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Detailed information for vg1125417163:

Variant ID: vg1125417163 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25417163
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACTAAAGATCATCTTTAGCCCCGGTTTTTATTGCATCCGGGACTATTGTGGAAATCGGCCGACCGACGAAAGATGGTTTCTCCACCGGTGTTAATTTG[T/G]
TGATGGCTACTAGCTTGTTGGATCTAAATACTGATCCTTGTTTCAAACATGGGTCGTTTTATAGCGTATACTCACTTTGTTTTGTTTTATTGTATAAGAC

Reverse complement sequence

GTCTTATACAATAAAACAAAACAAAGTGAGTATACGCTATAAAACGACCCATGTTTGAAACAAGGATCAGTATTTAGATCCAACAAGCTAGTAGCCATCA[A/C]
CAAATTAACACCGGTGGAGAAACCATCTTTCGTCGGTCGGCCGATTTCCACAATAGTCCCGGATGCAATAAAAACCGGGGCTAAAGATGATCTTTAGTCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.00%	17.50%	5.99%	1.52%	NA
All Indica	2759	84.50%	6.40%	7.32%	1.81%	NA
All Japonica	1512	60.80%	33.00%	4.83%	1.32%	NA
Aus	269	64.70%	33.50%	1.86%	0.00%	NA
Indica I	595	78.20%	9.10%	10.92%	1.85%	NA
Indica II	465	87.30%	8.60%	3.66%	0.43%	NA
Indica III	913	88.80%	3.30%	5.70%	2.19%	NA
Indica Intermediate	786	82.60%	6.60%	8.65%	2.16%	NA
Temperate Japonica	767	44.70%	51.40%	3.13%	0.78%	NA
Tropical Japonica	504	82.10%	8.90%	6.55%	2.38%	NA
Japonica Intermediate	241	67.60%	24.90%	6.64%	0.83%	NA
VI/Aromatic	96	51.00%	49.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	14.40%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125417163	T -> DEL	N	N	silent_mutation	Average:21.864; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1125417163	T -> G	LOC_Os11g42190.1	upstream_gene_variant ; 829.0bp to feature; MODIFIER	silent_mutation	Average:21.864; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1125417163	T -> G	LOC_Os11g42190-LOC_Os11g42200	intergenic_region ; MODIFIER	silent_mutation	Average:21.864; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125417163	3.09E-07	3.09E-07	mr1499	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
vg1125417163	1.34E-06	NA	mr1745	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