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Detailed information for vg1110154705:

Variant ID: vg1110154705 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 10154705
Reference Allele: T	Alternative Allele: TGTGAATAAAGAAAATTCCAAAGTATC,C
Primary Allele: T	Secondary Allele: TGTGAATAAAGAAAATTCCA AAGTATC

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.01, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

GATATACCGACTGCTTTGTAAAATATGATGCGAGCAACCTAAAGTTGTCTACATCTTTGAAAATTTACATAGCAAAAAACAACTATAAAAAAGCATGTAT[T/TGTGAATAAAGAAAATTCCAAAGTATC,C]
GGGCACACACCATGCACACACTGCTTTAACAAATGTGCTTAAGTCCCTAAAAGACACATAGTTTCACCACACTTAGAAATATATGGCATATGTGGTGTAA

Reverse complement sequence

TTACACCACATATGCCATATATTTCTAAGTGTGGTGAAACTATGTGTCTTTTAGGGACTTAAGCACATTTGTTAAAGCAGTGTGTGCATGGTGTGTGCCC[A/GATACTTTGGAATTTTCTTTATTCACA,G]
ATACATGCTTTTTTATAGTTGTTTTTTGCTATGTAAATTTTCAAAGATGTAGACAACTTTAGGTTGCTCGCATCATATTTTACAAAGCAGTCGGTATATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of TGTGAATAAAGAAAATTCCA AAGTATC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.30%	33.20%	14.49%	5.61%	C: 2.37%
All Indica	2759	20.50%	47.20%	21.13%	7.50%	C: 3.70%
All Japonica	1512	95.00%	1.30%	2.18%	1.26%	C: 0.26%
Aus	269	13.00%	73.20%	12.27%	0.00%	C: 1.49%
Indica I	595	25.00%	27.90%	36.47%	8.91%	C: 1.68%
Indica II	465	5.60%	73.50%	9.89%	1.94%	C: 9.03%
Indica III	913	20.70%	44.10%	19.39%	12.71%	C: 3.07%
Indica Intermediate	786	25.60%	49.70%	18.19%	3.69%	C: 2.80%
Temperate Japonica	767	97.10%	1.80%	0.52%	0.13%	C: 0.39%
Tropical Japonica	504	91.70%	0.60%	4.76%	2.78%	C: 0.20%
Japonica Intermediate	241	95.40%	0.80%	2.07%	1.66%	NA
VI/Aromatic	96	19.80%	16.70%	25.00%	38.54%	NA
Intermediate	90	41.10%	41.10%	13.33%	2.22%	C: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110154705	T -> TGTGAATAAAGAAAATTCCAAAGTATC	LOC_Os11g18070.1	downstream_gene_variant ; 2092.0bp to feature; MODIFIER	silent_mutation	Average:31.629; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg1110154705	T -> TGTGAATAAAGAAAATTCCAAAGTATC	LOC_Os11g18044-LOC_Os11g18070	intergenic_region ; MODIFIER	silent_mutation	Average:31.629; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg1110154705	T -> DEL	N	N	silent_mutation	Average:31.629; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg1110154705	T -> C	LOC_Os11g18070.1	downstream_gene_variant ; 2093.0bp to feature; MODIFIER	silent_mutation	Average:31.629; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg1110154705	T -> C	LOC_Os11g18044-LOC_Os11g18070	intergenic_region ; MODIFIER	silent_mutation	Average:31.629; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110154705	NA	8.28E-06	mr1879_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