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Detailed information for vg1220410178:

Variant ID: vg1220410178 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 20410178
Reference Allele: A	Alternative Allele: G,AG
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.14, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGAAACTCCCAAGGAACCGGTCCGTCCGGCCCATGGCCTGGTCTGACCGGTGGTCAGTGGTGCGGTTAGACCGGCCACAGGAGGCGCGATCTGGCCT[A/G,AG]
GATAGGGCACAGTCTGACCGGCTATGGTAGGCACGGTCTGACCGGCATAGGGTGCGGTTAGACCAGTGTCACGACCGGTCATACCGTGTTATGCCCAGAA

Reverse complement sequence

TTCTGGGCATAACACGGTATGACCGGTCGTGACACTGGTCTAACCGCACCCTATGCCGGTCAGACCGTGCCTACCATAGCCGGTCAGACTGTGCCCTATC[T/C,CT]
AGGCCAGATCGCGCCTCCTGTGGCCGGTCTAACCGCACCACTGACCACCGGTCAGACCAGGCCATGGGCCGGACGGACCGGTTCCTTGGGAGTTTCTCCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.30%	15.30%	2.41%	51.63%	AG: 0.32%
All Indica	2759	13.00%	24.00%	1.92%	61.00%	AG: 0.04%
All Japonica	1512	65.30%	1.00%	3.90%	28.97%	AG: 0.86%
Aus	269	13.40%	11.50%	0.74%	74.35%	NA
Indica I	595	33.90%	2.90%	2.02%	61.18%	NA
Indica II	465	11.00%	33.10%	1.29%	54.41%	AG: 0.22%
Indica III	913	1.00%	36.90%	1.53%	60.57%	NA
Indica Intermediate	786	12.30%	19.70%	2.67%	65.27%	NA
Temperate Japonica	767	94.30%	0.30%	0.13%	5.22%	AG: 0.13%
Tropical Japonica	504	20.40%	2.60%	6.94%	68.45%	AG: 1.59%
Japonica Intermediate	241	66.80%	0.00%	9.54%	21.99%	AG: 1.66%
VI/Aromatic	96	8.30%	3.10%	0.00%	88.54%	NA
Intermediate	90	46.70%	14.40%	0.00%	37.78%	AG: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220410178	A -> AG	LOC_Os12g33840.1	downstream_gene_variant ; 4844.0bp to feature; MODIFIER	silent_mutation	Average:13.625; most accessible tissue: Callus, score: 40.412	N	N	N	N
vg1220410178	A -> AG	LOC_Os12g33840-LOC_Os12g33870	intergenic_region ; MODIFIER	silent_mutation	Average:13.625; most accessible tissue: Callus, score: 40.412	N	N	N	N
vg1220410178	A -> DEL	N	N	silent_mutation	Average:13.625; most accessible tissue: Callus, score: 40.412	N	N	N	N
vg1220410178	A -> G	LOC_Os12g33840.1	downstream_gene_variant ; 4843.0bp to feature; MODIFIER	silent_mutation	Average:13.625; most accessible tissue: Callus, score: 40.412	N	N	N	N
vg1220410178	A -> G	LOC_Os12g33840-LOC_Os12g33870	intergenic_region ; MODIFIER	silent_mutation	Average:13.625; most accessible tissue: Callus, score: 40.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220410178	NA	8.04E-06	mr1123	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