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Detailed information for vg1110417102:

Variant ID: vg1110417102 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10417102
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.59, A: 0.41, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

CAACGAGTTGACCGAACCCGAGGTCTCAGTCGCCGCCTGTTTTCCCCTTGGGGGTTCAAGTAGTGAAAGGCGGGGGCCGAGAAGAGGGGGTTCGAACGCC[G/A]
CAAAGGCCGCTTCCACGACGCCTTCGGCAGAAGCAGAAGCACCTGCCCCGTAGCTCCCACCCACCTCACCGGCAGAACCAGCAGCGGAGGCGGCGGCCGG

Reverse complement sequence

CCGGCCGCCGCCTCCGCTGCTGGTTCTGCCGGTGAGGTGGGTGGGAGCTACGGGGCAGGTGCTTCTGCTTCTGCCGAAGGCGTCGTGGAAGCGGCCTTTG[C/T]
GGCGTTCGAACCCCCTCTTCTCGGCCCCCGCCTTTCACTACTTGAACCCCCAAGGGGAAAACAGGCGGCGACTGAGACCTCGGGTTCGGTCAACTCGTTG

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	62.30%	35.90%	0.04%	1.76%	NA
All Indica	2759	92.00%	7.00%	0.07%	0.94%	NA
All Japonica	1512	5.10%	94.60%	0.00%	0.33%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	94.30%	5.40%	0.00%	0.34%	NA
Indica II	465	98.50%	1.10%	0.00%	0.43%	NA
Indica III	913	97.20%	2.00%	0.00%	0.88%	NA
Indica Intermediate	786	80.50%	17.40%	0.25%	1.78%	NA
Temperate Japonica	767	2.50%	97.40%	0.00%	0.13%	NA
Tropical Japonica	504	10.50%	89.30%	0.00%	0.20%	NA
Japonica Intermediate	241	2.10%	96.70%	0.00%	1.24%	NA
VI/Aromatic	96	19.80%	29.20%	0.00%	51.04%	NA
Intermediate	90	62.20%	34.40%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110417102	G -> A	LOC_Os11g18480.1	downstream_gene_variant ; 2732.0bp to feature; MODIFIER	silent_mutation	Average:61.342; most accessible tissue: Zhenshan97 young leaf, score: 86.055	N	N	N	N
vg1110417102	G -> A	LOC_Os11g18470.1	intron_variant ; MODIFIER	silent_mutation	Average:61.342; most accessible tissue: Zhenshan97 young leaf, score: 86.055	N	N	N	N
vg1110417102	G -> DEL	N	N	silent_mutation	Average:61.342; most accessible tissue: Zhenshan97 young leaf, score: 86.055	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110417102	NA	1.01E-10	mr1595	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
vg1110417102	1.50E-06	5.33E-07	mr1860	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
vg1110417102	4.61E-06	4.61E-06	mr1918	Jap_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
vg1110417102	NA	5.61E-10	mr1595_2	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