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Detailed information for vg1223867548:

Variant ID: vg1223867548 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23867548
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAGCCCCGGTTTTTATTGCAACCGGGACTATTGTGGAATTTGGCCGACCGACGAAAGATGGTTTCTCCACCAGTGAAATGCTTATATTTTAGGACGGA[G/A]
GGAGTATATAATTGTGCTGTGAATGATGTTAAATCAGAGAGTAGGAAGATCTTAGGCTAAAAAAGCCATATATATTGTCTGCCAAAGTTATCGACAGGTG

Reverse complement sequence

CACCTGTCGATAACTTTGGCAGACAATATATATGGCTTTTTTAGCCTAAGATCTTCCTACTCTCTGATTTAACATCATTCACAGCACAATTATATACTCC[C/T]
TCCGTCCTAAAATATAAGCATTTCACTGGTGGAGAAACCATCTTTCGTCGGTCGGCCAAATTCCACAATAGTCCCGGTTGCAATAAAAACCGGGGCTAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	5.30%	1.29%	2.41%	NA
All Indica	2759	97.70%	0.30%	1.12%	0.83%	NA
All Japonica	1512	76.90%	15.70%	1.65%	5.82%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	91.00%	0.60%	4.95%	3.44%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.50%	0.60%	1.02%	0.89%	NA
Temperate Japonica	767	85.00%	12.10%	0.91%	1.96%	NA
Tropical Japonica	504	73.60%	11.70%	2.98%	11.71%	NA
Japonica Intermediate	241	57.70%	35.30%	1.24%	5.81%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	3.30%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223867548	G -> DEL	N	N	silent_mutation	Average:61.449; most accessible tissue: Zhenshan97 flower, score: 86.841	N	N	N	N
vg1223867548	G -> A	LOC_Os12g38840.1	upstream_gene_variant ; 1102.0bp to feature; MODIFIER	silent_mutation	Average:61.449; most accessible tissue: Zhenshan97 flower, score: 86.841	N	N	N	N
vg1223867548	G -> A	LOC_Os12g38840-LOC_Os12g38850	intergenic_region ; MODIFIER	silent_mutation	Average:61.449; most accessible tissue: Zhenshan97 flower, score: 86.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223867548	8.00E-07	NA	mr1907	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