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Detailed information for vg0816119183:

Variant ID: vg0816119183 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16119183
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTTTGTGTACGCGTTTTCAAGCTTCTCCTCGTGCTTCACATCGTCAAGCGGTCAAGCGAATAATGAGGTATTTGAATCATACACTTGAGTTTGGAATT[T/C]
GGTATTCTACTTCATCTTCTATATGCTTGAGTGGATATTCCGATGTTGATTTTGGTGGTTGTAGAATTGATAGGAAAAGTACTAGTGGAACATGTCATTT

Reverse complement sequence

AAATGACATGTTCCACTAGTACTTTTCCTATCAATTCTACAACCACCAAAATCAACATCGGAATATCCACTCAAGCATATAGAAGATGAAGTAGAATACC[A/G]
AATTCCAAACTCAAGTGTATGATTCAAATACCTCATTATTCGCTTGACCGCTTGACGATGTGAAGCACGAGGAGAAGCTTGAAAACGCGTACACAAACAC

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	96.70%	1.30%	1.90%	0.17%	NA
All Indica	2759	99.00%	0.40%	0.40%	0.18%	NA
All Japonica	1512	91.70%	3.10%	5.09%	0.13%	NA
Aus	269	98.50%	0.70%	0.37%	0.37%	NA
Indica I	595	99.20%	0.30%	0.17%	0.34%	NA
Indica II	465	98.30%	0.00%	1.51%	0.22%	NA
Indica III	913	99.20%	0.50%	0.11%	0.11%	NA
Indica Intermediate	786	99.10%	0.50%	0.25%	0.13%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	80.60%	7.50%	11.90%	0.00%	NA
Japonica Intermediate	241	89.20%	3.70%	6.64%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0816119183	T -> C	LOC_Os08g26470.1	upstream_gene_variant ; 3369.0bp to feature; MODIFIER	silent_mutation	Average:7.699; most accessible tissue: Callus, score: 24.644	N	N	N	N
vg0816119183	T -> C	LOC_Os08g26450.1	downstream_gene_variant ; 133.0bp to feature; MODIFIER	silent_mutation	Average:7.699; most accessible tissue: Callus, score: 24.644	N	N	N	N
vg0816119183	T -> C	LOC_Os08g26460.1	downstream_gene_variant ; 1588.0bp to feature; MODIFIER	silent_mutation	Average:7.699; most accessible tissue: Callus, score: 24.644	N	N	N	N
vg0816119183	T -> C	LOC_Os08g26450-LOC_Os08g26460	intergenic_region ; MODIFIER	silent_mutation	Average:7.699; most accessible tissue: Callus, score: 24.644	N	N	N	N
vg0816119183	T -> DEL	N	N	silent_mutation	Average:7.699; most accessible tissue: Callus, score: 24.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816119183	2.00E-07	NA	mr1496	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
vg0816119183	2.05E-06	NA	mr1496	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