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Detailed information for vg0814220368:

Variant ID: vg0814220368 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14220368
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTTTGCCAGTACTCACCTAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAGTGCACACCGGTGAATTTATCCGGC[C/T]
TCAATGTATCGGCAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTGGATTGTTGAGATTAAAGGCATATAATGATTTAATATATTCCA

Reverse complement sequence

TGGAATATATTAAATCATTATATGCCTTTAATCTCAACAATCCAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTGCCGATACATTGA[G/A]
GCCGGATAAATTCACCGGTGTGCACTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTAGGTGAGTACTGGCAAACCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.20%	19.50%	14.56%	12.70%	NA
All Indica	2759	81.10%	1.20%	16.96%	0.69%	NA
All Japonica	1512	11.90%	56.20%	4.76%	27.18%	NA
Aus	269	17.10%	2.20%	43.12%	37.55%	NA
Indica I	595	74.10%	0.70%	25.21%	0.00%	NA
Indica II	465	77.20%	1.70%	20.86%	0.22%	NA
Indica III	913	89.50%	1.10%	8.76%	0.66%	NA
Indica Intermediate	786	79.00%	1.50%	17.94%	1.53%	NA
Temperate Japonica	767	11.00%	84.60%	2.48%	1.96%	NA
Tropical Japonica	504	13.90%	24.00%	6.35%	55.75%	NA
Japonica Intermediate	241	10.80%	32.80%	8.71%	47.72%	NA
VI/Aromatic	96	11.50%	9.40%	26.04%	53.12%	NA
Intermediate	90	44.40%	27.80%	7.78%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0814220368	C -> T	LOC_Os08g23480.1	upstream_gene_variant ; 34.0bp to feature; MODIFIER	silent_mutation	Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0814220368	C -> T	LOC_Os08g23490.1	upstream_gene_variant ; 2457.0bp to feature; MODIFIER	silent_mutation	Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0814220368	C -> T	LOC_Os08g23480-LOC_Os08g23490	intergenic_region ; MODIFIER	silent_mutation	Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N
vg0814220368	C -> DEL	N	N	silent_mutation	Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814220368	2.34E-07	NA	mr1141	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
vg0814220368	NA	4.46E-07	mr1321	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
vg0814220368	NA	1.48E-09	mr1649_2	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
vg0814220368	NA	3.54E-06	mr1788_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