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Detailed information for vg1116841607:

Variant ID: vg1116841607 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16841607
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATCTAAAATCATGATCTACATGTTTGTTTACTTTATATGTATTGTTTATTTGGAGTTTCTTAGTCTTTTTCCTCGTTTTGCGTGTTAGCTTGTCATTTC[C/T]
GTCGTTTCGAAGGTTCGCGTGTGCGTCGGGAGTATTCAAGAAGATTAATTGAAGACCGATTATTGCAAGGCAAGTCACACAGATCCCAAACACAATACCT

Reverse complement sequence

AGGTATTGTGTTTGGGATCTGTGTGACTTGCCTTGCAATAATCGGTCTTCAATTAATCTTCTTGAATACTCCCGACGCACACGCGAACCTTCGAAACGAC[G/A]
GAAATGACAAGCTAACACGCAAAACGAGGAAAAAGACTAAGAAACTCCAAATAAACAATACATATAAAGTAAACAAACATGTAGATCATGATTTTAGATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.10%	2.10%	20.46%	14.37%	NA
All Indica	2759	47.40%	3.40%	29.29%	19.97%	NA
All Japonica	1512	94.10%	0.10%	2.12%	3.70%	NA
Aus	269	37.50%	0.00%	40.15%	22.30%	NA
Indica I	595	75.10%	10.40%	4.37%	10.08%	NA
Indica II	465	43.90%	0.60%	29.25%	26.24%	NA
Indica III	913	28.30%	0.50%	48.08%	23.11%	NA
Indica Intermediate	786	50.60%	2.90%	26.34%	20.10%	NA
Temperate Japonica	767	98.00%	0.10%	0.26%	1.56%	NA
Tropical Japonica	504	90.90%	0.00%	4.56%	4.56%	NA
Japonica Intermediate	241	88.40%	0.00%	2.90%	8.71%	NA
VI/Aromatic	96	95.80%	0.00%	3.12%	1.04%	NA
Intermediate	90	64.40%	5.60%	17.78%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116841607	C -> T	LOC_Os11g29074.1	upstream_gene_variant ; 1562.0bp to feature; MODIFIER	silent_mutation	Average:17.893; most accessible tissue: Zhenshan97 flag leaf, score: 33.231	N	N	N	N
vg1116841607	C -> T	LOC_Os11g29060.1	downstream_gene_variant ; 2819.0bp to feature; MODIFIER	silent_mutation	Average:17.893; most accessible tissue: Zhenshan97 flag leaf, score: 33.231	N	N	N	N
vg1116841607	C -> T	LOC_Os11g29060-LOC_Os11g29074	intergenic_region ; MODIFIER	silent_mutation	Average:17.893; most accessible tissue: Zhenshan97 flag leaf, score: 33.231	N	N	N	N
vg1116841607	C -> DEL	N	N	silent_mutation	Average:17.893; most accessible tissue: Zhenshan97 flag leaf, score: 33.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116841607	1.21E-06	6.06E-06	mr1695	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