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Detailed information for vg1015988276:

Variant ID: vg1015988276 (JBrowse)	Variation Type: INDEL
Chromosome: chr10	Position: 15988276
Reference Allele: A	Alternative Allele: ATG,G
Primary Allele: ATG	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.48, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

AACTTCAGATCTATTCTTAATGAAAATGATTGATCTTGAGTTATATCCAACCATAAGCTTAATTAAGGGCATTATCTCACAAGCATGCATGCATGCATAT[A/ATG,G]
TATAGTCCAGATATGCATAGGGAGGACCTTCTCTCTCTCTCTCGAAACGTTAAGAAGTATTAGTTTCCTAAAATGGAAACAAAAAGAAGCTGGAAACAAG

Reverse complement sequence

CTTGTTTCCAGCTTCTTTTTGTTTCCATTTTAGGAAACTAATACTTCTTAACGTTTCGAGAGAGAGAGAGAAGGTCCTCCCTATGCATATCTGGACTATA[T/CAT,C]
ATATGCATGCATGCATGCTTGTGAGATAATGCCCTTAATTAAGCTTATGGTTGGATATAACTCAAGATCAATCATTTTCATTAAGAATAGATCTGAAGTT

Allele Frequencies:

Populations	Population Size	Frequency of ATG(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.90%	26.60%	0.00%	0.00%	G: 6.52%
All Indica	2759	98.30%	1.50%	0.00%	0.00%	G: 0.25%
All Japonica	1512	4.40%	76.50%	0.00%	0.00%	G: 19.11%
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	96.30%	3.20%	0.00%	0.00%	G: 0.43%
Indica III	913	99.80%	0.10%	0.00%	0.00%	G: 0.11%
Indica Intermediate	786	96.80%	2.70%	0.00%	0.00%	G: 0.51%
Temperate Japonica	767	1.40%	89.20%	0.00%	0.00%	G: 9.39%
Tropical Japonica	504	5.60%	76.20%	0.00%	0.00%	G: 18.25%
Japonica Intermediate	241	11.20%	36.90%	0.00%	0.00%	G: 51.87%
VI/Aromatic	96	72.90%	25.00%	0.00%	0.00%	G: 2.08%
Intermediate	90	51.10%	37.80%	0.00%	0.00%	G: 11.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1015988276	A -> ATG	LOC_Os10g30690.1	downstream_gene_variant ; 285.0bp to feature; MODIFIER	silent_mutation	Average:35.622; most accessible tissue: Callus, score: 73.574	N	N	N	N
vg1015988276	A -> ATG	LOC_Os10g30700.1	downstream_gene_variant ; 1503.0bp to feature; MODIFIER	silent_mutation	Average:35.622; most accessible tissue: Callus, score: 73.574	N	N	N	N
vg1015988276	A -> ATG	LOC_Os10g30690-LOC_Os10g30700	intergenic_region ; MODIFIER	silent_mutation	Average:35.622; most accessible tissue: Callus, score: 73.574	N	N	N	N
vg1015988276	A -> G	LOC_Os10g30690.1	downstream_gene_variant ; 284.0bp to feature; MODIFIER	silent_mutation	Average:35.622; most accessible tissue: Callus, score: 73.574	N	N	N	N
vg1015988276	A -> G	LOC_Os10g30700.1	downstream_gene_variant ; 1504.0bp to feature; MODIFIER	silent_mutation	Average:35.622; most accessible tissue: Callus, score: 73.574	N	N	N	N
vg1015988276	A -> G	LOC_Os10g30690-LOC_Os10g30700	intergenic_region ; MODIFIER	silent_mutation	Average:35.622; most accessible tissue: Callus, score: 73.574	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1015988276	NA	5.47E-26	mr1617	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
vg1015988276	NA	4.65E-14	mr1191_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
vg1015988276	2.87E-06	8.38E-07	mr1594_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
vg1015988276	NA	8.79E-26	mr1617_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
vg1015988276	NA	3.95E-09	mr1705_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
vg1015988276	NA	3.58E-06	mr1745_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