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Detailed information for vg1200353183:

Variant ID: vg1200353183 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 353183
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAACTAATACTCTGGTGCTTACAGTTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCACTTGGTCTAGGAGTAAGTGGCGC[T/G]
GCATTGGCAACAGTGACTTCTGAGTATGTTGAACTTACTGTGAGACTTTACAACAAATTTACCTTTTCTTTCAATTGTAGTCTCTTCACTTATCTCAATA

Reverse complement sequence

TATTGAGATAAGTGAAGAGACTACAATTGAAAGAAAAGGTAAATTTGTTGTAAAGTCTCACAGTAAGTTCAACATACTCAGAAGTCACTGTTGCCAATGC[A/C]
GCGCCACTTACTCCTAGACCAAGTGGAAAAATAAATATAGCATCCAGCAATGCATTCACTAGGTTACCAGCAACTGTAAGCACCAGAGTATTAGTTTCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.90%	38.80%	0.25%	0.02%	NA
All Indica	2759	35.90%	63.70%	0.40%	0.04%	NA
All Japonica	1512	96.40%	3.60%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	47.20%	52.60%	0.17%	0.00%	NA
Indica II	465	18.10%	81.10%	0.65%	0.22%	NA
Indica III	913	38.20%	61.60%	0.22%	0.00%	NA
Indica Intermediate	786	35.10%	64.20%	0.64%	0.00%	NA
Temperate Japonica	767	94.70%	5.30%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.20%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg1200353183	T -> DEL	LOC_Os12g01580.2	N	frameshift_variant	Average:49.878; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353183	T -> DEL	LOC_Os12g01580.1	N	frameshift_variant	Average:49.878; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353183	T -> G	LOC_Os12g01580.1	synonymous_variant ; p.Ala302Ala; LOW	synonymous_codon	Average:49.878; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353183	T -> G	LOC_Os12g01580.2	synonymous_variant ; p.Ala91Ala; LOW	synonymous_codon	Average:49.878; most accessible tissue: Callus, score: 77.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200353183	NA	2.19E-08	mr1174	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