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Detailed information for vg1108587345:

Variant ID: vg1108587345 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8587345
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGCTCCATCGTAGTTGTCCAAATCACAAAACAAAATTACAAGAATCTCAATCACCATAGGAATCAGAATCATCAATCACAGTAGCAACAATTGGAACA[C/A]
CATGAACAGCACAAGACAAAATACATGGGTGAAAGAGGACTTGTTGGCACTGGATCTGAGCTCATTGTGTGCAGCTGGAGGCAAGTCAACGCATGTGGAT

Reverse complement sequence

ATCCACATGCGTTGACTTGCCTCCAGCTGCACACAATGAGCTCAGATCCAGTGCCAACAAGTCCTCTTTCACCCATGTATTTTGTCTTGTGCTGTTCATG[G/T]
TGTTCCAATTGTTGCTACTGTGATTGATGATTCTGATTCCTATGGTGATTGAGATTCTTGTAATTTTGTTTTGTGATTTGGACAACTACGATGGAGCAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.30%	5.10%	3.58%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.07%	0.00%	NA
All Japonica	1512	74.00%	15.10%	10.85%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	54.10%	27.80%	18.12%	0.00%	NA
Tropical Japonica	504	97.60%	0.40%	1.98%	0.00%	NA
Japonica Intermediate	241	88.00%	5.80%	6.22%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108587345	C -> A	LOC_Os11g15210.1	upstream_gene_variant ; 1109.0bp to feature; MODIFIER	silent_mutation	Average:39.631; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg1108587345	C -> A	LOC_Os11g15220.1	upstream_gene_variant ; 535.0bp to feature; MODIFIER	silent_mutation	Average:39.631; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg1108587345	C -> A	LOC_Os11g15210-LOC_Os11g15220	intergenic_region ; MODIFIER	silent_mutation	Average:39.631; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108587345	3.34E-06	3.34E-06	mr1955	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