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Detailed information for vg1109901210:

Variant ID: vg1109901210 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9901210
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATATGTTATTTTATACCTTAGCCCGCTTCCTGTTAATATCATCTATTATATATTGATAGTCCATTAAACATCCTACAAACGTACTCAGGACACCACGTA[T/G]
CACTCCTACAAATGCTCCTACGTCGCCACATGACATTTTAATAAATTAGAAAAATCACAAAAAATTTGAGAATAAATAAAACATTTGGCCATCGATTTTC

Reverse complement sequence

GAAAATCGATGGCCAAATGTTTTATTTATTCTCAAATTTTTTGTGATTTTTCTAATTTATTAAAATGTCATGTGGCGACGTAGGAGCATTTGTAGGAGTG[A/C]
TACGTGGTGTCCTGAGTACGTTTGTAGGATGTTTAATGGACTATCAATATATAATAGATGATATTAACAGGAAGCGGGCTAAGGTATAAAATAACATATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.00%	17.20%	5.46%	18.41%	NA
All Indica	2759	39.30%	28.00%	8.16%	24.50%	NA
All Japonica	1512	97.90%	0.70%	0.13%	1.32%	NA
Aus	269	33.50%	2.60%	2.60%	61.34%	NA
Indica I	595	48.10%	21.70%	15.13%	15.13%	NA
Indica II	465	48.20%	26.20%	5.81%	19.78%	NA
Indica III	913	20.70%	37.10%	6.35%	35.82%	NA
Indica Intermediate	786	49.10%	23.30%	6.36%	21.25%	NA
Temperate Japonica	767	97.70%	0.00%	0.13%	2.22%	NA
Tropical Japonica	504	98.00%	1.40%	0.00%	0.60%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	66.70%	10.40%	22.92%	0.00%	NA
Intermediate	90	74.40%	13.30%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109901210	T -> DEL	N	N	silent_mutation	Average:34.407; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg1109901210	T -> G	LOC_Os11g17720.1	upstream_gene_variant ; 2958.0bp to feature; MODIFIER	silent_mutation	Average:34.407; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg1109901210	T -> G	LOC_Os11g17730.1	downstream_gene_variant ; 3084.0bp to feature; MODIFIER	silent_mutation	Average:34.407; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg1109901210	T -> G	LOC_Os11g17720-LOC_Os11g17730	intergenic_region ; MODIFIER	silent_mutation	Average:34.407; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109901210	NA	5.05E-06	mr1044	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
vg1109901210	8.30E-07	2.63E-07	mr1741	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
vg1109901210	NA	1.71E-06	mr1154_2	Ind_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