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Detailed information for vg1119956594:

Variant ID: vg1119956594 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19956594
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.30, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTGTGTTCTATTGTTGGCTTAGCGGCGGTCGGTTACGCTTAGCGGCGGCCAGTCCGGTGCTAGCCTTCTCCTGGATCCGTGTTTGGCGCTGTCGGTGT[A/G]
TGGGTGGTGATATATTTTTTTTCGTTTTTCTAGTTACGACCTTTTAGGGTTGTAATATTGTAATATTTTCCTACTCTATCGATAGAACTTCGTCGTTCAA

Reverse complement sequence

TTGAACGACGAAGTTCTATCGATAGAGTAGGAAAATATTACAATATTACAACCCTAAAAGGTCGTAACTAGAAAAACGAAAAAAAATATATCACCACCCA[T/C]
ACACCGACAGCGCCAAACACGGATCCAGGAGAAGGCTAGCACCGGACTGGCCGCCGCTAAGCGTAACCGACCGCCGCTAAGCCAACAATAGAACACAGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.60%	18.50%	0.57%	58.32%	NA
All Indica	2759	2.00%	13.70%	0.87%	83.40%	NA
All Japonica	1512	60.60%	31.70%	0.00%	7.74%	NA
Aus	269	1.50%	0.00%	1.12%	97.40%	NA
Indica I	595	1.00%	9.70%	1.01%	88.24%	NA
Indica II	465	1.50%	2.20%	1.51%	94.84%	NA
Indica III	913	1.40%	21.90%	0.44%	76.23%	NA
Indica Intermediate	786	3.80%	14.00%	0.89%	81.30%	NA
Temperate Japonica	767	80.30%	13.80%	0.00%	5.87%	NA
Tropical Japonica	504	45.80%	43.80%	0.00%	10.32%	NA
Japonica Intermediate	241	28.60%	63.10%	0.00%	8.30%	NA
VI/Aromatic	96	67.70%	4.20%	0.00%	28.12%	NA
Intermediate	90	32.20%	13.30%	0.00%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119956594	A -> DEL	N	N	silent_mutation	Average:20.203; most accessible tissue: Zhenshan97 young leaf, score: 27.047	N	N	N	N
vg1119956594	A -> G	LOC_Os11g34090.1	downstream_gene_variant ; 3245.0bp to feature; MODIFIER	silent_mutation	Average:20.203; most accessible tissue: Zhenshan97 young leaf, score: 27.047	N	N	N	N
vg1119956594	A -> G	LOC_Os11g34100.1	downstream_gene_variant ; 749.0bp to feature; MODIFIER	silent_mutation	Average:20.203; most accessible tissue: Zhenshan97 young leaf, score: 27.047	N	N	N	N
vg1119956594	A -> G	LOC_Os11g34110.1	downstream_gene_variant ; 178.0bp to feature; MODIFIER	silent_mutation	Average:20.203; most accessible tissue: Zhenshan97 young leaf, score: 27.047	N	N	N	N
vg1119956594	A -> G	LOC_Os11g34100-LOC_Os11g34110	intergenic_region ; MODIFIER	silent_mutation	Average:20.203; most accessible tissue: Zhenshan97 young leaf, score: 27.047	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119956594	4.21E-07	4.21E-07	mr1417	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
vg1119956594	1.19E-06	6.07E-07	mr1988	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