Search for Variation information by Variation ID:

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

Detailed information for vg1205555271:

Variant ID: vg1205555271 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5555271
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCCATGCGAAGTCCTCCTGTGTGATGCGTGACAATGGCACTGTTATGAATTGCTTGCCAACAATGATTCCCAACAATTTGATATGCTGCAAACAGTGA[C/T]
AACCTCGTTTGATCAACTGCAGAGTCCACCCATGTTCATGATTATGTCCATTTATTGGCATGCCAATTTCATCAGTCAAGCATATGCATTGCCCAGTAGA

Reverse complement sequence

TCTACTGGGCAATGCATATGCTTGACTGATGAAATTGGCATGCCAATAAATGGACATAATCATGAACATGGGTGGACTCTGCAGTTGATCAAACGAGGTT[G/A]
TCACTGTTTGCAGCATATCAAATTGTTGGGAATCATTGTTGGCAAGCAATTCATAACAGTGCCATTGTCACGCATCACACAGGAGGACTTCGCATGGAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.90%	24.70%	16.31%	0.04%	NA
All Indica	2759	31.10%	41.90%	26.89%	0.07%	NA
All Japonica	1512	99.00%	0.20%	0.79%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	25.90%	28.70%	45.38%	0.00%	NA
Indica II	465	15.30%	55.30%	29.46%	0.00%	NA
Indica III	913	42.50%	47.30%	10.08%	0.11%	NA
Indica Intermediate	786	31.20%	37.80%	30.92%	0.13%	NA
Temperate Japonica	767	99.30%	0.30%	0.39%	0.00%	NA
Tropical Japonica	504	98.20%	0.00%	1.79%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	76.70%	7.80%	15.56%	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
vg1205555271	C -> DEL	N	N	silent_mutation	Average:12.499; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1205555271	C -> T	LOC_Os12g10490.1	upstream_gene_variant ; 2866.0bp to feature; MODIFIER	silent_mutation	Average:12.499; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1205555271	C -> T	LOC_Os12g10470.1	downstream_gene_variant ; 474.0bp to feature; MODIFIER	silent_mutation	Average:12.499; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1205555271	C -> T	LOC_Os12g10480.1	downstream_gene_variant ; 632.0bp to feature; MODIFIER	silent_mutation	Average:12.499; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1205555271	C -> T	LOC_Os12g10470-LOC_Os12g10480	intergenic_region ; MODIFIER	silent_mutation	Average:12.499; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205555271	5.05E-06	NA	mr1517	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
vg1205555271	6.08E-07	7.45E-09	mr1517	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
vg1205555271	NA	1.08E-07	mr1946	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
vg1205555271	NA	3.14E-07	mr1517_2	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