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Detailed information for vg0826953770:

Variant ID: vg0826953770 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26953770
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGCTGAATATGACATGGCGCTGAGGTGTCTAAGTTCAGCGCCAGGTGATTTGGCGCTGACCAAAAGAGTCATTTTTGAAATAAGTTTTGGCAGCGGTT[T/C]
ATTTGTAAAAAAAGTTTTTGCAAAGGGTCAAATTGTGAAAATTTCAGAAATAACTACATACTAGTTGTGTGGCACCTTTTTGGGGGAGCTCGACATGTCA

Reverse complement sequence

TGACATGTCGAGCTCCCCCAAAAAGGTGCCACACAACTAGTATGTAGTTATTTCTGAAATTTTCACAATTTGACCCTTTGCAAAAACTTTTTTTACAAAT[A/G]
AACCGCTGCCAAAACTTATTTCAAAAATGACTCTTTTGGTCAGCGCCAAATCACCTGGCGCTGAACTTAGACACCTCAGCGCCATGTCATATTCAGCGCC

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	71.40%	27.10%	0.06%	1.44%	NA
All Indica	2759	98.40%	1.10%	0.00%	0.47%	NA
All Japonica	1512	24.00%	75.80%	0.07%	0.13%	NA
Aus	269	80.70%	0.70%	0.74%	17.84%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	97.80%	0.40%	0.00%	1.72%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.40%	0.00%	0.64%	NA
Temperate Japonica	767	9.10%	90.90%	0.00%	0.00%	NA
Tropical Japonica	504	39.30%	60.10%	0.20%	0.40%	NA
Japonica Intermediate	241	39.40%	60.60%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	78.10%	0.00%	3.12%	NA
Intermediate	90	70.00%	27.80%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826953770	T -> C	LOC_Os08g42650.1	upstream_gene_variant ; 2774.0bp to feature; MODIFIER	silent_mutation	Average:52.973; most accessible tissue: Callus, score: 77.517	N	N	N	N
vg0826953770	T -> C	LOC_Os08g42640.1	downstream_gene_variant ; 255.0bp to feature; MODIFIER	silent_mutation	Average:52.973; most accessible tissue: Callus, score: 77.517	N	N	N	N
vg0826953770	T -> C	LOC_Os08g42640-LOC_Os08g42650	intergenic_region ; MODIFIER	silent_mutation	Average:52.973; most accessible tissue: Callus, score: 77.517	N	N	N	N
vg0826953770	T -> DEL	N	N	silent_mutation	Average:52.973; most accessible tissue: Callus, score: 77.517	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826953770	NA	4.74E-17	mr1116	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
vg0826953770	NA	1.49E-27	mr1148	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
vg0826953770	NA	1.65E-10	mr1307	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
vg0826953770	NA	7.87E-09	mr1575	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
vg0826953770	5.42E-07	3.64E-42	mr1601	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
vg0826953770	NA	2.52E-06	mr1646	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
vg0826953770	NA	2.06E-08	mr1776	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