Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1200812566:

Variant ID: vg1200812566 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 812566
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GCAACAAGTAAGCAAAACAAATTTCAACGTGTTGTCATCTGCTCCGGTTAGCTCTTCTTGTGTTCTTGGTGCTGATTGATTGGTTCTGTAGGTGGAACAC[G/A,C]
CACATCAAGCGCAAGCTCATGAGCCAGGGCATCGATCCGCAGACGCATCAGCCAGTTAGCGCCGGGACCAGCGTTGCCGCGGCAAGTGAGCTGATCACGA

Reverse complement sequence

TCGTGATCAGCTCACTTGCCGCGGCAACGCTGGTCCCGGCGCTAACTGGCTGATGCGTCTGCGGATCGATGCCCTGGCTCATGAGCTTGCGCTTGATGTG[C/T,G]
GTGTTCCACCTACAGAACCAATCAATCAGCACCAAGAACACAAGAAGAGCTAACCGGAGCAGATGACAACACGTTGAAATTTGTTTTGCTTACTTGTTGC

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	67.40%	14.00%	18.28%	0.28%	NA
All Indica	2759	48.60%	22.70%	28.56%	0.11%	NA
All Japonica	1512	93.80%	1.60%	3.97%	0.60%	NA
Aus	269	97.40%	0.40%	2.23%	0.00%	NA
Indica I	595	54.80%	17.60%	27.56%	0.00%	NA
Indica II	465	42.60%	17.40%	39.35%	0.65%	NA
Indica III	913	49.90%	30.10%	19.93%	0.00%	NA
Indica Intermediate	786	45.90%	21.10%	32.95%	0.00%	NA
Temperate Japonica	767	91.00%	1.60%	6.39%	1.04%	NA
Tropical Japonica	504	96.80%	2.00%	0.99%	0.20%	NA
Japonica Intermediate	241	96.70%	0.80%	2.49%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	8.90%	11.11%	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
vg1200812566	G -> C	LOC_Os12g02430.1	synonymous_variant ; p.Thr48Thr; LOW	N	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg1200812566	G -> C	LOC_Os12g02440.4	downstream_gene_variant ; 4437.0bp to feature; MODIFIER	N	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg1200812566	G -> C	LOC_Os12g02440.3	downstream_gene_variant ; 4437.0bp to feature; MODIFIER	N	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg1200812566	G -> C	LOC_Os12g02440.2	downstream_gene_variant ; 4437.0bp to feature; MODIFIER	N	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg1200812566	G -> C	LOC_Os12g02440.1	downstream_gene_variant ; 4437.0bp to feature; MODIFIER	N	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg1200812566	G -> DEL	LOC_Os12g02430.1	N	frameshift_variant	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg1200812566	G -> A	LOC_Os12g02430.1	synonymous_variant ; p.Thr48Thr; LOW	synonymous_codon	Average:53.479; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200812566	1.37E-06	NA	mr1471	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
vg1200812566	7.22E-06	NA	mr1684	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