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Detailed information for vg0805661208:

Variant ID: vg0805661208 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5661208
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCATTTGAGCAGGGGTGTTGAGTATTATGTGTTTAGGGGTATATTAGTAATTTCCTATCTCTATTGTACTCATATATGCCCTTTGGGCTAACACAATA[G/C]
CAACTGTTCATTCTCCAATTTCCCCCAAATTGTGACAACTCACACTGGCCACAGGCACTATTGTGCTTGATGATTCACTTTTATGTGCTGGTTTTGATTA

Reverse complement sequence

TAATCAAAACCAGCACATAAAAGTGAATCATCAAGCACAATAGTGCCTGTGGCCAGTGTGAGTTGTCACAATTTGGGGGAAATTGGAGAATGAACAGTTG[C/G]
TATTGTGTTAGCCCAAAGGGCATATATGAGTACAATAGAGATAGGAAATTACTAATATACCCCTAAACACATAATACTCAACACCCCTGCTCAAATGCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.60%	2.90%	1.61%	34.89%	NA
All Indica	2759	49.00%	0.00%	1.41%	49.51%	NA
All Japonica	1512	84.50%	9.10%	1.32%	5.09%	NA
Aus	269	53.90%	0.00%	1.49%	44.61%	NA
Indica I	595	50.60%	0.20%	2.02%	47.23%	NA
Indica II	465	81.90%	0.00%	1.72%	16.34%	NA
Indica III	913	24.80%	0.00%	0.77%	74.48%	NA
Indica Intermediate	786	56.60%	0.00%	1.53%	41.86%	NA
Temperate Japonica	767	82.70%	15.30%	1.83%	0.26%	NA
Tropical Japonica	504	85.10%	1.00%	0.40%	13.49%	NA
Japonica Intermediate	241	89.20%	6.20%	1.66%	2.90%	NA
VI/Aromatic	96	25.00%	0.00%	10.42%	64.58%	NA
Intermediate	90	70.00%	0.00%	3.33%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805661208	G -> C	LOC_Os08g09800.1	downstream_gene_variant ; 2370.0bp to feature; MODIFIER	silent_mutation	Average:28.327; most accessible tissue: Callus, score: 61.703	N	N	N	N
vg0805661208	G -> C	LOC_Os08g09790.1	intron_variant ; MODIFIER	silent_mutation	Average:28.327; most accessible tissue: Callus, score: 61.703	N	N	N	N
vg0805661208	G -> DEL	N	N	silent_mutation	Average:28.327; most accessible tissue: Callus, score: 61.703	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805661208	1.36E-06	1.36E-06	mr1465	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