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Detailed information for vg0819439793:

Variant ID: vg0819439793 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19439793
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTAAGGGGTATCTCTTTCCTTGCAGAGGCGAGATCCGGCCTTCACAAACTTCTCCCGGCCAACCACACGTAGATCGGTGGCTCGGGAGTGACACCTAGC[C/T]
ATCTAGGAGTCCTCAACCTCCAAGAGTAACAAACACCACACAACTCTTGGTCAAACCCTAGTGCTTAAGATCGAGTGAAACACACACTAGGTCCTCAAAT

Reverse complement sequence

ATTTGAGGACCTAGTGTGTGTTTCACTCGATCTTAAGCACTAGGGTTTGACCAAGAGTTGTGTGGTGTTTGTTACTCTTGGAGGTTGAGGACTCCTAGAT[G/A]
GCTAGGTGTCACTCCCGAGCCACCGATCTACGTGTGGTTGGCCGGGAGAAGTTTGTGAAGGCCGGATCTCGCCTCTGCAAGGAAAGAGATACCCCTTAGT

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	72.30%	0.90%	4.23%	22.56%	NA
All Indica	2759	55.80%	0.20%	6.45%	37.59%	NA
All Japonica	1512	99.40%	0.00%	0.00%	0.60%	NA
Aus	269	77.70%	14.50%	6.69%	1.12%	NA
Indica I	595	32.90%	0.20%	10.59%	56.30%	NA
Indica II	465	23.00%	0.00%	8.17%	68.82%	NA
Indica III	913	82.00%	0.00%	3.40%	14.57%	NA
Indica Intermediate	786	62.00%	0.50%	5.85%	31.68%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	0.00%	4.44%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819439793	C -> T	LOC_Os08g31420.1	upstream_gene_variant ; 2323.0bp to feature; MODIFIER	silent_mutation	Average:15.797; most accessible tissue: Callus, score: 25.29	N	N	N	N
vg0819439793	C -> T	LOC_Os08g31430.1	downstream_gene_variant ; 1445.0bp to feature; MODIFIER	silent_mutation	Average:15.797; most accessible tissue: Callus, score: 25.29	N	N	N	N
vg0819439793	C -> T	LOC_Os08g31420-LOC_Os08g31430	intergenic_region ; MODIFIER	silent_mutation	Average:15.797; most accessible tissue: Callus, score: 25.29	N	N	N	N
vg0819439793	C -> DEL	N	N	silent_mutation	Average:15.797; most accessible tissue: Callus, score: 25.29	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819439793	1.30E-06	1.02E-08	mr1383_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