Search for Variation information by Variation ID:

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

Detailed information for vg0217953192:

Variant ID: vg0217953192 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17953192
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAAAAAAAAAGACCCTTTCTCAACTAACAAAACAAATGAGCTACAAGAGTACTAACTACGGTTCTATAATAATTGATGCTTTGGACAAGGTTGAGGT[C/T]
AAACTTTTATAACTTTGACCATAAATAACTTTAAAAATATTTGGTTTAAAGAAACTAAAACAACATTTATAGATTTATCTTTCAAAGCACTATAATAAAA

Reverse complement sequence

TTTTATTATAGTGCTTTGAAAGATAAATCTATAAATGTTGTTTTAGTTTCTTTAAACCAAATATTTTTAAAGTTATTTATGGTCAAAGTTATAAAAGTTT[G/A]
ACCTCAACCTTGTCCAAAGCATCAATTATTATAGAACCGTAGTTAGTACTCTTGTAGCTCATTTGTTTTGTTAGTTGAGAAAGGGTCTTTTTTTTTTCTT

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	63.10%	36.50%	0.38%	0.06%	NA
All Indica	2759	45.70%	53.70%	0.51%	0.07%	NA
All Japonica	1512	97.20%	2.80%	0.00%	0.00%	NA
Aus	269	36.40%	63.20%	0.37%	0.00%	NA
Indica I	595	19.50%	80.50%	0.00%	0.00%	NA
Indica II	465	25.20%	74.00%	0.86%	0.00%	NA
Indica III	913	79.70%	19.90%	0.33%	0.00%	NA
Indica Intermediate	786	38.20%	60.70%	0.89%	0.25%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	64.40%	31.10%	3.33%	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
vg0217953192	C -> T	LOC_Os02g30190.1	downstream_gene_variant ; 2251.0bp to feature; MODIFIER	silent_mutation	Average:29.025; most accessible tissue: Callus, score: 56.286	N	N	N	N
vg0217953192	C -> T	LOC_Os02g30200.1	intron_variant ; MODIFIER	silent_mutation	Average:29.025; most accessible tissue: Callus, score: 56.286	N	N	N	N
vg0217953192	C -> DEL	N	N	silent_mutation	Average:29.025; most accessible tissue: Callus, score: 56.286	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217953192	NA	6.40E-08	mr1138	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
vg0217953192	NA	2.37E-07	mr1169	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
vg0217953192	NA	6.94E-06	mr1317	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
vg0217953192	NA	1.21E-06	mr1646	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
vg0217953192	9.70E-07	NA	mr1855	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
vg0217953192	NA	6.03E-12	mr1138_2	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
vg0217953192	NA	2.06E-06	mr1138_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
vg0217953192	9.56E-06	NA	mr1169_2	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
vg0217953192	2.36E-06	3.19E-07	mr1169_2	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
vg0217953192	NA	4.73E-07	mr1317_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
vg0217953192	NA	3.01E-07	mr1559_2	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
vg0217953192	NA	3.46E-10	mr1806_2	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
vg0217953192	NA	1.28E-08	mr1806_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
vg0217953192	NA	4.26E-07	mr1807_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
vg0217953192	NA	9.20E-07	mr1818_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
vg0217953192	1.53E-08	NA	mr1855_2	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
vg0217953192	NA	1.76E-06	mr1870_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