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Detailed information for vg0818406495:

Variant ID: vg0818406495 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18406495
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTATTTGCATGTTTTAAATGTATATAGCATTGCACTGTCTTGTGCATAAAAGAACAATTGGATATTCGGTTATTTTGGTAGAATTCTAGAGTTCTTTGC[T/C]
TTTTAAGTTTGGAATGCAAAAATTGAATATGTTTAAGTCAATTTCACATTCATTTCACAAAGCTGTTGAGCTTTTGTGCTGTGTTTTCTCCTCAATAAAA

Reverse complement sequence

TTTTATTGAGGAGAAAACACAGCACAAAAGCTCAACAGCTTTGTGAAATGAATGTGAAATTGACTTAAACATATTCAATTTTTGCATTCCAAACTTAAAA[A/G]
GCAAAGAACTCTAGAATTCTACCAAAATAACCGAATATCCAATTGTTCTTTTATGCACAAGACAGTGCAATGCTATATACATTTAAAACATGCAAATAAC

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	60.00%	11.40%	1.61%	26.96%	NA
All Indica	2759	43.70%	13.70%	2.61%	40.05%	NA
All Japonica	1512	87.70%	2.10%	0.20%	9.99%	NA
Aus	269	58.40%	40.50%	0.37%	0.74%	NA
Indica I	595	37.50%	1.30%	3.70%	57.48%	NA
Indica II	465	81.50%	7.70%	1.08%	9.68%	NA
Indica III	913	21.00%	27.60%	2.52%	48.85%	NA
Indica Intermediate	786	52.30%	10.30%	2.80%	34.61%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	72.00%	0.80%	0.60%	26.59%	NA
Japonica Intermediate	241	86.70%	6.20%	0.00%	7.05%	NA
VI/Aromatic	96	89.60%	8.30%	0.00%	2.08%	NA
Intermediate	90	67.80%	16.70%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818406495	T -> C	LOC_Os08g29960.1	upstream_gene_variant ; 3287.0bp to feature; MODIFIER	silent_mutation	Average:49.055; most accessible tissue: Callus, score: 76.987	N	N	N	N
vg0818406495	T -> C	LOC_Os08g29970.1	intron_variant ; MODIFIER	silent_mutation	Average:49.055; most accessible tissue: Callus, score: 76.987	N	N	N	N
vg0818406495	T -> DEL	N	N	silent_mutation	Average:49.055; most accessible tissue: Callus, score: 76.987	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818406495	4.18E-06	1.81E-07	mr1509_2	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