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Detailed information for vg0818684033:

Variant ID: vg0818684033 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18684033
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGACGTGTAAAACAAATATCATCGTCTTGATGAAGTTATGGAGTTATAGTTGTGGGACTCGTTTTTTTTACATAATGGATTAAACCGGCCTCTACATC[C/T]
AAACGGATGTACACAGCCAAAGTTGTGGGACTCATTTTAGTCGAGATAAATTCAAATGACACCTAAAATTAAAGATGGCCTTGTGAATTCTTACTCTGGA

Reverse complement sequence

TCCAGAGTAAGAATTCACAAGGCCATCTTTAATTTTAGGTGTCATTTGAATTTATCTCGACTAAAATGAGTCCCACAACTTTGGCTGTGTACATCCGTTT[G/A]
GATGTAGAGGCCGGTTTAATCCATTATGTAAAAAAAACGAGTCCCACAACTATAACTCCATAACTTCATCAAGACGATGATATTTGTTTTACACGTCCCA

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	79.30%	5.30%	0.61%	14.79%	NA
All Indica	2759	78.10%	2.00%	0.94%	19.03%	NA
All Japonica	1512	85.60%	3.00%	0.20%	11.18%	NA
Aus	269	48.30%	51.70%	0.00%	0.00%	NA
Indica I	595	95.30%	0.20%	0.00%	4.54%	NA
Indica II	465	92.90%	0.40%	0.86%	5.81%	NA
Indica III	913	67.10%	1.90%	1.64%	29.35%	NA
Indica Intermediate	786	69.00%	4.30%	0.89%	25.83%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	64.10%	4.80%	0.60%	30.56%	NA
Japonica Intermediate	241	85.90%	7.90%	0.00%	6.22%	NA
VI/Aromatic	96	91.70%	7.30%	0.00%	1.04%	NA
Intermediate	90	90.00%	5.60%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818684033	C -> T	LOC_Os08g30360.1	downstream_gene_variant ; 1375.0bp to feature; MODIFIER	silent_mutation	Average:49.484; most accessible tissue: Callus, score: 88.353	N	N	N	N
vg0818684033	C -> T	LOC_Os08g30370.1	downstream_gene_variant ; 1869.0bp to feature; MODIFIER	silent_mutation	Average:49.484; most accessible tissue: Callus, score: 88.353	N	N	N	N
vg0818684033	C -> T	LOC_Os08g30360-LOC_Os08g30370	intergenic_region ; MODIFIER	silent_mutation	Average:49.484; most accessible tissue: Callus, score: 88.353	N	N	N	N
vg0818684033	C -> DEL	N	N	silent_mutation	Average:49.484; most accessible tissue: Callus, score: 88.353	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818684033	2.38E-06	NA	mr1247_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