Search for Variation information by Variation ID:

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

Detailed information for vg1017569988:

Variant ID: vg1017569988 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17569988
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTCTAAACATGAGATTTGTTTTCTTGGGAACAAAATAAAAGGCCCACCCTTTTGCTTATTCCTGGAATAAGCGAAACGAAGTGATCTTTGAATAAAC[C/T]
TTTATATACATGTTCTTAACGATCTAAAAGCAAAGGTTGAAGAATAAACTTCGATGAAAAAAACCTTAAAATCACCTTCAAATTTAAGGTTAAAAATTTA

Reverse complement sequence

TAAATTTTTAACCTTAAATTTGAAGGTGATTTTAAGGTTTTTTTCATCGAAGTTTATTCTTCAACCTTTGCTTTTAGATCGTTAAGAACATGTATATAAA[G/A]
GTTTATTCAAAGATCACTTCGTTTCGCTTATTCCAGGAATAAGCAAAAGGGTGGGCCTTTTATTTTGTTCCCAAGAAAACAAATCTCATGTTTAGAATAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	30.90%	4.49%	6.64%	NA
All Indica	2759	79.90%	2.20%	7.29%	10.62%	NA
All Japonica	1512	13.30%	85.60%	0.46%	0.66%	NA
Aus	269	95.20%	1.90%	0.00%	2.97%	NA
Indica I	595	75.10%	0.70%	12.27%	11.93%	NA
Indica II	465	72.30%	4.10%	13.12%	10.54%	NA
Indica III	913	86.00%	1.10%	0.99%	11.94%	NA
Indica Intermediate	786	81.00%	3.40%	7.38%	8.14%	NA
Temperate Japonica	767	1.60%	97.80%	0.26%	0.39%	NA
Tropical Japonica	504	20.40%	79.00%	0.00%	0.60%	NA
Japonica Intermediate	241	35.70%	60.60%	2.07%	1.66%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	48.90%	43.30%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1017569988	C -> T	LOC_Os10g33380.1	upstream_gene_variant ; 4403.0bp to feature; MODIFIER	silent_mutation	Average:60.256; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg1017569988	C -> T	LOC_Os10g33390.1	downstream_gene_variant ; 2175.0bp to feature; MODIFIER	silent_mutation	Average:60.256; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg1017569988	C -> T	LOC_Os10g33370.1	intron_variant ; MODIFIER	silent_mutation	Average:60.256; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg1017569988	C -> DEL	N	N	silent_mutation	Average:60.256; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017569988	NA	6.52E-79	mr1135	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
vg1017569988	NA	2.91E-87	mr1504	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
vg1017569988	NA	4.11E-39	mr1645	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
vg1017569988	NA	2.44E-32	mr1647	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
vg1017569988	NA	6.81E-36	mr1670	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
vg1017569988	NA	8.13E-82	mr1672	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
vg1017569988	NA	3.82E-35	mr1682	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
vg1017569988	NA	2.52E-39	mr1873	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
vg1017569988	NA	2.79E-18	mr1657_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
vg1017569988	NA	2.34E-41	mr1689_2	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