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Detailed information for vg1106620010:

Variant ID: vg1106620010 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6620010
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCTCTAGCCGGGTGTCAGGTGGCGTGCGGTAGGTATGCCCTGTCCCGTCACGATGATGAGGGGTACAACACCTCTCAACTATTCAGCGTTGGCTTGAC[T/C]
GCCTTGAACATACCCGGGATGACATTCCCGGTGCACTAACACCCCAGAATCCACATCCATTAAATGGTGAATGACGGGGATCCTCCCCGTGTCGGCCTGC

Reverse complement sequence

GCAGGCCGACACGGGGAGGATCCCCGTCATTCACCATTTAATGGATGTGGATTCTGGGGTGTTAGTGCACCGGGAATGTCATCCCGGGTATGTTCAAGGC[A/G]
GTCAAGCCAACGCTGAATAGTTGAGAGGTGTTGTACCCCTCATCATCGTGACGGGACAGGGCATACCTACCGCACGCCACCTGACACCCGGCTAGAGCAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.30%	20.20%	1.31%	47.21%	NA
All Indica	2759	7.60%	25.40%	1.92%	65.06%	NA
All Japonica	1512	76.70%	1.90%	0.33%	21.10%	NA
Aus	269	0.40%	72.90%	0.00%	26.77%	NA
Indica I	595	7.60%	9.60%	1.34%	81.51%	NA
Indica II	465	2.60%	18.90%	1.51%	76.99%	NA
Indica III	913	10.30%	38.20%	1.42%	50.05%	NA
Indica Intermediate	786	7.50%	26.30%	3.18%	62.98%	NA
Temperate Japonica	767	71.10%	1.40%	0.65%	26.86%	NA
Tropical Japonica	504	87.10%	1.40%	0.00%	11.51%	NA
Japonica Intermediate	241	73.00%	4.10%	0.00%	22.82%	NA
VI/Aromatic	96	79.20%	7.30%	1.04%	12.50%	NA
Intermediate	90	36.70%	23.30%	3.33%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106620010	T -> DEL	N	N	silent_mutation	Average:12.04; most accessible tissue: Callus, score: 61.735	N	N	N	N
vg1106620010	T -> C	LOC_Os11g11920.1	upstream_gene_variant ; 3983.0bp to feature; MODIFIER	silent_mutation	Average:12.04; most accessible tissue: Callus, score: 61.735	N	N	N	N
vg1106620010	T -> C	LOC_Os11g11930.1	upstream_gene_variant ; 1513.0bp to feature; MODIFIER	silent_mutation	Average:12.04; most accessible tissue: Callus, score: 61.735	N	N	N	N
vg1106620010	T -> C	LOC_Os11g11940.1	upstream_gene_variant ; 1632.0bp to feature; MODIFIER	silent_mutation	Average:12.04; most accessible tissue: Callus, score: 61.735	N	N	N	N
vg1106620010	T -> C	LOC_Os11g11930-LOC_Os11g11940	intergenic_region ; MODIFIER	silent_mutation	Average:12.04; most accessible tissue: Callus, score: 61.735	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106620010	NA	2.53E-09	mr1336	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
vg1106620010	3.48E-06	7.44E-07	mr1790	Jap_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