA
Temperate Japonica	767	95.30%	0.00%	0.78%	3.91%	NA
Tropical Japonica	504	76.80%	0.00%	2.98%	20.24%	NA
Japonica Intermediate	241	77.60%	0.00%	1.66%	20.75%	NA
VI/Aromatic	96	13.50%	0.00%	44.79%	41.67%	NA
Intermediate	90	37.80%	2.20%	41.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808821817	C -> T	LOC_Os08g14670.1	upstream_gene_variant ; 799.0bp to feature; MODIFIER	silent_mutation	Average:25.311; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0808821817	C -> T	LOC_Os08g14660-LOC_Os08g14670	intergenic_region ; MODIFIER	silent_mutation	Average:25.311; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0808821817	C -> DEL	N	N	silent_mutation	Average:25.311; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808821817	NA	9.26E-07	mr1586	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